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Influence of Confinement on Dynamical Heterogeneities in Dense Colloidal
Samples: We study a dense colloidal suspension confined between two quasiparallel
glass plates as a model system for a supercooled liquid in confined geometries.
We directly observe the three-dimensional Brownian motion of the colloidal
particles using laser scanning confocal microscopy. The particles form dense
layers along the walls, but crystallization is avoided as we use a mixture of
two particle sizes. A normally liquid-like sample, when confined, exhibits
slower diffusive motion. Particle rearrangements are spatially heterogeneous,
and the shapes of the rearranging regions are strongly influenced by the
layering. These rearranging regions become more planar upon confinement. The
wall-induced layers and changing character of the spatially heterogeneous
dynamics appear strongly connected to the confinement induced glassiness. | cond-mat_soft |
Criterion for extensional necking instability in polymeric fluids: We study the linear instability with respect to necking of a filament of
polymeric fluid undergoing uniaxial extension. Contrary to the widely discussed
Considere criterion, we find the onset of instability to relate closely to the
onset of downward curvature in the time (and so strain) evolution of the zz
component of the molecular strain, for extension along the z axis. In
establishing this result numerically across five of the most widely used models
of polymer rheology, and by analytical calculation, we argue it to apply
generically. Particularly emphasized is the importance of polymer chain
stretching in partially mitigating necking. We comment finally on the
relationship between necking and the shape of the underlying steady state
constitutive curve for homogeneous extension. | cond-mat_soft |
Heat Transfer between Graphene and Amorphous SiO2: We study the heat transfer between graphene and amorphous SiO2. We include
both the heat transfer from the area of real contact, and between the surfaces
in the non-contact region. We consider the radiative heat transfer associated
with the evanescent electromagnetic waves which exist outside of all bodies,
and the heat transfer by the gas in the non-contact region. We find that the
dominant contribution to the heat transfer result from the area of real
contact, and the calculated value of the heat transfer coefficient is in good
agreement with the value deduced from experimental data. | cond-mat_soft |
Molecular Dynamics Simulation of Apolipoprotein E3 Lipid Nanodiscs: Nanodiscs are binary discoidal complexes of a phospholipid bilayer
circumscribed by belt-like helical scaffold proteins. Using coarse-grained and
all-atom molecular dynamics simulations, we explore the stability, size, and
structure of nanodiscs formed between the N-terminal domain of apolipoprotein
E3 (apoE3-NT) and variable number of
1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) molecules. We study both
parallel and antiparallel double-belt configurations, consisting of four
proteins per nanodisc. Our simulations predict nanodiscs containing between 240
and 420 DMPC molecules to be stable. The antiparallel configurations exhibit an
average of 1.6 times more amino acid interactions between protein chains and 2
times more ionic contacts, compared to the parallel configuration. With one
exception, DMPC order parameters are consistently larger in the antiparallel
configuration than in the parallel one. In most cases, the root mean square
deviation of the positions of the protein backbone atoms is smaller in the
antiparallel configuration. We further report nanodisc size, thickness, radius
of gyration, and solvent accessible surface area. Combining all investigated
parameters, we hypothesize the antiparallel protein configuration leading to
more stable and more rigid nanodiscs than the parallel one. | cond-mat_soft |
Phase Separation and Ripening in a Viscoelastic Gel: The process of phase separation in elastic solids and viscous fluids is of
fundamental importance to the stability and function of soft materials. We
explore the dynamics of phase separation and domain growth in a viscoelastic
material such as a polymer gel. Using analytical theory and Monte Carlo
simulations we report a new domain growth regime, in which the domain size
increases algebraically with a ripening exponent $\alpha$ that depends on the
viscoelastic properties of the material. For a prototypical Maxwell material,
we obtain $\alpha=1$, which is markedly different from the well-known Ostwald
ripening process with $\alpha=1/3$. We generalize our theory to systems with
arbitrary power-law relaxation behavior and discuss our findings in the context
of the long-term stability of materials as well as recent experimental results
on phase separation in cross-linked networks and cytoskeleton. | cond-mat_soft |
Steady state cyclic behaviour of a half-plane contact in partial slip
subject to varying normal load, moment, shear load, and moderate differential
bulk tension: A new solution for a general half-plane contact in the steady state is
presented. The contacting bodies are subject to a set of constant loads -
normal force, shear force and bulk tension parallel with the interface -
together with an oscillatory set of the same quantities. Partial slip
conditions are expected to ensue for a range of these quantities. In addition,
the line of action of the normal load component does not necessarily need to
pass the centre-line of the contact, thereby introducing a moment and asymmetry
in the contact extent. This advancement enables a mapping to be formalised
between the normal and tangential problem. An exact and easy to apply recipe is
defined. | cond-mat_soft |
Strong coupling electrostatics for randomly charged surfaces:
Antifragility and effective interactions: We study the effective interaction mediated by strongly coupled Coulomb
fluids between dielectric surfaces carrying quenched, random monopolar charges
with equal mean and variance, both when the Coulomb fluid consists only of
mobile multivalent counterions and when it consists of an asymmetric ionic
mixture containing multivalent and monovalent (salt) ions in equilibrium with
an aqueous bulk reservoir. We analyze the consequences that follow from the
interplay between surface charge disorder, dielectric and salt image effects,
and the strong electrostatic coupling that results from multivalent counterions
on the distribution of these ions and the effective interaction pressure they
mediate between the surfaces. In a dielectrically homogeneous system, we show
that the multivalent counterions are attracted towards the surfaces with a
singular, disorder-induced potential that diverges logarithmically on approach
to the surfaces, creating a singular counterion density profile with an
algebraic divergence at the surfaces. This effect drives the system towards a
state of lower thermal "disorder", one that can be described by a renormalized
temperature, exhibiting thus a remarkable antifragility. The interaction
pressure acting on the surfaces displays in general a highly non-monotonic
behavior as a function of the inter-surface separation with a prominent regime
of attraction at small to intermediate separations. This attraction is caused
directly by the combined effects from charge disorder and strong coupling
electrostatics of multivalent counterions, which can be quite significant even
with a small degree of surface charge disorder relative to the mean surface
charge. The strong coupling, disorder-induced attraction is typically far more
stronger than the van der Waals interaction between the surfaces, especially
within a range of several nanometers for the inter-surface separation. | cond-mat_soft |
Free-energy functional for freezing transitions: Hard sphere systems
freezing into crystalline and amorphous structures: A free-energy functional that contains both the symmetry conserved and
symmetry broken parts of the direct pair correlation function has been used to
investigate the freezing of a system of hard spheres into crystalline and
amorphous structures. The freezing parameters for fluid-crystal transition have
been found to be in very good agreement with the results found from
simulations. We considered amorphous structures found from the molecular
dynamics simulations at packing fractions $\eta$ lower than the glass close
packing fraction $\eta_{J}$ and investigated their stability compared to that
of a homogeneous fluid. The existence of free-energy minimum corresponding to a
density distribution of overlapping Gaussians centered around an amorphous
lattice depicts the deeply supercooled state with a heterogeneous density
profile. | cond-mat_soft |
Mobility in immersed granular materials upon cyclic loading: We study the mobility of objects embedded in an immersed granular packing and
subjected to cyclic loadings. In this aim, we conducted experiments using glass
beads immersed in water and a horizontal plate subjected to a cyclic uplift
force. Tests performed at different cyclic force frequencies and amplitudes
evidence the development of three mobility regimes whereby the plate stays
virtually immobile, moves up steadily or slowly creeps upwards. Results show
that steady plate uplift can occur at lower force magnitudes when the frequency
is increased. We propose an interpretation of this frequency-weakening
behaviour based on force relaxation experiments and on the analysis of the
mobility response of theoretical visco-elasto-plastic mechanical analogue.
These results and analysis point out inherent differences in mobility response
between steady and cyclic loadings in immersed granular materials. | cond-mat_soft |
Propagating compaction bands in confined compression of snow: Experiment
and Modelling: We show that the plastic deformation of snow under uniaxial compression is
characterized by complex spatio-temporal strain localization phenomena.
Deformation is characterized by repeated nucleation and propagation of
compaction bands. Compaction bands are also observed during the very first
stage of compression of solid foams where a single band moves across the sample
at approximately constant stress. However, snow differs from these materials as
repeated nucleation and propagation of bands occurs throughout the subsequent
hardening stage until the end of the deformation experiment. Band nucleation
and/or reflection of bands at the sample boundaries are accompanied by stress
drops which punctuate the stress strain curve. A constitutive model is proposed
which quantitatively reproduces all features of this oscillatory deformation
mode. To this end, a well-established compressive plasticity framework for
solid foams is generalized to account for shear softening behavior, time
dependence of microstructure (`rapid sintering') and non-locality of damage
processes in snow. | cond-mat_soft |
Low-Temperature and High-Pressure Induced Swelling of a Hydrophobic
Polymer-Chain in Aqueous Solution: We report molecular dynamics simulations of a hydrophobic polymer-chain in
aqueous solution between $260 {K}$ and $420 {K}$ at pressures of $1 {bar}$,
$3000 {bar}$, and $4500 {bar}$. The simulations reveal a hydrophobically
collapsed state at low pressures and high temperatures. At $3000 {bar}$ and
about $260 {K}$ and at $4500 {bar}$ and about $260 {K}$, however, a transition
to a swelled state is observed. The transition is driven by a smaller volume
and a remarkably strong lower enthalpy of the swelled state, indicating a steep
positive slope of the corresponding transition line. The swelling is stabilized
almost completely by the energetically favorable state of water in the polymers
hydrophobic first hydration shell at low temperatures. Although surprising,
this finding is consistent with the observation of a positive heat capacity of
hydrophobic solvation. Moreover, the slope and location of the observed
swelling transition for the collapsed hydrophobic chain coincides remarkably
well with the cold denaturation transition of proteins. | cond-mat_soft |
Soft particles at liquid interfaces: From molecular particle
architecture to collective phase behavior: Soft particles such as microgels and core-shell particles can undergo
significant and anisotropic deformations when adsorbed to a liquid interface.
This, in turn, leads to a complex phase behavior upon compression. Here we
develop a multiscale framework to rationally link the molecular particle
architecture to the resulting interfacial morphology and, ultimately, to the
collective interfacial phase behavior, enabling us to identify the key
single-particle properties underlying two-dimensional continuous,
heterostructural, and isostructural solid-solid transitions. Our approach
resolves existing discrepancies between experiments and simulations and thus
provides a unifying framework to describe phase transitions in interfacial
soft-particle systems. We establish proof-of-principle for our rational
approach by synthesizing three different poly(N-isopropylacrylamide)
soft-particle architectures, each of which corresponds to a different targeted
phase behavior. In parallel, we introduce a versatile and highly efficient
coarse-grained simulation method that adequately captures the qualitative key
features of each soft-particle system; the novel ingredient in our simulation
model is the use of auxiliary degrees of freedom to explicitly account for the
swelling and collapse of the particles as a function of surface pressure.
