text
stringlengths 89
2.49k
| category
stringclasses 19
values |
|---|---|
Absolute Measurement Of Laminar Shear Rate Using Photon Correlation
Spectroscopy: An absolute measurement of the components of the shear rate tensor
$\mathcal{S}$ in a fluid can be found by measuring the photon correlation
function of light scattered from particles in the fluid. Previous methods of
measuring $\mathcal{S}$ involve reading the velocity at various points and
extrapolating the shear, which can be time consuming and is limited in its
ability to examine small spatial scale or short time events. Previous work in
Photon Correlation Spectroscopy has involved only approximate solutions,
requiring free parameters to be scaled by a known case, or different cases,
such as 2-D flows, but here we present a treatment that provides quantitative
results directly and without calibration for full 3-D flow. We demonstrate this
treatment experimentally with a cone and plate rheometer. | cond-mat_soft |
The interplay between phase-separation and gene-enhancer communication:
a theoretical study: The phase-separation occurring in a system of mutually interacting proteins
that can bind on specific sites of a chromatin fiber is here investigated. This
is achieved by means of extensive Molecular Dynamics simulations of a simple
polymer model which includes regulatory proteins as interacting spherical
particles. Our interest is particularly focused on the role played by
phase-separation in the formation of molecule aggregates that can join distant
regulatory elements, such as gene promoters and enhancers, along the DNA. We
find that the overall equilibrium state of the system resulting from the mutual
interplay between binding molecules and chromatin can lead, under suitable
conditions that depend on molecules concentration, molecule-molecule and
molecule-DNA interactions, to the formation of phase-separated molecular
clusters allowing robust contacts between regulatory sites. Vice-versa, the
presence of regulatory sites can promote the phase-separation process.
Different dynamical regimes can generate the enhancer-promoter contact, either
by cluster nucleation at binding sites or by bulk spontaneous formation of the
mediating cluster to which binding sites are successively attracted. The
possibility that such processes can explain experimental live-cell imaging data
measuring distances between regulatory sites during time is also discussed. | cond-mat_soft |
Nonequilibrium thermodynamics versus model grain growth: derivation and
some physical implications: Nonequilibrium thermodynamics formalism is proposed to derive the flux of
grainy (bubbles-containing) matter, emerging in a nucleation growth process.
Some power and non-power limits, due to the applied potential as well as owing
to basic correlations in such systems, have been discussed. Some encouragement
for such a discussion comes from the fact that the nucleation and growth
processes studied, and their kinetics, are frequently reported in literature as
self-similar (characteristic of algebraic correlations and laws) both in basic
entity (grain; bubble) size as well as time scales. | cond-mat_soft |
On the relevance of numerical simulations to booming sand: We have performed a simulation study of 3D cohesionless granular flows down
an inclined chute. We find that the oscillations observed in [L.E. Silbert,
Phys. Rev. Lett., 94, 098002 (2005)] near the angle of repose are harmonic
vibrations of the lowest normal mode. Their frequencies depend on the contact
stiffness as well as on the depth of the flow. Could these oscillations account
for the phenomena of "booming sand"? We estimate an effective contact stiffness
from the Hertz law, but this leads to frequencies several times higher than
observed. However, the Hertz law also predicts interpenetrations of a few
nanometers, indicating that the oscillations frequencies are governed by the
surface stiffness, which can be much lower than the bulk one. This is in
agreement with previous studies ascribing the ability to sing to the presence
of a soft coating on the grain surface. | cond-mat_soft |
Dynamic heterogeneity in polydisperse systems: A comparative study of
the role of local structural order parameter and particle size: In polydisperse systems, describing the structure and any structural order
parameter (SOP) is not trivial as it varies with the number of species we use
to describe the system, M . Depending on the degree of polydispersity, there is
an optimum value of M = M0 where we show that the mutual information of the
system increases. However, surprisingly the correlation between a recently
proposed SOP and the dynamics is highest for M = 1. This effect increases with
polydispersity. We find that the SOP at M = 1 is coupled with the particle
size, {\sigma}, and this coupling increases with polydispersity and decreases
with an increase in M . Careful analysis shows that at lower polydispersity the
SOP is a good predictor of the dynamics. However, at higher polydispersity, the
dynamics is strongly dependent on {\sigma}. Since the coupling between the SOP
and {\sigma} is higher for M = 1 thus, it appears to be a better predictor of
the dynamics. We also study the Vibrality an order parameter independent of
structural information. Compared to SOP, at high polydispersity we find
Vibrality to be a marginally better predictor of the dynamics. However, this
high predictive power of Vibrality, which is not there at lower polydispersity,
appears to be due to its stronger coupling with {\sigma}. Thus our study
suggests that for systems with high polydispersity, the correlation of any
order parameter and {\sigma} will affect the correlation between the order
parameter and dynamics and need not project a generic predictive power of the
order parameter. | cond-mat_soft |
Biocompatible carbon nitride-based light-driven microswimmer propulsion
in biological and ionic media with responsive on-demand drug delivery: We propose two-dimensional organic poly(heptazine imide) (PHI) carbon nitride
microparticles as light-driven microswimmers in various ionic and biological
media. Their demonstrated high-speed (15-23 $\mu$m/s) swimming in
multi-component ionic solutions with concentrations up to 1 M and without
dedicated fuels is unprecedented, overcoming one of the bottlenecks of previous
light-driven microswimmers. Such high ion tolerance is attributed to a
favorable interplay between the particle's textural and structural nanoporosity
and optoionic properties, facilitating ionic interactions in solutions with
high salinity. Biocompatibility of the microswimmers is validated by cell
viability tests with three different cell types and primary cells. The
nanopores of the swimmers are loaded with a model cancer drug, doxorubicin
(DOX), in high (185%) loading efficiency without passive release. Controlled
drug release is reported in different pH conditions and can be triggered
on-demand also by illumination. Light-triggered, boosted release of DOX and its
active degradation products is demonstrated in oxygen-poor conditions using the
intrinsic, environmentally sensitive and light-induced charge storage
properties of PHI, which could enable future theranostic applications in
oxygen-deprived tumor regions. These organic PHI microswimmers simultaneously
solve the current light-driven microswimmer challenges of high ion tolerance,
fuel-free high-speed propulsion in biological media, biocompatibility and
controlled on-demand cargo release towards their biomedical, environmental and
other potential future applications. | cond-mat_soft |
Liquid-liquid phase separation of a surfactant-solubilized membrane
protein: The phase behavior of membrane proteins stems from a complex synergy with the
amphiphilic molecules required for their solubilization. We show that
ionization of a pH-sensitive surfactant, LDAO, bound to a bacterial
photosynthetic protein, the Reaction Center (RC), leads in a narrow pH range to
protein liquid-liquid phase separation in surprisingly stable `droplets',
forerunning reversible aggregation at lower pH. Phase segregation is promoted
by increasing temperature and hindered by adding salt. RC light-absorption and
photoinduced electron cycle are moreover strongly affected by phase
segregation. | cond-mat_soft |
Programmable phase behavior in fluids with designable interactions: We introduce a method for solving the "inverse" phase equilibria problem: How
should the interactions among a collection of molecular species be designed in
order to achieve a target phase diagram? Using techniques from convex
optimization theory, we show how to solve this problem for phase diagrams
containing a large number of components and many coexisting phases with
prescribed compositions. We apply our approach to commonly used mean-field
models of multicomponent fluids and then use molecular simulations to verify
that the designed interactions result in the target phase diagrams. Our
approach enables the rational design of "programmable" fluids, such as
biopolymer and colloidal mixtures, with complex phase behavior. | cond-mat_soft |
Early stage of Erythrocyte Sedimentation Rate test: Fracture of a
high-volume-fraction gel: Erythrocyte Sedimentation Rate (ESR) is a clinical parameter used as a
non-specific marker for inflammation, and recent studies have shown that it is
linked to the collapse of the gel formed by red blood cells (RBCs) at
physiological hematocrits (i.e. RBC volume fraction). Previous research has
suggested that the delay time before the sedimentation process is related to
the formation of fractures in the gel. Moreover, RBC gels present specific
properties due to the anisotropic shape and flexibility of the RBCs. Namely,
the onset of the collapse is reached earlier and the settling velocity of the
gel increases with increasing attraction between the RBCs, while gel of
spherical particles show the opposite trend. Here, we report experimental
observations of the gel structure during this onset and suggest an equation
modeling this initial process as fracturing of the gel. We demonstrate that
this equation provides a model for the motion of the interface between blood
plasma and the RBC gel, along the whole time span. We also observe that the
increase in the attraction between the RBCs modifies the density of fractures
in the gel, which explains why the gel displays a decrease in delay time when
the aggregation energy between the RBCs increases. Our work uncovers the
detailed physical mechanism underlying the ESR and provides insights into the
fracture dynamics of a RBC gel. These results can improve the accuracy of
clinical measurements. | cond-mat_soft |
Stability analysis of twist grain boundaries in lamellar phases of block
copolymers: Twist grain boundaries are widely observed in lamellar phases of block
copolymers. A mesoscopic model of the copolymer is used to obtain stationary
configurations that include a twist grain boundary, and to analyze their
stability against long wavelength perturbations. The analysis presented is
valid in the weak segregation regime, and includes direct numerical solution of
the governing equations as well as a multiple scale analysis. We find that a
twist boundary configuration with arbitrary misorientation angle can be well
described by two modes, and obtain the equations for their slowly varying
amplitudes. The width of the boundary region is seen to scale as
$\epsilon^{-1/4}$, with $\epsilon$ being the dimensionless distance to the
order-disorder transition. We finally present the results of the linear
stability analysis of the planar boundary. | cond-mat_soft |
Active Nematic Ratchet in Asymmetric Obstacle Arrays: We numerically investigate the effect of a periodic array of asymmetric
obstacles in a two-dimensional active nematic. We find that activity in
conjunction with the asymmetry leads to a ratchet effect or unidirectional flow
of the fluid along the asymmetry direction. The directional flow is still
present even in the active turbulent phase when the gap between obstacles is
sufficiently small. We demonstrate that the dynamics of the topological defects
transition from flow-mirroring to smectic-like as the gap between obstacles is
made smaller, and explain this transition in terms of the pinning of negative
winding number defects between obstacles. This also leads to a non-monotonic
ratchet effect magnitude as a function of obstacle size, so that there is an
optimal obstacle size for ratcheting at fixed activity. | cond-mat_soft |
Activation of a muscle as a mapping of stress-strain curves: The mathematical modeling of the contraction of a muscle is a crucial problem
in biomechanics. Several different models of muscle activation exist in
literature. A possible approach to contractility is the so-called active
strain: it is based on a multiplicative decomposition of the deformation
gradient into an active contribution, accounting for the muscle activation, and
an elastic one, due to the passive deformation of the body.
