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Microstructural origins of crushing strength for inherently anisotropic
brittle materials: We study the crushing strength of brittle materials whose internal structure
(e.g., mineral particles or graining) presents a layered arrangement
reminiscent of sedimentary and metamorphic rocks. Taking a discrete-element
approach, we probe the failure strength of circular-shaped samples intended to
reproduce specific mineral configurations. To do so, assemblies of cells,
products of a modified Voronoi tessellation, are joined in mechanically-stable
layerings using a bonding law. The cells' shape distribution allows us to set a
level of inherent anisotropy to the material. Using a diametral point loading,
and systematically changing the loading orientation with respect to the cells'
configuration, we characterize the failure strength of increasingly anisotropic
structures. This approach ends up reproducing experimental observations and
lets us quantify the statistical variability of strength, the consumption of
the fragmentation energy, and the induced anisotropies linked to the cell's
geometry and force transmission in the samples. Based on a fine description of
geometrical and mechanical properties at the onset of failure, we develop a
micromechanical breakdown of the crushing strength variability using an
analytical decomposition of the stress tensor and the geometrical and force
anisotropies. We can conclude that the origins of failure strength in
anisotropic layered media rely on compensations of geometrical and mechanical
anisotropies, as well as an increasing average radial force between minerals
indistinctive of tensile or compressive components. | cond-mat_soft |
Aging Dynamics of a Fractal Model Gel: Using molecular dynamics computer simulations we investigate the aging
dynamics of a gel. We start from a fractal structure generated by the DLCA-DEF
algorithm, onto which we then impose an interaction potential consisting of a
short-range attraction as well as a long-range repulsion. After relaxing the
system at T=0, we let it evolve at a fixed finite temperature. Depending on the
temperature T we find different scenarios for the aging behavior. For T>0.2 the
fractal structure is unstable and breaks up into small clusters which relax to
equilibrium. For T<0.2 the structure is stable and the dynamics slows down with
increasing waiting time. At intermediate and low T the mean squared
displacement scales as t^{2/3} and we discuss several mechanisms for this
anomalous time dependence. For intermediate T, the self-intermediate scattering
function is given by a compressed exponential at small wave-vectors and by a
stretched exponential at large wave-vectors. In contrast, for low T it is a
stretched exponential for all wave-vectors. This behavior can be traced back to
a subtle interplay between elastic rearrangements, fluctuations of chain-like
filaments, and heterogeneity. | cond-mat_soft |
Modelling segregation of flowing bidisperse granular mixtures varying
simultaneously in size and density: Flowing granular materials segregate due to differences in particle size
(driven by percolation) and density (driven by buoyancy). Modelling the
segregation of mixtures of large/heavy particles and small/light particles is
challenging due to the opposing effects of the two segregation mechanisms.
Using discrete element method (DEM) simulations of combined size and density
segregation we show that the segregation velocity is well described by a model
that depends linearly on the local shear rate and quadratically on the species
concentration. Concentration profiles predicted by incorporating this
segregation velocity model into a continuum advection-diffusion-segregation
transport model match DEM simulation results well for a wide range of particle
size and density ratios. Most surprisingly, the DEM simulations and the
segregation velocity model both show that the segregation direction for a range
of size and density ratios depends on the local species concentration. This
leads to a methodology to determine the combination of particle size ratio,
density ratio, and particle concentration for which a bidisperse mixture will
not segregate. | cond-mat_soft |
Simulation of a Single Polymer Chain in Solution by Combining Lattice
Boltzmann and Molecular Dynamics: In this paper we establish a new efficient method for simulating
polymer-solvent systems which combines a lattice Boltzmann approach for the
fluid with a continuum molecular dynamics (MD) model for the polymer chain. The
two parts are coupled by a simple dissipative force while the system is driven
by stochastic forces added to both the fluid and the polymer. Extensive tests
of the new method for the case of a single polymer chain in a solvent are
performed. The dynamic and static scaling properties predicted by analytical
theory are validated. In this context, the influence of the finite size of the
simulation box is discussed. While usually the finite size corrections scale as
L^{-1} (L denoting the linear dimension of the box), the decay rate of the
Rouse modes is only subject to an L^{-3} finite size effect. Furthermore, the
mapping to an existing MD simulation of the same system is done so that all
physical input values for the new method can be derived from pure MD
simulation. Both methods can thus be compared quantitatively, showing that the
new method allows for much larger time steps. Comparison of the results for
both methods indicates systematic deviations due to non-perfect match of the
static chain conformations. | cond-mat_soft |
Long-Tail Feature of DNA Words Over- and Under-Representation in Coding
Sequences: We have analyzed DNA sequences of known genes from 16 yeast chromosomes
(Saccharomyces cerevisiae) in terms of oligonucleotides. We have noticed that
the relative abundances of oligonucleotide usage in the genome follow a
long-tail Levy-like distribution. We have observed that long genes often use
strongly over-represented and under-represented nucleotides, whereas it was not
the case for the short genes (shorter than 300 nucleotides) under
consideration. If selection on the extremely over-represented/under-represented
oligonucleotides was strong, long genes would be more affected by spontaneous
mutations than short ones. | cond-mat_soft |
Microscopic derivation of the thin film equation using the Mori-Zwanzig
formalism: The hydrodynamics of thin films is typically described using phenomenological
models whose connection to the microscopic particle dynamics is a subject of
ongoing research. Existing methods based on density functional theory provide a
good description of static thin films, but are not sufficient for understanding
nonequilibrium dynamics. In this work, we present a microscopic derivation of
the thin film equation using the Mori-Zwanzig projection operator formalism.
This method allows to directly obtain the correct gradient dynamics structure
along with microscopic expressions for the mobility and the free energy. Our
results are verified against molecular dynamics simulations for both simple
fluids and polymers. | cond-mat_soft |
Mass separation in an asymmetric channel: We present a mechanism to sort out particles of different masses in an
asymmetric channel, where the entropic barriers arise naturally and control the
diffusion of these particles. When particles are subjected to an oscillatory
force, with the scaled amplitude $a$ and frequency $\omega$, the mean particle
velocity exhibits a bell-shaped behavior as a function of the particle mass,
indicating that particles with an optimal mass $m_{op}$ drift faster than other
particles. By tuning $a$ and $\omega$, we get an empirical relation to estimate
$m_{op} \sim (a\,\omega^2)^{-0.4}$. An additional static bias, applied in the
opposite direction of the rectified velocity, would push the particles of
lighter mass to move in its direction while the others drift opposite to it.
This study is useful to design lab-on-a-chip devices for separating particles
of different masses. | cond-mat_soft |
Microrheology of non mulberry silk varieties by optical tweezer and
video microscopy based techniques: We have carried out a comparative study of the microrheological properties of
silk fibroin solutions formed from a variety of silks indigenous to the Indian
subcontinent. We present the measured viscoelastic moduli of Tasar silk fibroin
solution using both a single and dual optical tweezer at 0.16% and 0.25% (w/v).
The bandwidth of the measurements carried out using optical tweezers is
extended down to the lower frequency regime by a video microscopy measurement.
Further, we have measured the viscoelastic moduli of Eri and Muga varieties of
silk fibroin solutions at a higher concentration (1.00% w/v) limiting the tool
of measurement to video microscopy, as the reduced optical transparencies of
these solutions at higher concentration preclude an optical tweezer based
investigation. The choice of a higher concentration of fibroin solution of the
latter silk varieties is so as to enable a comparison of the shear moduli
obtained from optical methods with their corresponding fibre stiffness obtained
from wide angle X-ray scattering data. We report a correlation between the
microstructure and microrheological parameters of these silk varieties for the
concentration of fibroin solutions studied. | cond-mat_soft |
Oscillating membranes: modeling and controlling autonomous
shape-transforming sheets: Living organisms have mastered the dynamic control of internal stresses to
perform an array of functions, such as change shape and locomote.
State-of-the-art attempts to replicate this ability in synthetic materials are
rudimentary in comparison. Here we present the first experimental realization
of a self-oscillating gel in a thin sheet configuration. We show that internal
signaling produces stresses that drive lifelike shape changes, that the
material's response is accurately modelled with the theory of non-Euclidean
elasticity and that the internal signaling can be programmed with light.
Together, our results demonstrate a complete route for developing fully
autonomous soft machines. | cond-mat_soft |
Capillary interactions between soft capsules protruding through thin
fluid films: When a suspension dries, the suspending fluid evaporates, leaving behind a
dry film composed of the suspended particles. During the final stages of
drying, the height of the fluid film on the substrate drops below the particle
size, inducing local interface deformations that lead to strong capillary
interactions among the particles. Although capillary interactions between rigid
particles are well studied, much is still to be understood about the behaviour
of soft particles and the role of their softness during the final stages of
film drying. Here, we use our recently-introduced numerical method that couples
a fluid described using the lattice Boltzmann approach to a finite element
description of deformable objects to investigate the drying process of a film
with suspended soft particles. Our measured menisci deformations and lateral
capillary forces, which agree well with previous theoretical and experimental
works in case of rigid particles, show the deformations become smaller with
increasing particles softness, resulting in weaker lateral interaction forces.
At large interparticle distances, the force approaches that of rigid particles.
Finally, we investigate the time dependent formation of particle clusters at
the late stages of the film drying. | cond-mat_soft |
Curvature-driven instabilities in thin active shells: Spontaneous material shape changes, such as swelling, growth or thermal
expansion, can be used to trigger dramatic elastic instabilities in thin
shells. These instabilities originate in geometric incompatibility between the
preferred extrinsic and intrinsic curvature of the shell, which may be modified
by active deformations through the thickness and in plane respectively. Here,
we solve the simplest possible model of such instabilities, which assumes the
shells are shallow, thin enough to bend but not stretch, and subject to
homogeneous preferred curvatures. We consider separately the cases of zero,
positive and negative Gaussian curvature. We identify two types of
super-critical symmetry breaking instability, in which the shell's principal
curvature spontaneously breaks discrete up-down symmetry and continuous planar
isotropy respectively. These are then augmented by inversion instabilities, in
which the shell jumps sub-critically between up/down broken symmetry states,
and rotation instabilities, in which the curvatures rotate by 90 degrees
between states of broken isotropy without release of energy. Each instability
has a thickness independent threshold value for the preferred extrinsic
curvature proportional to the square-root of Gauss curvature. Finally, we show
that the threshold for the isotropy-breaking instability is the same for deep
spherical caps, in good agreement with recently published data. | cond-mat_soft |
Critical aspects of hierarchical protein folding: We argue that the first order folding transitions of proteins observed at
physiological chemical conditions end in a critical point for a given
temperature and chemical potential of the surrounding water. We investigate
this critical point using a hierarchical Hamiltonian and determine its
universality class. This class differs qualitatively from those of other known
models. | cond-mat_soft |
Synchronized Fractionation and Phase Separation in Binary Colloids: Fractionation is necessary for self-assembly in multicomponent mixtures.