Notably, these combined efforts allow us to establish the first experimental
demonstration of a heterostructural transition to a chain phase in a
single-component system, as well as the first accurate in silico account of the
two-dimensional isostructural transition. Overall, our multiscale framework
provides a bridge between physicochemical soft-particle characteristics at the
molecular- and nanoscale and the collective self-assembly phenomenology at the
macroscale, paving the way towards novel materials with on-demand interfacial
behavior. | cond-mat_soft |
Arches and contact forces in a granular pile: Assemblies of granular particles mechanically stable under their own weight
contain arches. These are structural units identified as sets of mutually
stable grains. It is generally assumed that these arches shield the weight
above them and should bear most of the stress in the system. We test such
hypothesis by studying the stress born by in-arch and out-of-arch grains. We
show that, indeed, particles in arches withstand larger stresses. In
particular, the isotropic stress tends to be larger for in-arch-grains whereas
the anisotropic component is marginally distinguishable between the two types
of particles. The contact force distributions demonstrate that an exponential
tail (compatible with the maximization of entropy under no extra constraints)
is followed only by the out-of-arch contacts. In-arch contacts seem to be
compatible with a Gaussian distribution consistent with a recently introduced
approach that takes into account constraints imposed by the local force balance
on grains. | cond-mat_soft |
Anomalous Diffusion in a Monolayer of Lightweight Spheres Fluidized in
Airflow: This paper presents statistical analyses of random motions in a single layer
of fluidized lightweight spherical particles. Foam polystyrene spheres were
driven by an upward airflow through the sieve mesh, and their two-dimensional
motion was acquired using image analysis. In the bulk region, the particle
velocity distributions changed from Gaussian to heavy-tailed distribution as
the bulk packing fraction $\phi_b$ was increased. The mean square displacement
of the particles exhibited transition to subdiffusion at much lower $\phi_b$
than observed in previous studies using similar setup but with heavier
particles. A slight superdiffusion and significant growth of the correlation
length in the two-body velocity correlation was observed at further large
$\phi_b$. The effect of the wall on the dynamics of the particles was also
investigated and the anisotropy of the granular temperature was found to be a
useful index to discriminate between the wall region and the bulk. The
turbulence statistics in the wake of a particle indicated a strong wall-normal
asymmetry of aerodynamic forcing as the ``thermal'' agitation in the wall
region. | cond-mat_soft |
Novel Experimentally Observed Phenomena in Soft Matter: Soft materials such as colloidal suspensions, polymer solutions and liquid
crystals are constituted by mesoscopic entities held together by weak forces.
Their mechanical moduli are several orders of magnitude lower than those of
atomic solids. The application of small to moderate stresses to these materials
results in the disruption of their microstructures. The resulting flow is
non-Newtonian and is characterised by features such as shear rate-dependent
viscosities and non-zero normal stresses. This article begins with an
introduction to some unusual flow properties displayed by soft matter.
Experiments that report a spectrum of novel phenomena exhibited by these
materials, such as turbulent drag reduction, elastic turbulence, the formation
of shear bands and the existence of rheological chaos, flow-induced
birefringence and the unusual rheology of soft glassy materials, are reviewed.
The focus then shifts to observations of the liquid-like response of granular
media that have been subjected to external forces. The article concludes with
examples of the patterns that emerge when certain soft materials are vibrated,
or when they are displaced with Newtonian fluids of lower viscosities. | cond-mat_soft |
Pickering emulsions stabilized by oppositely charged colloids: stability
and pattern formation: Binary mixture of oppositely charged of colloids can be used to stabilize
water-in-oil or oil-in-water emulsions. A Monte Carlo simulation study to
address the effect of charge ratio of colloids on the stability of Pickering
emulsions is presented. The colloidal particles at the interface are modeled as
aligned dipolar hard spheres, with attractive interactions between
unlike-charged and repulsive interaction between like-charged particles. The
optimum composition (fraction of positively charged particles) required for the
stabilization corresponds to a minimum in the interaction energy per particle.
In addition, for each charge ratio, there is a range of compositions where
emulsions can be stabilized. The structural arrangement of particles or the
pattern formation at the emulsion interface is strongly influenced by the
charge ratio. We find well-mixed isotropic, square and hexagonal arrangement of
particles on emulsion surface for different compositions at a given charge
ratio. Distribution of coordination numbers is calculated to characterize
structural features. The simulation study is useful for rational design of
Pickering emulsifications wherein oppositely charged colloids are used, and for
the control of pattern formation that can be useful for the synthesis of
colloidosomes and porous-shells derived from thereof. | cond-mat_soft |
Coarse-grain Molecular Dynamics Study of Fullerene Transport across a
Cell Membrane: The study of the ability of drug molecules to enter cells through the
membrane is of vital importance in the field of drug delivery. In cases where
the transport of the drug molecules through the membrane is not easily
accomplishable, other carrier molecules are used. Spherical fullerene molecules
have been postulated as potential carriers of highly hydrophilic drugs across
the plasma membrane. Here we report the coarse-grain molecular dynamics study
of the translocation of C60 fullerene and its derivatives across a cell
membrane modeled as a 1, 2-distearoyl-sn-glycero-3-phosphocholine (DSPC)
bilayer. Simulation results indicate that pristine fullerene molecules enter
the bilayer quickly and reside within it. The addition of polar functionalized
groups makes the fullerenes less likely to reside within the bilayer but
increases their residence time in bulk water. Addition of polar functional
groups to one half of the fullerene surface, in effect creating a Janus
particle, offers the most promise in developing fullerene models that can
achieve complete translocation through the membrane bilayer. | cond-mat_soft |
Particle Size Effects in Flow-Stabilized Solids: Flow-stabilized solids are a class of fragile matter that forms when a dense
suspension of colloids accumulates against a semi-permeable barrier, for flow
rates above a critical value. In order to probe the effect of particle size on
the formation of these solids, we perform experiments on micron-sized
monodisperse spherical polystyrene spheres in a Hele-Shaw geometry. We examine
the spatial extent, internal fluctuations, and fluid permeability of the solids
deposited against the barrier, and find that these do not scale with the
P\'eclet number. Instead, we find distinct behaviors at higher Peclet numbers,
suggesting a transition from thermal- to athermal-solids which we connect to
particle-scale fluctuations in the liquid-like layer at the upstream surface of
the solid. We further observe that while the Carman-Kozeny model does not
accurately predict the permeability of flow-stabilized solids, we do find a new
scaling which predicts the permeability. | cond-mat_soft |
Pressure and Flow of Exponentially Self-Correlated Active Particles: Microscopic swimming particles, which dissipate energy to execute persistent
directed motion, are a classic example of a non-equilibrium system. We
investigate the non-interacting Ornstein--Uhlenbeck Particle (OUP), which is
propelled through a viscous medium by a force which is correlated over a finite
time. We obtain an exact expression for the steady state phase-space density of
a single OUP confined by a quadratic potential, and use the result to explore
more complex geometries, both through analytical approximations and numerical
simulations. In a "Casimir"-style setup involving two narrowly-spaced walls, we
describe a particle-trapping phenomenon, which leads to a repulsive effective
interaction between the walls; while in a two-dimensional annulus geometry, we
observe net stresses which resemble the Laplace pressure. | cond-mat_soft |
Cyclic annealing as an iterated random map: Disordered magnets, martensitic mixed crystals, and glassy solids can be
irreversibly deformed by subjecting them to external deformation. The
deformation produces a smooth, reversible response punctuated by abrupt
relaxation "glitches". Under appropriate repeated forward and reverse
deformation producing multiple glitches, a strict repetition of a single
sequence of microscopic configurations often emerges. We exhibit these features
by describing the evolution of the system configuration from glitch to glitch
as a mapping of $\mathcal{N}$ states into one-another. A map $\mathbf{U}$
controls forward deformation; a second map $\mathbf{D}$ controls reverse
deformation. Iteration of a given sequence of forward and reverse maps, e.g.
$\mathbf{DDDDUUU}$ necessarily produces a convergence to a fixed cyclic
repetition of states covering multiple glitches. The repetition may have a
period of more than one strain cycle, as recently observed in simulations.