We show that the active strain approach does not allow to recover the
experimental stress-stretch curve corresponding to a uniaxial deformation of a
skeletal muscle, whatever the functional form of the strain energy. To overcome
such difficulty, we introduce an alternative model, that we call mixture active
strain approach, where the muscle is composed of two different solid phases and
only one of them actively contributes to the active behavior of the muscle. | cond-mat_soft |
Can a Carbon Nanotube Pierce through a Phospholipid Bilayer?: Great efficiency to penetrate into living cells is attributed to carbon
nanotubes due to a number of direct and indirect observations of carbon
nanotubes inside the cells. However, a direct evidence of physical
translocation of nanotubes through phospholipid bilayers and the exact
microscopic mechanism of their penetration into cells are still lacking. In
order to test one of the inferred translocation mechanisms, namely the
spontaneous piercing through the membrane induced only by thermal motion, we
calculate the energy cost associated with the insertion of a carbon nanotube
into a model phospholipid bilayer using the Single Chain Mean Field theory
which is particularly suitable for the accurate measurements of equilibrium
free energies. We find that the energy cost of the bilayer rupture is quite
high compared to the energy of thermal motion. This conclusion may indirectly
support other energy dependent translocation mechanisms such as, for example,
endocytosis. | cond-mat_soft |
Anomalous fluctuations of active polar filaments: Using a simple model, we study the fluctuating dynamics of inextensible,
semiflexible polar filaments interacting with active and directed force
generating centres such as molecular motors. Taking into account the fact that
the activity occurs on time-scales comparable to the filament relaxation time,
we obtain some unexpected differences between both the steady-state and
dynamical behaviour of active as compared to passive filaments. For the
statics, the filaments have a {novel} length-scale dependent rigidity.
Dynamically, we find strongly enhanced anomalous diffusion. | cond-mat_soft |
Topology of Complex Bridges inside Vibrated Dry Granular Media: After some communications (EMAIL EXCHANGE) with the co-authors, this article
has been withdrawn (for appropriate reason, please refer to the comments
section). | cond-mat_soft |
Large heat-capacity jump in cooling-heating of fragile glass from
kinetic Monte Carlo simulations based on a two-state picture: The specific heat capacity $c_v$ of glass formers undergoes a hysteresis when
subjected to a cooling-heating cycle, with a larger $c_v$ and a more pronounced
hysteresis for fragile glasses than for strong ones. Here, we show that these
experimental features, including the unusually large magnitude of $c_v$ of
fragile glasses, are well reproduced by kinetic Monte Carlo and equilibrium
study of a distinguishable particle lattice model (DPLM) incorporating a
two-state picture of particle interactions. The large $c_v$ in fragile glasses
is caused by a dramatic transfer of probabilistic weight from high-energy
particle interactions to low-energy ones as temperature decreases. | cond-mat_soft |
Topology counts: force distributions in circular spring networks: Filamentous polymer networks govern the mechanical properties of many
biological materials. Force distributions within these networks are typically
highly inhomogeneous and, although the importance of force distributions for
structural properties is well recognized, they are far from being understood
quantitatively. Using a combination of probabilistic and graph-theoretical
techniques we derive force distributions in a model system consisting of
ensembles of random linear spring networks on a circle. We show that
characteristic quantities, such as mean and variance of the force supported by
individual springs, can be derived explicitly in terms of only two parameters:
(i) average connectivity and (ii) number of nodes. Our analysis shows that a
classical mean-field approach fails to capture these characteristic quantities
correctly. In contrast, we demonstrate that network topology is a crucial
determinant of force distributions in an elastic spring network. | cond-mat_soft |
Dissipative particle dynamics for coarse-grained models: We develop a computational method based on Dissipative Particle Dynamics
(DPD) that introduces solvent hydrodynamic interactions to coarse-grained
models of solutes, such as ions, molecules, or polymers. DPD-solvent (DPDS) is
a fully off-lattice method that allows straightforward incorporation of
hydrodynamics at desired solvent viscosity, compressibility and solute
diffusivity with any particle-based solute model. Solutes interact with the
solvent only through the DPD thermostat, which ensures that the equilibrium
properties of the solute system are not affected by the introduction of the DPD
solvent. Thus, DPDS can be used as a replacement for traditional molecular
dynamics thermostats such as Nos\'e-Hoover and Langevin. We demonstrate the
applicability of DPDS on the case of polymer dynamics and electroosmotic flow
through a nanopore. The method should be broadly useful as means to introduce
hydrodynamics to existing coarse-grained models of molecules and soft
materials. | cond-mat_soft |
Critical bending and magnetic shape memory effect in magnetoactive
elastomers: The results of a study of magnetoactive elastomers (MAEs) consisting of an
elastomer matrix with embedded ferromagnetic particles are presented. A
continuous critical bending induced by the magnetic field, characterized by a
critical exponent for the bending magnitude, and the derivative of which has a
singularity in the critical region is reported for the first time. The
mechanical stability loss and the symmetry reduction of the magnetic state,
which are interrelated with each other, take place at the critical point. The
magnetization in the high-symmetric state (below the critical point) is
directed along the magnetic field and the torque is absent. Above the critical
point, the magnetization and the magnetic field are noncollinear and there
arises a torque, which is self-consistent with the bending. The magnetic field
dependence of the MAE bending was found to have a hysteresis, which is
associated with the magneto-rheological effect. The shape memory effect was
also obtained for the MAE bending in a cycle consisting of magnetization,
cooling (at H=/0), and heating (at H=0). The influence of the critical glass
transition temperature of the matrix, as well as its melting/solidification
temperature, on the magnetic shape memory effect was studied. | cond-mat_soft |
Passive viscous flow selection via fluid-induced buckling: We study the buckling of a clamped beam immersed in a creeping flow within a
rectangular channel. Via a combination of precision experiments, simulations,
and theoretical modeling, we show how the instability depends on a pressure
feedback mechanism and rationalize it in terms of dimensionless parameters. As
the beam can bend until touching the wall above a critical flow rate, we
finally demonstrate how the system can be used as a tunable passive flow
selector, effectively redirecting the flow within a designed hydraulic circuit. | cond-mat_soft |
Intermittency, aging and record fluctuations: Aging in spin glasses is analyzed via the Probability Density Function (PDF)
of the heat transfer between system and bath over a small time $\delta t$. The
PDF contains a Gaussian part, describing reversible fluctuations, and an
exponential tail caused by intermittent events. We find that the relative
weight of these two parts depends, for fixed $\delta t$, on the ratio of the
total sampling time to the age $t_w$. Fixing this ratio, the intensity of the
intermittent events is proportional to $\delta t/t_w$ and independent of the
temperature. The Gaussian part has a variance with the same temperature
dependence as the variance of the equilibrium energy in a system with an
exponential density of states. All these observations are explained assuming
that, for any $t_w$, intermittent events are triggered by local energy
fluctuations exceeding those previously occurred. | cond-mat_soft |
Modelling chemotaxis of microswimmers: from individual to collective
behavior: We discuss recent progress in the theoretical description of chemotaxis by
coupling the diffusion equation of a chemical species to equations describing
the motion of sensing microorganisms. In particular, we discuss models for
autochemotaxis of a single microorganism which senses its own secretion leading
to phenomena such as self-localization and self-avoidance. For two
heterogeneous particles, chemotactic coupling can lead to predator-prey
behavior including chase and escape phenomena, and to the formation of active
molecules, where motility spontaneously emerges when the particles approach
each other. We close this review with some remarks on the collective behavior
of many particles where chemotactic coupling induces patterns involving
clusters, spirals or traveling waves. | cond-mat_soft |
Nonlinear Viscoelastic Modeling of Adhesive Failure for Polyacrylate
Pressure-Sensitive Adhesives: We investigate experimentally the adherence energy $\Gamma$ of model
polyacrylate Pressure Sensitive Adhesives (PSAs) with combined large strain
rheological measurements in uniaxial extension and an instrumented peel test.
We develop a nonlinear model for such peel test which captures the dependence
of $\Gamma(V)$ with peeling rate $V$ revealing the key role played by the
extensional rheology. Our model explains in particular why traditional linear
viscoelastic approaches correctly predict the slope of $\Gamma(V)$ curves for
sufficiently elastic PSAs characterized by a simple rate-independent debonding
criterion. However, for more viscoelastic adhesives, we identified a more
complex rate-dependent debonding criterion yielding a significant modification
of the $\Gamma(V)$ curves, an effect that has been largely overlooked so far.
This investigation opens the way towards the understanding of fibrils
debonding, which is the main missing block to predict the adherence of PSAs. | cond-mat_soft |
Mathematical Modeling of Electrolyte Flow Dynamic Patterns and
Volumetric Flow Penetrations in the Flow Channel over Porous Electrode
Layered System in Vanadium Flow Battery with Serpentine Flow Field Design: In this work, a two-dimensional mathematical model is developed to study the
flow patterns and volumetric flow penetrations in the flow channel over the
porous electrode layered system in vanadium flow battery with serpentine flow
field design. The flow distributions at the interface between the flow channel
and porous electrode are examined. It is found that the non-linear pressure
distributions can distinguish the interface flow distributions under the ideal
plug flow and ideal parabolic flow inlet boundary conditions. However, the
volumetric flow penetration within the porous electrode beneath the flow
channel through the integration of interface flow velocity reveals that this
value is identical under both ideal plug flow and ideal parabolic flow inlet
boundary conditions. The volumetric flow penetrations under the advection
effects of flow channel and landing/rib are estimated. The maximum current
density achieved in the flow battery can be predicted based on the 100% amount
of electrolyte flow reactant consumption through the porous electrode beneath
both flow channel and landing channel. The corresponding theoretical maximum
current densities achieved in vanadium flow battery with one and three layers
of SGL 10AA carbon paper electrode have reasonable agreement with experimental
results under a proper permeability. | cond-mat_soft |
Size distribution and waiting times for the avalanches of the Cell
Network Model of Fracture: The Cell Network Model is a fracture model recently introduced that resembles
the microscopical structure and drying process of the parenchymatous tissue of
the Bamboo Guadua angustifolia. The model exhibits a power-law distribution of
avalanche sizes, with exponent -3.0 when the breaking thresholds are randomly
distributed with uniform probability density. Hereby we show that the same
exponent also holds when the breaking thresholds obey a broad set of Weibull
distributions, and that the humidity decrements between successive avalanches
(the equivalent to waiting times for this model) follow in all cases an
exponential distribution. Moreover, the fraction of remaining junctures shows
an exponential decay in time. In addition, introducing partial breakings and
cumulative damages induces a crossover behavior between two power-laws in the
avalanche size histograms. This results support the idea that the Cell Network
Model may be in the same universality class as the Random Fuse Model. | cond-mat_soft |
Colloidal trains: Single and double paramagnetic colloidal particles are placed above a
magnetic square pattern and are driven with an external magnetic field
precessing around a high symmetry direction of the pattern. The external
magnetic field and that of the pattern confine the colloids into lanes parallel
to a lattice vector of the pattern. The precession of the external field causes
traveling minima of the magnetic potential along the direction of the lanes. At
sufficiently high frequencies of modulation only the doublets respond to the
external field and move in direction of the traveling minima along the lanes,
while the single colloids cannot follow and remain static. We show how the
doublets can induce a coordinated motion of the single colloids building
colloidal trains made of a chain of several single colloids transported by
doublets. | cond-mat_soft |
Random copolymer adsorption: Morita approximation compared to exact
numerical simulations: We study the adsorption of ideal random lattice copolymers with correlations
in the sequences on homogeneous substrates with two different methods: An
analytical solution of the problem based on the constrained annealed
approximation introduced by Morita in 1964 and the generating functional (GF)
technique, and direct numerical simulations of lattice chains averaged over
many realizations of random sequences. Both methods allow to calculate the free
energy and different conformational characteristics of the adsorbed chain. The
comparison of the results for random copolymers with different degree of
correlations and different types of nonadsorbing monomers (neutral or repelling
from the surface) shows not only qualitative but a very good quantitative
agreement, especially in the cases of Bernoullian and quasi-alternating random
sequences. | cond-mat_soft |
On the stability of 2 \sqrt{2} x 2 \sqrt{2} oxygen ordered
superstructures in YBa2Cu3O6+x: We have compared the ground-state energy of several observed or proposed " 2
\sqrt{2} x 2 \sqrt{2} oxygen (O) ordered superstructures " (from now on HS),
with those of "chain superstructures" (CS) (in which the O atoms of the basal
plane are ordered in chains), for different compositions x in YBa2Cu3O6+x. The
model Hamiltonian contains i) the Madelung energy, ii) a term linear in the
difference between Cu and O hole occupancies which controls charge transfer,
and iii) covalency effects based on known results for $t-J$ models in one and
two dimensions. The optimum distribution of charge is determined minimizing the
total energy, and depends on two parameters which are determined from known
results for x=1 and x=0.5. We obtain that on the O lean side, only CS are
stable, while for x=7/8, a HS with regularly spaced O vacancies added to the
x=1 structure is more stable than the corresponding CS for the same x. We find
that the detailed positions of the atoms in the structure, and long-range
Coulomb interactions, are crucial for the electronic structure, the mechanism
of charge transfer, the stability of the different phases, and the possibility
of phase separation. | cond-mat_soft |
Time-Rate-Transformation framework for targeted assembly of short-range
attractive colloidal suspensions: The aggregation of attractive colloids has been extensively studied from both
theoretical and experimental perspectives as the fraction of solid particles is
changed, and the range, type and strength of attractive or repulsive forces
between particles varies. The resulting gels consisting of disordered
assemblies of attractive colloidal particles, have also been investigated with
regards to percolation, phase separation, and the mechanical characteristics of
the resulting fractal networks. Despite tremendous progress in our
understanding of the gelation process, and the exploration of different routes
for arresting the dynamics of attractive colloids, the complex interplay
between convective transport processes and many-body effects in such systems
has limited our ability to drive the system towards a specific configuration.