Here, reversible fractionation and crystallization are realized and studied in
a two-dimensional binary colloids which is supersaturated by enhancing the
attraction between colloidal particles. As a deep and fast supersaturation
results in gels with a uniform distribution of binary particles, a gradual
quasistatic supersaturating process leads to a two-step crystallization in
which small particles and large particles are fractionated as coexisting
crystal and liquid phases respectively. Fractionation occurs as well in the
quasistatic melting of gel. We show that the synchronized fractionation and
phase separation arises from the competition between the size-dependent
repulsion and the tunable attraction. The results in this study demonstrate a
robust mechanism of fractionation via phase separation, and have important
implication in understanding the reversible formation of membraneless
organelles in living cells. | cond-mat_soft |
Glassy relaxation in de Vries smectic liquid crystal consisting of
bent-core molecules: We report the experimental investigations on a liquid crystal comprised of
thiophene-based achiral bent-core banana shaped molecules. The results reveal
the presence of a short range nematic phase at high temperatures and a
long-range SmA phase at lower temperatures, which transits to a SmC phase on
further cooling the sample. Practically no layer contraction was observed
across the SmA to SmC transition, indicating the de Vries nature of the SmA
phase. Interestingly, the crystallization does not occur on cooling the sample
till 223 K; instead, a glass transition at 271 K was observed. The dielectric
spectroscopy studies carried out on the sample reveal the presence of a
dielectric mode whose relaxation process is of the Cole-Cole type. The
relaxation frequency of the mode was found to drop rapidly with decreasing
temperature, further confirming the glassy behavior. The variation of
relaxation frequency with temperature follows the Vogel-Fulcher-Tammann
equation indicating the fragile glassy nature of the sample. | cond-mat_soft |
Shapes and singularities in triatic liquid crystal vesicles: Determining the equilibrium configuration and shape of curved two-dimensional
films with (generalized) liquid crystalline (LC) order is a difficult infinite
dimensional problem of direct relevance to the study of generalized
polymersomes, soft matter and the fascinating problem of understanding the
origin and formation of shape (morphogenesis). The symmetry of the free energy
of the LC film being considered and the topology of the surface to be
determined often requires that the equilibrium configuration possesses singular
structures in the form of topological defects such as disclinations for nematic
films. The precise number and type of defect plays a fundamental role in
restricting the space of possible equilibrium shapes. Flexible closed vesicles
with spherical topology and nematic or smectic order, for example, inevitably
possess four elementary strength $+1/2$ disclination defects positioned at the
four vertices of a tetrahedral shell. Here we address the problem of
determining the equilibrium shape of flexible vesicles with generalized LC
order. The order parameter in these cases is an element of $S^1/Z_p$, for any
positive integer $p$. We will focus on the case $p =3$, known as triatic LCs.
We construct the appropriate order parameter for triatics and find the
associated free energy. We then describe the structure of the elementary
defects of strength $+1/3$ in flat space. Finally, we prove that sufficiently
floppy triatic vesicles with the topology of the 2-sphere equilibrate to
octahedral shells with strength $+1/3$ defects at each of the six vertices,
independently of scale. | cond-mat_soft |
Geometric theory of topological defects: methodological developments and
new trends: Liquid crystals generally support orientational singularities of the director
field known as topological defects. These latter modifiy transport properties
in their vicinity as if the geometry was non-Euclidean. We present a state of
the art of the differential geometry of nematic liquid crystals, with a special
emphasis on linear defects. We then discuss unexpected but deep connections
with cosmology and high-energy-physics, and conclude with a review on defect
engineering for transport phenomena. | cond-mat_soft |
Topological packing statistics distinguish living and non-living matter: How much structural information is needed to distinguish living from
non-living systems? Here, we show that the statistical properties of Delaunay
tessellations suffice to differentiate prokaryotic and eukaroytic cell packings
from a wide variety of inanimate physical structures. By introducing a
mathematical framework for measuring topological distances between general 3D
point clouds, we construct a universal topological atlas encompassing bacterial
biofilms, snowflake yeast, plant shoots, zebrafish brain matter, organoids, and
embryonic tissues as well as foams, colloidal packings, glassy materials, and
stellar configurations. Living systems are found to localize within a bounded
island-like region, reflecting that growth memory essentially distinguishes
multicellular from physical packings. By detecting subtle topological
differences, the underlying metric framework enables a unifying classification
of 3D disordered media, from microbial populations, organoids and tissues to
amorphous materials and astrophysical systems. | cond-mat_soft |
Relaxation with long-period oscillation in defect turbulence of planar
nematic liquid crystals: Through experiments, we studied defect turbulence, a type of spatiotemporal
chaos in planar systems of nematic liquid crystals, to clarify the chaotic
advection of weak turbulence. In planar systems of large aspect ratio,
structural relaxation which is characterized by the dynamic structure factor
exhibits a long-period oscillation that is described well by a combination of a
simple exponential relaxation and underdamped oscillation. The simple
relaxation arises as a result of the roll modulation while the damped
oscillation is manifest in the repetitive gliding of defect pairs in a local
area. Each relaxation is derived analytically by the projection operator method
that separates turbulent transport into a macroscopic contribution and
fluctuations. The analysis proposes that the two relaxations are not
correlated. The nonthermal fluctuations of defect turbulence are consequently
separated into two independent Markov processes. Our approach sheds light on
diversity and universality from a unified viewpoint for weak turbulence. | cond-mat_soft |
The Excluded Area of Superellipse Sector Particles: Superellipse sector particles (SeSPs) are segments of superelliptical curves
that form a tunable set of hard-particle shapes for granular and colloidal
systems. SeSPs allow for continuous parameterization of corner sharpness,
aspect ratio, and particle curvature; rods, circles, rectangles, and staples
are examples of shapes SeSPs can model. We investigate the space of allowable
(non-overlapping) configurations of two SeSPs, which depends on both the
center-of-mass separation and relative orientation. Radial correlation plots of
the allowed configurations reveal circular regions centered at each of the
particle's two endpoints that indicate configurations of mutually-entangled
particle interactions. Simultaneous entanglement with both endpoints is
geometrically impossible; the overlap of these two regions therefore represents
an excluded area in which no particles can be placed regardless of orientation.
The regions' distinct boundaries indicates a translational frustration with
implications for the dynamics of particle rearrangements (e.g. under shear).
Representing translational and rotational degrees of freedom as a hypervolume,
we find a topological change that suggests geometric frustration arises a phase
transition in this space. The excluded area is a straightforward integration
over excluded states; for arbitrary relative orientation this decreases
sigmoidally with increasing opening aperture, with sharper SeSP corners
resulting in a sharper decrease. Together, this work offers a path towards a
unified theory for particle shape-control of bulk material properties. | cond-mat_soft |
Observation of Heteronuclear Feshbach Resonances in a Bose-Fermi Mixture: Three magnetic-field induced heteronuclear Feshbach resonances were
identified in collisions between bosonic 87Rb and fermionic 40K atoms in their
absolute ground states. Strong inelastic loss from an optically trapped mixture
was observed at the resonance positions of 492, 512, and 543 +/- 2 G. The
magnetic-field locations of these resonances place a tight constraint on the
triplet and singlet cross-species scattering lengths, yielding -281 +/- 15 Bohr
and -54 +/- 12 Bohr, respectively. The width of the loss feature at 543 G is
3.7 +/- 1.5 G wide; this broad Feshbach resonance should enable experimental
control of the interspecies interactions. | cond-mat_soft |
Testing quantum correlations in a confined atomic cloud by scattering
fast atoms: We suggest measuring one-particle density matrix of a trapped ultracold
atomic cloud by scattering fast atoms in a pure momentum state off the cloud.
The lowest-order probability of the inelastic process, resulting in a pair of
outcoming fast atoms for each incoming one, turns out to be given by a Fourier
transform of the density matrix. Accordingly, important information about
quantum correlations can be deduced directly from the differential scattering
cross-section. A possible design of the atomic detector is also discussed. | cond-mat_soft |
Shear Induced Pressure Determines a Reduction in Polymer Radius: Shear induced particle pressure has been measured and modelled for
concentrated suspensions of particles. Importantly, the significance of the
shear induced particle pressure has not been recognized in polymer rheology.
The shear induced particle pressure results in an inward pressure on the
polymer chains resulting in a shear dependent compressive force. The analytical
form of the force balance equations that incorporate the effect of shear
induced particle pressure predict a reduced polymer blob size and reducing
viscosity with increasing shear rate as has been observed experimentally. Power
law behavior is found for the viscosity in accord with the general behavior
observed for the rheology of concentrated polymer solutions and melts.