Using numerical sampling, we characterize the convergence properties of four
types of random maps implementing successive physical restrictions. The most
restrictive is the much-studied Preisach model. These maps show only the most
qualitative resemblance to annealing simulations. However, they suggest further
properties needed for a realistic mapping scheme. | cond-mat_soft |
Coarse Grained Computations for a Micellar System: We establish, through coarse-grained computation, a connection between
traditional, continuum numerical algorithms (initial value problems as well as
fixed point algorithms) and atomistic simulations of the Larson model of
micelle formation. The procedure hinges on the (expected) evolution of a few
slow, coarse-grained mesoscopic observables of the MC simulation, and on
(computational) time scale separation between these and the remaining "slaved",
fast variables. Short bursts of appropriately initialized atomistic simulation
are used to estimate the (coarse-grained, deterministic) local dynamics of the
evolution of the observables. These estimates are then in turn used to
accelerate the evolution to computational stationarity through traditional
continuum algorithms (forward Euler integration, Newton-Raphson fixed point
computation). This "equation-free" framework, bypassing the derivation of
explicit, closed equations for the observables (e.g. equations of state) may
provide a computational bridge between direct atomistic / stochastic simulation
and the analysis of its macroscopic, system-level consequences. | cond-mat_soft |
Tricritical behavior of soft nematic elastomers: We propose a lattice statistical model to investigate the phase diagrams and
the soft responses of nematic liquid-crystal elastomers. Using suitably scaled
infinite-range interactions, we obtain exact self-consistent equations for the
tensor components of the nematic order parameter in terms of temperature, the
distortion and stress tensors, and the initial nematic order. These equations
are amenable to simple numerical calculations, which are used to characterize
the low-temperature soft regime. We find a peculiar phase diagram, in terms of
temperature and the diagonal component of the distortion tensor along the
stretching direction, with first- and second-order transitions to the soft
phase, and the prediction of tricritical points. This behavior is not
qualitatively changed if we use different values of the initial nematic order
parameter. | cond-mat_soft |
Coarse-grain Molecular Dynamics Study of Fullerene Transport across a
Cell Membrane: The study of the ability of drug molecules to enter cells through the
membrane is of vital importance in the field of drug delivery. In cases where
the transport of the drug molecules through the membrane is not easily
accomplishable, other carrier molecules are used. Spherical fullerene molecules
have been postulated as potential carriers of highly hydrophilic drugs across
the plasma membrane. Here we report the coarse-grain molecular dynamics study
of the translocation of C60 fullerene and its derivatives across a cell
membrane modeled as a 1, 2-distearoyl-sn-glycero-3-phosphocholine (DSPC)
bilayer. Simulation results indicate that pristine fullerene molecules enter
the bilayer quickly and reside within it. The addition of polar functionalized
groups makes the fullerenes less likely to reside within the bilayer but
increases their residence time in bulk water. Addition of polar functional
groups to one half of the fullerene surface, in effect creating a Janus
particle, offers the most promise in developing fullerene models that can
achieve complete translocation through the membrane bilayer. | cond-mat_soft |
Dumb-bell swimmers: We investigate the way in which oscillating dumb-bells, a simple microscopic
model of apolar swimmers, move at low Reynold's number. In accordance with
Purcell's Scallop Theorem a single dumb-bell cannot swim because its stroke is
reciprocal in time. However the motion of two or more dumb-bells, with mutual
phase differences, is not time reversal invariant, and hence swimming is
possible. We use analytical and numerical solutions of the Stokes equations to
calculate the hydrodynamic interaction between two dumb-bell swimmers and to
discuss their relative motion. The cooperative effect of interactions between
swimmers is explored by considering first regular, and then random arrays of
dumb-bells. We find that a square array acts as a micropump. The long time
behaviour of suspensions of dumb-bells is investigated and compared to that of
model polar swimmers. | cond-mat_soft |
Dynamics of quasi-static collapse process of a binary granular column: The dynamical behavior of the column that made up binary granular beads is
investigated systematically by tracking the displacement of particles in the
collapse process. An experimental setup is first devised to control the
quasi-static collapse of a granular column, and then observe the trajectories
of tracer particles by using an industrial camera controlled by the image
acquisition program. It is found that there exist two zones in column: a
sliding region in which particles are moving in a layered structure; a static
region within which particles are stationary. According to this analytical
result, a dynamical model is developed to predict the trajectory evolution of
particles in the space-time. The calculating result for the trajectories of
particles on the selected layers is well consistent with the experimental
observation. | cond-mat_soft |
Tensile Fracture of Welded Polymer Interfaces: Miscibility,
Entanglements and Crazing: Large-scale molecular simulations are performed to investigate tensile
failure of polymer interfaces as a function of welding time $t$. Changes in the
tensile stress, mode of failure and interfacial fracture energy $G_I$ are
correlated to changes in the interfacial entanglements as determined from
Primitive Path Analysis. Bulk polymers fail through craze formation, followed
by craze breakdown through chain scission. At small $t$ welded interfaces are
not strong enough to support craze formation and fail at small strains through
chain pullout at the interface. Once chains have formed an average of about one
entanglement across the interface, a stable craze is formed throughout the
sample. The failure stress of the craze rises with welding time and the mode of
craze breakdown changes from chain pullout to chain scission as the interface
approaches bulk strength. The interfacial fracture energy $G_I$ is calculated
by coupling the simulation results to a continuum fracture mechanics model. As
in experiment, $G_I$ increases as $t^{1/2}$ before saturating at the average
bulk fracture energy $G_b$. As in previous simulations of shear strength,
saturation coincides with the recovery of the bulk entanglement density. Before
saturation, $G_I$ is proportional to the areal density of interfacial
entanglements. Immiscibiltiy limits interdiffusion and thus suppresses
entanglements at the interface. Even small degrees of immisciblity reduce
interfacial entanglements enough that failure occurs by chain pullout and $G_I
\ll G_b$. | cond-mat_soft |
Tension dynamics in semiflexible polymers. Part II: Scaling solutions
and applications: In Part I of this contribution, a systematic coarse-grained description of
the dynamics of a weakly-bending semiflexible polymer was developed. Here, we
discuss analytical solutions of the established deterministic partial
integro-differential equation for the spatio-temporal relaxation of the
backbone tension. For prototypal experimental situations, such as the sudden
application or release of a strong external pulling force, it is demonstrated
that the tensile dynamics reflects the self-affine conformational fluctuation
spectrum in a variety of intermediate asymptotic power laws. Detailed and
explicit analytical predictions for the tension propagation and relaxation and
corresponding results for common observables, such as the end-to-end distance,
are obtained. | cond-mat_soft |
Nonadditive Interactions Unlock Small-Particle Mobility in Binary
Colloidal Monolayers: We examine the organization and dynamics of binary colloidal monolayers
composed of micron-scale silica particles interspersed with smaller-diameter
silica particles that serve as minority component impurities. These binary
monolayers are prepared at the surface of ionic liquid droplets over a range of
size ratios ($\sigma=0.16-0.66$) and are studied with low-dose minimally
perturbative scanning electron microscopy (SEM). The high resolution of SEM
imaging provides direct tracking of all particle coordinates over time,
enabling a complete description of the microscopic state. In these bidisperse
size mixtures, particle interactions are non-additive because interfacial
pinning to the droplet surface causes the equators of differently sized
particles to lie in separate planes. By varying the size ratio we control the
extent of non-additivity in order to achieve phase behavior inaccessible to
additive 2D systems. Across the range of size ratios we tune the system from a
mobile small-particle phase ($\sigma<0.24$), to an interstitial solid
($0.24<\sigma<0.33$), to a disordered glass ($\sigma>0.33$). These distinct
phase regimes are classified through measurements of hexagonal ordering of the
large-particle host lattice and the lattice's capacity for small-particle
transport. Altogether, we explain these structural and dynamic trends by
considering the combined influence of interparticle interactions and the
colloidal packing geometry. Our measurements are reproduced in molecular
dynamics simulations of 2D non-additive disks, suggesting an efficient method
for describing confined systems with reduced dimensionality representations. | cond-mat_soft |
Vibrations of Jammed Disk Packings with Hertzian Interactions: Contact breaking and Hertzian interactions between grains can both give rise
to nonlinear vibrational response of static granular packings. We perform
molecular dynamics simulations at constant energy in 2D of frictionless
bidisperse disks that interact via Hertzian spring potentials as a function of
energy and measure directly the vibrational response from the Fourier transform
of the velocity autocorrelation function. We compare the measured vibrational
response of static packings near jamming onset to that obtained from the
eigenvalues of the dynamical matrix to determine the temperature above which
the linear response breaks down. We compare packings that interact via
single-sided (purely repulsive) and double-sided Hertzian spring interactions
to disentangle the effects of the shape of the potential from contact breaking.
Our studies show that while Hertzian interactions lead to weak nonlinearities
in the vibrational behavior (e.g. the generation of harmonics of the
eigenfrequencies of the dynamical matrix), the vibrational response of static
packings with Hertzian contact interactions is dominated by contact breaking as
found for systems with repulsive linear spring interactions. | cond-mat_soft |
Confinement Effects on Phase Behavior of Soft Matter Systems: When systems that can undergo phase separation between two coexisting phases
in the bulk are confined in thin film geometry between parallel walls, the
phase behavior can be profoundly modified. These phenomena shall be described
and exemplified by computer simulations of the Asakura-Oosawa model for
colloid-polymer mixtures, but applications to other soft matter systems (e.g.
confined polymer blends) will also be mentioned. Typically a wall will prefer
one of the phases, and hence the composition of the system in the direction
perpendicular to the walls will not be homogeneous. If both walls are of the
same kind, this effect leads to a distortion of the phase diagram of the system
in thin film geometry, in comparison with the bulk, analogous to the phenomenon
of "capillary condensation" of simple fluids in thin capillaries. In the case
of "competing walls", where both walls prefer different phases of the two
phases coexisting in the bulk, a state with an interface parallel to the walls
gets stabilized. The transition from the disordered phase to this "soft mode
phase" is rounded by the finite thickness of the film and not a sharp phase
transition. However, a sharp transition can occur where this interface gets
localized at (one of) the walls. The relation of this interface localization
transition to wetting phenomena is discussed. Finally, an outlook to related
phenomena is given, such as the effects of confinement in cylindrical pores on
the phase behavior, and more complicated ordering phenomena (lamellar
mesophases of block copolymers or nematic phases of liquid crystals under
confinement). | cond-mat_soft |
A simple analytical formula for the free-energy of ligand-receptor
mediated interactions: Recently \1, we presented a general theory for calculat- ing the strength and
properties of colloidal interactions mediated by ligand-receptor bonds (such as
those that bind DNA-coated colloids). In this communication, we derive a
surprisingly simple analytical form for the inter- action free energy, which
was previously obtainable only via a costly numerical thermodynamic
integration. As a result, the computational effort to obtain potentials of in-
teraction is significantly reduced. Moreover, we can gain insight from this
analytic expression for the free energy in limiting cases. In particular, the
connection of our general theory to other previous specialised approaches is
now made transparent. This important simplification will significantly broaden
the scope of our theory. | cond-mat_soft |
Vibrational lifetimes and viscoelastic properties of ultrastable glasses: Amorphous solids are viscoelastic. They dissipate energy when deformed at
finite rate and finite temperature. We here use analytic theory and molecular
simulations to demonstrate that linear viscoelastic dissipation can be directly
related to the static and dynamic properties of the fundamental vibrational
excitations of an amorphous system. We study ultrastable glasses that do not
age, i.e. that remain in stable minima of the potential energy surface at
finite temperature. Our simulations show four types of vibrational modes, which
differ in spatial localization, similarity to plane waves and vibrational
lifetimes. At frequencies below the Boson peak, the viscoelastic response can
be split into contributions from plane-wave and quasilocalized modes. We derive
a parameter-free expression for the viscoelastic storage and loss moduli for
both of these modes. Our results show that the dynamics of microscopic
dissipation, in particular the lifetimes of the modes, determine the
viscoelastic response only at high frequency. Quasilocalized modes dominate the
linear viscoelastic response at intermediate frequencies below the Boson peak. | cond-mat_soft |
Programming complex shapes in thin nematic elastomer and glass sheets: Nematic elastomers and glasses are solids that display spontaneous distortion
under external stimuli. Recent advances in the synthesis of sheets with
controlled heterogeneities have enabled their actuation into non-trivial shapes
with unprecedented energy density. Thus, these have emerged as powerful
candidates for soft actuators. To further this potential, we introduce the key
metric constraint which governs shape changing actuation in these sheets. We
then highlight the richness of shapes amenable to this constraint through two
broad classes of examples which we term nonisometric origami and lifted
surfaces. Finally, we comment on the derivation of the metric constraint, which
arises from energy minimization in the interplay of stretching, bending and
heterogeneity in these sheets. | cond-mat_soft |
Effect of particle exchange on the glass transition of binary hard
spheres: We investigate the replica theory of the liquid-glass transition for a binary
mixture of large and small additive hard spheres. We consider two different
ans\"atze for this problem: the frozen glass ansatz (FGA) in whichs the
exchange of large and small particles in a glass state is prohibited, and the
exchange glass ansatz (EGA), in which it is allowed. We calculate the dynamical
and thermodynamical glass transition points with the two ans\"atze. We show
that the dynamical transition density of the FGA is lower than that of the EGA,
while the thermodynamical transition density of the FGA is higher than that of
the EGA. We discuss the algorithmic implications of these results for the
density-dependence of the relaxation time of supercooled liquids. We
particularly emphasize the difference between the standard Monte Carlo and swap
Monte Carlo algorithms. Furthermore, we discuss the importance of particle
exchange for estimating the configurational entropy. | cond-mat_soft |
Quasicrystal vs Glass Transition: comparison structural and dynamical
properties: Quasicrystals are solid structures with symmetry forbidden by
crystallographic rules. Because of this some structural characteristics of
quasicrystals, for instance, radial distribution function, can look similar to
the ones of amorphous phases. This is of principal importance since radial
distribution function is the main property to characterize the structure in
molecular simulation. In the present paper we compare the radial distribution
functions and dynamical properties of three systems in the vicinity of glass
transition, quasicrystal formation and crystallization. We show that in spite
of similarity of radial distribution functions the dynamical properties of a
system in the vicinity of quasicrystal are qualitatively equivalent to the ones
of crystal. Because of this combination the radial distribution functions with
investigation of dynamics of the liquid allows unambiguously distinguish glass
and quasicrystal. | cond-mat_soft |
Perspective: Atomistic Simulations of Water and Aqueous Systems with
Machine Learning Potentials: As the most important solvent, water has been at the center of interest since
the advent of computer simulations. While early molecular dynamics and Monte
Carlo simulations had to make use of simple model potentials to describe the
atomic interactions, accurate ab initio molecular dynamics simulations relying
on the first-principles calculation of the energies and forces have opened the
way to predictive simulations of aqueous systems. Still, these simulations are
very demanding, which prevents the study of complex systems and their
properties. Modern machine learning potentials (MLPs) have now reached a mature
state, allowing to overcome these limitations by combining the high accuracy of
electronic structure calculations with the efficiency of empirical force
fields. In this Perspective we give a concise overview about the progress made
in the simulation of water and aqueous systems employing MLPs, starting from
early work on free molecules and clusters via bulk liquid water to electrolyte
solutions and solid-liquid interfaces. | cond-mat_soft |
Segregation forces in dense granular flows: Closing the gap from single
intruders to mixtures: Using simulations and a virtual-spring-based approach, we measure the
segregation force, Fseg, over a range of size-bidisperse mixture
concentrations, particle size ratios, and shear rates to develop a model for
Fseg that extends its applicability from the well-studied non-interacting
intruders regime to finite-concentration mixtures where cooperative phenomena
occur. The model predicts the concentration below which the single intruder
assumption applies and provides an accurate description of the pressure
partitioning between species. | cond-mat_soft |
A Percolation Model of Diagenesis: The restructuring process of diagenesis in the sedimentary rocks is studied
using a percolation type model. The cementation and dissolution processes are
modeled by the culling of occupied sites in rarefied and growth of vacant sites
in dense environments. Starting from sub-critical states of ordinary
percolation the system evolves under the diagenetic rules to critical
percolation configurations. Our numerical simulation results in two dimensions
indicate that the stable configuration has the same critical behaviour as the
ordinary percolation. | cond-mat_soft |
Large-scale critical behavior of the rippling phase transition for
graphene membranes: We analyze the spontaneous rippling of graphene membranes as function of the
coupling between lattice deformations and electrons.
