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From Molecular Dynamics to hydrodynamics - a novel Galilean invariant
thermostat: This article proposes a novel thermostat applicable to any particle-based
dynamic simulation. Each pair of particles is thermostated either (with
probability P) with a pairwise Lowe-Andersen thermostat, or (with probability
1-P) with a thermostat that is introduced here, which is based on a pairwise
interaction similar to the Nose-Hoover thermostat. When the pairwise
Nose-Hoover thermostat dominates (low P), the liquid has a high diffusion
coefficient and low viscosity, but when the Lowe-Andersen thermostat dominates,
the diffusion coefficient is low and viscosity is high. This novel
Nose-Hoover-Lowe-Andersen thermostat is Galilean invariant and preserves both
total linear and angular momentum of the system, due to the fact that the
thermostatic forces between each pair of the particles are pairwise additive
and central. We show by simulation that this thermostat also preserves
hydrodynamics. For the (non-interacting) ideal gas at P=0, the diffusion
coefficient diverges and viscosity is zero, while for P>0 it has a finite
value. By adjusting probability P, the Schmidt number can be varied by orders
of magnitude. The temperature deviation from the required value is at least an
order of magnitude smaller than in Dissipative Particle Dynamics (DPD), while
the equilibrium properties of the system are very well reproduced. Applications
of this thermostat include all standard molecular dynamic simulations of dense
liquids and solids with any type of force field, as well as hydrodynamic
simulation of multi-phase systems with largely different bulk viscosities,
including surface viscosity, and of dilute gases and plasmas. | cond-mat_soft |
Geometrically-protected reversibility in hydrodynamic Loschmidt-echo
experiments: We demonstrate an archetypal Loschmidt-echo experiment involving thousands of
droplets which interact in a reversible fashion via a viscous fluid. Firstly,
we show that, unlike equilibrium systems, periodically driven microfluidic
emulsions self-organize and geometrically protect their macroscopic
reversibility. Self-organization is not merely dynamical; we show that it has a
clear structural signature akin to that found in a mixture of molecular
liquids. Secondly, we show that, above a maximal shaking amplitude, structural
order and reversibility are lost simultaneously in the form of a first order
non-equilibrium phase transition. We account for this discontinuous transition
in terms of a memory-loss process. Finally, we suggest potential applications
of microfluidic echo as a robust tool to tailor colloidal self-assembly at
large scales. | cond-mat_soft |
Local stress and pressure in an inhomogeneous system of spherical active
Brownian particles: The stress of a fluid on a confining wall is given by the mechanical wall
forces, independent of the nature of the fluid being passive or active. At
thermal equilibrium, an equation of state exists and stress is likewise
obtained from intrinsic bulk properties; even more, stress can be calculated
locally. Comparable local descriptions for active systems require a particular
consideration of active forces. Here, we derive expressions for the stress
exerted on a local volume of a systems of spherical active Brownian particles
(ABPs). Using the virial theorem, we obtain two identical stress expressions, a
stress due to momentum flux across a hypothetical plane, and a bulk stress
inside of the local volume. In the first case, we obtain an active contribution
to momentum transport in analogy to momentum transport in an underdamped
passive system, and we introduce an active momentum. In the second case, a
generally valid expression for the swim stress is derived. By simulations, we
demonstrate that the local bulk stress is identical to the wall stress of a
confined system for both, non-interacting ABPs as well as ABPs with
excluded-volume interactions. This underlines the existence of an equation of
state for a system of spherical ABPs. Most importantly, our calculations
demonstrated that active stress is not a wall (boundary) effect, but is caused
by momentum transport. We demonstrate that the derived stress expression
permits the calculation of the local stress in inhomogeneous systems of ABPs. | cond-mat_soft |
On the rheology of a liquid-vapor interface: The mass and momentum balances are theoretically studied in heterogeneous
two-component systems. Following Gibbs the system is presented as two bulk and
a single surface phases. Comparing the equations derived with some typical
rheological models, useful information about the location of the interface is
obtained. It was demonstrated that the surface phase for insoluble surfactants
coincides with the equimolecular interface, while for soluble ones it is placed
on the surface of total mass density zero excess. In both cases the surface
phase is close to the surface of tension and kinematic surface. | cond-mat_soft |
Capillary-gravity waves: a "fixed-depth" analysis: We study the onset of the wave-resistance due to the generation of
capillary-gravity waves by a partially immersed moving object in the case where
the object is hold at a fixed immersion depth. We show that, in this case, the
wave resistance varies continuously with the velocity, in qualitative
accordance with recent experiments by Burghelea et al. (Phys. Rev. Lett. 86,
2557 (2001)). | cond-mat_soft |
Propagation velocity of slip front and emergence of macroscopic static
friction in the system with vanishing local static friction: We investigate the propagation of the slip front in the elastic body on the
rigid substrate. We first obtain the slip profile and the slip front velocity
of the steady state by employing the local friction law with the quadratic form
of the slip velocity and with vanishing static friction stress. The macroscopic
static friction stress emerges spontaneously, which is expressed in terms of
the parameter emerging in the friction law. For the model with viscosity, the
macroscopic static friction stress again emerges spontaneously. The analytical
treatment gives estimations for two slip front propagation velocities. They
corresponds to two different boundary conditions, and one of them describes the
framework employed here. Linear Marginal Stability Hypothesis based on the
linearized equation of motion shows that two slip front propagation velocities
exist in this system, both of which coincide with the analytical solutions
noted above. These imply that the linearized friction law dominantly governs
the slip front propagation behavior. Seismological implications are also given
based on the analytical and numerical results. | cond-mat_soft |
Surface Granular flows: Two Related Examples: Granular surface flows are common in industrial practice and natural systems,
however, theoretical description of such flows is at present incomplete. Two
prototype systems involving surface flow are compared: heap formation by
pouring at a point and rotating cylinders. Continuum models for analysis of
these flows are reviewed, and experimental results for quasi-2d systems are
presented. Experimental results in both systems are well described by continuum
models. | cond-mat_soft |
Current-Voltage Characteristics and non-Gaussian fluctuations in two
different protein light receptors: We investigate conductance and conductance fluctuations of two transmembrane
proteins, bacteriorhodopsin and proteorhodopsin, belonging to the family of
protein light receptors. These proteins are widely diffused in aqueous
environments, are sensitive to visible light and are promising biomaterials for
the realization of novel photodevices. The conductance exhibits a rapid
increase at increasing applied voltages, over a threshold value. Around the
threshold value the variance of conductance fluctuations shows a dramatic jump
of about 5 orders of magnitude: conductance and variance behaviours trace a
second order phase transition. Furthermore, the conductance fluctuations
evidence a non-Gaussian behaviour with a probability density function (PDF)
which follows a generalized Gumbel distribution, typical of extreme-value
statistics. The theoretical model is validated on existing current-voltage
measurements and the interpretation of the PDF of conductance fluctuations is
proven to be in line with the microscopic mechanisms responsible of charge
transport. | cond-mat_soft |
Tilting behavior of lamellar ice tip during unidirectional freezing of
aqueous solutions: Freezing of ice has been largely reported from many aspects, especially its
complex pattern formation. Ice grown from liquid phase is usually
characteristic of lamellar morphology which plays a significant role in various
domains. However, tilted growth of ice via transition from coplanar to
non-coplanar growth in directional solidification has been paid little
attention in previous studies and there is misleading explanation of the
formation of tilted lamellar ice. Here, we in-situ investigated the variations
of tilting behavior of lamellar ice tip under different conditions within a
single ice crystal with manipulated orientation via unidirectional freezing of
aqueous solutions. It is found that tilted growth of ice tips is sensitive to
pulling velocity and solute type. These experimental results reveal intrinsic
tilted growth behavior of lamellar ice and enrich our understanding in pattern
formation of ice. | cond-mat_soft |
Disjoining Pressure and the Film-Height-Dependent Surface Tension of
Thin Liquid Films: New Insight from Capillary Wave Fluctuations: In this paper we review simulation and experimental studies of thermal
capillary wave fluctuations as an ideal means for probing the underlying
disjoining pressure and surface tensions, and more generally, fine details of
the Interfacial Hamiltonian Model. We discuss recent simulation results that
reveal a film-height-dependent surface tension not accounted for in the
classical Interfacial Hamiltonian Model. We show how this observation may be
explained bottom-up from sound principles of statistical thermodynamics and
discuss some of its implications. | cond-mat_soft |
Signatures of granular microstructure in dense shear flows: Granular materials react to shear stresses differently than do ordinary
fluids. Rather than deforming uniformly, materials such as dry sand or
cohesionless powders develop shear bands: narrow zones containing large
relative particle motion leaving adjacent regions essentially rigid[1,2,3,4,5].
Since shear bands mark areas of flow, material failure and energy dissipation,
they play a crucial role for many industrial, civil engineering and geophysical
processes[6]. They also appear in related contexts, such as in lubricating
fluids confined to ultra-thin molecular layers[7]. Detailed information on
motion within a shear band in a three-dimensional geometry, including the
degree of particle rotation and inter-particle slip, is lacking. Similarly,
only little is known about how properties of the individual grains - their
microstructure - affect movement in densely packed material[5]. Combining
magnetic resonance imaging, x-ray tomography, and high-speed video particle
tracking, we obtain the local steady-state particle velocity, rotation and
packing density for shear flow in a three-dimensional Couette geometry. We find
that key characteristics of the granular microstructure determine the shape of
the velocity profile. | cond-mat_soft |
Multiscale modeling of polymers at interfaces: A brief review of modeling and simulation methods for a study of polymers at
interfaces is provided. When studying truly multiscale problems as provided by
realistic polymer systems, coarse graining is practically unavoidable. In this
process, degrees of freedom on smaller scales are eliminated to the favor of a
model suitable for efficient study of the system behavior on larger length and
time scales. We emphasize the need to distinguish between dynamic and static
properties regarding the model validation. A model which accurately reproduces
static properties may fail completely, when it comes to the dynamic behavior of
the system. Furthermore, we comment on the use of Monte Carlo method in polymer
science as compared to molecular dynamics simulations. Using the latter
approach, we also discuss results of recent computer simulations on the
properties of polymers close to solid substrates. This includes both generic
features (as also observed in the case of simpler molecular models) as well as
polymer specific properties. Predictive power of computer simulations is
highlighted by providing experimental evidence for these observations. Some
important implications of these results for an understanding of mechanical
properties of thin polymer films and coatings are also worked out. | cond-mat_soft |
Tree frog-inspired nanopillar arrays for enhancement of adhesion and
friction: Bioinspired structure adhesives have received increasing interest for many
applications, such as climbing robots and medical devices. Inspired by the
closely packed keratin nanopillars on the toe pads of tree frogs, tightly
arranged polycaprolactone nanorod arrays are prepared by mold process and
chemical modification. Nanorod arrays show enhanced adhesion and friction on
both smooth and rough surfaces compared to the arrays with hexagonal
micropillars. The bonding of nanorods results in a larger stiffness of the
nanorod surface,contributing mainly to friction rather than adhesion. The
results suggest the function of closely packed keratin nanopillars on the toe
pad of tree frogs and offer a guiding principle for the designing of new
structured adhesives with strong attaching abilities. | cond-mat_soft |
Influence of constraints on axial growth reduction of cylindrical Li-ion
battery electrode particles: Volumetric expansion of silicon anode particles in a lithium-ion battery
during charging may lead to the generation of undesirable internal stresses.