Differing powers are found for the behavior depending on the concentration
regime. | cond-mat_soft |
Self-assembly and crystallisation of indented colloids at a planar wall: We report experimental and simulation studies of the structure of a monolayer
of indented ("lock and key") colloids, on a planar surface. On adding a
non-absorbing polymer with prescribed radius and volume fraction, depletion
interactions are induced between the colloids, with controlled range and
strength. For spherical particles, this leads to crystallisation, but the
indented colloids crystallise less easily than spheres, in both simulation and
experiment. Nevertheless, simulations show that indented colloids do form
plastic (rotator) crystals. We discuss the conditions under which this occurs,
and the possibilities of lower-symmetry crystal states. We also comment on the
kinetic accessibility of these states. | cond-mat_soft |
Steady state particle distribution of a dilute sedimenting suspension: Sedimentation of a non-Brownian suspension of hard particles is studied. It
is shown that in the low concentration limit a two-particle distribution
function ensuring finite particle correlation length can be found and
explicitly calculated. The sedimentation coefficient is computed. Results are
compared with experiment. | cond-mat_soft |
The effect of inter-cluster interactions on the structure of colloidal
clusters: Colloidal systems present exciting opportunities to study clusters. Unlike
atomic clusters, which are frequently produced at extremely low density,
colloidal clusters may interact with one another. Here we consider the effect
of such interactions on the intra-cluster structure in simulations of colloidal
cluster fluids. A sufficient increase in density leads to a higher population
of clusters in the ground state. In other words, inter-cluster interactions
perturb the intra-cluster behaviour, such that each cluster may no longer be
considered as an isolated system. Conversely, for dilute, weakly interacting
cluster fluids little dependence on colloid concentration is observed, and we
thus argue that it is reasonable to treat each cluster as an isolated system. | cond-mat_soft |
Ion association in low-polarity solvents: comparisons between theory,
simulation, and experiment: The association of ions in electrolyte solutions at very low concentration
and low temperature is studied using computer simulations and quasi-chemical
ion-pairing theory. The specific case of the restricted primitive model
(charged hard spheres) is considered. Specialised simulation techniques are
employed that lead to efficient sampling of the arrangements and distributions
of clusters and free ions, even at conditions corresponding to nanomolar
solutions of simple salts in solvents with dielectric constants in the range
5-10, as used in recent experimental work on charged-colloid sus- pensions. A
direct comparison is effected between theory and simulation using a variety of
clustering criteria and theoretical approximations. It is shown that
conventional distance-based cluster criteria can give erroneous results. A
reliable set of theoretical and simulation estimators for the degree of
association is proposed. The ion-pairing theory is then compared to
experimental results for salt solutions in low-polarity solvents. The agreement
is excellent, and on this basis some calculations are made for the screening
lengths which will figure in the treatment of colloid-colloid interactions in
such solutions. The accord with available experimental results is complete. | cond-mat_soft |
Accelerating Copolymer Inverse Design using AI Gaming algorithm: There exists a broad class of sequencing problems, for example, in proteins
and polymers that can be formulated as a heuristic search algorithm that
involve decision making akin to a computer game. AI gaming algorithms such as
Monte Carlo tree search (MCTS) gained prominence after their exemplary
performance in the computer Go game and are decision trees aimed at identifying
the path (moves) that should be taken by the policy to reach the final winning
or optimal solution. Major challenges in inverse sequencing problems are that
the materials search space is extremely vast and property evaluation for each
sequence is computationally demanding. Reaching an optimal solution by
minimizing the total number of evaluations in a given design cycle is therefore
highly desirable. We demonstrate that one can adopt this approach for solving
the sequencing problem by developing and growing a decision tree, where each
node in the tree is a candidate sequence whose fitness is directly evaluated by
molecular simulations. We interface MCTS with MD simulations and use a
representative example of designing a copolymer compatibilizer, where the goal
is to identify sequence specific copolymers that lead to zero interfacial
energy between two immiscible homopolymers. We apply the MCTS algorithm to
polymer chain lengths varying from 10-mer to 30-mer, wherein the overall search
space varies from 210 (1024) to 230 (~1 billion). In each case, we identify a
target sequence that leads to zero interfacial energy within a few hundred
evaluations demonstrating the scalability and efficiency of MCTS in exploring
practical materials design problems with exceedingly vast chemical/material
search space. Our MCTS-MD framework can be easily extended to several other
polymer and protein inverse design problems, in particular, for cases where
sequence-property data is either unavailable and/or is resource intensive. | cond-mat_soft |
Random Isotropic Structures and Possible Glass Transitions in Diblock
Copolymer Melts: We study the microstructural glass transitions in diblock-copolymer melts
using a thermodynamic replica approach. Our approach performs an expansion in
terms of the natural smallness parameter -- the inverse of the scaled degree of
polymerization, which allows us to systematically study the approach to
mean-field behavior as the degree of polymerization increases. We find that in
the limit of infinite long polymer chains, both the onset of glassiness and the
vitrification transition (Kauzmann temperature) collapse to the mean-field
spinodal, suggesting that the spinodal can be regarded as the mean-field
signature for glass transitions in this class of systems. We also study the
order-disorder transitions (ODT) within the same theoretical framework; in
particular, we include the leading-order fluctuation corrections due to the
cubic interaction in the coarse-grained Hamiltonian, which has been ignored in
previous works on the ODT in block copolymers. We find that the cubic term
stabilizes both the ordered (body-centered-cubic) phase and the glassy state
relative to the disordered phase. While in melts of symmetric copolymers the
glass transition always occurs after the order-disorder transition (below the
ODT temperature), for asymmetric copolymers, it is possible that the glass
transition precedes the ordering transition. | cond-mat_soft |
Tensile elasticity of semiflexible polymers with hinge defects: It has become clear in recent years that the simple uniform wormlike chain
model needs to be modified in order to account for more complex behavior which
has been observed experimentally in some important biopolymers. For example,
the large flexibility of short ds-DNA has been attributed to kink or hinge
defects. In this paper, we calculate analytically, within the weak bending
approximation, the force-extension relation of a wormlike chain with a
permanent hinge defect along its contour. The defect is characterized by its
bending energy (which can be zero, in the completely flexible case) and its
position along the polymer contour. Besides the bending rigidity of the chain,
these are the only parameters which describe our model. We show that a hinge
defect causes a significant increase in the differential tensile compliance of
a pre-stressed chain. In the small force limit, a hinge defect significantly
increases the entropic elasticity. Our results apply to any pair of
semiflexible segments connected by a hinge. As such, they may also be relevant
to cytoskeletal filaments (F-actin, microtubules), where one may treat the
cross-link connecting two filaments as a hinge defect. | cond-mat_soft |
Transients in sheared granular matter: As dense granular materials are sheared, a shear band and an anisotropic
force network form. The approach to steady state behavior depends on the
history of the packing and the existing force and contact network. We present
experiments on shearing of dense granular matter in a 2D Couette geometry in
which we probe the history and evolution of shear bands by measuring particle
trajectories and stresses during transients. We find that when shearing is
stopped and restarted in the same direction, steady state behavior is
immediately reached, in agreement with the typical assumption that the system
is quasistatic. Although some relaxation of the force network is observed when
shearing is stopped, quasistatic behavior is maintained because the contact
network remains essentially unchanged. When the direction of shear is reversed,
a transient occurs in which stresses initially decrease, changes in the force
network reach further into the bulk, and particles far from the wheel become
more mobile. This occurs because the force network is fragile to changes
transverse to the force network established under previous shear; particles
must rearrange before becoming jammed again, thereby providing resistance to
shear in the reversed direction. The strong force network is reestablished
after displacing the shearing surface $\approx 3d$, where $d$ is the mean grain
diameter. Steady state velocity profiles are reached after a shear of $\leq
30d$. Particles immediately outside of the shear band move on average less than
1 diameter before becoming jammed again. We also examine particle rotation
during this transient and find that mean particle spin decreases during the
transient, which is related to the fact that grains are not interlocked as
strongly. | cond-mat_soft |
DNA capture into the ClyA nanopore: diffusion-limited versus
reaction-limited processes: The capture and translocation of biomolecules through nanometer-scale pores
are processes with a potential large number of applications, and hence they
have been intensively studied in the recent years. The aim of this paper is to
review existing models of the capture process by a nanopore, together with some
recent experimental data of short single- and double-stranded DNA captured by
Cytolysin A (ClyA) nanopore. ClyA is a transmembrane protein of bacterial
origin which has been recently engineered through site-specific mutations, to
allow the translocation of double- and single-stranded DNA. A comparison
between theoretical estimations and experiments suggests that for both cases
the capture is a reaction-limited process. This is corroborated by the observed
salt dependence of the capture rate, which we find to be in quantitative
agreement with the theoretical predictions. | cond-mat_soft |
Sedimentation stacking diagram of binary colloidal mixtures and bulk
phases in the plane of chemical potentials: We give a full account of a recently proposed theory that explicitly relates
the bulk phase diagram of a binary colloidal mixture to its phase stacking
phenomenology under gravity [Soft Matter 9, 8636 (2013)]. As we demonstrate,
the full set of possible phase stacking sequences in sedimentation-diffusion
equilibrium originates from straight lines (sedimentation paths) in the
chemical potential representation of the bulk phase diagram. From the analysis
of various standard topologies of bulk phase diagrams, we conclude that the
corresponding sedimentation stacking diagrams can be very rich, even more so
when finite sample height is taken into account. We apply the theory to obtain
the stacking diagram of a mixture of nonadsorbing polymers and colloids. We
also present a catalog of generic phase diagrams in the plane of chemical
potentials in order to facilitate the practical application of our concept,
which also generalizes to multi component mixtures. | cond-mat_soft |
W-potentials in nonlinear biophysics of microtubules: In the present article we investigate the nonlinear dynamics of microtubules,
the basic components of the eukaryotic cytoskeleton, and rely on the known
general model. A crucial interaction among constitutive particles is modelled
using W-potential. Three kinds of this potential are studied, symmetrical and
two non-symmetrical. We demonstrate an advantage of the latter ones. | cond-mat_soft |
Knots in Macromolecules in Constraint Space: We find a power law for the number of knot-monomers with an exponent $0.39
\pm0.13$ in agreement with previous simulations. For the average size of a knot
we also obtain a power law $N_m=2.56\cdot N^{0.20\pm0.04}$. We further present
data on the average number of knots given a certain chain length and confirm a
power law behaviour for the number of knot-monomers. Furthermore we study the
average crossing number for random and self-avoiding walks as well as for a
model polymer with and without geometric constraints. The data confirms the
$aN\log N + bN$ law in the case of without excluded volume and determines the
constants $a$ and $b$ for various cases. For chains with excluded volume the
data for chains up to N=1500 is consistent with $aN\log N + bN$ rather than the
proposed $N^{4/3}$ law. Nevertheless our fits show that the $N^{4/3}$ law is a
suitable approximation. | cond-mat_soft |
Glass transition in Ultrathin Polymer Films : A Thermal Expansion Study: Glass transition process gets affected in ultrathin films having thickness
comparable to the size of the molecules. We observe systematic broadening of
glass transition temperature (Tg) as the thickness of the polymer film reduces
below the radius of gyration but the change in the average Tg was found to be
very small. Existence of reversible negative and positive thermal expansion
below and above Tg increased the sensitivity of our thickness measurements
performed using energy dispersive x-ray reflectivity. A simple model of Tg
variation as a function of depth expected from sliding motion could explain the
results. We observe clear glass transition even for 4 nm polystyrene film that
was predicted to be absent from ellipsometry measurements of thicker films. | cond-mat_soft |
Anomalous Front Broadening During Spontaneous Imbibition in a Matrix
with Elongated Pores: During spontaneous imbibition a wetting liquid is drawn into a porous medium
by capillary forces. In systems with comparable pore length and diameter, such
as paper and sand, the front of the propagating liquid forms a continuous
interface. Sections of this interface advance in a highly correlated manner due
to an effective surface tension, which restricts front broadening. Here we
investigate water imbibition in a nanoporous glass (Vycor) in which the pores
are much longer than they are wide. In this case, no continuous liquid-vapor
interface with coalesced menisci can form. Anomalously fast imbibition front
roughening is experimentally observed by neutron imaging.We propose a
theoretical pore network model, whose structural details are adapted to the
microscopic pore structure of Vycor glass, and show that it displays the same
large scale roughening characteristics as observed in the experiment. The model
predicts that menisci movements are uncorrelated. This indicates that despite
the connectivity of the network the smoothening effect of surface tension on
the imbibition front roughening is negligible. These results suggest a new
universality class of imbibition behavior which is expected to occur in any
matrix with elongated, interconnected pores of random radii. | cond-mat_soft |
On Exact Solutions to the Cylindrical Poisson-Boltzmann Equation with
Applications to Polyelectrolytes: Using exact results from the theory of completely integrable systems of the
Painleve/Toda type, we examine the consequences for the theory of
polyelectrolytes in the (nonlinear) Poisson-Boltzmann approximation. | cond-mat_soft |
The Influence on Crystal Nucleation of an Order-Disorder Transition
among the Subcritical Clusters: Studies of nucleation generally focus on the properties of the critical
cluster, but the presence of defects within the crystal lattice means that the
population of nuclei necessarily evolve through a distribution of pre-critical
clusters with varying degrees of structural disorder on their way to forming a
growing stable crystal. To investigate the role pre-critical clusters play in
nucleation, we develop a simple thermodynamic model for crystal nucleation in
terms of cluster size and the degree of cluster order that allows us to alter
the work of forming the pre-critical clusters without effecting the properties
of the critical cluster. The steady state and transient nucleation behaviour of
the system are then studied numerically, for different microscopic ordering
kinetics. We find that the models exhibits a generic order-disorder transition
in the pre-critical clusters. Independent of the type of ordering kinetics,
increasing the accessibility of disordered pre-critical clusters decreases both
the steady state nucleation rate and the nucleation lag time. Furthermore, the
interplay between the free energy surface and the microscopic ordering kinetics
leads to three distinct nucleation pathways. | cond-mat_soft |
Plasticity of a colloidal polycrystal under cyclic shear: We use confocal microscopy and time-resolved light scattering to investigate
plasticity in a col- loidal polycrystal, following the evolution of the network
of grain boundaries as the sample is submitted to thousands of shear
deformation cycles. The grain boundary motion is found to be ballistic, with a
velocity distribution function exhibiting non-trivial power law tails. The
shear- induced dynamics initially slow down, similarly to the aging of the
spontaneous dynamics in glassy materials, but eventually reach a steady state.