We numerically study a model of an elastic membrane coupled to Dirac
fermions. We identify a phase transition from a flat to a rippled configuration
of the membrane when increasing the coupling and propose a scaling procedure
that allows us to effectively reach arbitrary large system sizes. We find that
the critical value of the coupling rapidly decays as the system increases its
size, in agreement with the experimental observation of an unavoidable stable
rippled state for suspended graphene membranes. This decay turns out to be
controlled by a power law with a critical exponent $\sim 1/2$. | cond-mat_soft |
Assembly and speed control in ion exchange based modular phoretic
micro-swimmers: We report an experimental study on ion-exchange based modular micro-swimmers
in low-salt water. Cationic ion-exchange particles and passive cargo particles
assemble into self-propelling complexes, showing self-propulsion at speeds of
several microns per second over extended distances and times. We quantify the
assembly and speed of the complexes for different combinations of ion exchange
particles and cargo particles, substrate types, salt types and concentrations,
and cell geometries. Irrespective of experimental boundary conditions, we
observe a regular development of the assembly shape with increasing number of
cargo. Moreover, the swimming speed increases stepwise upon increasing the
number of cargo and then saturates at a maximum speed, indicating an active
role of cargo in modular swimming. We propose a geometric model of
self-assembly to describe the experimental observations in a qualitative way.
Our study also provides some constraints for future theoretical modelling and
simulation. | cond-mat_soft |
Liquid dynamics in partially crystalline glycerol: We present a dielectric study on the dynamics of supercooled glycerol during
crystallization. We explore the transformation into a solid phase in real time
by monitoring the temporal evolution of the amplitude of the dielectric signal.
Neither the initial nucleation or the crystal growth influence the liquid
dynamics visibly. For one of the samples studied, a tiny fraction of glycerol
remained in the disordered state after the end of the transition. We examined
the nature of the alpha relaxation in this frustrated crystal and find that it
is virtually identical to the bulk dynamics. In addition to that, we have found
no evidence that supercooled glycerol transforms into a peculiar phase where
either a new solid amorphous state or nano-crystals dispersed in a liquid
matrix are formed. | cond-mat_soft |
Cluster and reentrant anomalies of nearly Gaussian core particles: We study through integral equation theory and numerical simulations the
structure and dynamics of fluids composed of ultrasoft, nearly Gaussian
particles. Namely, we explore the fluid phase diagram of a model in which
particles interact via the generalized exponential potential u(r)=\epsilon
exp[-(r/\sigma)^n], with a softness exponent n slightly larger than 2. In
addition to the well-known anomaly associated to reentrant melting, the
structure and dynamics of the fluid display two additional anomalies, which are
visible in the isothermal variation of the structure factor and diffusivity.
These features are correlated to the appearance of dimers in the fluid phase
and to the subsequent modification of the cluster structure upon compression.
We corroborate these results through an analysis of the local minima of the
potential energy surface, in which clusters appear as much tighter
conglomerates of particles. We find that reentrant melting and clustering
coexist for softness exponents ranging from 2^+ up to values relevant for the
description of amphiphilic dendrimers, i.e., n=3. | cond-mat_soft |
Kinetics of Loop Formation in Polymer Chains: We investigate the kinetics of loop formation in flexible ideal polymer
chains (Rouse model), and polymers in good and poor solvents. We show for the
Rouse model, using a modification of the theory of Szabo, Schulten, and
Schulten, that the time scale for cyclization is $\tau_c\sim \tau_0 N^2$ (where
$\tau_0$ is a microscopic time scale and $N$ is the number of monomers),
provided the coupling between the relaxation dynamics of the end-to-end vector
and the looping dynamics is taken into account. The resulting analytic
expression fits the simulation results accurately when $a$, the capture radius
for contact formation, exceeds $b$, the average distance between two connected
beads. Simulations also show that, when $a < b$, $\tau_c\sim N^{\alpha_\tau}$,
where $1.5<{\alpha_\tau}\le 2$ in the range $7<N<200$ used in the simulations.
By using a diffusion coefficient that is dependent on the length scales $a$ and
$b$ (with $a<b$), which captures the two-stage mechanism by which looping
occurs when $a < b$, we obtain an analytic expression for $\tau_c$ that fits
the simulation results well. The kinetics of contact formation between the ends
of the chain are profoundly affected when interactions between monomers are
taken into account. Remarkably, for $N < 100$ the values of $\tau_c$ decrease
by more than two orders of magnitude when the solvent quality changes from good
to poor. Fits of the simulation data for $\tau_c$ to a power law in $N$
($\tau_c\sim N^{\alpha_\tau}$) show that $\alpha_\tau$ varies from about 2.4 in
a good solvent to about 1.0 in poor solvents. Loop formation in poor solvents,
in which the polymer adopts dense, compact globular conformations, occurs by a
reptation-like mechanism of the ends of the chain. | cond-mat_soft |
Spontaneous knotting and unknotting of flexible linear polymers:
equilibrium and kinetic aspects: We report on a computational study of the statics and dynamics of long
flexible linear polymers that spontaneously knot and unknot. Specifically, the
equilibrium self-entanglement properties, such as the knotting probability,
knot length and position, are investigated with extensive Monte Carlo sampling
of chains of up to 15,000 beads. Tens of such equilibrated chains of up to 4,
096 beads are next used as starting points for Langevin dynamics simulations.
The complex interplay of chain dynamics and self-knotting is addressed by
monitoring the time evolution of various metric and entanglement properties. In
particular, the extensive duration of the simulations allows for observing the
spontaneous formation and disappearance of prime and composite physical knots
in linear chains. Notably, a sizeable fraction of self-knotting and unknotting
events is found to involve regions that are far away from the chain termini. To
the best of our knowledge this represents the first instance where spontaneous
changes in knotting for linear homopolymers are systematically characterized
using unbiased dynamics simulations. | cond-mat_soft |
Electrostatic Interactions in Strongly-Coupled Soft Matter: Charged soft-matter systems--such as colloidal dispersions and charged
polymers--are dominated by attractive forces between constituent like-charged
particles when neutralizing counterions of high charge valency are introduced.
Such counter-intuitive effects indicate strong electrostatic coupling between
like-charged particles, which essentially results from electrostatic
correlations among counterions residing near particle surfaces. In this paper,
the attraction mechanism and the structure of counterionic correlations are
discussed in the limit of strong coupling based on recent numerical and
analytical investigations and for various geometries (planar, spherical and
cylindrical) of charged objects. | cond-mat_soft |
Relation between the alpha-relaxation and the Johari-Goldstein
Beta-relaxation of a component in miscible blends of two glass-formers: It is well known that the \alpha-relaxation of each component in a miscible
mixtures of two glass-formers has its own dynamics, which change with the
composition of the blend. Lesser known are the corresponding change of the
Johari-Goldstein (JG) \beta-relaxation and its relation to the
\alpha-relaxation. Previously, in neat glass-formers, the relaxation time
\tauJG of JG \beta-relaxation was identified with the independent relaxation
time \tau0 of the coupling model. The correspondence between \tau0 and \tauJG
was supported by analysis of experimental data of many glass-formers. In this
work, this correspondence between \tau0 and \tauJG of a component in binary
mixtures and the relation between \tau0 and \tau\alpha of the coupling model
are used to generate predictions of the simultaneous changes of \tau\alpha and
\tau\JG of the component on varying the composition of the mixture. The
predictions are in accord with the experimental data of the component
2-picoline in mixtures with either tri-styrene or ortho-terphenyl by T.