For a cylindrical particle such growth may also lead to failure by buckling if
the expansion is constrained in the axial direction due to other particles or
supporting structures. To mitigate this problem, the possibility of reducing
axial growth is investigated theoretically by studying simple modifications of
the solid cylinder geometry. First, an annular cylinder is considered with
lithiation either from the inside or from the outside. In both cases, the
reduction of axial growth is not found to be significant. Next, explicit
physical constraints are studied by addition of a non-growing elasto-plastic
material: first, an outer annular constraint on a solid silicon cylinder, and
second a rod-like inner constraint for an annular silicon cylinder. In both
cases, it is found that axial growth can be reduced if the yield stress of the
constraining material is significantly higher than that of silicon and/or the
thickness of the constraint is relatively high. Phase diagrams are presented
for both the outer and the inner constraint cases to identify desirable
operating zones. Finally, to interpret the phase diagrams and isolate the key
physical principles two different simplified models are presented and are shown
to recover important qualitative trends of the numerical simulation results. | cond-mat_soft |
Stiff quantum polymers: At ultralow temperatures, polymers exhibit quantum behavior, which is
calculated here for the second and fourth moments of the end-to-end
distribution in the large-stiffness regime. The result should be measurable for
polymers in wide optical traps. | cond-mat_soft |
Complex Fluids with Mobile Charge-Regulated Macro-Ions: We generalize the concept of charge regulation of ionic solutions, and apply
it to complex fluids with mobile macro-ions having internal non-electrostatic
degrees of freedom. The suggested framework provides a convenient tool for
investigating systems where mobile macro-ions can self-regulate their charge
(e.g., proteins). We show that even within a simplified charge-regulation
model, the charge dissociation equilibrium results in different and notable
properties. Consequences of the charge regulation include a positional
dependence of the effective charge of the macro-ions, a non-monotonic
dependence of the effective Debye screening length on the concentration of the
monovalent salt, a modification of the electric double-layer structure, and
buffering by the macro-ions of the background electrolyte. | cond-mat_soft |
Flexible confinement leads to multiple relaxation regimes in glassy
colloidal liquids: Understanding relaxation of supercooled fluids is a major challenge and
confining such systems can lead to bewildering behaviour. Here we exploit an
optically confined colloidal model system in which we use reduced pressure as a
control parameter. The dynamics of the system are ``Arrhenius'' at low and
moderate pressure, but at higher pressures relaxation is faster than expected.
We associate this faster relaxation with a decrease in density adjacent to the
confining boundary due to local ordering in the system enabled by the flexible
wall. | cond-mat_soft |
Characterization of invariant patterns in a slowly rotated granular
tumbler: We report experimental results of the pattern developed by a mixture of two
types of grains in a triangular rotating tumbler operating in the avalanche
regime. At the centroid of the triangular tumbler an invariant zone appears
where the grains do not move relative to the tumbler. We characterize this
invariant zone by its normalized area, $A_i$, and its circularity index as a
function of the normalized filling area $A$. We find a critical filling area so
that only for $A>A_c$ invariant zones are obtained. These zones scale as
$A_i\sim (A-A_c)^2$ near $A_c$. We have obtained a maximum in the circularity
index for $A\approx 0.8$, for which the shape of the invariant zone is closer
to a circular one. The experimental results are reproduced by a simple model
which, based on the surface position, accounts for all the possible straight
lines within the triangle that satisfy the condition of constant $A$. We have
obtained an analytic expression for the contour of the invariant zone. | cond-mat_soft |
Implicit Chain Particle Model for Polymer Grafted Nanoparticles: Matrix-free nanocomposites made from polymer grafted nanoparticles (PGN)
represent a paradigm shift in materials science because they greatly improve
nanoparticle dispersion and offer greater tunability over rheological and
mechanical properties in comparison to neat polymers. Utilizing the full
potential of PGNs requires a deeper understanding of how polymer graft length,
density, and chemistry influence interfacial interactions between particles.
There has been great progress in describing these effects with molecular
dynamics (MD). However, the limitations of the length and time scales of MD
make it prohibitively costly to study systems involving more than a few PGNs.
Here, we address some of these challenges by proposing a new modeling paradigm
for PGNs using a strain-energy mapping framework involving potential of mean
force (PMF) calculations. In this approach, each nanoparticle is coarse-grained
into a representative particle with chains treated implicitly, namely, the
implicit chain particle model (ICPM). Using a chemistry-specific CG-MD model of
PMMA as a testbed, we derive the effective interaction between particles
arranged in a closed-packed lattice configuration by matching bulk
dilation/compression strain energy densities. The strain-rate dependence of the
mechanical work in ICPM is also discussed. Overall, the ICPM model increases
the computational speed by approximately 5-6 orders of magnitude compared to
the CG-MD models. This novel framework is foundational for particle-based
simulations of PGNs and their blends and accelerates the understanding and
predictions of emergent properties of PGN materials. | cond-mat_soft |
Universal Particle Kinetic Distribution in Crowded Environments: We study many-particle transport in heterogeneous, crowded environments at
different particle P\'{e}clet numbers ($Pe^*$). We demonstrate that a modified
Nakagami-$m$ function describes particle velocity probability distributions
when particle deposition occurs. We assess the universality of said function
through comparison against new Lagrangian simulations of various particle types
as well as experimental data from the literature. We construe the function's
physical meaning as its ability to explain particle deposition in terms of
$Pe^*$ and the competition between distributions of energy barriers for
particle release and particles' diffusive energy. | cond-mat_soft |
Time dependent current in a nonstationary environment: A microscopic
approach: Based on a microscopic system reservoir model,where the associated bath is
not in thermal equilibrium, we simulate the nonstationary Langevin dynamics and
obtained the generalized nonstationary fluctuation dissipation relation (FDR)
which asymptotically reduces to the traditional form. Our Langevin dynamics
incorporates non-Markovian process also, the origin of which lies on the
decaying term of the nonstationary FDR. We then follow the stochastic dynamics
of the Langevin particle based on the Fokker-Planck-Smoluchowski description,
in ratchet potential to obtain the steady and time dependent current in an
analytic form. We also examine the influence of initial excitation and
subsequent relaxation of bath modes on the transport of the Langevin particle
to show that the nonequilibrium nature of the bath leads to both strong
non-exponential dynamics as well as nonstationary current. | cond-mat_soft |
Oscillations and damping in the fractional Maxwell materials: This paper examines the oscillatory behaviour of complex viscoelastic systems
with power law-like relaxation behaviour. Specifically, we use the fractional
Maxwell model, consisting of a spring and fractional dashpot in series, which
produces a power-law creep behaviour and a relaxation law following the
Mittag-Leffler function. The fractional dashpot is characterised by a parameter
beta, continuously moving from the pure viscous behaviour when beta=1 to the
purely elastic response when beta=0. In this work, we study the general
response function and focus on the oscillatory behaviour of a fractional
Maxwell system in four regimes: stress impulse, strain impulse, step stress,
and driven oscillations. The solutions are presented in a format analogous to
the classical oscillator, showing how the fractional nature of relaxation
changes the long-time equilibrium behaviour and the short-time transient
solutions. We specifically test the critical damping conditions in the
fractional regime, since these have a particular relevance in biomechanics. | cond-mat_soft |
Self-assembly of anisotropic soft particles in two dimensions: The self assembly of core-corona discs interacting via anisotropic potentials
is investigated using Monte Carlo computer simulations. A minimal interaction
potential that incorporates anisotropy in a simple way is introduced. It
consists in a core-corona architecture in which the center of the core is
shifted with respect to the center of the corona. Anisotropy can thus be tuned
by progressively shifting the position of the core. Despite its simplicity, the
system self organize in a rich variety of structures including stripes,
triangular and rectangular lattices, and unusual plastic crystals. Our results
indicate that the amount of anisotropy does not alter the lattice spacing and
only influences the type of clustering (stripes, micells, etc.) of the
individual particles. | cond-mat_soft |
Effective charge versus bare charge for colloids in the infinite
dilution limit: We propose an analytical approximation for the dependence of the effective
charge on the bare charge for spherical and cylindrical macro-ions as a
function of the size of the colloid and salt content, for the situation of a
unique colloid immersed in a sea of electrolyte (where the definition of an
effective charge is non ambiguous).
Our approach is based on the Poisson-Boltzmann (PB) mean-field theory.