Surprisingly, the cross-over time between the ini- tial aging regime and the
steady state decreases with increasing probed length scale, hinting at a
hierarchical organization of the grain boundary dynamics. | cond-mat_soft |
Current rectification and ionic selectivity of alpha-hemolysin:
Coarse-Grained Molecular Dynamics simulations: In order to understand the physical processes of nanopore experiments at the
molecular level, microscopic information from molecular dynamics is greatly
needed. Coarse-grained models are a good alternative to classical all-atom
models since they allow longer simulations and application of lower electric
potentials, closer to the experimental ones. We performed coarse-grained
molecular dynamics of the ionic transport through the $\alpha$-hemolysin
protein nanopore, inserted into a lipid bilayer surrounded by solvent and ions.
For this purpose, we used the MARTINI coarse-grained force field and its
polarizable water solvent (PW). Moreover, the electric potential difference
applied experimentally was mimicked by the application of an electric field to
the system. We present, in this study, the results of 1.5 microsecond
long-molecular dynamics simulations of twelve different systems for which
different charged amino acids were neutralized, each of them in the presence of
nine different electric fields ranging between +/- 0.04 V/nm (a total of around
100 simulations). We were able to observe several specific features of this
pore, current asymmetry and anion selectivity, in agreement with previous
studies and experiments, and identified the charged amino acids responsible for
these current behaviors, therefore validating our coarse-grain approach to
study ionic transport through nanopores. We also propose a microscopic
explanation of these ionic current features using ionic density maps. | cond-mat_soft |
Dynamic Control of Particle Deposition in Evaporating Droplets by an
External Point Source of Vapor: The deposition of particles on a surface by an evaporating sessile droplet is
important for phenomena as diverse as printing, thin-film deposition and
self-assembly. The shape of the final deposit depends on the flows within the
droplet during evaporation. These flows are typically determined at the onset
of the process by the intrinsic physical, chemical and geometrical properties
of the droplet and its environment. Here, we demonstrate deterministic
emergence and real-time control of Marangoni flows within the evaporating
droplet by an external point-source of vapor. By varying the source location,
we can modulate these flows in space and time to pattern colloids on surfaces
in a controllable manner. | cond-mat_soft |
Optimized Constant Pressure Stochastic Dynamics: A recently proposed method for computer simulations in the
isothermal-isobaric (NPT) ensemble, based on Langevin-type equations of motion
for the particle coordinates and the ``piston'' degree of freedom, is
re-derived by straightforward application of the standard Kramers-Moyal
formalism. An integration scheme is developed which reduces to a
time-reversible symplectic integrator in the limit of vanishing friction. This
algorithm is hence expected to be quite stable for small friction, allowing for
a large time step. We discuss the optimal choice of parameters, and present
some numerical test results. | cond-mat_soft |
Dense granular flow of mixtures of spheres and dumbbells down a rough
inclined plane: Segregation and rheology: We study the flow of equal-volume binary granular mixtures of spheres and
dumbbells with different aspect ratios down a rough inclined plane, using the
discrete element method. We consider two types of mixtures -- in the first type
the particles of the two species have equal volume but different aspect ratios
(EV) and in the second type they have variable volumes and aspect ratios (VV).
We also use mixtures of spheres of two different sizes (SS) with the same
volume ratios as in the mixtures of the second type, as the base case. Based on
the study of Guillard, Forterre and Pouliquen [\textit{J. Fluid Mech.}
\textbf{807}, R1--R11 (2016)], the inclination angle of the base for each
mixture is adjusted and maintained at a high value to yield the same pressure
and shear stress gradients for all mixtures and a high effective friction
($\mu$) for each. This ensures that the segregation force and resulting extent
of segregation depend only the size and shape of the particles. The species
with larger effective size, computed in terms of the geometric mean diameter,
floats up in all cases and the dynamics of the segregation process for all the
mixtures are reported. The concentration profiles of the species at steady
state agree well with the predictions of a continuum theory. The $\mu-I$ and
$\phi-I$ scaling relations, where $I$ is the inertial number and $\phi$ is the
solid volume fraction, extended to the case of mixtures, are shown to describe
the rheology for all the cases. | cond-mat_soft |
Confinement-mediated phase behavior of hydrocarbon fluids: Insights from
Monte Carlo simulations: The phase behavior of hydrocarbon fluids confined in porous media has been
reported to deviate significantly from that in the bulk environment due to the
existence of sub-10nm pores. Though experiments and simulations have measured
the bubble/dew points and sorption isotherms of hydrocarbons confined in both
natural and synthetic nanopores, the confinement effects in terms of the
strength of fluid-pore interactions tuned by surface wettability and chemistry
have received comparably less discussion. More importantly, the underlying
physics of confinement-induced phenomena remain obfuscated. In this work, we
studied the phase behavior and capillary condensation of n-hexane to understand
the effects of confinement at the molecular level. To systematically
investigate the pore effects, we constructed two types of wall confinements;
one is a structureless virtual wall described by the Steele potential and the
other one is an all-atom amorphous silica structure with surface modified by
hydroxyl groups. Our numerical results demonstrated the importance of
fluid-pore interaction, pore size, and pore morphology effects in mediating the
pressure-volume-temperature (PVT) properties of hydrocarbons. The most
remarkable finding of this work was that the saturation pressure predicted from
the van der Waals-type adsorption isothermal loop could be elevated or
suppressed relative to the bulk phase, as illustrated in the graphical
abstract. As the surface energy (i.e., fluid-pore interaction) decreased, the
isothermal vapor pressure increased, indicating a greater preference for the
fluid to exist in the vapor state. Sufficient reduction of the fluid-pore
interactions could even elevate the vapor pressure above that of the bulk
fluid. | cond-mat_soft |
Self-assembly of anisotropic soft particles in two dimensions: The self assembly of core-corona discs interacting via anisotropic potentials
is investigated using Monte Carlo computer simulations. A minimal interaction
potential that incorporates anisotropy in a simple way is introduced. It
consists in a core-corona architecture in which the center of the core is
shifted with respect to the center of the corona. Anisotropy can thus be tuned
by progressively shifting the position of the core. Despite its simplicity, the
system self organize in a rich variety of structures including stripes,
triangular and rectangular lattices, and unusual plastic crystals. Our results
indicate that the amount of anisotropy does not alter the lattice spacing and
only influences the type of clustering (stripes, micells, etc.) of the
individual particles. | cond-mat_soft |
Long-range interactions & parallel scalability in molecular simulations: Typical biomolecular systems such as cellular membranes, DNA, and protein
complexes are highly charged. Thus, efficient and accurate treatment of
electrostatic interactions is of great importance in computational modelling of
such systems. We have employed the GROMACS simulation package to perform
extensive benchmarking of different commonly used electrostatic schemes on a
range of computer architectures (Pentium-4, IBM Power 4, and Apple/IBM G5) for
single processor and parallel performance up to 8 nodes - we have also tested
the scalability on four different networks, namely Infiniband, GigaBit
Ethernet, Fast Ethernet, and nearly uniform memory architecture, i.e.,
communication between CPUs is possible by directly reading from or writing to
other CPUs' local memory. It turns out that the particle-mesh Ewald method
(PME) performs surprisingly well and offers competitive performance unless
parallel runs on PC hardware with older network infrastructure are needed.