Blochowicz and E.A. Rossler, Phys.Rev.Lett. in press(2004). | cond-mat_soft |
Anomalous Thermomechanical Properties of a Self-propelled Colloidal
Fluid: We use numerical simulations to compute the equation of state of a suspension
of spherical, self-propelled nanoparticles. We study in detail the effect of
excluded volume interactions and confinement as a function of the system
temperature, concentration and strength of the propulsion. We find a striking
non-monotonic dependence of the pressure with the temperature, and provide
simple scaling arguments to predict and explain the occurrence of such an
anomalous behavior. We conclude the paper by explicitly showing how our results
have an important implications for the effective forces exerted by fluids of
self-propelled particles on passive, larger components. | cond-mat_soft |
Generating multi-chain configurations of an inhomogeneous melt from the
knowledge of single-chain properties: Mean-field techniques provide a rather accurate description of single-chain
conformations in spatially inhomogeneous polymer systems containing interfaces
or surfaces. Intermolecular correlations, however, are not described by the
mean-field approach and information about the distribution of distance between
different molecules is lost. Based on the knowledge of the exact equilibrium
single-chain properties in contact with solid substrates, we generate
multi-chain configurations that serve as nearly equilibrated starting
configurations for molecular dynamics simulations by utilizing the packing
algorithm of Auhl and co-workers [J. Chem. Phys. 119, 12718 (2003)] for
spatially inhomogeneous systems, i.e., a thin polymer film confined between two
solid substrates. The single-chain conformations are packed into the thin film
conserving the single-chain properties and simultaneously minimizing local
fluctuations of the density. The extent to which enforcing the
near-incompressibility of a dense polymer liquid during the packing process is
able to re-establish intermolecular correlations is investigated by monitoring
intermolecular correlation functions and the structure function of density
fluctuations as a function of the distance from the confining solid substrates. | cond-mat_soft |
Coarse-grained modeling of polymers with end-on and side-on liquid
crystal moieties: effect of architecture: Mesogens, which are typically stiff rodlike or disklike molecules, are able
to self-organize into liquid crystal (LC) phases in a certain temperature
range. Such mesogens, or LC groups, can be attached to polymer chains in
various configurations including within the backbone (main-chain LC polymers)
or at the ends of side-chains attached to the backbone in an end-on or side-on
configuration (side-chain LC polymers or SCLCPs), which can display synergistic
properties arising from both their LC and polymeric character. At lower
temperatures, chain conformations may be significantly altered due to the
mesoscale LC ordering, thus, when heating from the LC ordered state through the
LC to isotropic phase transition, the chains return from a more stretched to a
more random coil conformation. This can cause macroscopic shape changes, which
depend significantly on the type of LC attachment and other architectural
properties of the polymer. Here, to study the structure-property relationships
for SCLCPs with a range of different architectures, we develop a coarse-grained
model that includes torsional potentials along with LC interactions of a
Gay--Berne form. We create systems of different side chain lengths, chain
stiffnesses, and LC attachment types, and track their structural properties as
a function of temperature. Our modeled systems indeed form a variety of
well-organized mesophase structures at low temperatures, and we predict higher
LC to isotropic transition temperatures for the end-on side-chain systems than
for analogous side-on side-chain systems. Understanding these phase transitions
and their dependence on polymer architecture can be useful in designing
materials with reversible and controllable deformations. | cond-mat_soft |
On the thickness of the double layer in ionic liquids: In this study, we examined the thickness of the electrical double layer (EDL)
in ionic liquids using density functional theory (DFT) calculations and
molecular dynamics (MD) simulations. We focused on the BF4- anion adsorption
from 1-ethyl-3-methylimidazolium tetrafluoroborate (EMImBF4) ionic liquid on
the Au(111) surface. At both DFT and MD levels, we evaluated the
capacitance-potential dependence for the Helmholtz model of the interface.
Using MD simulations, we also explored a more realistic, multilayer EDL model
accounting for the ion layering. Concurrent analysis of the DFT and MD results
provides a ground for thinking whether the electrical double layer in ionic
liquids is one- or multi-ionic-layer thick. | cond-mat_soft |
In Situ Ion Induced Gelation of Colloidal Dispersion of Laponite:
Relating Microscopic Interactions to Macroscopic Behavior: Aqueous dispersion of Laponite, when exposed to carbon dioxide environment
leads to in situ inducement of magnesium and lithium ions, which is, however
absent when dispersion is exposed to air. Consequently, in the rheological
experiments, Laponite dispersion preserved under carbon dioxide shows more
spectacular enhancement in the elastic and viscous moduli as a function of time
compared to that exposed to air. By measuring concentration of all the ions
present in a dispersion as well as change in pH, the evolving inter-particle
interactions among the Laponite particles is estimated. DLVO analysis of a
limiting case is performed, wherein two particles approach each other in a
parallel fashion a situation with maximum repulsive interactions. Interestingly
it is observed that DLVO analysis explains the qualitative details of an
evolution of elastic and viscous moduli remarkably well thereby successfully
relating the macroscopic phenomena to the microscopic interactions. | cond-mat_soft |
Ordering kinetics in active polar fluid: We model the active polar fluid as a collection of orientable objects
supplied with active stresses and momentum damping coming from the viscosity of
bulk fluid medium. The growth kinetics of local orientation field is studied.
The effect of active fluid is contractile or extensile depending upon the sign
of the active stress. We explore the growth kinetics for different activities.
We observe that for both extensile and contractile cases the growth is altered
by a prefactor when compared to the equilibrium Model A. We find that the
extensile fluid enhances the domain growth whereas the contractile fluid
supresses it. The asymptotic growth becomes pure algebraic for large magnitudes
of activity. We also find that the domain morphology remains unchanged due to
activity and system shows the good dynamic scaling for all activities. Our
study provides the understanding of ordering kinetics in active polar gel. | cond-mat_soft |
A model for the atomic-scale structure of a dense, nonequilibrium fluid:
the homogeneous cooling state of granular fluids: It is shown that the equilibrium Generalized Mean Spherical Model of fluid
structure may be extended to nonequilibrium states with equation of state
information used in equilibrium replaced by an exact condition on the two-body
distribution function. The model is applied to the homogeneous cooling state of
granular fluids and upon comparison to molecular dynamics simulations is found
to provide an accurate picture of the pair distribution function. | cond-mat_soft |
Viscoelasticity of reversibly crosslinked networks of semiflexible
polymers: We present a theoretical framework for the linear and nonlinear visco-elastic
properties of reversibly crosslinked networks of semiflexible polymers. In
contrast to affine models where network strain couples to the polymer
end-to-end distance, in our model strain rather serves to locally distort the
network structure. This induces bending modes in the polymer filaments, the
properties of wich are slaved to the surrounding network structure.
Specifically, we investigate the frequency-dependent linear rheology, in
particular in combination with crosslink binding/unbinding processes. We also
develop schematic extensions to describe the nonlinear response during creep
measurements as well as during constant-strainrate ramps. | cond-mat_soft |
An alternative scenario for the formation of specialized protein
nano-domains (cluster phases) in biomembranes: We discuss a realistic scenario, accounting for the existence of
sub-micrometric protein domains in cell membranes. At the biological level,
such membrane domains have been shown to be specialized, in order to perform a
determined biological task, in the sense that they gather one or a few protein
species out of the hundreds of different ones that a cell membrane may contain.
By analyzing the balance between mixing entropy and protein affinities, we
propose that such protein sorting in distinct domains can be explained without
appealing to pre-existing lipidic micro-phase separations, as in the lipid raft
scenario. We show that the proposed scenario is compatible with known physical
interactions between membrane proteins, even if thousands of different species
coexist. | cond-mat_soft |
Entropy and Barrier-Hopping Determine Conformational Viscoelasticity in
Single Biomolecules: Biological macromolecules have complex and non-trivial energy landscapes,
endowing them a unique conformational adaptability and diversity in function.
Hence, understanding the processes of elasticity and dissipation at the
nanoscale is important to molecular biology and also emerging fields such as
nanotechnology. Here we analyse single molecule fluctuations in an atomic force
microscope (AFM) experiment using a generic model of biopolymer viscoelasticity
that importantly includes sources of local `internal' conformational
dissipation. Comparing two biopolymers, dextran and cellulose, polysaccharides
with and without the well-known `chair-to-boat' transition, reveals a signature
of this simple conformational change as minima in both the elasticity and
internal friction around a characteristic force. A calculation of two-state
populations dynamics offers a simple explanation in terms of an elasticity
driven by the entropy, and friction by barrier-controlled hopping, of
populations on a landscape. The microscopic model, allows quantitative mapping
of features of the energy landscape, revealing unexpectedly slow dynamics,
suggestive of an underlying roughness to the free energy. | cond-mat_soft |
Unzipping of a double-stranded block copolymer DNA by a periodic force: Using Monte Carlo simulations, we study the hysteresis in unzipping of a
double stranded block copolymer DNA with $-A_n B_n-$ repeat units. Here $A$ and
$B$ represent two different types of base pairs having two- and three-bonds,
respectively, and $2n$ represents the number of such base pairs in a unit. The
end of the DNA are subjected to a time dependent periodic force with frequency
($\omega$) and amplitude ($g_0$) keeping the other end fixed. We find that the
equilibrium force-temperature phase diagram for the static force is independent
of the DNA sequence. For the periodic force case, the results are found to be
dependent on the block copolymer DNA sequence and also on the base pair type on
which the periodic force is acting. We observe hysteresis loops of various
shapes and sizes and obtain the scaling of loop area both at low and high
frequency regimes. | cond-mat_soft |
Effect of total and pair configurational entropy in determining dynamics
of supercooled liquids over a range of densities: In this paper, we present a study of supercooled liquids interacting with the
Lennard Jones (LJ) potential and the corresponding purely repulsive
(Weeks-Chandler-Andersen or WCA) potential, over a range of densities and
temperatures, in order to understand the origin of their different dynamics in
spite of their structures being similar. Using the configurational entropy as
the thermodynamic marker via the Adam Gibbs (AG) relation, we show that the
difference in the dynamics of these two systems at low temperatures can be
explained from thermodynamics. At higher densities both the thermodynamical and
dynamical difference between these model systems decrease, which is
quantitatively demonstrated in this paper by calculating different parameters.
The study also reveals the origin of the difference in pair entropy despite the
similarity in the structure. Although the maximum difference in structure is
obtained in the partial radial distribution function (rdf) of the B type of
particles, the rdf of AA pairs and AB pairs give rise to the differences in the
entropy and dynamics. This work supports the observation made in an earlier
study (Phys. Rev. Lett.,\textbf {113}, 225701, 2014) and shows that they are
generic in nature, independent of density. | cond-mat_soft |
Two-State Folding, Folding through Intermediates, and Metastability in a
Minimalistic Hydrophobic-Polar Model for Proteins: Within the frame of an effective, coarse-grained hydrophobic-polar protein
model, we employ multicanonical Monte Carlo simulations to investigate
free-energy landscapes and folding channels of exemplified heteropolymer
sequences, which are permutations of each other. Despite the simplicity of the
model, the knowledge of the free-energy landscape in dependence of a suitable
system order parameter enables us to reveal complex folding characteristics
known from real bioproteins and synthetic peptides, such as two-state folding,
folding through weakly stable intermediates, and glassy metastability. | cond-mat_soft |
Growing timescales and lengthscales characterizing vibrations of
amorphous solids: Low-temperature properties of crystalline solids can be understood using
harmonic perturbations around a perfect lattice, as in Debye's theory.