Mathematically speaking, our estimate is asymptotically exact in the limit
$\kappa a\gg 1$, where $a$ is the radius of the colloid and $\kappa$ the
inverse screening length. In practice, a careful comparison with effective
charges parameters obtained by numerically solving the full non-linear PB
theory proves that it is good down to $\kappa a\sim 1$. This is precisely the
limit appropriate to treat colloidal suspensions. A particular emphasis is put
on the range of parameters suitable to describe both single and double strand
DNA molecules under physiological conditions. | cond-mat_soft |
Non-Gaussian statistics of electrostatic fluctuations of hydration
shells: We report the statistics of electric field fluctuations produced by SPC/E
water inside a Kihara solute given as a hard-sphere core with a Lennard-Jones
layer at its surface. The statistics of electric field fluctuations, obtained
from numerical simulations, are studied as a function of the magnitude of a
point dipole placed close to the solute-water interface. The free energy
surface as a function of the electric field projected on the dipole direction
shows a cross-over with the increasing dipole magnitude. While it is a
single-well harmonic function at low dipole values, it becomes a double-well
surface at intermediate dipole moment magnitudes, transforming to a single-well
surface, with a non-zero minimum position, at still higher dipoles. A broad
intermediate region where the interfacial waters fluctuate between the two
minima is characterized by intense field fluctuations, with non-Gaussian
statistics and the variance far exceeding the linear-response expectations. The
excited state of the surface water is found to be lifted above the ground state
by the energy required to break approximately two hydrogen bonds. This state is
pulled down in energy by the external electric field of the solute dipole,
making it readily accessible to thermal excitations. The excited state is a
localized surface defect in the hydrogen-bond network creating a stress in the
nearby network, but otherwise relatively localized in the region closest to the
solute dipole. | cond-mat_soft |
Molecular and all solid DFT studies of the magnetic and chemical bonding
properties within KM[Cr(CN)$_6$] (M = V, Ni) complexes: A study at both the molecular and extended solid level in the framework DFT
is carried out for KM[Cr(CN)$_6$] (M = V, Ni). From molecular calculations, the
exchange parameters J are obtained, pointing to the expected magnetic ground
states, i.e., antiferromagnetic for M = V with J = -296.5 cm$^{-1}$ and
ferromagnetic for M = Ni with J = +40.5 cm$^{-1}$. From solid state
computations the same ground states and J magnitudes are confirmed from energy
differences. Furthermore an analysis of the site projected density of states
and of the chemical bonding is developed in which the cyanide ion linkage is
analyzed addressing some isomerism aspects. | cond-mat_soft |
A geometrically controlled rigidity transition in a model for confluent
3D tissues: The origin of rigidity in disordered materials is an outstanding open problem
in statistical physics. Previously, a class of 2D cellular models has been
shown to undergo a rigidity transition controlled by a mechanical parameter
that specifies cell shapes. Here, we generalize this model to 3D and find a
rigidity transition that is similarly controlled by the preferred surface area:
the model is solid-like below a dimensionless surface area of
$s_0^\ast\approx5.413$, and fluid-like above this value. We demonstrate that,
unlike jamming in soft spheres, residual stresses are necessary to create
rigidity. These stresses occur precisely when cells are unable to obtain their
desired geometry, and we conjecture that there is a well-defined minimal
surface area possible for disordered cellular structures. We show that the
behavior of this minimal surface induces a linear scaling of the shear modulus
with the control parameter at the transition point, which is different from the
scaling observed in particulate matter. The existence of such a minimal surface
may be relevant for biological tissues and foams, and helps explain why cell
shapes are a good structural order parameter for rigidity transitions in
biological tissues. | cond-mat_soft |
Membrane lateral structure: The influence of immobilized particles on
domain size: In experiments on model membranes, a formation of large domains of different
lipid composition is readily observed. However, no such phase separation is
observed in the membranes of intact cells. Instead, a structure of small
transient inhomogeneities called lipid rafts are expected in these systems. One
of the numerous attempts to explain small domains refers to the coupling of the
membrane to its surroundings, which leads to the immobilization of some of the
membrane molecules. These immobilized molecules then act as static obstacles
for the remaining mobile ones. We present detailed Molecular Dynamics
simulations demonstrating that this can indeed account for small domains. This
confirms previous Monte Carlo studies based on simplified models. Furthermore,
by directly comparing domain structures obtained using Molecular Dynamics to
Monte Carlo simulations of the Ising model, we demonstrate that domain
formation in the presence of obstacles is remarkably insensitive to the details
of the molecular interactions. | cond-mat_soft |
Stabilization of frictional sliding by normal load modulation: A
bifurcation analysis: This paper presents the stability analysis of a system sliding at low
velocities ($< 100 \mu$m.s$^{-1}$) under a periodically modulated normal load,
preserving interfacial contact. Experiments clearly evidence that normal
vibrations generally stabilize the system against stick-slip oscillations, at
least for a modulation frequency much larger than the stick-slip one. The
mechanical model of Bureau {\it et al.} (2000), validated on the steady-state
response of the system, is used to map its stability diagram. The model takes
explicitly into account the finite shear stiffness of the load-bearing
asperities, in addition to a classical state- and rate-dependent friction
force. The numerical results are in excellent quantitative agreement with the
experimental data obtained from a multicontact frictional system between glassy
polymer materials. Simulations at larger amplitude of modulation (typically 20%
of the mean normal load) suggest that the non-linear coupling between normal
and sliding motion could have a destabilizing effect in restricted regions of
the parameter space. | cond-mat_soft |
Stresses in lipid membranes: The stresses in a closed lipid membrane described by the Helfrich
hamiltonian, quadratic in the extrinsic curvature, are identified using
Noether's theorem. Three equations describe the conservation of the stress
tensor: the normal projection is identified as the shape equation describing
equilibrium configurations; the tangential projections are consistency
conditions on the stresses which capture the fluid character of such membranes.
The corresponding torque tensor is also identified. The use of the stress
tensor as a basis for perturbation theory is discussed. The conservation laws
are cast in terms of the forces and torques on closed curves. As an
application, the first integral of the shape equation for axially symmetric
configurations is derived by examining the forces which are balanced along
circles of constant latitude. | cond-mat_soft |
On the interaction of viscoelasticity and waviness in enhancing the
pull-off force in sphere/flat contacts: Motivated by roughness-induced adhesion enhancement (toughening and
strengthening) in low modulus materials, we study the detachment of a sphere
from a substrate in the presence of both viscoelastic dissipation at the
contact edge, and roughness in the form of a single axisymmetric waviness. We
show that the roughness-induced enhancement found by Guduru and coworkers for
the elastic case (i.e. at very small detachment speeds) tends to disappear with
increasing speeds, where the viscoelastic effect dominates and the problem
approaches that of a smooth sphere. This is in qualitative agreement with the
original experiments of Guduru's group with gelatin. The cross-over velocity is
where the two separate effects are comparable. Viscoelasticity effectively
damps roughness-induced elastic instabilities, and make their effects much less
important. | cond-mat_soft |
Separation of long DNA chains using non-uniform electric field: a
numerical study: We study migration of DNA molecules through a microchannel with a series of
electric traps controlled by an ac electric field. We describe the motion of
DNA based on Brownian dynamics simulations of a beads-spring chain. Our
simulation demonstrates that the chain captured by an electrode escapes from
the binding electric field due to thermal fluctuation. We find that the
mobility of chain would depend on the chain length; the mobility sharply
increases when the length of a chain exceeds a critical value, which is
strongly affected by the amplitude of the applied ac field. Thus we can adjust
the length regime, in which this microchannel well separates DNA molecules,
without changing the structure of the channel. We also present a theoretical
insight into the relation between the critical chain length and the field
amplitude. | cond-mat_soft |
Spontaneous chiralization of polar active colloids: Polar active particles constitute a wide class of synthetic colloids that are
able to propel along a preferential direction, given by their polar axis. Here,
we demonstrate a generic self-phoretic mechanism that leads to their
spontaneous chiralization through a symmetry breaking instability. We find that
the transition of an active particle from a polar to a chiral symmetry is
characterized by the emergence of active rotation and of circular trajectories.
We show that the instability is driven by the advection of a solute that
interacts differently with the two portions of the particle surface and it
occurs through a supercritical pitchfork bifurcation. | cond-mat_soft |
Phase behaviour of the confined lattice gas Lebwohl-Lasher model: The phase behaviour of the Lebwohl-Lasher lattice gas model (one of the
simplest representations of a nematogenic fluid) confined in a slab is
investigated by means of extensive Monte Carlo simulations. The model is known
to yield a first order gas-liquid transition in both the 2D and 3D limits, that
is coupled with an orientational order-disorder transition. This latter
transition happens to be first order in the 3D limit and it shares some
characteristic features with the continuous defect mediated
Berezinskii-Kosterlitz-Thouless transition in 2D. In this work we will analyze
in detail the behaviour of this system taking full advantage of the lattice
nature of the model and the particular symmetry of the interaction potential,
which allows for the use of efficient cluster algorithms. | cond-mat_soft |
Analytical approach to chiral active systems: suppressed phase
separation of interacting Brownian circle swimmers: We consider chirality in active systems by exemplarily studying the phase
behavior of planar systems of interacting Brownian circle swimmers with a
spherical shape. Continuing previous work presented in [G.-J. Liao, S. H. L.
Klapp, Soft Matter, 2018, 14, 7873-7882], we derive a predictive field theory
that is able to describe the collective dynamics of circle swimmers. The theory
yields a mapping between circle swimmers and noncircling active Brownian
particles and predicts that the angular propulsion of the particles leads to a
suppression of their motility-induced phase separation, being in line with
previous simulation results. In addition, the theory provides analytical
expressions for the spinodal corresponding to the onset of motility-induced
phase separation and the associated critical point as well as for their
dependence on the angular propulsion of the circle swimmers. We confirm our
findings by Brownian dynamics simulations and an analysis of the collective
dynamics using a weighted graph-theoretical network. The agreement between
results from theory and simulation is found to be good. | cond-mat_soft |
Field-mediated interactions of passive and conformation-active
particles: multibody and retardation effects: Particles in soft matter often interact through the deformation field they
create, as in the "cheerios" effect or the curvature-mediated interactions of
membrane proteins. Using a simple model for field-mediated interactions between
passive particles, or active particles that switch conformation randomly or
synchronously, we derive generic results concerning multibody interactions,
activity driven patterns, and retardation effects. | cond-mat_soft |
Spin polarizability of a trapped superfluid Fermi gas: The polarization produced by the relative displacement of the potentials
trapping two spin species of a dilute Fermi gas with $N_\ua=N_\da$ is
calculated at unitarity by assuming phase separation between the superfluid and
a spin polarized phase at zero temperature. Due to the energy cost associated
with pair breaking, the dipole magnetic polarizability vanishes in the linear
limit and exhibits important deviations from the ideal gas behaviour even for
displacements of the order of the size of the atomic cloud. The magnetic
behaviour in the presence of different trapping frequencies for the two spin
species is also discussed. | cond-mat_soft |
Ordering at two length scales in comb-coil diblock copolymers consisting
of only two different monomers: The microphase separated morphology of a melt of a specific class of
comb-coil diblock copolymers, consisting of an AB comb block and a linear
homopolymer A block, is analyzed in the weak segregation limit. On increasing
the length of the homopolymer A block, the systems go through a characteristic
series of structural transitions. Starting from the pure comb copolymer the
first series of structures involve the short length scale followed by
structures involving the large length scale. A maximum of two critical points
exists. Furthermore, in the two parameter space, characterizing the comb-coil
diblock copolymer molecules considered, a non-trivial bifurcation point exists
beyond which the structure factor can have two maxima (two correlation hole
peaks). | cond-mat_soft |
Exotic states of matter in an oscillatory driven liquid crystal cell: Matter under different equilibrium conditions of pressure and temperature
exhibits different states such as solid, liquid, gas, and plasma. Exotic states
of matter, such as Bose- Einstein condensates, superfluidity, chiral magnets,
superconductivity, and liquid crystalline blue phases are observed in
thermodynamic equilibrium. Rather than being a result of an aggregation of
matter, their emergence is due to a change of a topological state of the
system. Here we investigate topological states of matter in a system with
injection and dissipation of energy. In an experiment involving a liquid
crystal cell under the influence of a low-frequency oscillatory electric field,
we observe a transition from non-vortex state to a state in which vortices
persist. Depending on the period and the type of the forcing, the vortices
self-organise forming square lattices, glassy states, and disordered vortex
structures. Based on a stochastic amplitude equation, we recognise the origin
of the transition as the balance between stochastic creation and deterministic
annihilation of vortices. Our results show that the matter maintained out of
equilibrium by means of the temporal modulation of parameters can exhibit
exotic states. | cond-mat_soft |
A Simple Tensorial Theory of Smectic C Liquid Crystals: The smectic C (smC) phase represents a unique class of liquid crystal phases
characterised by the layered arrangement of molecules with tilted orientations
with respect to layer normals. Building upon the real-valued tensorial smectic
A (smA) model in [Xia et al., PRL, 126, 177801 (2021)], we propose a new
continuous mathematical model for smC (and smA) by introducing a novel coupling
term between the real tensor containing orientational information and density
variation, to control the tilt angle between directors and the layer normal
(the tilt angle is zero for smA and nonzero for smC). To validate our proposed
model, we conduct a series of two- and three-dimensional numerical experiments
that account for typical structures in smectics: chevron patterns, defects,
dislocations and toroidal focal conic domains (TFCDs). These results also
reveal the phenomenological differences between smA and smC configurations. | cond-mat_soft |
A threshold model of plastic waste fragmentation: New insights into the
distribution of microplastics in the ocean and its evolution over time: Plastic pollution in the aquatic environment has been assessed for many years
by ocean waste collection expeditions around the globe or by river sampling.