Lipid bilayers of sizes 128, 512 and 2048 lipid molecules were used as the test
systems representing typical cases encountered in biomolecular simulations. Our
results enable an accurate prediction of computational speed on most current
computing systems, both for serial and parallel runs. These results should be
helpful in, for example, choosing the most suitable configuration for a small
departmental computer cluster. | cond-mat_soft |
Collective states of active particles with elastic dipolar interactions: Many types of mammalian cells exert active contractile forces and
mechanically deform their elastic substrate, to accomplish biological functions
such as cell migration. These substrate deformations provide a mechanism by
which cells can sense other cells, leading to long range mechanical intercell
interactions and possible self organization. Here, we treat cells as noisy
motile particles that exert contractile dipolar stresses on elastic substrates
as they move. By combining this minimal model for the motility of individual
cells with a linear elastic model that accounts for substrate mediated cell
cell interactions, we examine emergent collective states that result from the
interplay of cell motility and long range elastic dipolar interactions. In
particular, we show that particles self assemble into flexible, motile chains
which can cluster to form diverse larger scale compact structures with polar
order. By computing key structural and dynamical metrics, we distinguish
between the collective states at weak and strong elastic interactions, as well
as at low and high motility. We also show how these states are affected by
confinement, an important characteristic of the complex mechanical
microenvironment inhabited by cells. Our model predictions are generally
applicable to active matter with dipolar interactions ranging from biological
cells to synthetic colloids endowed with electric or magnetic dipole moments. | cond-mat_soft |
Transport and phase separation of active Brownian particles in
fluctuating environments: In this work, we study the dynamics of a single active Brownian particle, as
well as the collective behavior of interacting active Brownian particles, in a
fluctuating heterogeneous environment. We employ a variant of the diffusing
diffusivity model where the equation of motion of the active particle involves
a time-dependent motility and diffusivities. Within our model, those
fluctuations are coupled to each other. Using analytical methods, we obtain the
probability distribution function of particle displacement and its moments for
a single particle. We then investigate the impact of the environmental
fluctuations on the collective behavior of the active Brownian particles by
means of extensive numerical simulations. Our results show that the
fluctuations hinder the motility-induced phase separation, accompanied by a
significant change of the density dependence of particle velocities. These
effects are interpreted using our analytical results for the dynamics of a
single particle. | cond-mat_soft |
Molecular theory of hydrophobic mismatch between lipids and peptides: Effects of the mismatch between the hydrophobic length, d, of transmembrane
alpha helices of integral proteins and the hydrophobic thickness, D_h, of the
membranes they span are studied theoretically utilizing a microscopic model of
lipids. In particular, we examine the dependence of the period of a lamellar
phase on the hydrophobic length and volume fraction of a rigid, integral,
peptide. We find that the period decreases when a short peptide, such that
d<D_h, is inserted. More surprising, we find that the period increases when a
long peptide, such that d>D_h, is inserted. The effect is due to the
replacement of extensible lipid tails by rigid peptide. As the peptide length
is increased, the lamellar period continues to increase, but at a slower rate,
and can eventually decrease. The amount of peptide which fails to incorporate
and span the membrane increases with the magnitude of the hydrophobic mismatch
|d-D_h|. We explicate these behaviors which are all in accord with experiment.
Predictions are made for the dependence of the tilt of a single trans-membrane
alpha helix on hydrophobic mismatch and helix density. | cond-mat_soft |
A Discotic Disguised as a Smectic: A Hybrid Columnar Bragg Glass: We show that discotics, lying deep in the columnar phase, can exhibit an
x-ray scattering pattern which mimics that of a somewhat unusual smectic liquid
crystal. This exotic, new glassy phase of columnar liquid crystals, which we
call a ``hybrid columnar Bragg glass'', can be achieved by confining a columnar
liquid crystal in an anisotropic random environment of e.g., strained aerogel.
Long-ranged orientational order in this phase makes {\em single domain} x-ray
scattering possible, from which a wealth of information could be extracted. We
give detailed quantitative predictions for the scattering pattern in addition
to exponents characterizing anomalous elasticity of the system. | cond-mat_soft |
Manifestation of the collective drift of molecules in argon according to
their mean square displacements: The mean square displacement (MSD) of an argon molecule as a function of time
is studied. Its deviations from the standard asymptotic law for intermediate
times are analyzed in details. It is shown that these deviations are mainly
connected with the square-root contribution to the MSD which is proportional
the ratio of the collective part to the full self-diffusion coefficient. It is
established that the relative value of the collective contribution to the
self-diffusion coefficient of argon changes from 0.23 near the triple point up
to 0.4 at approaching the critical point. A new method for the determination of
the Maxwell relaxation time is proposed. Its temperature dependence on the
coexistence curve and one of isochors is investigated. | cond-mat_soft |
Friction Scaling Laws for Transport in Bacterial Turbulence: Understanding the role of frictional drag in diffusive transport is an
important problem in the field of active turbulence. Using a continuum model
that applies well to bacterial suspensions, we investigate the role of Ekmann
friction on the transport of passive (Lagrangian) tracers that go with the
local flow. We find that the crossover from ballistic to diffusive regime
happens at a time scale $\tau_c$ that attains a minimum at zero friction,
meaning that both injection and dissipation of energy delay the relaxation of
tracers. We explain this by proposing that $\tau_c \sim 2
\ell^*/u_{\text{rms}}$, where $\ell^*$ is a dominant length scale extracted
from energy spectrum peak, and $u_{\text{rms}}$ is a velocity scale that sets
the kinetic energy at steady state, both scales monotonically decrease with
friction. Finally, we predict robust scaling laws for $\ell^*$,
$u_{\text{rms}}$ and the diffusion coefficient $\mathcal{D} \sim \ell^*
u_{\text{rms}} / 2$, that are valid over a wide range of fluid friction. Our
findings might be relevant to transport phenomena in a generic active fluid. | cond-mat_soft |
Liquid droplets on a free-standing glassy membrane: deformation through
the glass transition: In this study, micro-droplets are placed on thin, glassy, free-standing films
where the Laplace pressure of the droplet deforms the free-standing film,
creating a bulge. The film's tension is modulated by changing temperature
continuously from well below the glass transition into the melt state of the
film. The contact angle of the liquid droplet with the planar film as well as
the angle of the bulge with the film are measured and found to be consistent
with the contact angles predicted by a force balance at the contact line. | cond-mat_soft |
Topology of Complex Bridges inside Vibrated Dry Granular Media: After some communications (EMAIL EXCHANGE) with the co-authors, this article
has been withdrawn (for appropriate reason, please refer to the comments
section). | cond-mat_soft |
Cooperative rheological state-switching of enzymatically-driven
composites of circular DNA and dextran: Polymer topology, which plays a principal role in the rheology of polymeric
fluids, and non-equilibrium materials, which exhibit time-varying rheological
properties, are topics of intense investigation. Here, we push composites of
circular DNA and dextran out-of-equilibrium via enzymatic digestion of DNA
rings to linear fragments. Our time-resolved rheology measurements reveal
discrete state-switching, with composites undergoing abrupt transitions between
dissipative and elastic-like states. The gating time and lifetime of the
elastic-like states, and the magnitude and sharpness of the transitions, are
surprisingly decorrelated from digestion rates and non-monotonically depend on
the DNA fraction. We model our results using sigmoidal two-state functions to
show that bulk state-switching can arise from continuous molecular-level
activity due to the necessity for cooperative percolation of entanglements to
support macroscopic stresses. Our platform, coupling the tunability of
topological composites with the power of enzymatic reactions, may be leveraged
for diverse material applications from wound-healing to self-repairing
infrastructure. | cond-mat_soft |
Temperature (de)activated patchy colloidal particles: We present a new model of patchy particles in which the interaction sites can
be activated or deactivated by varying the temperature of the system. We study
the thermodynamics of the system by means of Wertheim's first order
perturbation theory, and use Flory-Stockmayer theory of polymerization to
analyse the percolation threshold. We find a very rich phase behaviour
including lower critical points and reentrant percolation. | cond-mat_soft |
When is a surface foam-phobic or foam-philic?: By integrating the Young-Laplace equation, including the effects of gravity,
we have calculated the equilibrium shape of the two-dimensional Plateau borders
along which a vertical soap film contacts two flat, horizontal solid substrates
of given wettability. We show that the Plateau borders, where most of a foam's
liquid resides, can only exist if the values of the Bond number ${\rm Bo}$ and
of the liquid contact angle $\theta_c$ lie within certain domains in
$(\theta_c,{\rm Bo})$ space: under these conditions the substrate is
foam-philic. For values outside these domains, the substrate cannot support a
soap film and is foam-phobic. In other words, on a substrate of a given
wettability, only Plateau borders of a certain range of sizes can form. For
given $(\theta_c,{\rm Bo})$, the top Plateau border can never have greater
width or cross-sectional area than the bottom one. Moreover, the top Plateau
border cannot exist in a steady state for contact angles above 90$^\circ$. Our
conclusions are validated by comparison with both experimental and numerical
(Surface Evolver) data. We conjecture that these results will hold, with slight
modifications, for non-planar soap films and bubbles. Our results are also
relevant to the motion of bubbles and foams in channels, where the friction
force of the substrate on the Plateau borders plays an important role. | cond-mat_soft |
Instabilities and shape variation phase transitions in tubular lipid
membranes: Changes of external parameters in proximity of critical point can increase
thermal fluctuations of tubular lipid membrane (TLM) and result in variation of
the membrane shape. The phase transitions in the system are shown to be
controlled by a single effective parameter, which depends on the pressure
difference between inner and outer regions of membrane and the applied
stretching force. We determine an interval of the parameter values
corresponding to the stability region of the cylindrical shape of TLM and
investigate the behavior of the system in the vicinity of critical
instabilities, where the cylindrical shape of membrane becomes unstable with
respect to thermal fluctuations. The applied boundary conditions strongly
influence the behavior of TLM. For example, small negative effective parameter
corresponds to chiral shape of TLM only in the case of periodic boundary
conditions. We also discuss other three types of phase transitions emerging in
the system. | cond-mat_soft |
Partial clustering prevents global crystallization in a binary 2D
colloidal glass former: A mixture of two types of super-paramagnetic colloidal particles with long
range dipolar interaction is confined by gravity to a flat interface of a
hanging water droplet. The particles are observed by video microscopy and the
dipolar interaction strength is controlled via an external magnetic field. The
system is a model system to study the glass transition in 2D, and it exhibits
partial clustering of the small particles. This clustering is strongly
dependent on the relative concentration $\xi$ of big and small particles.