Here we study a model attractive colloidal system over a wide range of particle
characteristics and flow conditions undergoing aggregation far from
equilibrium. The complex multiscale dynamics of the system can be understood
using a Time-Rate-Transformation diagram adapted from understanding of
materials processing in block copolymers, supercooled liquids and much stiffer
glassy metals to direct targeted assembly of attractive colloidal particles. | cond-mat_soft |
Effect of topology on the collapse transition and the instantaneous
shape of a model heteropolymer: The effect of topology on the collapse transition and instantaneous shape of
an energy polydisperse polymer (a model heteropolymer) is studied by means of
computer simulations. In particular, we consider three different chain
topology, namely, linear (L), ring (R) and trefoil knot (T). The heteropolymer
is modeled by assigning each monomer an interaction parameter, $\varepsilon_i$,
drawn randomly from a Gaussian distribution. Through chain size scaling the
transition temperature, $\theta$, is located and compared among the chains of
different topogies. The influence of topology is reflected in the value of
$\theta$ and observed that $\theta(\text{L}) > \theta(\text{R}) >
\theta(\text{T})$ in a similar fashion to that of the homopolymer counterpart.
Also studied chain size distributions, and the shape changes across the
transition temperature characterised through shape parameters based on the
eigenvalues of the gyration tensor. It is observed that, for the model
heteropolymer, in addition to chain topology the $\theta$-temperature also
depends on energy polydispersity. | cond-mat_soft |
Structure and dynamics of colloidal depletion gels: coincidence of
transitions and heterogeneity: Transitions in structural heterogeneity of colloidal depletion gels formed
through short-range attractive interactions are correlated with their dynamical
arrest. The system is a density and refractive index matched suspension of 0.20
volume fraction poly(methyl methacyrlate) colloids with the non-adsorbing
depletant polystyrene added at a size ratio of depletant to colloid of 0.043.
As the strength of the short-range attractive interaction is increased,
clusters become increasingly structurally heterogeneous, as characterized by
number-density fluctuations, and dynamically immobilized, as characterized by
the single-particle mean-squared displacement. The number of free colloids in
the suspension also progressively declines. As an immobile cluster to gel
transition is traversed, structural heterogeneity abruptly decreases.
Simultaneously, the mean single-particle dynamics saturates at a localization
length on the order of the short-range attractive potential range. Both
immobile cluster and gel regimes show dynamical heterogeneity. Non-Gaussian
distributions of single particle displacements reveal enhanced populations of
dynamical trajectories localized on two different length scales. Similar
dependencies of number density fluctuations, free particle number and dynamical
length scales on the order of the range of short-range attraction suggests a
collective structural origin of dynamic heterogeneity in colloidal gels. | cond-mat_soft |
Effect of bond length fluctuations on crystal nucleation of hard bead
chains: We study the spontaneous nucleation and crystallization of linear and cyclic
chains of flexibly connected hard spheres using extensive molecular dynamics
simulations. To this end, we present a novel event-driven molecular dynamics
simulation method, which is easy to implement and very efficient. We find that
the nucleation rates are predominately determined by the number of bonds per
sphere in the system, rather than the precise details of the chain topology,
chain length, and polymer composition. O ur results thus show that the crystal
nucleation rate of bead chains can be enhanced by adding monomers to the
system. In addition, we find that the resulting crystal n uclei contain
significantly more face-centered-cubic than hexagonal-close-packed ordered
particles. More surprisingly, the resulting crystal nuclei possess a range of
crystal morphologies including structures with a five-fold symmetry. | cond-mat_soft |
Liquid Crystal Distortions Revealed by an Octupolar Tensor: The classical theory of liquid crystal elasticity as formulated by Oseen and
Frank describes the (orientable) optic axis of these soft materials by a
director $\mathbf{n}$. The ground state is attained when $\mathbf{n}$ is
uniform in space; all other states, which have a non-vanishing gradient
$\nabla\mathbf{n}$, are distorted. This paper proposes an algebraic (and
geometric) way to describe the local distortion of a liquid crystal by
constructing from $\mathbf{n}$ and $\nabla\mathbf{n}$ a third-rank, symmetric
and traceless tensor $\mathbf{A}$ (the octupolar tensor). The (nonlinear)
eigenvectors of $\mathbf{A}$ associated with the local maxima of its cubic form
$\Phi$ on the unit sphere (its octupolar potential) designate the directions of
distortion concentration. The octupolar potential is illustrated geometrically
and its symmetries are charted in the space of distortion characteristics, so
as to educate the eye to capture the dominating elastic modes. Special
distortions are studied, which have everywhere either the same octupolar
potential or one with the same shape, but differently inflated. | cond-mat_soft |
Swelling, Structure, and Phase Stability of Compressible Microgels: Microgels are soft colloidal particles that, when dispersed in a solvent,
swell and deswell in response to changes in environmental conditions, such as
temperature, concentration, and $p$H. Using Monte Carlo simulation, we model
bulk suspensions of microgels that interact via Hertzian elastic interparticle
forces and can expand or contract via trial moves that allow particles to
change size in accordance with the Flory-Rehner free energy of cross-linked
polymer gels. We monitor the influence of particle compressibility, size
fluctuations, and concentration on bulk structural and thermal properties by
computing particle swelling ratios, radial distribution functions, static
structure factors, osmotic pressures, and freezing densities. For microgels in
the nanoscale size range, particle compressibility and associated size
fluctuations suppress crystallization, shifting the freezing transition to a
higher density than for the hard-sphere fluid. As densities increase beyond
close packing, microgels progressively deswell, while their intrinsic size
distribution grows increasingly polydisperse. | cond-mat_soft |
Effect of stretching-induced changes in hydrodynamic screening on
coil-stretch hysteresis of unentangled polymer solutions: Extensional rheometry and Brownian Dynamics simulations of flexible polymer
solutions confirm predictions based on blob concepts that coil--stretch
hysteresis in extensional flows increases with concentration, reaching a
maximum at the critical overlap concentration $c^\ast$ before progressively
vanishing in the semidilute regime. These observations demonstrate that chain
stretching strengthens intermolecular hydrodynamic screening in dilute
solutions, but weakens it in semidilute solutions. Flow can thus strongly
modify the concentration dependence of viscoelastic properties of polymer
solutions. | cond-mat_soft |
Critical behavior of a water monolayer under hydrophobic confinement: The properties of water can have a strong dependence on the confinement.
Here, we consider a water monolayer nanoconfined between hydrophobic parallel
walls under conditions that prevent its crystallization. We investigate, by
simulations of a many-body coarse-grained water model, how the properties of
the liquid are affected by the confinement. We show, by studying the response
functions and the correlation length and by performing finite-size scaling of
the appropriate order parameter, that at low temperature the monolayer
undergoes a liquid-liquid phase transition ending in a critical point in the
universality class of the two-dimensional (2D) Ising model. Surprisingly, by
reducing the linear size L of the walls, keeping the walls separation h
constant, we find a 2D-3D crossover for the universality class of the
liquid-liquid critical point for L/h~50, i.e. for a monolayer thickness that is
small compared to its extension. This result is drastically different from what
is reported for simple liquids, where the crossover occurs for L/h ~ 5, and is
consistent with experimental results and atomistic simulations. We shed light
on these findings showing that they are a consequence of the strong
cooperativity and the low coordination number of the hydrogen bond network that
characterizes water. | cond-mat_soft |
Electric field unbinding of solid-supported lipid multilayers: We studied by X-ray reflectivity the behaviour of fully hydrated
solid-supported lipid multilayers under the influence of a transverse electric
field, under conditions routinely used in the electroformation process. The
kinetics of sample loss (unbinding) was measured as a function of the amplitude
and frequency of the applied field by monitoring the integrated intensity of
the Bragg peaks. We also performed a time-resolved analysis of the intensity of
the first Bragg peak and characterized the final state of the sample. | cond-mat_soft |
From ageing to immortality: cluster growth in stirred colloidal
solutions: This model describes cluster aggregation in a stirred colloidal solution
Interacting clusters compete for growth in this 'winner-takes-all' model; for
finite assemblies, the largest cluster always wins, i.e. there is a uniform
sediment. In mean-field, the model exhibits glassy dynamics, with two
well-separated time scales, corresponding to individual and collective
behaviour; the survival probability of a cluster eventually falls off according
to a universal law $(\ln t)^{-1/2}$. In finite dimensions, the glassiness is
enhanced: the dynamics manifests both {\it ageing} and metastability, where
pattern formation is manifested in each metastable state by a fraction of {\it
immortal} clusters. | cond-mat_soft |
Hydrodynamic Coupling of Two Brownian Spheres to a Planar Surface: We describe direct imaging measurements of the collective and relative
diffusion of two colloidal spheres near a flat plate. The bounding surface
modifies the spheres' dynamics, even at separations of tens of radii. This
behavior is captured by a stokeslet analysis of fluid flow driven by the
spheres' and wall's no-slip boundary conditions. In particular, this analysis
reveals surprising asymmetry in the normal modes for pair diffusion near a flat
surface. | cond-mat_soft |
Nucleation-induced transition to collective motion in active systems: While the existence of polar ordered states in active systems is well
established, the dynamics of the self-assembly processes are still elusive. We
study a lattice gas model of self-propelled elongated particles interacting
through excluded volume and alignment interactions, which shows a phase
transition from an isotropic to a polar ordered state. By analyzing the
ordering process we find that the transition is driven by the formation of a
critical nucleation cluster and a subsequent coarsening process. Moreover, the
time to establish a polar ordered state shows a power-law divergence. | cond-mat_soft |
Non-Gaussian Dynamics in Smectic Liquid Crystals of Parallel Hard Rods: Using computer simulations, we studied the diffusion and structural
relaxation in equilibrium smectic liquid crystal bulk phases of parallel hard
spherocylinders. These systems exhibit a non-Gaussian layer-to-layer diffusion
due to the presence of periodic barriers and transient cages, and show
remarkable similarities with the behavior of out-of-equilibrium supercooled
liquids. We detect a very slow inter-layer relaxation dynamics over the whole
density range of the stable smectic phase which spans a time interval of four
time decades. The intrinsic nature of the layered structure yields a
hopping-type diffusion which becomes more heterogeneous for higher packing
fractions. In contrast, the in-layer dynamics is typical of a dense fluid with
a relatively fast decay. Our results on the dynamic behavior agree well with
that observed in systems of freely rotating hard rods, but differ quantitavely,
as the height of the periodic barriers reduces to zero at the nematic-smectic
transition for aligned rods, while it remains finite for freely rotating rods. | cond-mat_soft |
Velocity Distribution and the Effect of Wall Roughness in Granular
Poiseuille Flow: From event-driven simulations of a gravity-driven channel flow of inelastic
hard-disks, we show that the velocity distribution function remains close to a
Gaussian for a wide range densities (even when the Knudsen number is of order
one) if the walls are smooth and the particle collisions are nearly elastic.