While the total amount of plastic produced worldwide is well documented, the
amount of plastic found in the ocean, the distribution of particles on its
surface and its evolution over time are still the subject of much debate. In
this article, we propose a general fragmentation model, postulating the
existence of a critical size below which particle fragmentation becomes
extremely unlikely. In the frame of this model, an abundance peak appears for
sizes around 1mm, in agreement with real environmental data. Using, in
addition, a realistic exponential waste feed to the ocean, we discuss the
relative impact of fragmentation and feed rates, and the temporal evolution of
microplastics (MP) distribution. New conclusions on the temporal trend of MP
pollution are drawn. | cond-mat_soft |
Theory of helicoids and skyrmions in confined cholesteric liquid
crystals: Cholesteric liquid crystals experience geometric frustration when they are
confined between surfaces with anchoring conditions that are incompatible with
the cholesteric twist. Because of this frustration, they develop complex
topological defect structures, which may be helicoids or skyrmions. We develop
a theory for these structures, which extends previous theoretical research by
deriving exact solutions for helicoids with the assumption of constant azimuth,
calculating numerical solutions for helicoids and skyrmions with varying
azimuth, and interpreting the results in terms of competition between terms in
the free energy. | cond-mat_soft |
Fractional solitons in non-Euclidian elastic plates: We show that minimal-surface non-Euclidean elastic plates share the same
low-energy effective theory as Haldane's dimerized quantum spin chain. As a
result, such elastic plates support fractional excitations, which take the form
of charge-$1/2$ solitons between degenerate states of the plates, in strong
analogy to their quantum counterpart. These fractional solitons exhibit
properties similar to fractional excitations in quantum fractional topological
states, including deconfinement and braiding, as well as unique new features
such as holographic properties and diode-like nonlinear response, demonstrating
great potentials for applications as mechanical metamaterials. | cond-mat_soft |
Fluctuations of particle motion in granular avalanches - from the
microscopic to the macroscopic scales: In this study, we have investigated the fluctuations of particle motion, i.e.
the non-affine motion, during the avalanche process, discovering a rich
dynamics from the microscopic to the macroscopic scales. We find that there is
strong correlation between the magnitude of the velocity fluctuation and the
velocity magnitude in the spatial and temporal domains. The possible connection
between this finding and STZ is discussed based on the direct measurement of
the T1 events. In addition, the velocity magnitude of the system and the stress
fluctuations of the system are strongly correlated temporally. Our finding will
pose challenges to the development of more rigorous theories to describe the
avalanche dynamics based on the microscopic approach. Moreover, our finding
presents a plausible mechanism of the particle entrainment in a simple system. | cond-mat_soft |
Dynamics of a deformable self-propelled domain: We investigate the dynamical coupling between the motion and the deformation
of a single self-propelled domain based on two different model systems in two
dimensions. One is represented by the set of ordinary differential equations
for the center of gravity and two tensor variables characterizing deformations.
The other is an active cell model which has an internal mechanism of motility
and is represented by the partial differential equation for deformations.
Numerical simulations show a rich variety of dynamics, some of which are common
to the two model systems. The origin of the similarity and the difference is
discussed. | cond-mat_soft |
Influence of nano confinement on nematic liquid crystals: We explore the nematic ordering of the rod-like liquid crystals 5CB and 6CB,
embedded into parallel-aligned nanochannels in mesoporous silicon and silica
membranes as a function of mean channel radius (4.7<=R <=8.3 nm), and thus
geometrical confinement strength, by optical birefringence measurements in the
infrared region. The orientational order inside the nanochannels results in an
excess birefringence, which is proportional to the nematic order parameter. It
evolves continuously upon cooling with a precursor behavior, typical of a
paranematic state at high temperatures. These observations are compared with
the bulk behavior and analyzed within a phenomenological model. Such an
approach indicates that the strength of the nematic ordering fields sigma is
beyond a critical threshold sigma_c =1/2, that separates discontinuous from
continuous paranematic-to-nematic behavior. In agreement with the predictions
of the phenomenological approach a linear dependency of sigma on the inverse
channel radius is found and we can infer therefrom the critical channel radii,
R_c, separating continuous from discontinuous paranematic-to-isotropic
behavior, for 5CB (12.1 nm) and 6CB (14.0 nm). Our analysis suggests that the
tangential anchoring at the channel walls is of similar strength in mesoporous
silicon and mesoporous silica membranes. A comparison with the bulk phase
behavior reveals that the nematic order in nanoconfinement is significantly
affected by channel wall roughness leading to a reduction of the effective
nematic ordering. | cond-mat_soft |
Perturbation Theory for Path Integrals of Stiff Polymers: The wormlike chain model of stiff polymers is a nonlinear $\sigma$-model in
one spacetime dimension in which the ends are fluctuating freely. This causes
important differences with respect to the presently available theory which
exists only for periodic and Dirichlet boundary conditions. We modify this
theory appropriately and show how to perform a systematic large-stiffness
expansions for all physically interesting quantities in powers of $L/\xi$,
where $L$ is the length and $\xi$ the persistence length of the polymer. This
requires special procedures for regularizing highly divergent Feynman integrals
which we have developed in previous work. We show that by adding to the
unperturbed action a correction term ${\cal A}^{\rm corr}$, we can calculate
all Feynman diagrams with Green functions satisfying Neumann boundary
conditions. Our expansions yield, order by order, properly normalized
end-to-end distribution function in arbitrary dimensions $d$, its even and odd
moments, and the two-point correlation function. | cond-mat_soft |
Overdamped thermal ratchets in one and more dimensions. Kinesin
transport and protein folding: The overdamped thermal ratchet driven by an external (Orstein-Uhlenbeck)
noise is revisited. The ratchet we consider is unbounded in space and not
necessarily periodic . We briefly discuss the conditions under which current is
obtained by analyzing the corresponding Fokker-Planck equation and its lack of
stationary states. Next, two examples in more than one dimension and related to
biological systems are presented. First, a two-dimensional model of a ``kinesin
protein'' on a ``microtubule'' is analyzed and, second, we suggest that a
ratchet mechanism may be behind the folding of proteins; the latter is
elaborated with a multidimensional ratchet model. | cond-mat_soft |
Casimir and pseudo-Casimir interactions in confined polyelectrolytes: We investigate the pseudo-Casimir force acting between two charged surfaces
confining a single polyelectrolyte chain with opposite charge. We expand the
exact free energy to the second order in the local electrostatic field as well
as the replicated polymer density field around the mean-field (saddle-point)
solution. The quadratic terms lead to a fluctuation interaction that is partly
due to the (thermal) Casimir effect for the confined electrostatic field and
partly due to the pseudo-Casimir effect due to the confined replicated polymer
density field. We study the intersurface separation dependence of both effects
and show that the pseudo-Casimir effect leads to a long range attraction
between the surfaces that decays with an anomalous algebraic exponent of $\sim
1.7$, smaller than the standard exponent of 2 in the case of Casimir
interactions. | cond-mat_soft |
Protein-Polymer Mixtures in the Colloid Limit: Aggregation,
Sedimentation and Crystallization: While proteins have been treated as particles with a spherically symmetric
interaction, of course in reality the situation is rather more complex. A
simple step towards higher complexity is to treat the proteins as
non--spherical particles and that is the approach we pursue here. We
investigate the phase behavior of enhanced green fluorescent protein (eGFP)
under the addition of a non--adsorbing polymer, polyethylene glycol (PEG). From
small angle x-ray scattering we infer that the eGFP undergoes dimerization and
we treat the dimers as spherocylinders with aspect ratio $L/D-1 = 1.05$.