However, changing the interaction strength $\Gamma$ reveals that the clustering
does not depend on the interaction strength. The partial clustering scenario is
quantified using Minkowski functionals and partial structure factors. Evidence
that partial clustering prevents global crystallization is discussed. | cond-mat_soft |
Nonequilibrium steady states in fluids of platelike colloidal particles: Nonequilibrium steady states in an open system connecting two reservoirs of
platelike colloidal particles are investigated by means of a recently proposed
phenomenological dynamic density functional theory [M. Bier and R. van Roij,
Phys. Rev. E 76, 021405 (2007)]. The platelike colloidal particles are
approximated within the Zwanzig model of restricted orientations, which
exhibits an isotropic-nematic bulk phase transition. Inhomogeneities of the
local chemical potential generate a diffusion current which relaxes to a
nonvanishing value if the two reservoirs coupled to the system sustain
different chemical potentials. The relaxation process of initial states towards
the steady state turns out to comprise two regimes: a smoothening of initial
steplike structures followed by an ultimate relaxation of the slowest diffusive
mode. The position of a nonequilibrium interface and the particle current of
steady states depend nontrivially on the structure of the reservoirs due to the
coupling between translational and orientational degrees of freedom of the
fluid. | cond-mat_soft |
Impact of dipole-dipole interactions on motility-induced phase
separation: We present a hydrodynamic theory for systems of dipolar active Brownian
particles which, in the regime of weak dipolar coupling, predicts the onset of
motility-induced phase separation (MIPS), consistent with Brownian dynamics
(BD) simulations. The hydrodynamic equations are derived by explicitly
coarse-graining the microscopic Langevin dynamics, thus allowing for a
quantitative comparison of parameters entering the coarse-grained model and
particle-resolved simulations. Performing BD simulations at fixed density, we
find that dipolar interactions tend to hinder MIPS, as first reported in [Liao
et al., Soft Matter, 2020, 16, 2208]. Here we demonstrate that the theoretical
approach indeed captures the suppression of MIPS. Moreover, the analysis of the
numerically obtained, angle-dependent correlation functions sheds light into
the underlying microscopic mechanisms leading to the destabilization of the
homogeneous phase. | cond-mat_soft |
Minimum Entropy Production by Microswimmers with Internal Dissipation: The energy dissipation and entropy production by self-propelled microswimmers
differ profoundly from passive particles pulled by external forces. The
difference extends both to the shape of the flow around the swimmer, as well as
to the internal dissipation of the propulsion mechanism. Here we derive a
general theorem that provides an exact lower bound on the total, external and
internal, dissipation by a microswimmer. The problems that can be solved
include an active surface-propelled droplet, swimmers with an extended
propulsive layer and swimmers with an effective internal dissipation. We apply
the theorem to determine the swimmer shapes that minimize the total dissipation
while keeping the volume constant. Our results show that the entropy production
by active microswimmers is subject to different fundamental limits than the
entropy production by externally driven particles. | cond-mat_soft |
Hidden symmetries generate rigid folding mechanisms in periodic origami: We consider the zero-energy deformations of periodic origami sheets with
generic crease patterns. Using a mapping from the linear folding motions of
such sheets to force-bearing modes in conjunction with the Maxwell-Calladine
index theorem we derive a relation between the number of linear folding motions
and the number of rigid body modes that depends only on the average
coordination number of the origami's vertices. This supports the recent result
by Tachi which shows periodic origami sheets with triangular faces exhibit
two-dimensional spaces of rigidly foldable cylindrical configurations. We also
find, through analytical calculation and numerical simulation, branching of
this configuration space from the flat state due to geometric compatibility
constraints that prohibit finite Gaussian curvature. The same counting argument
leads to pairing of spatially varying modes at opposite wavenumber in
triangulated origami, preventing topological polarization but permitting a
family of zero energy deformations in the bulk that may be used to reconfigure
the origami sheet. | cond-mat_soft |
Fractional Debye-Stokes-Einstein behaviour in an ultraviscous
nanocolloid: glycerol and silver nanoparticles: One of hallmark features of glass forming ultraviscous liquids is the
decoupling between translational and orientational dynamics. This report
presents studies of this phenomenon in glycerol, a canonical molecular glass
former, heading for the impact of two exogenic factors: high pressures up to
extreme 1.5 GPa and silver (Ag) nanoparticles (NP). The analysis is focused on
the fractional Debye-Stokes-Einstein (FDSE) relation $\sigma(T,P)*(\tau(T,P))^S
= const$, linking DC electric conductivity $(\sigma)$ and primary $(\alpha)$
relaxation time $(\tau_\alpha)$. In glycerol and its nanocolloid (glycerol with
Ag-NP) under atmospheric pressure only the negligible decoupling $(S = 1)$ was
detected. However, in the compressed nanocolloid a well-defined transformation
(at P = 1.2 GPa) from $S \thickapprox 1$ to the very strongly decoupled
dynamics $(S \thickapprox 0.5)$ occurred. For comparison, in pressurized 'pure'
glycerol the stretched shift from $S \thickapprox 1$ to $S \thickapprox 0.7$
took place. This report presents also the general discussion of FDSE behavior
in ultraviscous liquids, including the new link between FDSE exponent,
fragility and the apparent activation enthalpy and volume. | cond-mat_soft |
Enhanced stability of tetratic phase due to clustering: We show that the relative stability of the nematic tetratic phase with
respect to the usual uniaxial nematic phase can be greatly enhanced by
clustering effects. Two--dimensional rectangles of aspect ratio $\kappa$
interacting via hard interactions are considered, and the stability of the two
nematic phases (uniaxial and tetratic) is examined using an extended
scaled--particle theory applied to a polydispersed fluid mixture of $n$
species. Here the $i$--th species is associated with clusters of $i$
rectangles, with clusters defined as stacks of rectangles containing
approximately parallel rectangles, with frozen internal degrees of freedom. The
theory assumes an exponential cluster size distribution (an assumption fully
supported by Monte Carlo simulations and by a simple chemical--reaction model),
with fixed value of the second moment. The corresponding area distribution
presents a shoulder, and sometimes even a well-defined peak, at cluster sizes
approximately corresponding to square shape (i.e. $i\simeq\kappa$), meaning
that square clusters have a dominant contribution to the free energy of the
hard--rectangle fluid. The theory predicts an enhanced region of stability of
the tetratic phase with respect to the standard scaled--particle theory, much
closer to simulation and to experimental results, demonstrating the importance
of clustering in this fluid. | cond-mat_soft |
Statistical field theory for a multicomponent fluid: The collective
variables approach: Using the collective variables (CV) method the basic relations of statistical
field theory of a multicomponent non-homogeneous fluids are reconsidered. The
corresponding CV action depends on two sets of scalar fields - fields
$\rho_{\alpha}$ connected to the local density fluctuations of the $\alpha$th
species of particles and fields $\omega_{\alpha}$ conjugated to
$\rho_{\alpha}$. The explicit expressions for the CV field correlations and
their relation to the density correlation functions are found. The perturbation
theory is formulated and a mean field level (MF) of the theory is considered in
detail. | cond-mat_soft |
Smectic-$A$ elastomers with weak director anchoring: Experimentally it is possible to manipulate the director in a (chiral)
smectic-$A$ elastomer using an electric field. This suggests that the director
is not necessarily locked to the layer normal, as described in earlier papers
that extended rubber elasticity theory to smectics. Here, we consider the case
that the director is weakly anchored to the layer normal assuming that there is
a free energy penalty associated with relative tilt between the two. We use a
recently developed weak-anchoring generalization of rubber elastic approaches
to smectic elastomers and study shearing in the plane of the layers, stretching
in the plane of the layers, and compression and elongation parallel to the
layer normal. We calculate, inter alia, the engineering stress and the tilt
angle between director and layer normal as functions of the applied
deformation. For the latter three deformations, our results predict the
existence of an instability towards the development of shear accompanied by
smectic-$C$-like order. | cond-mat_soft |
A systematically coarse-grained model for DNA, and its predictions for
persistence length, stacking, twist, and chirality: We introduce a coarse-grained model of DNA with bases modeled as rigid-body
ellipsoids to capture their anisotropic stereochemistry. Interaction potentials
are all physicochemical and generated from all-atom simulation/parameterization
with minimal phenomenology. Persistence length, degree of stacking, and twist
are studied by molecular dynamics simulation as functions of temperature, salt
concentration, sequence, interaction potential strength, and local position
along the chain, for both single- and double-stranded DNA where appropriate.