For dense flows, a transition from a Gaussian to a power-law distribution for
the high velocity tails occurs with increasing dissipation in the center of the
channel, irrespective of wall-roughness. For a rough wall, the near-wall
distribution functions are distinctly different from those in the bulk even in
the quasielastic limit. | cond-mat_soft |
Dynamic path dependence of phase behaviors in dense active system: There are rich emergent phase behaviors in non-equilibrium active systems.
Flocking and clustering are two representative dynamic phases. The relationship
between these two phases is still unclear. In the paper, we numerically
investigate the evolution of flocking and clustering in a system consisting of
self-propelled particles with active reorientation. We consider the interplay
between flocking and clustering phases under different initial states, and
observe an unstable domain in order parameters phase diagrams due to initial
states even in the absence of an explicit attraction. This point is different
from the previous finding that active angular fluctuations lead to an earlier
breakdown of collective motion and the emergence of a new bi-stable regime in
the aligned active particles [R.Grossmann et al, New J. Phys.073033,14 (2012)].
In particular, we find that the existence of bi-stable states is due to the
diversity of dynamic paths arising from different initial states. By increasing
(decreasing) the initial degree of ordering, the bi-stable state can be shifted
to a more ordered flocking (disordered clustering) state. These results
enlighten us pave the way to manipulate emergent behaviors and collective
motions of active system. | cond-mat_soft |
Shear-induced ordering of nano-pores and instabilities in concentrated
surfactant mesh phases: Mixed surfactant systems with strongly bound counterions show many
interesting phases such as the random mesh phase consisting of a disordered
array of defects (water-filled nano-pores in the bilayers). The present study
addresses the non-equilibrium phase transition of the random mesh phase under
shear to an ordered mesh phase with a high degree of coherence between
nano-pores in three-dimension. In-situ small-angle synchrotron X-ray study
under different shear stress conditions shows sharp Bragg peaks in the X-ray
diffraction, successfully indexed to the rhombohedral lattice with R$\bar{3}$m
space group symmetry. The ordered mesh phase shows isomorphic twinning and
buckling at higher shear stress. Our experimental studies bring out rich
non-equilibrium phase transitions in concentrated cationic surfactant systems
with strongly bound counterions hitherto not well-explored and provide
motivation for a quantitative understanding. | cond-mat_soft |
How reciprocity impacts ordering and phase separation in active
nematics?: Active nematics undergo spontaneous symmetry breaking and show phase
separation instability. Within the prevailing notion that macroscopic
properties depend only on symmetries and conservation laws, different
microscopic models are used out of convenience. Here, we test this notion
carefully by analyzing three different microscopic models of apolar active
nematics. They share the same symmetry but differ in implementing reciprocal or
non-reciprocal interactions, including a Vicsek-like implementation. We show
how such subtle differences in microscopic realization determine if the
ordering transition is continuous or first order. Despite the difference in the
type of phase transition, all three models exhibit fluctuation-dominated phase
separation and quasi-long-range order in the nematic phase. | cond-mat_soft |
Controlling the self-assembly of binary copolymer mixtures in solution
through molecular architecture: We present a combined experimental and theoretical study on the role of
copolymer architecture in the self-assembly of binary PEO-PCL mixtures in
water-THF, and show that altering the chain geometry and composition of the
copolymers can control the form of the self-assembled structures and lead to
the formation of novel aggregates. First, using transmission electron
microscopy and turbidity measurements, we study a mixture of sphere-forming and
lamella-forming PEO-PCL copolymers, and show that increasing the molecular
weight of the lamella-former at a constant ratio of its hydrophilic and
hydrophobic components leads to the formation of highly-curved structures even
at low sphere-former concentrations. This result is explained using a simple
argument based on the effective volumes of the two sections of the diblock and
is reproduced in a coarse-grained mean-field model: self-consistent field
theory (SCFT). Using further SCFT calculations, we study the distribution of
the two copolymer species within the individual aggregates and discuss how this
affects the self-assembled structures. We also investigate a binary mixture of
lamella-formers of different molecular weights, and find that this system forms
vesicles with a wall thickness intermediate to those of the vesicles formed by
the two copolymers individually. This result is also reproduced using SCFT.
Finally, a mixture of sphere-former and a copolymer with a large hydrophobic
block is shown to form a range of structures, including novel elongated
vesicles. | cond-mat_soft |
Hexatic phase and water-like anomalies in a two-dimensional fluid of
particles with a weakly softened core: We study a two-dimensional fluid of particles interacting through a
spherically-symmetric and marginally soft two-body repulsion. This model can
exist in three different crystal phases, one of them with square symmetry and
the other two triangular. We show that, while the triangular solids first melt
into a hexatic fluid, the square solid is directly transformed on heating into
an isotropic fluid through a first-order transition, with no intermediate
tetratic phase. In the low-pressure triangular and square crystals melting is
reentrant provided the temperature is not too low, but without the necessity of
two competing nearest-neighbor distances over a range of pressures. A whole
spectrum of water-like fluid anomalies completes the picture for this model
potential. | cond-mat_soft |
Phase Dependent Forcing and Synchronization in the three-sphere model of
Chlamydomonas: The green alga {\it Chlamydomonas} swims with synchronized beating of its two
flagella, and is experimentally observed to exhibit run-and-tumble behaviour
similar to bacteria. Recently we studied a simple hydrodynamic three-sphere
model of {\it Chlamydomonas} with a phase dependent driving force which can
produce run-and-tumble behaviour when intrinsic noise is added, due to the
non-linear mechanics of the system. Here, we consider the noiseless case and
explore numerically the parameter space in the driving force profiles, which
determine whether or not the synchronized state evolves from a given initial
condition, as well as the stability of the synchronized state. We find that
phase dependent forcing, or a beat pattern, is necessary for stable
synchronization in the geometry we work with. | cond-mat_soft |
Non-Equilibrium Effects of Molecular Motors on Polymers: We present a generic coarse-grained model to describe molecular motors acting
on polymer substrates, mimicking, for example, RNA polymerase on DNA or kinesin
on microtubules. The polymer is modeled as a connected chain of beads; motors
are represented as freely diffusing beads which, upon encountering the
substrate, bind to it through a short-ranged attractive potential. When bound,
motors and polymer beads experience an equal and opposite active force,
directed tangential to the polymer; this leads to motion of the motors along
the polymer contour. The inclusion of explicit motors differentiates our model
from other recent active polymer models. We study, by means of Langevin
dynamics simulations, the effect of the motor activity on both the
conformational and dynamical properties of the substrate. We find that activity
leads, in addition to the expected enhancement of polymer diffusion, to an
effective reduction of its persistence length. We discover that this effective
"softening" is a consequence of the emergence of double-folded branches, or
hairpins, and that it can be tuned by changing the number of motors or the
force they generate. Finally, we investigate the effect of the motors on the
probability of knot formation. Counter-intuitively our simulations reveal that,
even though at equilibrium a more flexible substrate would show an increased
knotting probability, motor activity leads to a marked decrease in the
occurrence of knotted conformations with respect to equilibrium. | cond-mat_soft |
How granular materials deform in quasistatic conditions: Based on numerical simulations of quasistatic deformation of model granular
materials, two rheological regimes are distinguished, according to whether
macroscopic strains merely reflect microscopic material strains within the
grains in their contact regions (type I strains), or result from instabilities
and contact network rearrangements at the microscopic level (type II strains).
We discuss the occurrence of regimes I and II in simulations of model materials
made of disks (2D) or spheres (3D). The transition from regime I to regime II
in monotonic tests such as triaxial compression is different from both the
elastic limit and from the yield threshold. The distinction between both types
of response is shown to be crucial for the sensitivity to contact-level
mechanics, the relevant variables and scales to be considered in
micromechanical approaches, the energy balance and the possible occurrence of
macroscopic instabilities | cond-mat_soft |
Confocal microscopy of colloidal particles: towards reliable, optimum
coordinates: Over the last decade, the light microscope has become increasingly useful as
a quantitative tool for studying colloidal systems. The ability to obtain
particle coordinates in bulk samples from micrographs is particularly
appealing. In this paper we review and extend methods for optimal image
formation of colloidal samples, which is vital for particle coordinates of the
highest accuracy, and for extracting the most reliable coordinates from these
images. We discuss in depth the accuracy of the coordinates, which is sensitive
to the details of the colloidal system and the imaging system. Moreover, this
accuracy can vary between particles, particularly in dense systems. We
introduce a previously unreported error estimate and use it to develop an
iterative method for finding particle coordinates. This individual-particle
accuracy assessment also allows comparison between particle locations obtained
from different experiments. Though aimed primarily at confocal microscopy
studies of colloidal systems, the methods outlined here should transfer readily
to many other feature extraction problems, especially where features may
overlap one another. | cond-mat_soft |
Microstructures and Dynamics of Tetraalkylphosphonium Chloride Ionic
Liquids: Atomistic simulations have been performed to investigate the effect of
aliphatic chain length in tetraalkylphosphonium cations on liquid morphologies,
microscopic ionic structures and dynamical properties of tetraalkylphosphonium
chloride ionic liquids. The liquid morphologies are characterized by
sponge-like interpenetrating polar and apolar networks in ionic liquids
consisting of tetraalkylphosphonium cations with short aliphatic chains. The
lengthening aliphatic chains in tetraalkylphosphonium cations leads to polar
domains consisting of chloride anions and central polar groups in cations being
partially or totally segregated in ionic liquid matrices due to a progressive
expansion of apolar domains in between. Prominent polarity alternation peaks
and adjacency correlation peaks are observed at low and high $q$ range in total
X-ray scattering structural functions, respectively, and their peak positions
gradually shift to lower q values with lengthening aliphatic chains in
tetraalkylphosphonium cations. The charge alternation peaks registered in
intermediate q range exhibit complicated tendencies due to the complete
cancellations of peaks and anti-peaks in partial structural functions for ionic
subcomponents. The particular microstructures and liquid morphologies in
tetraalkylphosphonium chloride ionic liquids intrinsically contribute to
distinct dynamics characterized by translational diffusion coefficients, van
Hove correlation functions, and non-Gaussian parameters for ionic species in
heterogeneous ionic environment. The increase of aliphatic chain length in
tetraalkylphosphonium cations leads to concomitant shift of van Hove
correlation functions and non-Gaussian parameters to larger radial distances
and longer timescales, respectively, indicating the enhanced translational
dynamical heterogeneities of tetraalkylphosphonium cations and the
corresponding chloride anions. | cond-mat_soft |
New Field Model of Polymer/Nanoparticle Mixture-Realizing Discreteness
in the Continuous Description: Field-theoretical method is efficient in predicting the assembling structures
of polymeric systems. However, for the polymer/nanoparticle mixture, the
continuous density description is not suitable to capture the realistic
assembly of particles, especially when the size of particle is much larger than
the polymer segment. Here, we developed a field-based model, in which the
particles are eventually discrete and hence it can overcome the drawbacks of
the conventional field descriptions, e.g., inadequate and crude treatment on
the polymer-particle interface and the excluded-volume interaction. We applied
the model to study the simplest system of nanoparticles immersed in dense
homopolymer solution. Our model can address the depletion effect and
interfacial interaction in a more delicate way. Insights into the enthalpic
and/or entropic origin of the structural variation due to the competition
between depletion and interfacial interaction are obtained. New phenomena such
as depletion-enhanced bridging aggregation are observed in the case of strong
interfacial attraction and large depletion length. This approach is readily
extendable to studying more complex polymer-based nanocomposites or
biology-related systems, such as dendrimer/drug encapsulation and
membrane/particle assembly. | cond-mat_soft |
Mediated interactions between rigid inclusions in two-dimensional
elastic or fluid films: Interactions between rigid inclusions in continuous three-dimensional
linearly elastic solids and low-Reynolds-number viscous fluids have largely
been quantified during the past. Prime example systems are given by
functionalized elastic composite materials or fluid colloidal suspensions.