Despite the complex nature of the proteins, we find that the phase behaviour is
similar to that of hard spherocylinders with ideal polymer depletant,
exhibiting aggregation and, in a small region of the phase diagram,
crystallization. By comparing our measurements of the onset of aggregation with
predictions for hard colloids and ideal polymers [S.V. Savenko and M. Dijkstra,
J. Chem. Phys 124, 234902 (2006) and F. lo Verso et al., Phys. Rev. E 73,
061407 (2006)] we find good agreement, which suggests that the eGFP proteins
are consistent with hard spherocylinders and ideal polymer. | cond-mat_soft |
Dielectric relaxation of thin films of polyamide random copolymers: We investigate the relaxation behavior of thin films of a polyamide random
copolymer, PA66/6I, with various film thicknesses using dielectric relaxation
spectroscopy. Two dielectric signals are observed at high temperatures, the
$\alpha$-process and the relaxation process due to electrode polarization (the
EP-process). The relaxation time of the EP-process has a Vogel-Fulcher-Tammann
type of temperature dependence, and the glass transition temperature, $T_{\rm
g}$, evaluated from the EP-process agrees very well with the $T_{\rm g}$
determined from the thermal measurements. The fragility index derived from the
EP-process increases with decreasing film thickness. The relaxation time and
the dielectric relaxation strength of the EP-process are described by a linear
function of the film thickness $d$ for large values of $d$, which can be
regarded as experimental evidence for the validity of attributing the observed
signal to the EP-process. Furthermore, there is distinct deviation from this
linear law for thicknesses smaller than a critical value. This deviation
observed in thinner films is associated with an increase in the mobility and/or
diffusion constant of the charge carriers responsible for the EP-process. The
$\alpha$-process is located in a high frequency region than the EP-process at
high temperatures, but merges with the EP-process at lower temperatures near
the glass transition region. The thickness dependence of the relaxation time of
the $\alpha$-process is different from that of the EP-process. This suggests
that there is decoupling between the segmental motion of the polymers and the
translational motion of the charge carriers in confinement. | cond-mat_soft |
Coarse-Grained Simulation of DNA using LAMMPS: During the last decade coarse-grained nucleotide models have emerged that
allow us to DNA and RNA on unprecedented time and length scales. Among them is
oxDNA, a coarse-grained, sequence-specific model that captures the
hybridisation transition of DNA and many structural properties of single- and
double-stranded DNA. oxDNA was previously only available as standalone
software, but has now been implemented into the popular LAMMPS molecular
dynamics code. This article describes the new implementation and analyses its
parallel performance. Practical applications are presented that focus on
single-stranded DNA, an area of research which has been so far
under-investigated. The LAMMPS implementation of oxDNA lowers the entry barrier
for using the oxDNA model significantly, facilitates future code development
and interfacing with existing LAMMPS functionality as well as other
coarse-grained and atomistic DNA models. | cond-mat_soft |
Stretching necklaces: Polyelectrolytes in poor solvents show a necklace structure where collapsed
polymer pearls are linked to stretched strings. In the present paper the
elasticity of such chains is studied in detail. Different deformation regimes
are addressed. The first is the continuous regime, where many pearls are
present. A continuous force extension relation ship is calculated. The main
contribution comes from the tension balance and the electrostatic repulsion of
consecutive pearls. The main correction term stems from the finite size of the
pearls, which monitors their surface energy. For a finite amount of pearls
discontinuous stretching is predicted. Finally counterion effects are discussed
qualitatively. | cond-mat_soft |
Mean field analysis of Williams-Bjerknes type growth: We investigate a class of stochastic growth models involving competition
between two phases in which one of the phases has a competitive advantage. The
equilibrium populations of the competing phases are calculated using a mean
field analysis. Regression probabilities for the extinction of the advantaged
phase are calculated in a leading order approximation. The results of the
calculations are in good agreement with simulations carried out on a square
lattice with periodic boundaries. The class of models are variants of the
Williams- Bjerknes model for the growth of tumours in the basal layer of an
epithelium. In the limit in which only one of the phases is unstable the class
of models reduces to the well known variants of the Eden model. | cond-mat_soft |
Non-uniqueness of local stress of three-body potentials in molecular
simulations: Microscopic stress fields are widely used in molecular simulations to
understand mechanical behavior. Recently, decomposition methods of multibody
forces to central force pairs between the interacting particles have been
proposed. Here, we introduce a force center of a three-body potential and
propose different force decompositions that also satisfy the conservation of
translational and angular momentum. We compare the force decompositions by
stress-distribution magnitude and discuss their difference in the stress
profile of a bilayer membrane using coarse-grained and atomistic molecular
dynamics simulations. | cond-mat_soft |
Bending and Twisting Elasticity: a Revised Marko-Siggia Model on DNA
Chirality: A revised Marko-Siggia elastic model for DNA double helix [Macromolecules 27,
981 (1994)] is proposed, which includes the WLC bending energy and a new chiral
twisting energy term. It is predicted that the mean helical repeat length (HRL)
for short DNA rings increases with the decreasing of chain length; while for
very long chains, their mean HRL is the same, independent of both the chain
length and whether the ends are closed, it is longer than the value for
rectilinear DNAs. Our results are in good agreement with experiments. | cond-mat_soft |
Unfolding designable structures: Among an infinite number of possible folds, nature has chosen only about 1000
distinct folds to form protein structures. Theoretical studies suggest that
selected folds are intrinsically more designable than others; these selected
folds are unusually stable, a property called the designability principle. In
this paper we use the 2D hydrophobic-polar lattice model to classify structures
according to their designability, and Langevin dynamics to account for their
time evolution. We demonstrate that, among all possible folds, the more
designable ones are easier to unfold due to their large number of surface-core
bonds. | cond-mat_soft |
Depinning and heterogeneous dynamics of colloidal crystal layers under
shear flow: Using Brownian dynamics (BD) simulations and an analytical approach we
investigate the shear-induced, nonequilibrium dynamics of dense colloidal
suspensions confined to a narrow slit-pore. Focusing on situations where the
colloids arrange in well-defined layers with solidlike in-plane structure, the
confined films display complex, nonlinear behavior such as collective depinning
and local transport via density excitations. These phenomena are reminiscent of
colloidal monolayers driven over a periodic substrate potential. In order to
deepen this connection, we present an effective model which maps the dynamics
of the shear-driven colloidal layers to the motion of a single particle driven
over an effective substrate potential. This model allows to estimate the
critical shear rate of the depinning transition based on the equilibrium
configuration, revealing the impact of important parameters such as the
slit-pore width and the interaction strength. We then turn to heterogeneous
systems where a layer of small colloids is sheared with respect to bottom
layers of large particles. For these incommensurate systems we find that the
particle transport is dominated by density excitations resembling the so-called
"kink" solutions of the Frenkel-Kontorova (FK) model. In contrast to the FK
model, however, the corresponding "antikinks" do not move. | cond-mat_soft |
Yield drag in a two-dimensional foam flow around a circular obstacle:
Effect of liquid fraction: We study the two-dimensional flow of foams around a circular obstacle within
a long channel. In experiments, we confine the foam between liquid and glass
surfaces. In simulations, we use a deterministic software, the Surface Evolver,
for bubble details and a stochastic one, the extended Potts model, for
statistics. We adopt a coherent definition of liquid fraction for all studied
systems. We vary it in both experiments and simulations, and determine the
yield drag of the foam, that is, the force exerted on the obstacle by the foam
flowing at very low velocity. We find that the yield drag is linear over a
large range of the ratio of obstacle to bubble size, and is independent of the
channel width over a large range. Decreasing the liquid fraction, however,
strongly increases the yield drag; we discuss and interpret this dependence. | cond-mat_soft |
Active nematic flows confined in a two dimensional channel with hybrid
alignment at the walls: a unified picture: Active nematic fluids confined in narrow channels generate spontaneous flows
when the activity is sufficiently intense. Recently, it was shown that if the
molecular anchoring at the channel walls is conflicting flows are initiated
even in the zero activity limit. An analytical laminar velocity profile for
this specific configuration was derived within a simplified nematohydrodynamic
model in which the nematic order parameter is a fixed-magnitude unit vector n.
In this study we explore systematically active flows in this confined geometry
with a more general theoretical model that uses a second-rank tensor order
parameter Q to express both the magnitude and orientation of the nematic phase.
The Q-model allows for the presence of defects and biaxial, in addition to
uniaxial, molecular arrangements. Our aim is to provide a unified picture,
beyond the limiting regime explored previously, to serve as a guide for
potential microfluidic applications. We reveal how the nematic-flow coupling is
not only dependent on geometrical constraints but also highly sensitive to
material and flow parameters. We specifically stress the key role played by the
activity and the flow aligning parameter and we show that solutions depend on
two dimensionless parameters. We find that for large values of the activity
parameter the flow is suppressed for contractile particles while is either
sustained or suppressed for extensile particles depending on whether they tend
to align or tumble when subject to shear. We explain these distinct behaviors
by an argument based on the results of the stability analysis applied to
simpler configurations. We finally provide a numerical example of a biaxial
three-dimensional thresholdless active flow for which we show that biaxiality
is specially relevant for a weakly first-order isotropic-nematic phase
transition. | cond-mat_soft |
Comparing simulated specific heat of liquid polymers and oligomers to
experiments: The specific heat is a central property of condensed matter systems including
polymers and oligomers in their condensed phases. Yet, predictions of this
quantity from molecular simulations and successful comparisons to experimental
data are scarce if existing at all. One reason for this may be that the
internal energy and thus the specific heat cannot be coarse-grained so that
they defy their rigorous computation with united-atom models. Moreover, many
modes in a polymer barely contribute to the specific heat because of their
quantum mechanical nature. Here, we demonstrate that an analysis of the
mass-weighted velocity autocorrelation function allows specific heat
predictions to be corrected for quantum effects so that agreement with
experimental data is on par with predictions of other routinely computed
quantities. We outline how to construct corrections for both all-atom and
united-atom descriptions of chain molecules. Corrections computed for eleven
hydrocarbon oligomers and commodity polymers deviate by less than
$k_\textrm{B}/10$ within a subset of nine molecules. Our results may benefit
the prediction of heat conductivity. | cond-mat_soft |
Effect of shear force on the separation of double stranded DNA: Using the Langevin Dynamics simulation, we have studied the effects of the
shear force on the rupture of short double stranded DNA at different
temperatures. We show that the rupture force increases linearly with the chain
length and approaches to the asymptotic value in accordance with the
experiment. The qualitative nature of these curves almost remains same for
different temperatures but with a shift in the force. We observe three
different regimes in the extension of covalent bonds (back bone) under the
shear force. | cond-mat_soft |
Acoustic emission signals resulting from the drying induced fractures of
Phyllostachys Pubescens bamboo, Evidence of scale free phenomena: I have performed experimental measurements of acoustic emission signals
resulting from the drying process of Phyllostachys Pubescens bamboo. The
emphasis was on identifying individual events, and characterize them according
to their time span and energy release. My results show a histogram of
experimental squared voltage distributions nicely fit into a power law with
exponent of $-1.16$, reminiscent of scale free phenomena. I have also
calculated the average signal shape, for different time spans of the system,
and found an asymmetrical form. The experimental evidence points to the system
having an isolated large crack at the beginning of the simulation. | cond-mat_soft |
Multidimensional optical fractionation with holographic verification: The trajectories of colloidal particles driven through a periodic potential
energy landscape can become kinetically locked in to directions dictated by the
landscape's symmetries. When the landscape is realized with forces exerted by a
structured light field, the path a given particle follows has been predicted to
depend exquisitely sensitively on such properties as the particle's size and
refractive index These predictions, however, have not been tested
experimentally. Here, we describe measurements of colloidal silica spheres'
transport through arrays of holographic optical traps that use holographic
video microscopy to track individual spheres' motions in three dimensions and
simultaneously to measure each sphere's radius and refractive index with
part-per-thousand resolution. These measurements confirm previously untested
predictions for the threshold of kinetically locked-in transport, and
demonstrate the ability of optical fractionation to sort colloidal spheres with
part-per-thousand resolution on multiple characteristics simultaneously. | cond-mat_soft |
Defect-mediated morphologies in growing cell colonies: Morphological trends in growing colonies of living cells are at the core of
physiological and evolutionary processes. Using active gel equations, which
include cell division, we show that shape changes during the growth can be
regulated by the dynamics of topological defects in the orientation of cells.