Low-temperature properties of amorphous solids, however, strongly depart from
such descriptions, displaying enhanced transport, activated slow dynamics
across energy barriers, excess vibrational modes with respect to Debye's theory
(i.e., a Boson Peak), and complex irreversible responses to small mechanical
deformations. These experimental observations indirectly suggest that the
dynamics of amorphous solids becomes anomalous at low temperatures. Here, we
present direct numerical evidence that vibrations change nature at a
well-defined location deep inside the glass phase of a simple glass former. We
provide a real-space description of this transition and of the rapidly growing
time and length scales that accompany it. Our results provide the seed for a
universal understanding of low-temperature glass anomalies within the
theoretical framework of the recently discovered Gardner phase transition. | cond-mat_soft |
Active colloidal propulsion over a crystalline surface: We study both experimentally and theoretically the dynamics of chemically
self-propelled Janus colloids moving atop a two-dimensional crystalline
surface. The surface is a hexagonally close-packed monolayer of colloidal
particles of the same size as the mobile one. The dynamics of the
self-propelled colloid reflects the competition between hindered diffusion due
to the periodic surface and enhanced diffusion due to active motion. Which
contribution dominates depends on the propulsion strength, which can be
systematically tuned by changing the concentration of a chemical fuel. The
mean-square displacements obtained from the experiment exhibit enhanced
diffusion at long lag times. Our experimental data are consistent with a
Langevin model for the effectively two-dimensional translational motion of an
active Brownian particle in a periodic potential, combining the confining
effects of gravity and the crystalline surface with the free rotational
diffusion of the colloid. Approximate analytical predictions are made for the
mean-square displacement describing the crossover from free Brownian motion at
short times to active diffusion at long times. The results are in
semi-quantitative agreement with numerical results of a refined Langevin model
that treats translational and rotational degrees of freedom on the same
footing. | cond-mat_soft |
Simulation of a two-dimensional model for colloids in a uniaxial
electric field: We perform Monte Carlo simulations of a simplified two-dimensional model for
colloidal hard spheres in an external uniaxial AC electric field.
Experimentally, the external field induces dipole moments in the colloidal
particles, which in turn form chains. We therefore approximate the system as
composed of well formed chains of dipolar hard spheres of a uniform length. The
dipolar interaction between colloidal spheres gives rise to an effective
interaction between the chains, which we treat as disks in a plane, that
includes a short range attraction and long range repulsion. Hence, the system
favors finite clustering over bulk phase separation and indeed we observe at
low temperature and density that the system does form a cluster phase. As
density increases, percolation is accompanied by a pressure anomaly. The
percolated phase, despite being composed of connected, locally crystalline
domains, does not bear the typical signatures of a hexatic phase. At very low
densities, we find no indication of a "void phase" with a cellular structure
seen recently in experiments. | cond-mat_soft |
Geometric Mechanics of Curved Crease Origami: Folding a sheet of paper along a curve can lead to structures seen in
decorative art and utilitarian packing boxes. Here we present a theory for the
simplest such structure: an annular circular strip that is folded along a
central circular curve to form a three-dimensional buckled structure driven by
geometrical frustration. We quantify this shape in terms of the radius of the
circle, the dihedral angle of the fold and the mechanical properties of the
sheet of paper and the fold itself. When the sheet is isometrically deformed
everywhere except along the fold itself, stiff folds result in creases with
constant curvature and oscillatory torsion. However, relatively softer folds
inherit the broken symmetry of the buckled shape with oscillatory curvature and
torsion. Our asymptotic analysis of the isometrically deformed state is
corroborated by numerical simulations which allow us to generalize our analysis
to study multiply folded structures. | cond-mat_soft |
Strong dynamical effects during stick-slip adhesive peeling: We consider the classical problem of the stick-slip dynamics observed when
peeling a roller adhesive tape at a constant velocity. From fast imaging
recordings, we extract the dependencies of the stick and slip phases durations
with the imposed peeling velocity and peeled ribbon length. Predictions of
Maugis and Barquins [in Adhesion 12, edited by K.W. Allen, Elsevier ASP,
London, 1988, pp. 205--222] based on a quasistatic assumption succeed to
describe quantitatively our measurements of the stick phase duration. Such
model however fails to predict the full stick-slip cycle duration, revealing
strong dynamical effects during the slip phase. | cond-mat_soft |
Dissipation induced transitions in two dimensional elastic membranes: Stochastic thermodynamics provides a useful set of tools to analyze and
constrain the behavior of far from equilibrium systems. In this paper, we
report an application of ideas from stochastic thermodynamics to the problem of
membrane growth. Non-equilibrium forcing of the membrane can cause it to buckle
and undergo a morphological transformation. We show how ideas from stochastic
thermodynamics, in particular the recently derived thermodynamic uncertainty
relations, can be used to phenomenologically describe and constrain the
parameters required to excite morphological changes during a non-equilibrium
growth process. | cond-mat_soft |
Structural and dynamical features of multiple metastable glassy states
in a colloidal system with competing interactions: Systems in which a short-ranged attraction and long-ranged repulsion compete
are intrinsically frustrated, leading their structure and dynamics to be
dominated either by mesoscopic order or by metastable disorder. Here we report
the latter case in a colloidal system with long-ranged electrostatic repulsions
and short-ranged depletion attractions. We find a variety of states exhibiting
slow non-diffusive dynamics: a gel, a glassy state of clusters, and a state
reminiscent of a Wigner glass. Varying the interactions, we find a continuous
crossover between the Wigner and cluster glassy states, and a sharp
discontinuous transition between the Wigner glassy state and gel. This
difference reflects the fact that dynamic arrest is driven by repulsion for the
two glassy states and attraction in the case of the gel. | cond-mat_soft |
Snapping elastic disks as microswimmers: swimming at low Reynolds
numbers by shape hysteresis: We illustrate a concept for shape-changing microswimmers, which exploits the
hysteresis of a shape transition of an elastic object, by an elastic disk
undergoing cyclic localized swelling. Driving the control parameter of a
hysteretic shape transition in a completely time-reversible manner gives rise
to a non-time-reversible shape sequence and a net swimming motion if the
elastic object is immersed into a viscous fluid. We prove this concept with a
microswimmer which is a flat circular elastic disk that undergoes a transition
into a dome-like shape by localized swelling of an inner disk. The control
parameter of this shape transition is a scalar swelling factor of the disk
material. With a fixed outer frame with an additional attractive interaction in
the central region, the shape transition between flat and dome-like shape
becomes hysteretic and resembles a hysteretic opening and closing of a scallop.
Employing Stokesian dynamics simulations of a discretized version of the disk
we show that the swimmer is effectively moving into the direction of the
opening of the dome in a viscous fluid if the swelling parameter is changed in
a time-reversible manner. The swimming mechanism can be qualitatively
reproduced by a simple 9-bead model. | cond-mat_soft |
A soft departure from jamming: the compaction of deformable granular
matter under high pressures: The high-pressure compaction of three dimensional granular packings is
simulated using a bonded particle model (BPM) to capture linear elastic
deformation. In the model, grains are represented by a collection of point
particles connected by bonds. A simple multibody interaction is introduced to
control Poisson's ratio and the arrangement of particles on the surface of a
grain is varied to model both high- and low-frictional grains. At low
pressures, the growth in packing fraction and coordination number follow the
expected behavior near jamming and exhibit friction dependence. As the pressure
increases, deviations from the low-pressure power-law scaling emerge after the
packing fraction grows by approximately 0.1 and results from simulations with
different friction coefficients converge. These results are compared to
predictions from traditional discrete element method simulations which,
depending on the definition of packing fraction and coordination number, may
only differ by a factor of two. As grains deform under compaction, the average
volumetric strain and asphericity, a measure of the change in the shape of
grains, are found to grow as power laws and depend heavily on the Poisson's
ratio of the constituent solid. Larger Poisson's ratios are associated with
less volumetric strain and more asphericity and the apparent power-law exponent
of the asphericity may vary. The elastic properties of the packed grains are
also calculated as a function of packing fraction. In particular, we find the
Poisson's ratio near jamming is 1/2 but decreases to 1/4 before rising again as
systems densify. | cond-mat_soft |
Connectivity of the Hexagonal, Cubic, and Isotropic Phases of the
C$_{12}$EO$_6$/H$_2$O Lyotropic Mixture Investigated by Tracer Diffusion and
X-ray Scattering: The connectivity of the hydrophobic medium in the nonionic binary system
C$_{12}$EO$_6$/H$_2$O is studied by monitoring the diffusion constants of
tracer molecules at the transition between the hexagonal mesophase and the
fluid isotropic phase. The increase in the transverse diffusion coefficient on
approaching the isotropic phase reveals the proliferation of bridgelike defects
connecting the surfactant cylinders. This suggests that the isotropic phase has
a highly connected structure. Indeed, we find similar diffusion coefficients in
the isotropic and cubic bicontinuous phases. The temperature dependence of the
lattice parameter in the hexagonal phase confirms the change in connectivity
close to the hexagonal-isotropic transition. Finally, an X-ray investigation of
the isotropic phase shows that its structure is locally similar to that of the
hexagonal phase. | cond-mat_soft |
Exact curvilinear diffusion coefficients in the repton model: The Rubinstein-Duke or repton model is one of the simplest lattice model of
reptation for the diffusion of a polymer in a gel or a melt. Recently, a
slightly modified model with hardcore interactions between the reptons has been
introduced. The curvilinear diffusion coefficients of both models are exactly
determined for all chain lengths. The case of periodic boundary conditions is
also considered. | cond-mat_soft |
Controlling cell motion and microscale flow with polarized light fields: We investigate how light polarization affects the motion of photo-responsive
algae, \textit{Euglena gracilis}. In a uniformly polarized field, cells swim
approximately perpendicular to the polarization direction and form a nematic
state with zero mean velocity. When light polarization varies spatially, cell
motion is modulated by local polarization. In such light fields, cells exhibit
complex spatial distribution and motion patterns which are controlled by
topological properties of the underlying fields; we further show that ordered
cell swimming can generate directed transporting fluid flow. Experimental
results are quantitatively reproduced by an active Brownian particle model in
which particle motion direction is nematically coupled to local light
polarization. | cond-mat_soft |
Note: Relaxation time below jamming: Like other critical phenomena, the jamming transition accompanies the
divergence of the relaxation time $\tau$. A recent numerical study of
frictionless spherical particles proves that $\tau$ is inversely proportional
to the lowest non-zero eigenvalue $\lambda_1$ of the dynamical matrix. In this
note, we derive the scaling of $\lambda_1$ below the jamming transition point
$\varphi_J$ by solving the linearized dynamical equation. The resultant
critical exponent agrees with a previous theoretical result for sheared
suspension obtained by applying the virtual work theorem to a simple shear,
highlighting the universality of the relaxation dynamics below jamming. | cond-mat_soft |
Ludwig: A parallel Lattice-Boltzmann code for complex fluids: This paper describes `Ludwig', a versatile code for the simulation of
Lattice-Boltzmann (LB) models in 3-D on cubic lattices. In fact `Ludwig' is not