Here, we address the significantly less frequently studied situation of rigid
inclusions in two-dimensional elastic or low-Reynolds-number fluid films. We
concentrate on the situation in which disk-like inclusions remain well
separated from each other and do not get into contact. Specifically, we
demonstrate and explain that the logarithmic divergence of the associated
Green's function is removed in the absence of net external forces on the
inclusions, in line with physical intuition. For instance, this situation
applies when only pairwise mutual interactions between the inclusions prevail.
Our results will support, for example, investigations on membranes
functionalized by appropriate inclusions, both of technical or biological
origin, or the dynamics of active microswimmers in appropriately prepared thin
films. | cond-mat_soft |
Repulsive and attractive depletion forces mediated by nonadsorbing
polyelectrolytes in the Donnan limit: In mixtures of colloids and nonadsorbing polyelectrolytes, a Donnan potential
arises across the region between surfaces that are depleted of polyelectrolyte
and the rest of the system. This Donnan potential tends to shift the
polyelectrolyte density profile towards the colloidal surface and leads to
local accumulation of polyelectrolytes. We derive a zero-field theory for the
disjoining pressure between two parallel flat plates. Polyelectrolyte is
allowed to enter the confined interplate region at the cost of a conformational
free energy penalty. The resulting disjoining pressure shows a crossover to a
repulsive regime when the interplate separation gets smaller than the size of
the polyelectrolyte chain, followed by an attractive part. We find a
quantitative match between the model and self-consistent field computations
that take into account the full Poisson-Boltzmann electrostatics. | cond-mat_soft |
Frustrated colloidal ordering and fully packed loops in arrays of
optical traps: We propose that a system of colloidal particles interacting with a honeycomb
array of optical traps that each contain three wells can be used to realize a
fully packed loop model. One of the phases in this system can be mapped to
Baxter's three-coloring problem, offering an easily accessible physical
realization of this problem. As a function of temperature and interaction
strength, we find a series of phases, including long range ordered loop or
stripe states, stripes with sliding symmetries, random packed loop states, and
disordered states in which the loops break apart. Our geometry could be
constructed using ion trap arrays, BEC vortices in optical traps, or magnetic
vortices in nanostructured superconductors. | cond-mat_soft |
Construction and calibration of a goniometer to measure contact angles
and calculate the surface free energy in solids with uncertainty analysis: Here, we present the construction and calibration of a low-cost goniometer to
measure contact angles by the sessile drop method. Besides, we propose a simple
and fast method to calculate the uncertainty in the determination of the
surface free energy (SFE) and its polar and dispersive components through the
Owens-Wendt model and tested it by using two testing liquids. The goniometer
performance and the SFE uncertainty were determined on two polymers:
polytetrafluorethylene (PTFE) and polyoxymethylene (POM), by using water and
methylene iodide. The values of contact angle measured were used to calculate
the SFE and its components with their errors. The SFE values obtained for PTFE
were 17.57-17.91 mJ/m^2, with a relative error lower than 5.5 %, whereas those
for POM were 42.80-43.23 mJ/m^2, with a relative error lower than 4.3%. Both
the SFE values and the errors were in the range of those previously reported.
Based on the mathematical analysis of the uncertainty propagation in the
determination of SFE, we concluded that the uncertainty is minimized when the
testing liquids are an apolar liquid and water. | cond-mat_soft |
Micro/Nano Motor Navigation and Localization via Deep Reinforcement
Learning: Efficient navigation and precise localization of Brownian micro/nano
self-propelled motor particles within complex landscapes could enable future
high-tech applications involving for example drug delivery, precision surgery,
oil recovery, and environmental remediation. Here we employ a model-free deep
reinforcement learning algorithm based on bio-inspired neural networks to
enable different types of micro/nano motors to be continuously controlled to
carry out complex navigation and localization tasks. Micro/nano motors with
either tunable self-propelling speeds or orientations or both, are found to
exhibit strikingly different dynamics. In particular, distinct control
strategies are required to achieve effective navigation in free space and
obstacle environments, as well as under time constraints. Our findings provide
fundamental insights into active dynamics of Brownian particles controlled
using artificial intelligence and could guide the design of motor and robot
control systems with diverse application requirements. | cond-mat_soft |
Bubble Relaxation Dynamics in Double-Stranded DNA: The paper deals with the two-state (opening-closing of base pairs) model used
to describe the fluctuation dynamics of a single bubble formation. We present
an exact solution for the discrete and finite size version of the model that
includes end effects and derive analytic expressions of the correlation
function, survival probability and lifetimes for the bubble relaxation
dynamics. It is shown that the continuous and semi-infinite limit of the model
becomes a good approximation to exact result when a^N << 1, where N is bubble
size and a, the ratio of opening to closing rates of base pairs, is the control
parameter of DNA melting. | cond-mat_soft |
Force Dipole Interactions in Tubular Fluid Membranes: We construct viscous fluid flow sourced by a force dipole embedded in a
cylindrical fluid membrane, coupled to external embedding fluids. We find
analytic expressions for the flow, in the limit of infinitely long and thin
tubular membranes. We utilize this solution to formulate the in-plane dynamics
of a pair of pusher-type dipoles along the cylinder surface. We find that a
mutually perpendicular dipole pair generically move together along helical
geodesics. Since the cylindrical geometry breaks the in-plane rotational
symmetry of the membrane, there is a difference in flows along the axial and
transverse directions of the cylinder. This in turn leads to anisotropic
hydrodynamic interaction between the dipoles and is remarkably different from
flat and spherical fluid membranes. In particular, the flow along the compact
direction of the cylinder has a local rigid rotation term (independent of the
angular coordinate but decays along the axis of the cylinder). Due to this
feature of the flow, we observe that the interacting dipole pair initially
situated along the axial direction exhibits an overall drift along the compact
angular direction of the tubular fluid membrane. We find that the drift for the
dipole pair increases linearly with time. Our results are relevant for
non-equilibrium dynamics of motor proteins in tubular membranes arising in
nature, as well as in-vitro experiments (25). | cond-mat_soft |
The FCC-BCC-Fluid triple point for model pair interactions with variable
softness: It is demonstrated that the coordinates of the fcc-bcc-fluid triple point of
various model systems are located in a relatively narrow region, when expressed
in terms of the two proper variables, characterizing the softness and strength
of the interaction force at the mean interparticle separation. This can be
regarded as a consequence of the "corresponding states principle" for strongly
interacting particle systems we have put forward recently [S. A. Khrapak, M.
Chaudhuri, and G. E. Morfill, J. Chem. Phys. {\bf 134}, 241101 (2011)]. The
related possibilities to predict the existence and approximate location of the
fcc-bcc-fluid triple point for a wide range of pair interactions with variable
softness are illustrated. Relation of the obtained results to experimental
studies of complex (dusty) plasmas are briefly discussed. | cond-mat_soft |
Active particle dynamics beyond the jamming density: Many biological systems form colonies at high density. Passive granular
systems will be jammed at such densities, yet for the survival of biological
systems it is crucial that they are dynamic. We construct a phase diagram for a
system of active particles interacting via Vicsek alignment, and vary the
density, self-propulsion force, and orientational noise. We find that the
system exhibits four different phases, characterized by transitions in the
effective diffusion constant and in the orientational order parameter. Our
simulations show that there exists an optimal noise such that particles require
a minimal force to unjam, allowing for rearrangements. | cond-mat_soft |
Topology of protocells: do nanoholes catalyse fission ?: We propose a mechanism with a low activation energy for lipid translocation,
based on a change of topology of the membrane of a protocell. The inner and
outer layers are connected and form toroidal nanoholes stabilised by repulsive
electrostatic forces for small radius and attractive elastic forces for large
radius. Thanks to these holes, the energy barrier of translocation is
drastically reduced and a difference of temperature between the inside and the
outside of the protocell can induce a differential growth of these layers,
until the vesicle splits in two. | cond-mat_soft |
Sequence Dependence of Electronic Transport in DNA: We study electronic transport in long DNA chains using the tight-binding
approach for a ladder-like model of DNA. We find insulating behavior with
localizaton lengths xi ~ 25 in units of average base-pair seperation.
Furthermore, we observe small, but significant differences between lambda-DNA,
centromeric DNA, promoter sequences as well as random-ATGC DNA. | cond-mat_soft |
Counter-ions at single charged wall: Sum rules: For inhomogeneous classical Coulomb fluids in thermal equilibrium, like the
jellium or the two-component Coulomb gas, there exists a variety of exact sum
rules which relate the particle one-body and two-body densities. The necessary
condition for these sum rules is that the Coulomb fluid possesses good
screening properties, i.e. the particle correlation functions or the averaged
charge inhomogeneity, say close to a wall, exhibit a short-range (usually
exponential) decay. In this work, we study equilibrium statistical mechanics of
an electric double layer with counter-ions only, i.e. a globally neutral system
of equally charged point-like particles in the vicinity of a plain hard wall
carrying a fixed uniform surface charge density of opposite sign. At large
distances from the wall, the one-body and two-body counter-ion densities go to
zero slowly according to the inverse-power law. In spite of the absence of
screening, all known sum rules are shown to hold for two exactly solvable cases
of the present system: in the weak-coupling Poisson-Boltzmann limit (in any
spatial dimension larger than one) and at a special free-fermion coupling
constant in two dimensions. This fact indicates an extended validity of the sum
rules and provides a consistency check for reasonable theoretical approaches. | cond-mat_soft |
Topological Linking Drives Anomalous Thickening of Ring Polymers In Weak
Extensional Flows: Molecular dynamics simulations confirm recent extensional flow experiments
showing ring polymer melts exhibit strong extension-rate thickening of the
viscosity at Weissenberg numbers $Wi<<1$. Thickening coincides with the extreme
elongation of a minority population of rings that grows with $Wi$. The large
susceptibility of some rings to extend is due to a flow-driven formation of
topological links that connect multiple rings into supramolecular chains. Links
form spontaneously with a longer delay at lower $Wi$ and are pulled tight and
stabilized by the flow. Once linked, these composite objects experience larger
drag forces than individual rings, driving their strong elongation. The
fraction of linked rings generated by flow depends non-monotonically on $Wi$,
increasing to a maximum when $Wi\sim1$ before rapidly decreasing when the
strain rate approaches the relaxation rate of the smallest ring loops $\sim
1/\tau_e$. | cond-mat_soft |
Lattice models of directed and semiflexible polymers in anisotropic
environment: We study the conformational properties of polymers in presence of extended
columnar defects of parallel orientation. Two classes of macromolecules are
considered: the so-called partially directed polymers with preferred
orientation along direction of the external stretching field and semiflexible
polymers. We are working within the frames of lattice models: partially
directed self-avoiding walks (PDSAWs) and biased self-avoiding walks (BSAWs).