The friction between the dividing cells and underlying substrate drives
anisotropic colony shapes toward more isotropic morphologies, by mediating the
number density and velocity of topological defects. We show that the defects
interact with the interface at a specific interaction range, set by the
vorticity length scale of flows within the colony, and that the cells
predominantly reorient parallel to the interface due to division-induced active
stresses. | cond-mat_soft |
An Ising-Like model for protein mechanical unfolding: The mechanical unfolding of proteins is investigated by extending the
Wako-Saito-Munoz-Eaton model, a simplified protein model with binary degrees of
freedom, which has proved successful in describing the kinetics of protein
folding. Such a model is generalized by including the effect of an external
force, and its thermodynamics turns out to be exactly solvable. We consider two
molecules, the 27th immunoglobulin domain of titin and protein PIN1. In the
case of titin we determine equilibrium force-extension curves and study
nonequilibrium phenomena in the frameworks of dynamic loading and force clamp
protocols, verifying theoretical laws and finding the position of the kinetic
barrier which hinders the unfolding of the molecule. The PIN1 molecule is used
to check the possibility of computing the free energy landscape as a function
of the molecule length by means of an extended form of the Jarzynski equality. | cond-mat_soft |
Liquid-Crystal Transitions: A First Principles Multiscale Approach: A rigorous theory of liquid-crystal transitions is developed starting from
the Liouville equation. The starting point is an all-atom description and a set
of order parameter field variables that are shown to evolve slowly via Newton's
equations. The separation of timescales between that of atomic collisions and
the order parameter fields enables the derivation of rigorous equations for
stochastic order parameter field dynamics. When the fields provide a measure of
the spatial profile of the probability of molecular position, orientation, and
internal structure, a theory of liquid-crystal transitions emerges. The theory
uses the all-atom/continuum approach developed earlier to obtain a functional
generalization of the Smoluchowski equation wherein key atomic details are
embedded. The equivalent non-local Langevin equations are derived and
computational aspects are discussed. The theory enables simulations that are
much less computationally intensive than molecular dynamics and thus does not
require oversimplification of the system's constituent components. The
equations obtained do not include factors that require calibration and can thus
be applicable to various phase transitions which overcomes the limitations of
phenomenological field models. The relation of the theory to phenomenological
descriptions of Nematic and Smectic phase transitions, and the possible
existence of other types of transitions involving intermolecular structural
parameters are discussed. | cond-mat_soft |
Diffusion constant for the repton model of gel electrophoresis: The repton model is a simple model of the "reptation" motion by which DNA
diffuses through a gel during electrophoresis. In this paper we show that the
model can be mapped onto a system consisting of two types of particles with
hard-sphere interactions diffusing on a one-dimensional lattice. Using this
mapping we formulate an efficient Monte Carlo algorithm for the model which
allows us to simulate systems more than twice the size of those studied before.
Our results confirm scaling hypotheses which have previously been put forward
for the model. We also show how the particle version of the model can be used
to construct a transfer matrix which allows us to solve exactly for the
diffusion constant of small repton systems. We give results for systems of up
to 20 reptons. | cond-mat_soft |
Classifying the age of a glass based on structural properties: A machine
learning approach: It is well established that physical aging of amorphous solids is governed by
a marked change in dynamical properties as the material becomes older.
Conversely, structural properties such as the radial distribution function
exhibit only a very weak age dependence, usually deemed negligible with respect
to the numerical noise. Here we demonstrate that the extremely weak
age-dependent changes in structure are in fact sufficient to reliably assess
the age of a glass with the support of machine learning. We employ a supervised
learning method to predict the age of a glass based on the system's
instantaneous radial distribution function. Specifically, we train a multilayer
perceptron for a model glassformer quenched to different temperatures, and find
that this neural network can accurately classify the age of our system across
at least four orders of magnitude in time. Our analysis also reveals which
structural features encode the most useful information. Overall, this work
shows that through the aid of machine learning, a simple structure-dynamics
link can indeed be established for physically aged glasses. | cond-mat_soft |
Dynamics of cylindrical droplets on flat substrate: Lattice Boltzmann
modeling versus simple analytic models: The steady state motion of cylindrical droplets under the action of external
body force is investigated both theoretically and via lattice Boltzmann
simulation. As long as the shape-invariance of droplet is maintained, the
droplet's center-of-mass velocity linearly scales with both the force density
and the square of droplet radius. However, a non-linear behavior appears as the
droplet deformation becomes significant. This deformation is associated with
the drop elongation occurring at sufficiently high external forcing. Yet,
independent of either the force density or the droplet size, the center-of-mass
velocity is found to be linear in terms of the inverse of dynamic viscosity. In
addition, it is shown that the energy is mainly dissipated in a region near the
substrate particularly close to the three phase contact line. The total viscous
dissipation is found to be proportional to both the square of force density and
the inverse of dynamic viscosity. Moreover, the dependence of the
center-of-mass velocity on the equilibrium contact angle is investigated. A
simple analytic model is provided reproducing the observed behavior. | cond-mat_soft |
Friction of viscoelastic elastomers with rough surfaces under torsional
contact conditions: Frictional properties of contacts between a smooth viscoelastic rubber and
rigid surfaces are investigated using a torsional contact configuration where a
glass lens is continuously rotated on the rubber surface. From the inversion of
the displacement field measured at the surface of the rubber, spatially
resolved values of the steady state frictional shear stress are determined
within the non homogeneous pressure and velocity fields of the contact. For
contacts with a smooth lens, a velocity dependent but pressure independent
local shear stress is retrieved from the inversion. On the other hand, the
local shear stress is found to depend both on velocity and applied contact
pressure when a randomly rough (sand blasted) glass lens is rubbed against the
rubber surface. As a result of changes in the density of micro-asperity
contacts, the amount of light transmitted by the transparent multi-contact
interface is observed to vary locally as a function of both contact pressure
and sliding velocity. Under the assumption that the intensity of light
transmitted by the rough interface is proportional to the proportion of area
into contact, it is found that the local frictional stress can be expressed
experimentally as the product of a purely velocity dependent term, $k(v)$, by a
term representing the pressure and velocity dependence of the actual contact
area, $A/A_0$. A comparison between $k(v)$ and the frictional shear stress of
smooth contacts suggests that nanometer scale dissipative processes occurring
at the interface predominate over viscoelastic dissipation at micro-asperity
scale. | cond-mat_soft |
Rotational and translational dynamics in dense fluids of patchy
particles: We explore the effect of directionality on rotational and translational
relaxation in glassy systems of patchy particles. Using molecular dynamics
simulations we analyze the impact of two distinct patch geometries, one that
enhance local icosahedral structure and one which does not strongly affect
local order. We find that in nearly all investigated cases, rotational
relaxation takes place on a much faster time scale than translational
relaxation. By comparing to a simplified dynamical Monte Carlo model, we
illustrate that rotational diffusion can be qualitatively explained as purely
local motion within a fixed environment, which is not coupled strongly to the
cage-breaking dynamics required for translational relaxation. Nonetheless,
icosahedral patch placement has a profound effect on the local structure of the
system, resulting in a dramatic slowdown at low temperatures which is strongest
at an intermediate "optimal" patch size. | cond-mat_soft |
Directed transport of active particles over asymmetric energy barriers: We theoretically and numerically investigate the transport of active colloids
to target regions, delimited by asymmetric energy barriers. We show that it is
possible to introduce a generalized effective temperature that is related to
the local variance of particle velocities. The stationary probability
distributions can be derived from a simple diffusion equation in the presence
of an inhomogeneous effective temperature resulting from the action of external
force fields. In particular, transitions rates over asymmetric energy barriers
can be unbalanced by having different effective temperatures over the two
slopes of the barrier. By varying the type of active noise, we find that equal
values of diffusivity and persistence time may produce strongly varied
effective temperatures and thus stationary distributions. | cond-mat_soft |
Quantum Theory of Chiral Interactions in Cholesteric Liquid Crystals: We study the effective chiral interaction between molecules arising from
quantum dispersion interactions within a model in which a) the dominant excited
states of a molecule form a band whose width is small compared to the average
excitation energy and b) biaxial orientational correlation between adjacent
molecules can be neglected. Previous treatments of quantum chiral interactions
were based on a multipole expansion of the intermolecular interaction. However,
because real liquid crystals are composed of elongated molecules, we utilize an
expansion in terms of only coordinates transverse to the long molecular axes.
We identify two distinct physical limits depending on whether one or both of
the interacting molecules are excited in the virtual state. When both molecules
are excited, our results are similar to those found previously by van der Meer
et al. Previously unidentified terms in which only one molecule is excited
involve the interactions of local dipole moments, which exist even when the
global dipole moment of the molecule vanishes. We present analytic and
numerical results for helical molecules. Our results do not indicate whether
the dominant chiral interaction in cholesterics results from quantum or from
steric interactions. | cond-mat_soft |
Phase transitions and ordering of confined dipolar fluids: We apply a modified mean-field density functional theory to determine the
phase behavior of Stockmayer fluids in slitlike pores formed by two walls with
identical substrate potentials. Based on the Carnahan-Starling equation of
state, a fundamental-measure theory is employed to incorporate the effects of
short-ranged hard sphere - like correlations while the long-ranged
contributions to the fluid interaction potential are treated perturbatively.
The liquid-vapor, ferromagnetic liquid - vapor, and ferromagnetic liquid -
isotropic liquid first-order phase separations are investigated. The local
orientational structure of the anisotropic and inhomogeneous ferromagnetic
liquid phase is also studied. We discuss how the phase diagrams are shifted and
distorted upon varying the pore width. | cond-mat_soft |
Fabrication of Fiber-Reinforced Polymer Ceramic Composites by Wet
Electrospinning: We propose a novel approach of wet electrospinning to yield fiber-reinforced
polymer ceramic composites, where a reactive ceramic precursor gel is used as a
collector. We illustrate our approach by generating polyethylene oxide (PEO)
fibers in a potassium silicate gel; the gel is later activated using metakaolin
to yield a ceramic-0.5 wt% PEO fiber composite. An increase of 29% and 22% is
recorded for the fabricated polymer ceramic composites in terms of indentation
modulus and indentation hardness respectively. Our initial findings demonstrate
the process viability and might lead to a potentially scalable manufacturing
approach for fiber-reinforced polymer ceramic composites. | cond-mat_soft |
Novel polymer nanocomposite composed of organic nanoparticles via
self-assembly: We report a novel class of polymer nanocomposite composed of organic
nanoparticles dispersed in polymer matrix, with the particle sizes of 30-120 nm
in radius. The organic nanoparticles were formed by the self-assembly of
protonated poly(4-vinyl-pyridine)-r-poly(acrylonitrile) and amphiphilic metanil
yellow dye molecules through electrostatic interactions in aqueous solution. A
strongly broadened Raman shift band was probed, suggesting the presence of
enhanced optoelectronic property from the polymer nanocomposite. Here, using
random-copolymer polyelectrolytes and mesogenic amphiphiles as the designed
building blocks for self-assembly, a new approach is acutally provided to
fabricate organic nanoparticles. | cond-mat_soft |
Colloidal Particles at Chiral Liquid Crystal Interfaces: Colloidal particles trapped at an interface between two fluids can form a
wide range of different structures. Replacing one of the fluid with a liquid
crystal increases the complexity of interactions and results in a greater range
of possible structures. New behaviour emerges when colloidal particles interact
with defects in the liquid crystal phases. Here we discuss the templating of
colloids at a cholesteric isotropic interface. | cond-mat_soft |
Vesiculation mechanisms mediated by anisotropic proteins: Endocytosis is an essential biological process for the trafficking of
macromolecules (cargo) and membrane proteins in cells. In yeast cells, this
involves the invagination of a tubular structure on the membrane and the
formation of endocytic vesicles. Bin/Amphiphysin/Rvs (BAR) proteins holding a
crescent-shape are generally assumed to be the active player to squeeze the
tubular structure and pinch off the vesicle by forming a scaffold on the side
of the tubular membrane. Here we use the extended Helfrich model to
theoretically investigate how BAR proteins help drive the formation of vesicles
via generating anisotropic curvatures. Our results show that, within the
classical Helfrich model, increasing the spontaneous curvature at the side of a
tubular membrane is unable to reduce the tube radius to a critical size to
induce membrane fission. However, membranes coated with proteins that generate
anisotropic curvatures are prone to experience an hourglass-shaped necking or a
tube-shaped necking process, an important step leading to membrane fission and
vesicle formation. In addition, our study shows that depending on the type of
anisotropic curvatures generated by a protein, the force to maintain the
protein coated membrane at a tubular shape exhibits qualitatively different
relationship with the spontaneous curvature. This result provides an
experimental guidance to determine the type of anisotropic curvatures of a
protein. | cond-mat_soft |
Motility and Swimming: Universal Description and Generic Trajectories: Autonomous locomotion is a ubiquitous phenomenon in biology and in physics of
active systems at microscopic scale. This includes prokaryotic, eukaryotic
cells (crawling and swimming) and artificial swimmers. An outstanding feature
is the ability of these entities to follow complex trajectories, ranging from
straight, curved (circular, helical...), to random-like ones. The non-straight
nature of these trajectories is often explained as a consequence of the
asymmetry of the particle or the medium in which it moves, or due to the
presence of bounding walls, etc... Here, we show that straight, circular and
helical trajectories emerge naturally in the absence of asymmetry of the
swimmer or that of suspending medium. Our first proof is based on general
considerations, without referring to an explicit form of a model. We show that
these three trajectories correspond to self-congruent solutions.