The model of DNA shows several phase transitions and crossover regimes in
addition to dehybridization, including unstacking, untwisting, and collapse
which affect mechanical properties such as rigidity and persistence length. The
model also exhibits chirality with a stable right-handed and metastable
left-handed helix. | cond-mat_soft |
General theory of charge regulation within the Poisson-Boltzmann
framework: study of a sticky-charged wall model: This work introduces a sticky-charge wall model as a simple and intuitive
representation of charge regulation. Implemented within the mean-field level of
description, the model modifies the boundary conditions without affecting the
underlying Poisson-Boltzmann (PB) equation of an electrolyte. Employing various
modified PB equations, we are able to assess how various structural details of
an electrolyte influence charge regulation. | cond-mat_soft |
Jet-driven viscous locomotion of confined thermoresponsive microgels: We consider the dynamics of micro-sized, asymmetrically-coated
thermoresponsive hydrogel ribbons (microgels) under periodic heating and
cooling in the confined space between two planar surfaces. As the result of the
temperature changes, the volume and thus the shape of the slender microgel
change, which lead to repeated cycles of bending and elastic relaxation, and to
net locomotion. Small devices designed for biomimetic locomotion need to
exploit flows that are not symmetric in time (non-reciprocal) to escape the
constraints of the scallop theorem and undergo net motion. Unlike other
biological slender swimmers, the non-reciprocal bending of the gel centreline
is not sufficient here to explain for the overall swimming motion. We show
instead that the swimming of the gel results from the flux of water
periodically emanating from (or entering) the gel itself due to its shrinking
(or swelling). The associated flows induce viscous stresses that lead to a net
propulsive force on the gel. We derive a theoretical model for this hypothesis
of jet-driven propulsion, which leads to excellent agreement with our
experiments. | cond-mat_soft |
Universal criterion for designability of heteropolymers: Proteins are an example of heteropolymers able to self-assemble in specific
target structures. The self-assembly of designed artificial heteropolymers is
still, to the best of our knowledge, not possible with control over the single
chain self-assembling properties comparable to what natural proteins can
achieve. What artificial heteropolymers lacks compared to bio-heteropolymers
that grants the latter such a versatility? Is the geometry of the protein
skeleton the only a particular choice to be designable? Here we introduce a
general criteria to discriminate which polymer backbones can be designed to
adopt a predetermined structure. With our approach we can explore different
polymer backbones and different amino acids alphabets. By comparing the radial
distribution functions of designable and not-designable scenarios we identify
as designability criteria the presence of a particular peak in the radial
distribution function that dominates over the random packing of the
heteropolymer. We show that the peak is a universal feature of all designable
heteropolymers, as it is dominating also the radial distribution function of
natural proteins. Our finding can help in understanding the key features that
make proteins a highly designable system. The criteria that we present can be
applied to engineer new types of self-assembling modular polymers that will
open new applications for polymer based material science. | cond-mat_soft |
Surface-Mediated Molecular Transport of a Lipophilic Fluorescent Probe
in Polydisperse Oil-in-Water Emulsions: Emulsions often act as carriers for water-insoluble solutes that are
delivered to a specific target. The molecular transport of solutes in emulsions
can be facilitated by surfactants and is often limited by diffusion through the
continuous phase. We here investigate this transport on a molecular scale by
using a lipophilic molecular rotor as a proxy for solutes. Using fluorescence
lifetime microscopy we track the transport of these molecules from the
continuous phase towards the dispersed phase in polydisperse oil-in-water
emulsions. We show that this transport comprises two timescales, which vary
significantly with droplet size and surfactant concentration, and, depending on
the type of surfactant used, can be limited either by transport across the
oil-water interface, or by diffusion through the continuous phase. By studying
the time-resolved fluorescence of the fluorophore, accompanied by molecular
dynamics simulations, we demonstrate how the rate of transport observed on a
macroscopic scale can be explained in terms of the local environment that the
probe molecules are exposed to. | cond-mat_soft |
Constraints on fundamental physical constants from bio-friendly
viscosity and diffusion: The problem of understanding fundamental physical constants was discussed in
particle physics, astronomy and cosmology. Here, I show that a new insight
comes from condensed matter physics and liquid physics in particular:
fundamental constants have a bio-friendly window constrained by bio-friendly
viscosity and diffusion setting the motion in essential life processes in and
across cells. I also show that bounds on viscosity, diffusion and the
fundamental velocity gradient in a biochemical machine can all be varied while
keeping the fine-structure constant and the proton-to-electron mass ratio
intact, with no implication for the production of heavy nuclei in stars. This
leads to a conjecture of multiple tuning and an evolutionary mechanism. | cond-mat_soft |
Wall-Fluid and Liquid-Gas Interfaces of Model Colloid-Polymer Mixtures
by Simulation and Theory: We perform a study of the interfacial properties of a model suspension of
hard sphere colloids with diameter $\sigma_c$ and non-adsorbing ideal polymer
coils with diameter $\sigma_p$. For the mixture in contact with a planar hard
wall, we obtain from simulations the wall-fluid interfacial free energy,
$\gamma_{wf}$, for size ratios $q=\sigma_p/\sigma_c=0.6$ and 1, using
thermodynamic integration, and study the (excess) adsorption of colloids,
$\Gamma_c$, and of polymers, $\Gamma_p$, at the hard wall. The interfacial
tension of the free liquid-gas interface, $\gamma_{lg}$, is obtained following
three different routes in simulations: i) from studying the system size
dependence of the interfacial width according to the predictions of capillary
wave theory, ii) from the probability distribution of the colloid density at
coexistence in the grand canonical ensemble, and iii) for statepoints where the
colloidal liquid wets the wall completely, from Young's equation relating
$\gamma_{lg}$ to the difference of wall-liquid and wall-gas interfacial
tensions, $\gamma_{wl}-\gamma_{wg}$. In addition, we calculate $\gamma_{wf},
\Gamma_c$, and $\Gamma_p$ using density functional theory and a scaled particle
theory based on free volume theory. Good agreement is found between the
simulation results and those from density functional theory, while the results
from scaled particle theory quantitatively deviate but reproduce some essential
features. Simulation results for $\gamma_{lg}$ obtained from the three
different routes are all in good agreement. Density functional theory predicts
$\gamma_{lg}$ with good accuracy for high polymer reservoir packing fractions,
but yields deviations from the simulation results close to the critical point. | cond-mat_soft |
The role of the extra cellular matrix on memory: We expose first a biological model of memory based on one hand of the
mechanical oscillations of axons during action potential and on the other hand
on the changes in the extra cellular matrix composition when a mechanical
strain is applied on it. Due to these changes, the stiffness of the extra
cellular matrix along the most excited neurons will increase close to these
neurons due to the growth of astrocytes around them and to the elastoplastic
behavior of collagen. This will create preferential paths linked to a memory
effect. In a second part, we expose a physical model based on random walk of
the action potential on the array composed of dendrites and axons. This last
model shows that repetition of the same event leads to long time memory of this
event and that paradoxical sleep leads to the linking of different events put
into memory. | cond-mat_soft |
Adhesion of microcapsules: The adhesion of microcapsules to an attractive contact potential is studied
theoretically. The axisymmetric shape equations are solved numerically. Beyond
a universal threshold strength of the potential, the contact radius increases
like a square root of the strength. Scaling functions for the corresponding
amplitudes are derived as a function of the elastic parameters. | cond-mat_soft |
Relaxation in homogeneous and non-homogeneous polarized systems. A
mesoscopic entropy approach: The dynamics of a degree of freedom associated to an axial vector in contact
with a heat bath is decribed by means of a probability distribution function
obeying a Fokker-Planck equation. The equation is derived by using mesoscopic
non-equilibrium thermodynamics and permits a formulation of a dynamical theory
for the axial degree of freedom (orientation, polarization) and its associated
order parameter. The theory is used to describe dielectric relaxation in
homogeneous and non-homogeneous systems in the presence of strong electric
fields. In the homogeneous case, we obtain the dependence of the relaxation
time on the external field as observed in experiments. In the non-homogeneous
case, our model account for the two observed maxima of the dielectric loss
giving a good quantitative description of experimental data at all frequencies,
especially for systems with low molecular mass. | cond-mat_soft |
Measurements of the self-assembly kinetics of individual viral capsids
around their RNA genome: The formation of a viral capsid -- the highly-ordered protein shell that
surrounds the genome of a virus -- is the canonical example of self-assembly.
The capsids of many positive-sense RNA viruses spontaneously assemble from in
vitro mixtures of the coat protein and RNA. The high yield of proper capsids
that assemble is remarkable, given their structural complexity: 180 identical
proteins must arrange into three distinct local configurations to form an
icosahedral capsid with a triangulation number of 3 (T = 3). Despite a wealth
of data from structural studies and simulations, even the most fundamental
questions about how these structures assemble remain unresolved. Experiments
have not determined whether the assembly pathway involves aggregation or
nucleation, or how the RNA controls the process. Here we use interferometric
scattering microscopy to directly observe the in vitro assembly kinetics of
individual, unlabeled capsids of bacteriophage MS2. By measuring how many coat
proteins bind to individual MS2 RNA strands over time scales from 1 ms to 900
s, we find that the start of assembly is broadly distributed in time and is
followed by a rapid increase in the number of bound proteins. These
measurements provide strong evidence for a nucleation-and-growth pathway. We
also find that malformed structures assemble when multiple nuclei appear on the
same RNA before the first nucleus has finished growing. Our measurements reveal
the complex assembly pathways for viral capsids around RNA in quantitative
detail, including the nucleation threshold, nucleation time, growth time, and
constraints on the critical nucleus size. These results may inform strategies
for engineering synthetic capsids or for derailing the assembly of pathogenic
viruses. | cond-mat_soft |
A molecular dynamics computer simulation study of room-temperature ionic
liquids. I. Equilibrium solvation structure and free energetics: Solvation in 1-ethyl-3-methylmidazolium chloride and in
1-ethyl-3-methylimidazolium hexafluorophosphate near equilibrium is
investigated via molecular dynamics computer simulations with diatomic and
benzenelike molecules employed as probe solutes. It is found that
electrostriction plays an important role in both solvation structure and free
energetics. The angular and radial distributions of cations and anions become
more structured and their densities near the solute become enhanced as the
solute charge separation grows. Due to the enhancement in structural rigidity
induced by electrostriction, the force constant associated with solvent
configuration fluctuations relevant to charge shift and transfer processes is
also found to increase. The effective polarity and reorganization free energies
of these ionic liquids are analyzed and compared with those of highly polar
acetonitrile. Their screening behavior of electric charges is also
investigated. | cond-mat_soft |
Orientational relaxation in a discotic liquid crystal: We investigate orientational relaxation of a model discotic liquid crystal,
consists of disc-like molecules, by molecular dynamics simulations along two
isobars starting from the high temperature isotropic phase. The two isobars
have been so chosen that (A) the phase sequence isotropic (I)-nematic
(N)-columnar (C) appears upon cooling along one of them and (B) the sequence
isotropic (I)-columnar (C) along the other. While the orientational relaxation
in the isotropic phase near the I-N phase transition in system (A) shows a
power law decay at short to intermediate times, such power law relaxation is
not observed in the isotropic phase near the I-C phase boundary in system (B).