Our numerical analysis of PDSAWs reveals, that competition between the
stretching field and anisotropy caused by presence of extended defects leads to
existing of three characteristic length scales in the system. At each fixed
concentration of disorder we found a transition point, where the influence of
extended defects is exactly counterbalanced by the stretching field. Numerical
simulations of BSAWs in anisotropic environment reveal an increase of polymer
stiffness. In particular, the persistence length of semiflexible polymers
increases in presence of disorder. | cond-mat_soft |
Correlation between ordering and shear thinning in confined liquids: Despite the extensive research that has been conducted for decades on the
behavior of confined liquids, detailed knowledge of this phenomenon,
particularly in the mixed/boundary lubrication regime, remains limited. This
can be attributed to several factors including the difficulty of direct
experimental observations of the behavior of lubricant molecules under
non-equilibrium conditions, the high computational cost of molecular
simulations to reach steady state, and the low signal-to-noise ratio at
extremely low shear rates corresponding to actual operating conditions. To this
end, we studied the correlation between the structure formation and shear
viscosity of octamethylcyclotetrasiloxane confined between two mica surfaces in
a mixed/boundary lubrication regime. Three different surface separations
corresponding to two-, three-, and five-layered structures were considered to
analyze the effect of confinement. The orientational distributions with one
specific peak for $n=2$ and two distributions, including a parallel orientation
with the surface normal for $n>2$, were observed at rest. The confined liquids
exhibited a distinct shear-thinning behavior independent of surface separations
for a relatively low sliding velocity, $V_{\rm x}\lesssim 10^{-1}\,{\rm m/s}$.
However, the shear viscosities at $V_{\rm x}\lesssim 10^{-1}\,{\rm m/s}$
depended on the number of layered structures. Newtonian behavior was observed
with a further increase in the sliding velocity. Furthermore, we found a strong
correlation between the degree of molecular orientation and the shear viscosity
of the confined liquids. The magnitude of the shear viscosity of the confined
liquids can primarily be determined by the degree of molecular orientation, and
shear-thinning originates from the vanishing of specific orientational
distributions with increasing sliding velocity. | cond-mat_soft |
Predicting Pair Correlation Functions of Glasses using Machine Learning: Glasses offer a broad range of tunable thermophysical properties that are
linked to their compositions. However, it is challenging to establish a
universal composition-property relation of glasses due to their enormous
composition and chemical space. Here, we address this problem and develop a
metamodel of composition-atomistic structure relation of a class of glassy
material via a machine learning (ML) approach. Within this ML framework, an
unsupervised deep learning technique, viz. convolutional neural network (CNN)
autoencoder, and a regression algorithm, viz. random forest (RF), are
integrated into a fully automated pipeline to predict the spatial distribution
of atoms in a glass. The RF regression model predicts the pair correlation
function of a glass in a latent space. Subsequently, the decoder of the CNN
converts the latent space representation to the actual pair correlation
function of the given glass. The atomistic structures of silicate (SiO2) and
sodium borosilicate (NBS) based glasses with varying compositions and dopants
are collected from molecular dynamics (MD) simulations to establish and
validate this ML pipeline. The model is found to predict the atom pair
correlation function for many unknown glasses very accurately. This method is
very generic and can accelerate the design, discovery, and fundamental
understanding of composition-atomistic structure relations of glasses and other
materials. | cond-mat_soft |
Force balance of particles trapped at fluid interfaces: We study the effective forces acting between colloidal particles trapped at a
fluid interface which itself is exposed to a pressure field. To this end we
apply what we call the ``force approach'', which relies solely on the condition
of mechanical equilibrium and turns to be in a certain sense less restrictive
than the more frequently used ``energy approach'', which is based on the
minimization of a free energy functional. The main goal is to elucidate the
advantages and disadvantages of the force approach as compared to the energy
approach. First, we derive a general stress-tensor formulation of the forces at
the interface and work out a useful analogy with 2D electrostatics in the
particular case of small deformations of the interface relative to its flat
configuration. We apply this analogy to compute the asymptotic decay of the
effective force between particles trapped at a fluid interface, extending the
validity of previous results. Second, we address the case of deformations of a
non-flat interface. We compute the deformation of a spherical droplet due to
the electric field of a charged particle trapped at its surface and conclude
that the interparticle capillary force is unlikely to explain certain recent
experimental observations. Finally we discuss the application to a generally
curved interface and show as an illustrative example that a nonspherical
particle deposited on an interface forming a minimal surface is pulled to
regions of larger curvature. | cond-mat_soft |
Weak Viscoelastic Nematodynamics of Maxwell Type: A constitutive theory for weak viscoelastic nematodynamics of Maxwell type is
developed using the standard local approach of non-equilibrium thermodynamics.
Along with particular viscoelastic and nematic kinematics, the theory uses the
weakly elastic potential proposed by de Gennes for nematic solids and the LEP
constitutive equations for viscous nematic liquids, while ignoring the Frank
(orientation) elasticity and inertia effects. In spite of many basic
parameters, algebraic properties of nematic operations investigated in
Appendix, allowed us to reveal a general group structure of the theory and
present it in a simple form. It is shown that the evolution equation for
director is also viscoelastic. An example of magnetization clarifies the
situation with non-symmetric stresses. When the sources of stress asymmetry are
absent, the theory is simplified and its relaxation properties are described by
a symmetric subgroup of nematic algebraic operations. A purely linear
constitutive behavior exemplifies the symmetric situation. | cond-mat_soft |
Open and anisotropic soft regions in a model polymer glass: The vibrational dynamics of a model polymer glass is studied by Molecular
Dynamics simulations. The focus is on the "soft" monomers with high
participation to the lower-frequency vibrational modes contributing to the
thermodynamic anomalies of glasses. To better evidence their role, the
threshold to qualify monomers as soft is made severe, allowing for the use of
systems with limited size. A marked tendency of soft monomers to form
quasi-local clusters involving up to 15 monomers is evidenced. Each chain
contributes to a cluster up to about three monomers and a single cluster
involves monomer belonging to about 2-3 chains. Clusters with monomers
belonging to a single chain are rare. The open and tenuous character of the
clusters is revealed by their fractal dimension $d_f < 2$. The inertia tensor
of the soft clusters evidences their strong anisotropy in shape and remarkable
linear correlation of the two largest eigenvalues. Owing to the limited size of
the system, finite-size effects, as well as dependence of the results on the
adopted polymer length, cannot be ruled out. | cond-mat_soft |
Macroscopic forces in inhomogeneous polyelectrolyte solutions: In this paper, we present a self-consistent field theory of macroscopic
forces in spatially inhomogeneous flexible chain polyelectrolyte solutions. We
derive an analytical expression for a stress tensor which consists of three
terms: isotropic hydrostatic stress, electrostatic (Maxwell) stress, and stress
rising from conformational entropy of polymer chains -- conformational stress.
We apply our theory to the description of polyelectrolyte solutions confined in
a conductive slit nanopore and observe anomalous behavior of disjoining
pressure and electric differential capacitance. | cond-mat_soft |
Self-propelled Worm-like Filaments: Spontaneous Spiral Formation,
Structure, and Dynamics: Worm-like filaments that are propelled homogeneously along their tangent
vector are studied by Brownian dynamics simulations. Systems in two dimensions
are investigated, corresponding to filaments adsorbed to interfaces or
surfaces. A large parameter space covering weak and strong propulsion, as well
as flexible and stiff filaments is explored. For strongly propelled and
flexible filaments, the free-swimming filaments spontaneously form stable
spirals. The propulsion force has a strong impact on dynamic properties, such
as the rotational and translational mean square displacement and the rate of
conformational sampling. In particular, when the active self-propulsion
dominates thermal diffusion, but is too weak for spiral formation, the
rotational diffusion coefficient has an activity-induced contribution given by
$v_c/\xi_P$, where $v_c$ is the contour velocity and $\xi_P$ the persistence
length. In contrast, structural properties are hardly affected by the activity
of the system, as long as no spirals form. The model mimics common features of
biological systems, such as microtubules and actin filaments on motility assays
or slender bacteria, and artificially designed microswimmers. | cond-mat_soft |
A microscopic model for chemically-powered Janus motors: Very small synthetic motors that make use of chemical reactions to propel
themselves in solution hold promise for new applications in the development of
new materials, science and medicine. The prospect of such potential
applications, along with the fact that systems with many motors or active
elements display interesting cooperative phenomena of fundamental interest, has
made the study of synthetic motors an active research area. Janus motors,
comprising catalytic and noncatalytic hemispheres, figure prominently in
experimental and theoretical studies of these systems. While continuum models
of Janus particle systems are often used to describe motor dynamics,
microscopic models that are able to account for intermolecular interactions,
many-body concentration gradients, fluid flows and thermal fluctuations provide
a way to explore the dynamical behavior of these complex out-of-equilibrium
systems that does not rely on approximations that are often made in continuum
theories. The analysis of microscopic models from first principles provides a
foundation from which the range of validity and limitations of approximate
theories of the dynamics may be assessed. In this paper, a microscopic model
for the diffusiophoretic propulsion of Janus motors, where motor interactions
with the environment occur only through hard collisions, is constructed,
analyzed and compared to theoretical predictions. Microscopic simulations of
both single-motor and many-motor systems are carried out to illustrate the
results. | cond-mat_soft |
Intercellular Friction and Motility Drive Orientational Order in Cell
Monolayers: Spatiotemporal patterns in multicellular systems are important to
understanding tissue dynamics, for instance, during embryonic development and
disease. Here, we use a multiphase field model to study numerically the
behavior of a near-confluent monolayer of deformable cells with intercellular
friction. Varying friction and cell motility drives a solid-liquid transition,
and near the transition boundary, we find the emergence of nematic order of
cell deformation driven by shear-aligning cellular flows. Intercellular
friction endows the monolayer with a finite viscosity, which significantly
increases the spatial correlation in the flow and, concomitantly, the extent of
nematic order. We also show that hexatic and nematic order are tightly coupled
and propose a mechanical-geometric model for the colocalization of +1/2 nematic
defects and 5-7 disclination pairs, which are the structural defects in the
hexatic phase. Such topological defects coincide with regions of high cell-cell
overlap, suggesting that they may mediate cellular extrusion from the
monolayer, as found experimentally. Our results delineate a mechanical basis
for the recent observation of nematic and hexatic order in multicellular
collectives in experiments and simulations and pinpoint a generic pathway to
couple topological and physical effects in these systems. | cond-mat_soft |
Healing of polymer interfaces: Interfacial dynamics, entanglements, and
strength: Self-healing of polymer films often takes place as the molecules diffuse
across a damaged region, above their melting temperature. Using molecular