Self-congruency means that the states of the system at different moments of
time can be made identical by an appropriate combination of rotation and
translation of the coordinate space. We show that these solutions are exhibited
by spherically symmetric particles as a result of a series of pitchfork
bifurcations as the activity is increased. Self-congruent dynamics in one and
two dimensions are analyzed as well. Finally, we present a simple explicit
nonlinear exactly solvable model of fully isotropic phoretic particle that
shows the transitions from a non-motile state to straight motion to circular
motion to helical motion as a series of spontaneous symmetry-breaking
bifurcations. Whether a system exhibits or not a given trajectory only depends
on the numerical values of parameters entering the model, while asymmetry of
swimmer shape, or anisotropy of the suspending medium , or influence of
bounding walls are not necessary. | cond-mat_soft |
Spheroid Model for Molecular Packing in Crystalline Phase: Dense packing of particles has provided important models to study the
structure of matter in various systems such as liquid, glassy and crystalline
phase, etc. The simplest sphere packing models are able to represent and
capture salient properties of the building blocks for covalent, metallic and
ionic crystals; it however becomes insufficient to reflect the broken symmetry
of the commonly anisotropic molecules in complex molecular crystals. Here we
develop spheroid models with the minimal degree of anisotropy, which serve as a
simple geometrical representation for a rich spectrum of molecules--including
both isotropic and anisotropic, convex and concave ones--in crystalline phases.
Our models are determined via an inverse packing approach: given a molecular
crystal, an optimal spheroid model is constructed using a contact diagram,
which depicts packing relationship between neighboring molecules within the
crystal. The spheroid models are capable of accurately capturing the broken
symmetry and characterizing the equivalent volume of molecules in the
crystalline phases. Our model also allows to retrieve such molecular
information from poor-quality crystal X-ray diffraction data that otherwise
would be simply discarded. | cond-mat_soft |
Spectral holographic trapping: Creating dynamic force landscapes with
polyphonic waves: Acoustic trapping uses forces exerted by sound waves to transport small
objects along specified trajectories in three dimensions. The structure of the
acoustic force landscape is governed by the amplitude and phase profiles of the
sound's pressure wave. These profiles can be controlled through deliberate
spatial modulation of monochromatic waves, by analogy to holographic optical
trapping. Alternatively, spatial and temporal control can be achieved by
interfering a small number of sound waves at multiple frequencies to create
acoustic holograms based on spectral content. We demonstrate spectral
holographic trapping by projecting acoustic conveyor beams that move
millimeter-scale objects along prescribed paths, and control the complexity of
particle trajectories by tuning the strength of weak reflections. Illustrative
spectral superpositions of static and dynamic force landscapes enable us to
realize two variations on the theme of a wave-driven oscillator, a deceptively
simple dynamical system with surprisingly complex phenomenology. | cond-mat_soft |
Multi-valent Ion Mediated Polyelectrolyte Association and Structure: Polyelectrolytes are commonly used to chelate multi-valent ions in aqueous
solutions, playing a critical role in water softening and the prevention of
mineralization. At sufficient ionic strength, ion-mediated
polyelectrolyte--polyelectrolyte interactions can precipitate
polyelectrolyte--ion complexes, a phenomenon known as "like-charge attraction".
While the significant influence of small ions on polyelectrolyte solution phase
behavior is recognized, the precise molecular mechanisms driving the
counterintuitive phenomenon remain largely elusive. In this study, we employ
all-atom molecular dynamics simulations to investigate the molecular mechanism
of like-charge attraction between two poly(acrylic acid) (PAA) chains in
solution. We find that moderate quantities of Ca$^{2+}$ ions induce attraction
between PAA chains, facilitated by the formation of PAA--Ca$^{2+}$--PAA bridges
and a significant increase in the coordination of Ca$^{2+}$ ions by the PAA
chains. At high Ca$^{2+}$ number densities, ion bridges are disfavored due to
electrostatic screening, yet the chains are still attracted to each other due
to solvent-mediated interactions between the chains and their chelated ions.
The insights gleaned from this study not only enrich our understanding of the
intricate mechanism of like-charge attraction between polyanions in solution
but also illuminate the influence of multi-valent ions on polyelectrolyte
interactions. | cond-mat_soft |
Phase behaviour of coarse-grained fluids: Soft condensed matter structures often challenge us with complex many-body
phenomena governed by collective modes spanning wide spatial and temporal
domains. In order to successfully tackle such problems mesoscopic
coarse-grained (CG) statistical models are being developed, providing a
dramatic reduction in computational complexity. CG models provide an
intermediate step in the complex statistical framework of linking the
thermodynamics of condensed phases with the properties of their constituent
atoms and molecules. These allow us to offload part of the problem to the CG
model itself and reformulate the remainder in terms of reduced CG phase space.
However, such exchange of pawns to chess pieces, or ``Hamiltonian
renormalization'', is a radical step and the thermodynamics of the primary
atomic and CG models could be markedly different. Here, we present a
comprehensive study of the phase diagram including binodal and interfacial
properties of a novel soft CG model, which includes finite-range attraction and
supports liquid phases. Although the model is rooted in similar arguments to
the Lennard-Jones (LJ) atomic pair potential, its phase behaviour is
qualitatively different from that of LJ and features several anomalies such as
an unusually broad liquid range, change in concavity of the liquid coexistence
branch with variation of the model parameters, volume contraction on fusion,
temperature of maximum density in the liquid phase and negative thermal
expansion in the solid phase. These results provide new insight into the
connection between simple potential models and complex emergent condensed
matter phenomena. | cond-mat_soft |
Nanoparticles modulate contact angle hysteresis in electrowetting: The pinning of the contact line adversely influences the electrowetting
performance of sessile liquid droplets. In this paper, we report the
electrowetting hysteresis characteristics of 100 mM aq. KCl sessile liquid
droplet placed on a hydrophobic PDMS surface. The effect of nanoparticles on
the contact angle hysteresis under the imposed electric potential is further
investigated. This study reveals that the contact angle hysteresis decreases
beyond a certain threshold value of nanoparticles concentration. Therefore,
nanoparticle suspension in the liquid droplet can be used to enhance or
suppress the electrowetting hysteresis and consequentially rate of heat
transfer during hot spot cooling. | cond-mat_soft |
Drag Law of Two Dimensional Granular Fluids: The drag force law acting on a moving circular disk in a two-dimensional
granular medium is analyzed based on the discrete element method (DEM). It is
remarkable that the drag force on the moving disk in moderate dense and pure
two-dimensional granular medium can be well reproduced by a perfect fluid with
separation from the surface of the tracer. A yield force, being independent of
the moving speed of the disk, appears if a dry friction between the granular
disks and the bottom plate exists. The perfect fluidity is violated in this
case. The yield force and the drag force diverge at the jamming point. | cond-mat_soft |
Numerical and Experimental Investigation of Static Wetting Morphologies
of Aqueous Drops on Lubricated Slippery Surfaces Using a Quasi-Static
Approach: Due to the slow dynamics of the wetting ridge, it is challenging to predict
the wetting morphology of liquid drops on thin lubricant coated surfaces. It is
hypothesized that when a drop sinks on a lubricated surface, quasi-static
wetting morphology can be numerically computed only from the knowledge of
interfacial energies, lubricant thickness, and drop volume. We used Surface
Evolver software for the numerical computation of the interface profiles for a
four-phase system. For the experiments, we used drops of 80 wt% formamide on
silicone oil coated substrates with varying lubricant thickness, substrate
wettability and drop volume. Optical images of drops were used to compare the
experimental interfacial profiles and apparent contact angles with the
numerically computed ones. We found good agreement between the experiments and
the simulations for the interfacial profiles and apparent contact angles as a
function of various systems parameters except for very thin lubricating films.