a single code, but a set of codes that share certain common routines, such as
I/O and communications. If `Ludwig' is used as intended, a variety of complex
fluid models with different equilibrium free energies are simple to code, so
that the user may concentrate on the physics of the problem, rather than on
parallel computing issues. Thus far, `Ludwig''s main application has been to
symmetric binary fluid mixtures. We first explain the philosophy and structure
of `Ludwig' which is argued to be a very effective way of developing large
codes for academic consortia. Next we elaborate on some parallel implementation
issues such as parallel I/O, and the use of MPI to achieve full portability and
good efficiency on both MPP and SMP systems. Finally, we describe how to
implement generic solid boundaries, and look in detail at the particular case
of a symmetric binary fluid mixture near a solid wall. We present a novel
scheme for the thermodynamically consistent simulation of wetting phenomena, in
the presence of static and moving solid boundaries, and check its performance. | cond-mat_soft |
Continuum mechanics at nanoscale. A tool to study trees' watering and
recovery: The cohesion-tension theory expounds the crude sap ascent thanks to the
negative pressure generated by evaporation of water from leaves. Nevertheless,
trees pose multiple challenges and seem to live in unphysical conditions: the
negative pressure increases cavitation; it is possible to obtain a water
equilibrium between connected parts where one is at a positive pressure and the
other one is at negative pressure; no theory is able to satisfactorily account
for the refilling of vessels after embolism events. A theoretical form of our
paper in the Journal of Theoretical Biology is proposed together with new
results: a continuum mechanics model of the disjoining pressure concept refers
to the Derjaguin School of physical chemistry. A comparison between liquid
behaviour both in tight-filled microtubes and in liquid thin-films is offered
when the pressure is negative in liquid bulks and is positive in liquid
thin-films and vapour bulks. In embolized xylem microtubes, when the air-vapour
pocket pressure is greater than the air-vapour bulk pressure, a refilling flow
occurs between the air-vapour domains to empty the air-vapour pockets although
the liquid-bulk pressure remains negative. The model has a limit of validity
taking the maximal size of trees into account. These results drop inkling that
the disjoining pressure is an efficient tool to study biological liquids in
contact with substrates at a nanoscale range. | cond-mat_soft |
Linear and angular motion of self-diffusiophoretic Janus particles: We theoretically study the active motion of self-diffusiophoretic Janus
particles (JPs) using the Onsager-Casimir reciprocal relations. The linear and
angular velocity of a single JP are shown to respectively result from a
coupling of electrochemical forces to the fluid flow fields induced by a force
and torque on the JP. A model calculation is provided for half-capped JPs
catalysing a chemical reaction of solutes at their surface, by reducing the
continuity equations of the reacting solutes to Poisson equations for the
corresponding electrochemical fields. We find that an anisotropic chemical
activity alone is enough to give rise to active linear motion of a JP, whereas
active rotation only occurs if the JP is not axisymmetric. In the absence of
specific interactions with the solutes, the active linear velocity of the JP is
shown to be related to the stoichiometrically weighted sum of the friction
coefficients (or hydrodynamic radii) of the reacting solutes. Our reciprocal
treatment further suggests that a specific interaction with the solutes is
required to observe far-field diffusiophoretic interactions between JPs, which
rely on an interfacial solute excess at the JP surface. Most notably, our
approach applies beyond the boundary-layer approximation and accounts for both
the diffusio- and electrophoretic nature of active motion. | cond-mat_soft |
Autonomous elastic microswimmer: A model of an autonomous three-sphere microswimmer is proposed by
implementing a coupling effect between the two natural lengths of an elastic
microswimmer. Such a coupling mechanism is motivated by the previous models for
synchronization phenomena in coupled oscillator systems. We numerically show
that a microswimmer can acquire a nonzero steady state velocity and a finite
phase difference between the oscillations in the natural lengths. These
velocity and phase difference are almost independent of the initial phase
difference. There is a finite range of the coupling parameter for which a
microswimmer can have an autonomous directed motion. The stability of the phase
difference is investigated both numerically and analytically in order to
determine its bifurcation structure. | cond-mat_soft |
Active actions: effective field theory for active nematics: Active matter consumes energy from the environment and transforms it into
mechanical work. Notable examples from biology include cell division, bacterial
swarms, and muscle contraction. In this work, we investigate the nature of
active matter systems using the powerful effective field theory toolbox. This
allows us to construct the most general theory without ambiguity up to a given
order in the derivative expansion. Our primary focus is active nematics --
liquid crystal systems that spontaneously break rotational but not
translational symmetry -- in two spatial dimensions. (Such spontaneous symmetry
breaking is allowed if the nematic is embedded in a higher dimensional space.)
While we focus on this one particular class of physical system, the tools
developed here can in principle be applied to any active matter system. Our
theories give unambiguous predictions for the relationship between fluctuations
and equations of motion in the presence of activity, generalizing the standard
fluctuation-dissipation relations characteristic of passive systems. | cond-mat_soft |
Importance of hydrodynamic shielding for the dynamic behavior of short
polyelectrolyte chains: The dynamic behavior of polyelectrolyte chains in the oligomer range is
investigated with coarse-grained molecular dynamics simulation and compared to
data obtained by two different experimental methods, namely capillary
electrophoresis and electrophoresis NMR. We find excellent agreement of
experiments and simulations when hydrodynamic interactions are accounted for in
the simulations. We show that the electrophoretic mobility exhibits a maximum
in the oligomer range and for the first time illustrate that this maximum is
due to the hydrodynamical shielding between the chain monomers. Our findings
demonstrate convincingly that it is possible to model dynamic behavior of
polyelectrolytes using coarse grained models for both, the polyelectrolyte
chains and the solvent induced hydrodynamic interactions. | cond-mat_soft |
Flow-Induced Shift of the Donnan Equilibrium for Ultra-Sensitive Mass
Transport Measurement Through a Single Nanochannel: Despite mass flow is arguably the most elementary transport associated to
nanofluidics, its measurement still constitutes a significant bottleneck for
the development of this promising field. Here, we investigate how a liquid flow
perturbs the ubiquitous enrichment-or depletion-of a solute inside a single
nanochannel. Using Fluorescence Correlation Spectroscopy to access the local
solute concentration, we demonstrate that the initial enrichment-the so-called
Donnan equilibrium-is depleted under flow thus revealing the underlying mass
transport. Combining theoretical and numerical calculations beyond the
classical 1D treatments of nanochannels, we rationalize quantitatively our
observations and demonstrate unprecedented flow rate sensitivity. Because the
present mass transport investigations are based on generic effects, we believe
they can develop into a versatile approach for nanofluidics. | cond-mat_soft |
Universality of Osmotic Equation of State in Star Polymer Solutions: We experimentally measure the osmotic pressures of linear polymers and
three-, four-, and eight-arm star polymers in a good solvent via membrane
osmometry. These results reveal that the osmotic equations of state in the star
polymer solutions are universally described by the same scaling function that
describes linear polymer solutions. This universality is achieved by canceling
increasing overlap concentrations and decreasing osmotic pressure, owing to the
increased arm number. We further clarify the molar mass and arm number
dependencies of the gyration radius and interpenetration factor, ensuring
universality in star polymer solutions. | cond-mat_soft |
Computational Pipeline to probe NaV1.7 gain-of-functions variants in
neuropathic painful syndromes: Applications of machine learning and graph theory techniques to neuroscience
have witnessed an increased interest in the last decade due to the large data
availability and unprecedented technology developments. Their employment to
investigate the effect of mutational changes in genes encoding for proteins
modulating the membrane of excitable cells, whose biological correlates are
assessed at electrophysiological level, could provide useful predictive clues.
We apply this concept to the analysis of variants in sodium channel NaV1.7
subunit found in patients with chronic painful syndromes, by the implementation
of a dedicated computational pipeline empowering different and complementary
techniques including homology modeling, network theory, and machine learning.
By testing three templates of different origin and sequence identities, we
provide an optimal condition for its use. Our findings reveal the usefulness of
our computational pipeline in supporting the selection of candidates for cell
electrophysiology assay and with potential clinical applications. | cond-mat_soft |
Theory of small-polaron band conduction in ultrapure organic crystals: We present a novel theory of charge-carrier mobilities in organic molecular
crystals of high purity. Our approach is based on Holstein's original concept
of small-polaron bands but generalized with respect to the inclusion of
nonlocal electron-phonon coupling. We derive an explicit expression for the
mobilities as a function of temperature and, using ab-initio methods to obtain
the material parameters, we demonstrate its predictive power by applying it to
naphthalene. The results show a remarkably good agreement with experiments and
provide new insight into the difference between electron and hole mobilities as
well as their peculiar algebraic and anisotropic temperature dependences. | cond-mat_soft |
Nonlinear Force Propagation during Granular Impact: We experimentally study nonlinear force propagation into granular material
during impact from an intruder, and we explain our observations in terms of the
nonlinear grain-scale force relation. Using high-speed video and photoelastic
particles, we determine the speed and spatial structure of the force response
just after impact. We show that these quantities depend on a dimensionless
parameter, $M'=t_c v_0/d$, where $v_0$ is the intruder speed at impact, $d$ is
the particle diameter, and $t_c$ is the collision time for a pair of grains
impacting at relative speed $v_0$. The experiments access a large range of $M'$
by using particles of three different materials. When $M' \ll 1$, force
propagation is chain-like with a speed, $v_f$, satisfying $v_f \propto d/t_c$.
For larger $M'$, the force response becomes spatially dense and the force
propagation speed departs from $v_f\propto d/t_c$, corresponding to collective
stiffening of a strongly compressed packing of grains. | cond-mat_soft |
Universality and stability phase-diagram of two-dimensional brittle
fracture: The two-dimensional oscillatory crack instability, experimentally observed in
a class of brittle materials under strongly dynamic conditions, has been
recently reproduced by a nonlinear phase-field fracture theory. Here we
highlight the universal character of this instability by showing that it is
present in materials exhibiting widely different near crack tip elastic
nonlinearity, and by demonstrating that the oscillations wavelength follows a
universal master curve in terms of dissipation-related and nonlinear elastic
intrinsic length scales. Moreover, we show that upon increasing the driving
force for fracture, a high-velocity tip-splitting instability emerges, as
experimentally demonstrated. The analysis culminates in a comprehensive
stability phase-diagram of two-dimensional brittle fracture, whose salient
properties and topology are independent of the form of near tip nonlinearity. | cond-mat_soft |
Band-gaps in electrostatically controlled dielectric laminates subjected
to incremental shear motions: The thickness vibrations of a finitely deformed infinite periodic laminate
made out of two layers of dielectric elastomers is studied. The laminate is
pre-stretched by inducing a bias electric field perpendicular the the layers.
Incremental time-harmonic fields superimposed on the initial finite deformation
are considered next. Utilizing the Bloch-Floquet theorem along with the
transfer matrix method we determine the dispersion relation which relates the
incremental fields frequency and the phase velocity.