dynamics simulations we probe the healing of polymer films and compare the
results with those for thermal welding of homopolymer slabs. The two processes
differ in their interfacial structure since damage leads to increased
polydispersity and more short chains. A polymer sample was cut into two
separate films that were then held together in the melt state. The recovery of
the damaged film was followed as time elapsed and polymer molecules diffused
across the interface. The mass uptake and formation of entanglements, as
obtained from primitive path analysis, are extracted and correlated with the
interfacial strength obtained from shear simulations. We find that the
interdiffusion is significantly faster in the damaged film compared to welding
because of the presence of short chains. Though interfacial entanglements
increase more rapidly for the damaged films, a large fraction of them are near
chain ends. As a result, the interfacial strength of the healing film increases
more slowly than for welding. For both healing and welding, the interfacial
strength saturates as the bulk entanglement density is recovered across the
interface. However, the saturation strength of the damaged film is below the
bulk strength for the polymer sample. At saturation, cut chains remain near the
healing interface. They are less entangled and thus mechanically weaken the
interface. When the interfacial strength saturates, the number of interfacial
entanglements scales with the corresponding bulk entanglement density. Chain
stiffness increases the density of entanglements, which increases the
interfacial strength. Our results show that a few entanglements across the
interface are sufficient to resist interfacial chain pullout and enhance the
mechanical strength. | cond-mat_soft |
First-order layering and critical wetting transitions in non-additive
hard sphere mixtures: Using fundamental-measure density functional theory we investigate entropic
wetting in an asymmetric binary mixture of hard spheres with positive
non-additivity. We consider a general planar hard wall, where preferential
adsorption is induced by a difference in closest approach of the different
species and the wall. Close to bulk fluid-fluid coexistence the phase rich in
the minority component adsorbs either through a series of first-order layering
transitions, where an increasing number of liquid layers adsorbs sequentially,
or via a critical wetting transition, where a thick film grows continuously. | cond-mat_soft |
Partial osmotic pressures of ions in electrolyte solutions: The concept of the partial osmotic pressure of ions in an electrolyte
solution is critically examined. In principle these can be defined by
introducing a solvent-permeable wall and measuring the force per unit area
which can certainly be attributed to individual ions. Here I demonstrate that
although the total wall force balances the bulk osmotic pressure as required by
mechanical equilibrium, the individual partial osmotic pressures are
extra-thermodynamic quantities dependent on the electrical structure at the
wall, and as such they resemble attempts to define individual ion activity
coefficients. The limiting case where the wall is a barrier to only one species
of ion is also considered, and with ions on both sides the classic Gibbs-Donnan
membrane equilibrium is recovered thus providing a unifying treatment. The
analysis can be extended to illustrate how the electrical state of the bulk is
affected by the nature of the walls and the sample handling history, thus
supporting the 'Gibbs-Guggenheim uncertainty principle' (the notion that the
electrical state is unmeasurable and usually accidentally determined). Since
this uncertainty is conferred also onto individual ion activities, it has
implications for the current (2002) IUPAC definition of pH. | cond-mat_soft |
Soft self-assembled nanoparticles with temperature-dependent properties: The fabrication of versatile building blocks that are reliably self-assemble
into desired ordered and disordered phases is amongst the hottest topics in
contemporary material science. To this end, microscopic units of varying
complexity, aimed at assembling the target phases, have been thought, designed,
investigated and built. Such a path usually requires laborious fabrication
techniques, especially when a specific funcionalisation of the building blocks
is required. Telechelic star polymers, i.e., star polymers made of a number $f$
of di-block copolymers consisting of solvophobic and solvophilic monomers
grafted on a central anchoring point, spontaneously self-assemble into soft
patchy particles featuring attractive spots (patches) on the surface. Here we
show that the tunability of such a system can be widely extended by controlling
the physical and chemical parameters of the solution. Indeed, at fixed external
conditions the self-assembly behaviour depends only on the number of arms
and/or on the ratio of solvophobic to solvophilic monomers. However, changes in
temperature and/or solvent quality makes it possible to reliably change the
number and size of the attractive patches. This allows to steer the mesoscopic
self-assembly behaviour without modifying the microscopic constituents.
Interestingly, we also demonstrate that diverse combinations of the parameters
can generate stars with the same number of patches but different radial and
angular stiffness. This mechanism could provide a neat way of further
fine-tuning the elastic properties of the supramolecular network without
changing its topology. | cond-mat_soft |
Different scenarios of dynamic coupling in glassy colloidal mixtures: Colloidal mixtures represent a versatile model system to study transport in
complex environments. They allow for a systematic variation of the control
parameters, namely size ratio, total volume fraction and composition. We study
the effects of these parameters on the dynamics of dense suspensions using
molecular dynamics simulations and differential dynamic microscopy experiments.
We investigate the motion of the small particles through the matrix of large
particles as well as the motion of the large particles. A particular focus is
on the coupling of the collective dynamics of the small and large particles and
on the different mechanisms leading to this coupling. For large size ratios,
about 1:5, and an increasing fraction of small particles, the dynamics of the
two species become increasingly coupled and reflect the structure of the large
particles. This is attributed to the dominant effect of the large particles on
the motion of the small particles which is mediated by the increasing crowding
of the small particles. Furthermore, for moderate size ratios, about 1:3, and
sufficiently high fractions of small particles, mixed cages are formed and
hence the dynamics are also strongly coupled. Again, the coupling becomes
weaker as the fraction of small particles is decreased. In this case, however,
the collective intermediate scattering function of the small particles shows a
logarithmic decay corresponding to a broad range of relaxation times. | cond-mat_soft |
Elasticity in strongly interacting soft solids: polyelectrolyte network: This paper discusses the elastic behavior of a very long crosslinked
polyelectrolyte chain (Debye-H\"uckel chain), which is weakly charged.
Therefore the response of the crosslinked chain (network) on an external
constant force $f$ acting on the ends of the chain is considered. A
selfconsistent variational computation of an effective field theory is
employed. It is shown, that the modulus of the polyelectrolyte network has two
parts: the first term represents the usual entropy elasticity of connected
flexible chains and the second term takes into account the electrostatic
interaction of the monomers. It is proportional to the squared crosslink
density and the Debye - screening parameter. | cond-mat_soft |
Effective dynamics of twisted and curved scroll waves using virtual
filaments: Scroll waves are three-dimensional excitation patterns that rotate around a
central filament curve; they occur in many physical, biological and chemical
systems. We explicitly derive the equations of motion for scroll wave filaments
in reaction-diffusion systems with isotropic diffusion up to third order in the
filament's twist and curvature. The net drift components define at every
instance of time a virtual filament which lies close to the instantaneous
filament. Importantly, virtual filaments obey simpler, time-independent laws of
motion which we analytically derive here and illustrate with numerical
examples. Stability analysis of scroll waves is performed using virtual
filaments, showing that filament curvature and twist add as quadratic terms to
the nominal filament tension. Applications to oscillating chemical reactions
and cardiac tissue are discussed. | cond-mat_soft |
Elastic monopoles and external torques in nematic liquid crystal
colloids: Up to now it is commonly believed that a colloidal particle suspended in a
nematic liquid crystal never produces elastic monopoles because this violates
the mechanical equilibrium condition. And the only way to obtain deformations
of director field falling off with distance as r^{-1} is to exert an external
torque \Gamma_{ext} on the colloid \cite{de_Gennes}. In this paper we
demonstrate that this statement is not quite correct and elastic monopoles, as
well as dipoles and quadrupoles, can be induced without any external influence
just by the particle itself. A behavior of a spherical colloidal particle with
asymmetric anchoring strength distribution is considered theoretically. It is
demonstrated that such a particle when suspended in a nematic host can produce
director deformations decreasing as $r^{-1}$, i.e. elastic monopoles, by itself
without any external influence. | cond-mat_soft |
Force density functional theory in- and out-of-equilibrium: When a fluid is subject to an external field, as is the case near an
interface or under spatial confinement, then the density becomes spatially
inhomogeneous. Although the one-body density provides much useful information,
a higher level of resolution is provided by the two-body correlations. These
give a statistical description of the internal microstructure of the fluid and
enable calculation of the average interparticle force, which plays an essential
role in determining both the equilibrium and dynamic properties of interacting
fluids. We present a theoretical framework for the description of inhomogeneous
(classical) many-body systems, based explicitly on the two-body correlation
functions. By consideration of local Noether-invariance against spatial
distortion of the system we demonstrate the fundamental status of the
Yvon-Born-Green (YBG) equation as a local force-balance within the fluid. Using
the inhomogeneous Ornstein-Zernike equation we show that the two-body
correlations are density functionals and, thus, that the average interparticle
force entering the YBG equation is also a functional of the one-body density.
The force-based theory we develop provides an alternative to standard density
functional theory for the study of inhomogeneous systems both in- and
out-of-equilibrium. We compare force-based density profiles to the results of
the standard potential-based (dynamical) density functional theory. In
equilibrium, we confirm both analytically and numerically that the standard
approach yields profiles that are consistent with the compressibility pressure,
whereas the force-density functional gives profiles consistent with the virial
pressure. The structure of the theory offers deep insights into the nature of
correlation in dense and inhomogeneous systems. | cond-mat_soft |
Electrohydrodynamic Quincke rotation of a prolate ellipsoid: We experimentally study the occurrence of spontaneous spinning (Quincke
rotation) of an ellipsoid in a uniform DC electric field. For an ellipsoid
suspended in an unbounded fluid, we find two stable states characterized by the
orientation of the ellipsoid long axis relative to the applied electric field :
spinless (parallel) and spinning (perpendicular). The phase diagram of
ellipsoid behavior as a function of field strength and aspect ratio is in close
agreement with the theory of Cebers et al. Phys. Rev .E 63:016301 (2000). We
also investigated the dynamics of the ellipsoidal Quincke rotor resting on a
planar surface with normal perpendicular to the field direction. We find novel
behaviors, such as swinging (long axis oscillating around the applied field
direction) and tumbling, due to the confinement. | cond-mat_soft |
Crystallography on Curved Surfaces: We study static and dynamical properties that distinguish two dimensional
crystals constrained to lie on a curved substrate from their flat space
counterparts. A generic mechanism of dislocation unbinding in the presence of
varying Gaussian curvature is presented in the context of a model surface
amenable to full analytical treatment. We find that glide diffusion of isolated
dislocations is suppressed by a binding potential of purely geometrical origin.