Apparent contact angles varied non-linearly as a function of substrate
wettability and lubricant thickness, however, were found constant with the drop
volume. | cond-mat_soft |
Aggregation of magnetic holes in a rotating magnetic field: We have experimentally investigated field induced aggregation of nonmagnetic
particles confined in a magnetic fluid layer when rotating magnetic fields were
applied. After application of a magnetic field rotating in the plane of the
fluid layer, the single particles start to form two-dimensional (2D) clusters,
like doublets, triangels, and more complex structures. These clusters
aggregated again and again to form bigger clusters. During this nonequilibrium
process, a broad range of cluster sizes was formed, and the scaling exponents,
$z$ and $z'$, of the number of clusters $N(t)\sim t^{z'}$and average cluster
size $S(t)\sim t^{z}$ were calculated. The process could be characterized as
diffusion limited cluster-cluster aggregation. We have found that all sizes of
clusters that occured during an experiment, fall on a single curve as the
dynamic scaling theory predicts. Hovewer, the characteristic scaling exponents
$z',\: z$ and crossover exponents $\Delta$ were not universal. A particle
tracking method was used to find the dependence of the diffusion coefficients
$D_{s}$ on cluster size $s$. The cluster motions show features of
\textit{\emph{Brownian}} motion. The average diffusion coefficients $<D_{s}>$
depend on the cluster sizes $s$ as a power law $<D_{s}>\propto s^{\gamma}$
where values of $\gamma$ as different as $\gamma=-0.62\pm0.19$ and
$\gamma=-2.08\pm0. were found in two of the experiments. | cond-mat_soft |
Phase Separation by Entanglement of Active Polymerlike Worms: We investigate the aggregation and phase separation of thin, living T.
tubifex worms that behave as active polymers. Randomly dispersed active worms
spontaneously aggregate to form compact, highly entangled blobs, a process
similar to polymer phase separation, and for which we observe power-law growth
kinetics. We find that the phase separation of active polymerlike worms does
not occur through Ostwald ripening, but through active motion and coalescence
of the phase domains. Interestingly, the growth mechanism differs from
conventional growth by droplet coalescence: the diffusion constant
characterizing the random motion of a worm blob is independent of its size, a
phenomenon that can be explained from the fact that the active random motion
arises from the worms at the surface of the blob. This leads to a fundamentally
different phase-separation mechanism that may be unique to active polymers. | cond-mat_soft |
Critical scaling for dense granular flow between parallel plates near
jamming: We numerically study the flow of dense granular materials between parallel
plates driven by an external force. The granular materials form a jammed
solid-like state when the external force is below a critical force, while they
flow like fluids above the critical force. The transition is characterized by
the mass flux. The critical force depends on the average packing fraction and
the distance between the plates. The scaling laws for the critical force and
the mass flux are predicted theoretically based on a continuum model. They are
numerically verified. | cond-mat_soft |
Dynamic buckling and fragmentation in brittle rods: We present experiments on the dynamic buckling and fragmentation of slender
rods axially impacted by a projectile. By combining the results of Saint-Venant
and elastic beam theory, we derive a preferred wavelength lambda for the
buckling instability, and experimentally verify the resulting scaling law for a
range of materials including teflon, dry pasta, glass, and steel. For brittle
materials, buckling leads to the fragmentation of the rod. Measured fragment
length distributions show two clear peaks near lambda/2 and lambda/4. The
non-monotonic nature of the distributions reflect the influence of the
deterministic buckling process on the more random fragmentation processes. | cond-mat_soft |
Tilting behavior of lamellar ice tip during unidirectional freezing of
aqueous solutions: Freezing of ice has been largely reported from many aspects, especially its
complex pattern formation. Ice grown from liquid phase is usually
characteristic of lamellar morphology which plays a significant role in various
domains. However, tilted growth of ice via transition from coplanar to
non-coplanar growth in directional solidification has been paid little
attention in previous studies and there is misleading explanation of the
formation of tilted lamellar ice. Here, we in-situ investigated the variations
of tilting behavior of lamellar ice tip under different conditions within a
single ice crystal with manipulated orientation via unidirectional freezing of
aqueous solutions. It is found that tilted growth of ice tips is sensitive to
pulling velocity and solute type. These experimental results reveal intrinsic
tilted growth behavior of lamellar ice and enrich our understanding in pattern
formation of ice. | cond-mat_soft |
Shear recovery and temperature stability of Ca2+ and Ag+ glycolipid
fibrillar metallogels with unusual $β$-sheet-like domains: Low-molecular weight gelators (LMWG) are small molecules (Mw < ~1 kDa), which
form self-assembled fibrillar networks (SAFiN) hydrogels in water. The great
majority of SAFiN gels is described by an entangled network of self-assembled
fibers, in analogy to a polymer in a good solvent. Here, fibrillation of a
biobased glycolipid bolaamphiphile is triggered by Ca2+ or Ag+ ions, added to
its diluted micellar phase. The resulting SAFiN, which forms hydrogel above 0.5
wt%, has a ``nano-fishnet'' structure, characterized by a fibrous network of
both entangled fibers and $\beta$-sheets-like rafts, generally observed for
silk fibroin, actin hydrogels or mineral imogolite nanotubes, but generally not
known for SAFiN. This work focuses on the strength of the SAFIN gels, their
fast recovery after applying a mechanical stimulus (strain) and their unusual
resistance to temperature, studied by coupling rheology to small angle X-ray
scattering (rheo-SAXS) using synchrotron radiation. The Ca2+-based hydrogel
keeps its properties up to 55{\textdegree}C, while the Ag+-based gel shows a
constant elastic modulus up to 70{\textdegree}C, without appearance of any
gel-to-sol transition temperature. Furthermore, the glycolipid is obtained by
fermentation from natural resources (glucose, rapeseed oil), thus showing that
naturally-engineered compounds can have unprecedented properties, when compared
to the wide range of chemically derived amphiphiles. | cond-mat_soft |
Anomalous distribution functions in sheared suspensions: We investigate velocity probability distribution functions (PDF) of sheared
hard-sphere suspensions. As observed in our Stokes flow simulations and
explained by our single-particle theory, these PDFs can show pronounced
deviations from a Maxwell-Boltzmann distribution. The PDFs are symmetric around
zero velocity and show a Gaussian core and exponential tails over more than six
orders of magnitude of probability. Following the excellent agreement of our
theory and simulation data, we demonstrate that the distribution functions
scale with the shear rate, the particle volume concentration, as well as the
fluid viscosity. | cond-mat_soft |
Synchronized molecular dynamics simulation via macroscopic heat and
momentum transfer: an application to polymer lubrication: The synchronized molecular dynamics simulation via macroscopic heat and
momentum transfer is proposed for the non-isothermal flow behaviors of complex
fluids. In this method, the molecular dynamics simulations are assigned to
small fluid elements to calculate the local stresses and temperatures and are
synchronized at certain time intervals to satisfy the macroscopic heat- and
momentum- transport equations. This method is applied to the lubrication of a
polymeric liquid composed of short chains with ten beads between parallel
plates. The rheological properties and conformation of polymer chains coupled
with the local viscous heating are investigated with a non-dimensional
parameter, i.e., the Nahme-Griffith number, which is defined by the ratio of
the viscous heating to the thermal conduction at the characteristic temperature
required to sufficiently change the viscosity. The present simulation
demonstrates that strong shear thinning and transitional behavior of the
conformation of the polymer chains occur with a rapid temperature rise when the
Nahme-Griffith number exceeds unity. The results also clarify that the
reentrant transition of the linear stress-optical relation occurs for large
shear stresses due to the coupling of the conformation of polymer chains and
heat generation under shear flows. | cond-mat_soft |
Embryo as an active granular fluid: stress-coordinated cellular
constriction chains: Mechanical stress plays an intricate role in gene expression in individual
cells and sculpting of developing tissues. However, systematic methods of
studying how mechanical stress and feedback help to harmonize cellular
activities within a tissue have yet to be developed. Motivated by our
observation of the cellular constriction chains (CCCs) during the initial phase
of ventral furrow formation in the Drosophila melanogaster embryo, we propose
an active granular fluid (AGF) model that provides valuable insights into
cellular coordination in the apical constriction process. In our model, cells
are treated as circular particles connected by a predefined force network, and
they undergo a random constriction process in which the particle constriction
probability P is a function of the stress exerted on the particle by its
neighbors. We find that when P favors tensile stress, constricted particles
tend to form chain-like structures. In contrast, constricted particles tend to
form compact clusters when P favors compression. A remarkable similarity of
constricted-particle chains and CCCs observed in vivo provides indirect
evidence that tensile-stress feedback coordinates the apical constriction
activity. We expect that our particle-based AGF model will be useful in
analyzing mechanical feedback effects in a wide variety of morphogenesis and
organogenesis phenomena. | cond-mat_soft |
Gap maps and intrinsic diffraction losses in one-dimensional photonic
crystal slabs: A theoretical study of photonic bands for one-dimensional (1D) lattices
embedded in planar waveguides with strong refractive index contrast is
presented. The approach relies on expanding the electromagnetic field on the
basis of guided modes of an effective waveguide, and on treating the coupling
to radiative modes by perturbation theory. Photonic mode dispersion, gap maps,
and intrinsic diffraction losses of quasi-guided modes are calculated for the
case of self-standing membranes as well as for Silicon-on-Insulator structures.
Photonic band gaps in a waveguide are found to depend strongly on the core
thickness and on polarization, so that the gaps for transverse electric and
transverse magnetic modes most often do not overlap. Radiative losses of
quasi-guided modes above the light line depend in a nontrivial way on structure
parameters, mode index and wavevector. The results of this study may be useful
for the design of integrated 1D photonic structures with low radiative losses. | cond-mat_soft |
From Liquid Structure to Configurational Entropy: Introducing Structural
Covariance: We connect the configurational entropy of a liquid to the geometrical
properties of its local energy landscape, using a high-temperature expansion.
It is proposed that correlations between local structures arises from their
overlap and, being geometrical in nature, can be usefully determined using the
inherent structures of high temperature liquids. We show quantitatively how the
high-temperature covariance of these local structural fluctuations arising from
their geometrical overlap, combined with their energetic stability, control the
decrease of entropy with decreasing energy. We apply this formalism to a family
of Favoured Local Structure (FLS) lattice models with two low symmetry FLS's
which are found to either crystallize or form a glass on cooling. The
covariance, crystal energy and estimated freezing temperature are tested as
possible predictors of glass-forming ability in the model system. | cond-mat_soft |
Four-boson scale near a Feshbach resonance: We show that an independent four-body momentum scale $\mu_{(4)}$ drives the
tetramer binding energy for fixed trimer energy (or three-body scale
$\mu_{(3)}$) and large scattering length ($a$). The three- and four-body forces
from the one-channel reduction of the atomic interaction near a Feshbach
resonance disentangle $\mu_{(4)}$ and $\mu_{(3)}$. The four-body independent
scale is also manifested through a family of Tjon-lines, with slope given by
$\mu_{(4)}/\mu_{(3)}$ for $a^{-1}=0$. There is the possibility of a new
renormalization group limit cycle due to the new scale. | cond-mat_soft |
Viscous dynamics of drops and bubbles in Hele-Shaw cells: drainage, drag
friction, coalescence, and bursting: In this review article, we discuss recent studies on drops and bubbles in
Hele-Shaw cells, focusing on how scaling laws exhibit crossovers from the
three-dimensional counterparts and focusing on topics in which viscosity plays
an important role. By virtue of progresses in analytical theory and high-speed
imaging, dynamics of drops and bubbles have actively been studied with the aid
of scaling arguments. However, compared with three dimensional problems,
studies on the corresponding problems in Hele-Shaw cells are still limited.
This review demonstrates that the effect of confinement in the Hele-Shaw cell
introduces new physics allowing different scaling regimes to appear. For this
purpose, we discuss various examples that are potentially important for
industrial applications handling drops and bubbles in confined spaces by
showing agreement between experiments and scaling theories. As a result, this
review provides a collection of problems in hydrodynamics that may be
analytically solved or that may be worth studying numerically in the near
future. | cond-mat_soft |
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