Ranges of frequencies at which waves cannot propagate are identified whenever
the Bloch-parameter is complex. These band-gaps depend on the phases
properties, their volume fraction, and most importantly on the electric bias
field. Our analysis reveals how these band-gaps can be shifted and their width
can be modified by changing the bias electric field. This implies that by
controlling the electrostatic bias field desired frequencies can be filtered
out. Representative examples of laminates with different combinations of
commercially available dielectric elastomers are examined. | cond-mat_soft |
Evaluation of bistable systems versus matched filters in detecting
bipolar pulse signals: This paper presents a thorough evaluation of a bistable system versus a
matched filter in detecting bipolar pulse signals. The detectability of the
bistable system can be optimized by adding noise, i.e. the stochastic resonance
(SR) phenomenon. This SR effect is also demonstrated by approximate statistical
detection theory of the bistable system and corresponding numerical
simulations. Furthermore, the performance comparison results between the
bistable system and the matched filter show that (a) the bistable system is
more robust than the matched filter in detecting signals with disturbed pulse
rates, and (b) the bistable system approaches the performance of the matched
filter in detecting unknown arrival times of received signals, with an
especially better computational efficiency. These significant results verify
the potential applicability of the bistable system in signal detection field. | cond-mat_soft |
Array of Bose-Einstein condensates under time-periodic
Feshbach-resonance management: The dynamics of a discrete soliton in an array of Bose-Einstein condensates
under the action of a periodically time-modulated atomic scattering length
(``Feshbach-resonance management, FRM'') is investigated. The cases of both
slow and rapid modulation, in comparison with the tunneling frequency, are
considered. We employ a discrete variational approach for the analysis of the
system. The existence of nonlinear resonances and chaos is predicted at special
values of the driving frequency. Soliton splitting is observed in numerical
simulations. In the case of the rapid modulation, we derive an averaged
equation, which is a generalized discrete nonlinear Schroedinger equation,
including higher-order effective nonlinearities and intersite nonlinear
interactions. Thus the predicted discrete FRM solitons are a direct matter-wave
analog of recently investigated discrete diffraction-managed optical solitons. | cond-mat_soft |
Phase-field-crystal model for liquid crystals: Based on static and dynamical density functional theory, a
phase-field-crystal model is derived which involves both the translational
density and the orientational degree of ordering as well as a local director
field. The model exhibits stable isotropic, nematic, smectic A, columnar,
plastic crystalline and orientationally ordered crystalline phases. As far as
the dynamics is concerned, the translational density is a conserved order
parameter while the orientational ordering is non-conserved. The derived
phase-field-crystal model can serve for efficient numerical investigations of
various nonequilibrium situations in liquid crystals. | cond-mat_soft |
Universal scaling for disordered viscoelastic matter II: Collapses,
global behavior and spatio-temporal properties: Disordered viscoelastic materials are ubiquitous and exhibit fascinating
invariant scaling properties. In a companion article, we have presented
comprehensive new results for the critical behavior of the dynamic
susceptibility of disordered elastic systems near the onset of rigidity. Here
we provide additional details of the derivation of the singular scaling forms
of the longitudinal response near both jamming and rigidity percolation. We
then discuss global aspects associated with these forms, and make scaling
collapse plots for both undamped and overdamped dynamics in both the rigid and
floppy phases. We also derive critical exponents, invariant scaling
combinations and analytical formulas for universal scaling functions of several
quantities such as transverse and density responses, elastic moduli,
viscosities, and correlation functions. Finally, we discuss tentative
experimental protocols to measure these behaviors in colloidal suspensions. | cond-mat_soft |
Numerical studies of triangulated vesicles with anisotropic membrane
inclusions: In this study, we implement the deviatoric curvature model to examine
dynamically triangulated surfaces with anisotropic membrane inclusions. The
Monte-Carlo numerical scheme is devised to not only minimize the total bending
energy of the membrane but also the in-plane nematic order of the inclusions by
considering the mismatch between the curvature of the membrane and the
intrinsic curvature of the inclusion. Neighboring inclusions can either attract
with nearest-neighbor interaction or with a nematic interaction derived from
liquid crystal theory. Orientational order determines whether vesicles fully
covered with inclusions result in bulbs connected by necks or long tubes.
Remarkably, when inclusions on vesicles with no vacancies interact
non-nematically, a spontaneous local order can lead to a bulb transition which
may have implications in cell or organelle division. Furthermore we find that
average nematic order is inversely proportional to the number of thin necks
formed in the vesicles. Our method shows good convergence and is suitable for
further upgrades, for example to vesicles constrained by volume. | cond-mat_soft |
Localized and Delocalized Charge Transport in Single-Wall
Carbon-Nanotube Mats: We measured the complex dielectric constant in mats of single-wall
carbon-nanotubes between 2.7 K and 300 K up to 0.5 THz. The data are well
understood in a Drude approach with a negligible temperature dependence of the
plasma frequency (omega_p) and scattering time (tau) with an additional
contribution of localized charges. The dielectric properties resemble those of
the best ''metallic'' polypyrroles and polyanilines. The absence of metallic
islands makes the mats a relevant piece in the puzzle of the interpretation of
tau and omega_p in these polymers. | cond-mat_soft |
The near and far of a pair of magnetic capillary disks: Control on microscopic scales depends critically on our ability to manipulate
interactions with different physical fields. The creation of micro-machines
therefore requires us to understand how multiple fields, such as surface
capillary or electro-magnetic, can be used to produce predictable behaviour.
Recently, a spinning micro-raft system was developed that exhibited both static
and dynamic self-assembly [Wang et al. (2017) Sci. Adv. 3, e1602522]. These
rafts employed both capillary and magnetic interactions and, at a critical
driving frequency, would suddenly change from stable orbital patterns to static
assembled structures. In this paper, we explain the dynamics of two interacting
micro-rafts through a combination of theoretical models and experiments. This
is first achieved by identifying the governing physics of the orbital patterns,
the assembled structures, and the collapse separately. We find that the orbital
patterns are determined by the short range capillary interactions between the
disks, while the explanations of the other two behaviours only require the
capillary far field. Finally we combine the three models to explain the
dynamics of a new micro-raft experiment. | cond-mat_soft |
Wetting of ferrofluids: phenomena and control: Ferrofluids are liquids exhibiting remarkably strong response to magnetic
fields, which leads to fascinating properties useful in various applications.
Understanding the wetting properties and spreading of ferrofluids is important
for their use in microfluidics and magnetic actuation. However, this is
challenging as magnetically induced deformation of the ferrofluid surface can
affect contact angles, which are commonly used to characterize wetting
properties in other systems. In addition, interaction of the magnetic
nanoparticles and solid surface at nanoscale can have surprising effects on
ferrofluid spreading. In this review we discuss these issues with focus on
interpretation of ferrofluid contact angles. We review recent literature
examining ferrofluid wetting phenomena and outline novel wetting related
ferrofluid applications. To better understand wetting of ferrofluids, more
careful experimental work is needed. | cond-mat_soft |
Forceless Sadowsky strips are spherical: We show that thin rectangular ribbons, defined as energy-minimising
configurations of the Sadowsky functional for narrow developable elastic
strips, have a propensity to form spherical shapes in the sense that forceless
solutions lie on a sphere. This has implications for ribbonlike objects in
(bio)polymer physics and nanoscience that cannot be described by the classical
wormlike chain model. A wider class of functionals with this property is
identified. | cond-mat_soft |
Model studies on motion of respiratory droplets driven through a face
mask: Face masks are used to intercept respiratory droplets to prevent spreading of
air-borne diseases. Designing face masks with better efficiency needs
microscopic understanding on how respiratory droplets move through a mask. Here
we study a simple model on the interception of droplets by a face mask. The
mask is treated as a polymeric network in an asymmetric confinement, while the
droplet is taken as a micrometer sized tracer colloidal particle, subject to
driving force that mimics the breathing. We study numerically, using the
Langevin dynamics, the tracer particle permeation through the polymeric
network. We show that the permeation is an activated process following an
Arrhenius dependence on temperature. The potential energy profile responsible
for the activation process increases with tracer size, tracer bead interaction,
network rigidity and decreases with the driving force and confinement length. A
deeper energy barrier led to better efficiency to intercept the tracer
particles of a given size in the presence of driving force at room temperature.
Our studies may help to design mask with better efficiency. | cond-mat_soft |
Statistical Mechanics of Splay Flexoelectricity in Nematic Liquid
Crystals: We develop a lattice model for the splay flexoelectric effect in nematic
liquid crystals. In this model, each lattice site has a spin representing the
local molecular orientation, and the interaction between neighboring spins
represents pear-shaped molecules with shape polarity. We perform Monte Carlo
simulations and mean-field calculations to find the behavior as a function of
interaction parameters, temperature, and applied electric field. The resulting
phase diagram has three phases: isotropic, nematic, and polar. In the nematic
phase, there is a large splay flexoelectric effect, which diverges as the
system approaches the transition to the polar phase. These results show that
flexoelectricity is a statistical phenomenon associated with the onset of polar
order. | 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 |
Microparticles self-assembly induced by travelling surface acoustic
waves: We present an acoustofluidic method based on travelling surface acoustic
waves (TSAWs) for the induction of the self-assembly of microparticles inside a
microfluidic channel. The particles are trapped above an interdigitated
transducer, placed directly beneath the microchannel, by the TSAW-based direct
acoustic radiation force (ARF). This approach was applied to 10 {\mu}m
polystyrene particles, which were pushed towards the ceiling of the
microchannel by 72 MHz TSAWs to form single- and multiple-layer colloidal
structures. The repair of cracks and defects within the crystal lattice occurs
as part of the self-assembly process. The sample flow through the first inlet
can be switched with a buffer flow through a second inlet to control the number
of particles in the crystalline structure. The constant flow-induced Stokes
drag force on the parti-cles is balanced by the opposing TSAW-based ARF. This
force balance is essential for the acoustics-based self-assembly of
microparticles inside the microchannel. Moreover, we studied the effects of
varying the input voltage and fluid flow rate on the position and shape of the
colloidal structure. The active self-assembly of microparticles into crystals
with multiple layers can be used in the bottom-up fabrication of colloidal
structures with dimensions greater than 500 {\mu}m x 500 {\mu}m, which is
expected to have important applications in various fields. | cond-mat_soft |
Spontaneous sense inversion in helical mesophases: We investigate the pitch sensitivity of cholesteric phases of helicoidal
patchy cylinders as a generic model for chiral (bio-)polymers and helix-shaped
colloidal rods. The behaviour of the macroscopic cholesteric pitch is studied
from microscopic principles by invoking a simple density functional theory
generalised to accommodate weakly twisted director fields. Upon changing the
degree of alignment along the local helicoidal director we find that
cholesteric phases exhibit a sudden sense inversion whereby the cholesteric
phase changes from left- to right-handed and vice versa. Since the local
alignment is governed by thermodynamic variables such as density, temperature
or the amplitude of an external directional field such pitch sense inversions
can be expected in systems of helical mesogens of both thermotropic and
lyotropic origin. We show that the spontaneous change of helical symmetry is a
direct consequence of an antagonistic effective torque between helical
particles with a certain prescribed internal helicity. The results may help
opening up new routes towards precise control of the helical handedness of
chiral assemblies by a judicious choice of external control parameters. | 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 |
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