Finally, the energetics and biased diffusion dynamics of point defects such as
vacancies and interstitials is explained in terms of their geometric potential. | cond-mat_soft |
History-dependent growth and reduction of the ripples formed on a swept
granular track: When a solid object or wheel is repeatedly dragged on a dry sandy surface,
ripple patterns are formed. Although the conditions to form ripple patterns
have been studied well, methods to eliminate the developed ripple patterns have
not been understood thus far. Therefore, history-dependent stability of the
ripple patterns formed on a sandy surface is investigated in this study. First,
the ripple patterns are formed by sweeping the flat sandy surface with a
flexible plow at a constant speed. Then, the sweeping speed is reduced, and the
variation of ripple patterns is measured. As a result, we find that the ripple
patterns show hysteresis. Specifically, the increase in amplitude of ripples is
observed when the reduced velocity is close to the initial velocity forming the
ripple pattern. In addition, splitting of ripples is found when the reduced
velocity is further decreased. From a simple analysis of the plow's motion, we
discuss the physical mechanism of the ripple splitting. | cond-mat_soft |
Blinking statistics of a molecular beacon triggered by end-denaturation
of DNA: We use a master equation approach based on the Poland-Scheraga free energy
for DNA denaturation to investigate the (un)zipping dynamics of a denaturation
wedge in a stretch of DNA, that is clamped at one end. In particular, we
quantify the blinking dynamics of a fluorophore-quencher pair mounted within
the denaturation wedge. We also study the behavioural changes in the presence
of proteins, that selectively bind to single-stranded DNA. We show that such a
setup could be well-suited as an easy-to-implement nanodevice for sensing
environmental conditions in small volumes. | cond-mat_soft |
Granular Response to Impact: Topology of the Force Networks: Impact of an intruder on granular matter leads to formation of mesoscopic
force networks seen particularly clearly in the recent experiments carried out
with photoelastic particles, e.g., Clark et al., Phys. Rev. Lett., 114 144502
(2015). These force networks are characterized by complex structure and evolve
on fast time scales. While it is known that total photoelastic activity in the
granular system is correlated with the acceleration of the intruder, it is not
known how the structure of the force network evolves during impact, and if
there is a dominant features in the networks that can be used to describe
intruder's dynamics. Here, we use topological tools, in particular persistent
homology, to describe these features. Persistent homology allows quantification
of both structure and time evolution of the resulting force networks. We find
that there is a clear correlation of the intruder's dynamics and some of the
topological measures implemented. This finding allows us to discuss which
properties of the force networks are most important when attempting to describe
intruder's dynamics. Regarding temporal evolution of the networks, we are able
to define the upper bound on the relevant time scale on which the networks
evolve. | cond-mat_soft |
Smectic ordering in liquid crystal - aerosil dispersions II. Scaling
analysis: Liquid crystals offer many unique opportunities to study various phase
transitions with continuous symmetry in the presence of quenched random
disorder (QRD). The QRD arises from the presence of porous solids in the form
of a random gel network. Experimental and theoretical work support the view
that for fixed (static) inclusions, quasi-long-range smectic order is destroyed
for arbitrarily small volume fractions of the solid. However, the presence of
porous solids indicates that finite-size effects could play some role in
limiting long-range order. In an earlier work, the nematic - smectic-A
transition region of octylcyanobiphenyl (8CB) and silica aerosils was
investigated calorimetrically. A detailed x-ray study of this system is
presented in the preceding Paper I, which indicates that pseudo-critical
scaling behavior is observed. In the present paper, the role of finite-size
scaling and two-scale universality aspects of the 8CB+aerosil system are
presented and the dependence of the QRD strength on the aerosil density is
discussed. | cond-mat_soft |
Toroidal Crystals: Crystalline assemblages of identical sub-units packed together and
elastically bent in the form of a torus have been found in the past ten years
in a variety of systems of surprisingly different nature, such as viral
capsids, self-assembled monolayers and carbon nanomaterials. In this Letter we
analyze the structural properties of toroidal crystals and we provide a unified
description based on the elastic theory of defects in curved geometries. We
find ground states characterized by the presence of 5-fold disclinations on the
exterior of the torus and 7-fold disclinations in the interior. The number of
excess disclinations is controlled primarily by the aspect ratio of the torus,
suggesting a novel mechanism for creating toroidal templates with precisely
controlled valency via functionalization of the defect sites. | cond-mat_soft |
Defects and Metric Anomalies in Föppl-von Kármán Surfaces: A general framework is developed to study the deformation and stress response
in F{\"o}ppl-von K{\'a}rm{\'a}n shallow shells for a given distribution of
defects, such as dislocations, disclinations, and interstitials, and metric
anomalies, such as thermal and growth strains. The theory includes dislocations
and disclinations whose defect lines can both pierce the two-dimensional
surface and lie within the surface. An essential aspect of the theory is the
derivation of strain incompatibility relations for stretching and bending
strains with incompatibility sources in terms of various defect and metric
anomaly densities. The incompatibility relations are combined with balance laws
and constitutive assumptions to obtain the inhomogeneous F{\"o}ppl-von
K{\'a}rm{\'a}n equations for shallow shells. Several boundary value problems
are posed, and solved numerically, by first considering only dislocations and
then disclinations coupled with growth strains. | cond-mat_soft |
Nonlinear screening and gas-liquid separation in suspensions of charged
colloids: We calculate phase diagrams of charged colloidal spheres (valency $Z$ and
radius $a$) in a 1:1 electrolyte from multi-centered nonlinear
Poisson-Boltzmann theory. Our theory takes into account charge-renormalization
of the colloidal interactions and volume terms due to many-body effects. For
valencies as small as Z=1 and as large as $10^4$ we find a gas--liquid spinodal
instability in the colloid-salt phase diagram provided $Z\lB/a\gtrsim24\pm1$,
where $\lB$ is the Bjerrum length. | cond-mat_soft |
Maier-Saupe nematogenic fluid with isotropic Yukawa repulsion at a hard
wall: Mean field approximation: The mean field approximation is formulated within the framework of the
density field theory to study the properties of a Maier-Saupe nematogenic fluid
near a hard wall. The density and the order parameter profiles are obtained
using the analytical expressions derived in the linearized mean field
approximation. The temperature dependencies of the contact values of the
density and order parameter profiles are analyzed in detail. To estimate a
validity of the applied approximations, the obtained theoretical results are
compared with the original computer simulation data. | cond-mat_soft |
Nonlinear optical properties of a channel waveguide produced with
crosslinkable ferroelectric liquid crystals: A binary mixture of ferroelectric liquid crystals (FLCs) was used for the
design of a channel waveguide. The FLCs possess two important functionalities:
a chromophore with a high hyperpolarizability $\beta$ and photoreactive groups.
The smectic liquid crystal is aligned in layers parallel to the glass plates in
a sandwich geometry. This alignment offers several advantages, such as that
moderate electric fields are sufficient to achieve a high degree of polar
order. The arrangement was then permanently fixed by photopolymerization which
yielded a polar network possessing a high thermal and mechanical stability
which did not show any sign of degradation within the monitored period of
several months. The linear and nonlinear optical properties have been measured
and all four independent components of the nonlinear susceptibility tensor
$\bar d$ have been determined. The off-resonant $d$-coefficients are remarkably
high and comparable to those of the best known inorganic materials. The
alignment led to an inherent channel waveguide for p-polarized light without
additional preparation steps. The photopolymerization did not induce scattering
sites in the waveguide and the normalized losses were less than 2 dB/cm. The
material offers a great potential for the design of nonlinear optical devices
such as frequency doublers of low power laser diodes. | cond-mat_soft |
RheoSpeckle: a new tool to investigate local flow and microscopic
dynamics of soft matter under shear: To investigate the interplay between microscopic dynamics and macroscopic
rheology in soft matter, we couple a stress-controlled-rheometer equipped with
a Couette cell to a light scattering setup in the imaging geometry, which
allows us to measure both the deformation field and the microscopic dynamics.
To validate our setup, we test two model systems. For an elastic solid sample,
we recover the expected deformation field within 1 micron. For a pure viscous
fluid seeded with tracer particles, we measure the velocity profile and the
dynamics of the tracers, both during shear and at rest. The velocity profile is
acquired over a gap of 5 mm with a temporal and spatial resolution of 1 s and
100 microns, respectively. At rest, the tracer dynamics have the expected
diffusive behavior. Under shear, the microscopic dynamics corrected for the
average drift due to solid rotation scale with the local shear rate,
demonstrating that our setup captures correctly the relative motion of the
tracers due to the affine deformation. | cond-mat_soft |
Narrow escape in composite domains forming heterogeneous networks: Cellular networks are often composed of thin tubules connecting much larger
node compartments. These structures serve for active or diffusion transport of
proteins. Examples are glial networks in the brain, the endoplasmic reticulum
in cells or dendritic spines located on dendrites. In this latter case, a large
ball forming the head is connected by a narrow passage. In all cases, how the
transport of molecules, ions or proteins is regulated determines the time scale
of chemical reactions or signal transduction. In the present study, based on
modeling diffusion in three dimensions, we compute the mean time for a Brownian
particle to reach a narrow target inside such a composite network made of
tubules connected to spherical nodes. We derive asymptotic formulas by solving
a mixed Neumann-Dirichlet boundary value problem with small Dirichlet part. We
first consider the case of a network domain organized in a 2-D lattice
structure that consists of spherical ball compartments connected via narrow
cylindrical passages. When there is a single target we derive a matrix equation
for each Mean First Passage Time (MFPT) averaged over each spherical
compartment. We then consider a composite domain consisting of a spherical
head-like domain connected to a large cylinder via a narrow cylindrical neck.
For Brownian particles starting within the narrow neck, we derive formulas for
the MFPT to reach a target on the spherical head. When diffusing particles can
be absorbed upon hitting additional absorbing boundaries of the large cylinder,
we compute the probability and conditional MFPT to reach a target. We compare
these formulas with numerical solutions of the mixed boundary value problem and
with Brownian simulations. To conclude, the present analysis reveals that the
mean arrival time, driven by diffusion in heterogeneous networks, is controlled
by the target and narrow passage sizes. | cond-mat_soft |
Elastic disk with isoperimetric Cosserat coating: A circular elastic disk is coated with an elastic beam, absorbing shear and
normal forces without deformation and linearly reacting to a bending moment
with a change in curvature. The inexstensibility of the elastic beam introduces
an isoperimetric constraint, so that the length of the initial circumference of
the disk is constrained to remain fixed during the loading of the disk/coating
system. The mechanical model for this system is formulated, solved for general
loading, and particularized to the case of two equal and opposite traction
distributions, each applied on a small boundary segment (thus modelling
indentation of a coated fiber). The stress fields, obtained via complex
potentials, are shown to evidence a nice correspondence with photoelastic
experiments, ad hoc designed and performed. The presented results are useful
for the design of coated fibers at the micro and nano scales. | cond-mat_soft |
Influence of Micro-mixing on the Size of Liposomes Self-Assembled from
Miscible Liquid Phases: Ethanol injection and variations of it are a class of methods where two
miscible phases---one of which contains dissolved lipids---are mixed together
leading to the self-assembly of lipid molecules to form liposomes. This method
has been suggested, among other applications, for in-situ synthesis of
liposomes as drug delivery capsules. However, the mechanism that leads to a
specific size selection of the liposomes in solution based self-assembly in
general, and in flow-focussing microfluidic devices in particular, has so far
not been established. Here we report two aspects of this problem. A simple and
easily fabricated device for synthesis of monodisperse unilamellar liposomes in
a co-axial flow-focussing microfluidic geometry is presented. We also show that
the size of liposomes is dependent on the extent of micro-convective mixing of
the two miscible phases. Here, a viscosity stratification induced hydrodynamic
instability leads to a gentle micro-mixing which results in larger liposome
size than when the streams are mixed turbulently. The results are in sharp
contrast to a purely diffusive mixing in macroscopic laminar flow that was
believed to occur under these conditions. Further precise quantification of the
mixing characteristics should provide the insights to develop a general theory
for size selection for the class of ethanol injection methods. This will also
lay grounds for obtaining empirical evidence that will enable better control of
liposome sizes and for designing drug encapsulation and delivery devices. | cond-mat_soft |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.