In order to understand this difference (the existence or the absence of the
power law decay), we calculated the the growth of the orientational pair
distribution functions (OPDF) near the I-N phase boundary and also near the I-C
phase boundary. We find that OPDF shows a marked growth in long range
correlation as the I-N phase boundary is approached in the I-N-C system (A),
but such a growth is absent in the I-C system, which appears to be consistent
with the result that I-N phase transition in the former is weakly first order
while the the I-C phase transition in the later is not weak. As the system
settles into the nematic phase, the decay of the single-particle second-rank
orientational OTCF follows a pattern that is similar to what is observed with
calamitic liquid crystals and supercooled molecular liquids. | cond-mat_soft |
Length distribution of stiff, self-assembled polymers at thermal
equilibrium: We investigate the length distribution of self-assembled, long and stiff
polymers at thermal equilibrium. Our analysis is based on calculating the
partition functions of stiff polymers of variable lengths in the elastic
regime. Our conclusion is that the length distribution of this self-assembled
system follows closely the exponential distribution, except at the short length
limit. We then discuss the implications of our results on the experimentally
observed length distributions in amyloid fibrils. | cond-mat_soft |
Electrophoretic separation of large DNAs using steric confinement: We report an alternative method for electrophoretic separation of large DNAs
using steric confinement between solid walls, without gel or obstacles. The
change of electrophoretic mobility vs confinement thickness is investigated
using fluorescence video microscopy. We observe separation at small confinement
thicknesses followed by a transition to the bulk behaviour (no separation) at a
thickness of about 4 μm (a few radii of gyration for the studied DNA
chains). We present tentative explanations of our original observations. | cond-mat_soft |
Effect of shear flow on Wormlike micelles: We use a hybrid method that combines the Multiparticle collision dynamics
(MPCD) for solvent particles with the molecular dynamics for equilibrium
polymers to simulate the shearing of the equilibrium polymers (or Wormlike
micelles) at a mesoscopic length scale. The MPCD method incorporates the
hydrodynamic interaction with the polymeric chains. We show successful
implementation of the method on the model equilibrium polymers (or Wormlike
micelles) and observe that the order of the Iso-Nem transition of the polymeric
system is affected by the shear rate. Moreover, the chains of the equilibrium
polymers first increase in their average length with the increase in shear rate
but then show a decrease in their average length after crossing a particular
value of the shear rate which shows the breaking of chains due to shear stress
when their nematic order remains unchanged. This model and method can be
further used to investigate the shear banding in Wormlike micelles or other
interesting properties of such systems. | cond-mat_soft |
Charge and hydration structure of dendritic polyelectrolytes: molecular
simulations of polyglycerol sulphate: Macromolecules based on dendritic or hyperbranched polyelectrolytes have been
emerging as high potential candidates for biomedical applications. Here we
study the charge and solvation structure of dendritic polyglycerol sulphate
(dPGS) of generations 0 to 3 in aqueous sodium chloride solution by
explicit-solvent molecular dynamics computer simulations. We characterize dPGS
by calculating several important properties such as relevant dPGS radii,
molecular distributions, the solvent accessible surface area, and the partial
molecular volume. In particular, as the dPGS exhibits high charge
renormalization effects, we address the challenges of how to obtain a
well-defined effective charge and surface potential of dPGS for practical
applications. We compare implicit- and explicit-solvent approaches in our
all-atom simulations with the coarse-grained simulations from our previous
work. We find consistent values for the effective electrostatic size (i.e., the
location of the effective charge of a Debye--H\"{u}ckel sphere) within all the
approaches, deviating at most by the size of a water molecule. Finally, the
excess chemical potential of water insertion into dPGS and its thermodynamic
signature are presented and rationalized. | cond-mat_soft |
Membrane budding driven by intra-cellular ESCRT-III filaments: Exocytosis is a common transport mechanism via which cells transport out
non-essential macro-molecules (cargo) into the extra cellular space. ESCRT-III
proteins are known to help in this. They polymerize into a conical spring like
structure and help deform the cell membrane locally into a bud which wrapps the
outgoing cargo. we model this process using a continuum energy functional. It
consists of elastic energies of the membrane and the semi-rigid ESCRT-III
filament, favorable adhesion energy between the cargo and the membrane, and
affinity among the ESCRT-III filaments. We take the free energy minimization
route to identify the sequence of composite structures which form during the
process. We show that membrane adhesion of the cargo is the driving force for
this budding process and not the buckling of ESCRT-III filaments from flat
spiral to conical spring shape. However ESCRT-III stabilizes the bud once it
forms. Further we conclude that a non-equilibrium process is needed to pinch
off/separate the stable bud (containing the cargo) from the cell body. | cond-mat_soft |
Ordering in granular rod monolayers driven far from thermodynamic
equilibrium: The orientational order in vertically agitated granular rod monolayers is
investigated experimentally and compared quantitatively with equilibrium Monte
Carlo simulations and density functional theory. At sufficiently high number
density, short rods form a tetratic state and long rods form a uniaxial nematic
state. The length-to-width ratio at which the order changes from tetratic to
uniaxial is around $7.3$ in both experiments and simulations. This agreement
illustrates the universal aspects of the ordering of rod-shaped particles
across equilibrium and nonequilibrium systems. Moreover, the assembly of
granular rods into ordered states is found to be independent of the agitation
frequency and strength, suggesting that the detailed nature of energy injection
into such a nonequilibrium system does not play a crucial role. | cond-mat_soft |
Effective Landau theory of ferronematics: An effective Landau-like description of ferronematics, i.e., suspensions of
magnetic colloidal particles in a nematic liquid crystal (NLC), is developed in
terms of the corresponding magnetization and nematic director fields. The study
is based on a microscopic model and on classical density functional theory.
Ferronematics are susceptible to weak magnetic fields and they can exhibit a
ferromagnetic phase, which has been predicted several decades ago and which has
recently been found experimentally. Within the proposed effective Landau theory
of ferronematics one has quantitative access, e.g., to the coupling between the
magnetization of the magnetic colloids and the nematic director of the NLC. On
mesoscopic length scales this generates complex response patterns. | cond-mat_soft |
Estimating the density-scaling exponent of a monatomic liquid from its
pair potential: This paper investigates two conjectures for calculating the density
dependence of the density-scaling exponent of a single-component,
pair-potential liquid with strong virial potential-energy correlations. The
first conjecture gives an analytical expression for the density-scaling
exponent directly in terms of the pair potential. The second conjecture is a
refined version of this, which involves the most likely nearest-neighbor
distance determined from the pair-correlation function. The two conjectures for
the density-scaling exponent are tested by simulations of three systems, one of
which is the standard Lennard-Jones liquid. While both expressions give
qualitatively correct results, the second expression is more accurate. | cond-mat_soft |
Translocation Dynamics with Attractive Nanopore-Polymer Interactions: Using Langevin dynamics simulations, we investigate the influence of
polymer-pore interactions on the dynamics of biopolymer translocation through
nanopores. We find that an attractive interaction can significantly change the
translocation dynamics. This can be understood by examining the three
components of the total translocation time $\tau \approx \tau_1+\tau_2+\tau_3$
corresponding to the initial filling of the pore, transfer of polymer from the
\textit{cis} side to the \textit{trans} side, and emptying of the pore,
respectively. We find that the dynamics for the last process of emptying of the
pore changes from non-activated to activated in nature as the strength of the
attractive interaction increases, and $\tau_3$ becomes the dominant
contribution to the total translocation time for strong attraction. This leads
to a new dependence of $\tau$ as a function of driving force and chain length.
Our results are in good agreement with recent experimental findings, and
provide a possible explanation for the different scaling behavior observed in
solid state nanopores {\it vs.} that for the natural $\alpha$-hemolysin
channel. | cond-mat_soft |
Dielectric study on mixtures of ionic liquids: Ionic liquids are promising candidates for electrolytes in energy-storage
systems. We demonstrate that mixing two ionic liquids allows to precisely tune
their physical properties, like the dc conductivity. Moreover, these mixtures
enable the gradual modification of the fragility parameter, which is believed
to be a measure of the complexity of the energy landscape in supercooled
liquids. The physical origin of this index is still under debate; therefore,
mixing ionic liquids can provide further insights. From the chemical point of
view, tuning ionic liquids via mixing is an easy and thus an economic way. For
this study, we performed detailed investigations by broadband dielectric
spectroscopy and differential scanning calorimetry on two mixing series of
ionic liquids. One series combines an imidazole based with a pyridine based
ionic liquid and the other two different anions in an imidazole based ionic
liquid. The analysis of the glass-transition temperatures and the thorough
evaluations of the measured dielectric permittivity and conductivity spectra
reveal that the dynamics in mixtures of ionic liquids are well defined by the
fractions of their parent compounds. | cond-mat_soft |
Steady vs. Dynamic Contributions of Different Doped Conducting Polymers
in the Principal Components of an Electronic Nose's Response: Multivariate data analysis and machine-learning classification become popular
tools to extract features without physical models for complex environments
recognition. For electronic noses, time sampling over multiple sensors must be
a fair compromise between a period sufficiently long to output a meaningful
information pattern, and sufficiently short to minimize training time for
practical applications. Particularly when reactivity's kinetics differ from
thermodynamics' in sensitive materials, finding the best compromise to get the
most from data is not obvious. Here, we investigate on the influence of data
acquisition to improve or alter data clustering for molecular recognition on a
conducting polymer electronic nose. We found out that waiting for the sensors
to reach their steady state is not required for classification, and that
reducing data acquisition down to the first dynamical information suffice to
recognize molecular gases by principal component analysis with the same
materials. Particularly for online inference, this study shows that a good
sensing array is no array of good sensors, and that new figure-of-merits shall
be defined for sensing hardware aiming machine-learning pattern-recognition
rather than metrology. | cond-mat_soft |
Viscous Mechano-Electric Response of Ferroelectric Nematic Liquid: Direct viscous mechano-electric response is demonstrated for a
room-temperature ferroelectric nematic liquid, which combines large spontaneous
electric polarization with 3D fluidity. The mechano-electric transduction is
observed in the frequency range 1-200 Hz via a simple demonstrator device. The
liquid is placed into a deformable container with electrodes and the electric
current induced by both periodic and irregular actuation of the container is
examined. The experiments reveal a rich interplay of several distinct viscous
mechano-electric phenomena, where both shape deformations and material flow
cause changes in the electric polarization structure of a ferroelectric nematic
liquid. The results show that the mechano-electric features of the material
promise a considerable applicative perspective spanning from sensitive tactile
sensors to energy harvesting devices. | cond-mat_soft |
Onset of glassiness in two-dimensional ring polymers: interplay of
stiffness and crowding: The effect of ring stiffness and pressure on the glassy dynamics of a thermal
assembly of two-dimensional ring polymers is investigated using extensive
coarse-grained molecular dynamics simulations. In all cases, dynamical slowing
down is observed with increasing pressure and thereby a phase space for
equilibrium dynamics is identified in the plane of obtained monomer density and
ring stiffness. When the rings are highly flexible, i.e. low ring stiffness,
glassiness sets in via crowding of crumpled polymers which take a globular
form. In contrast, at large ring stiffness, when the rings tend to have large
asphericity under compaction, we observe the emergence of local domains having
orientational ordering, at high pressures. Thus, our simulations highlight how
varying the deformability of rings leads to contrasting mechanisms in driving
the system towards the glassy regime. | cond-mat_soft |
Thermodynamics of protein folding: a random matrix formulation: The process of protein folding from an unfolded state to a biologically
active, folded conformation is governed by many parameters e.g the sequence of
amino acids, intermolecular interactions, the solvent, temperature and chaperon
molecules. Our study, based on random matrix modeling of the interactions,
shows however that the evolution of the statistical measures e.g Gibbs free
energy, heat capacity, entropy is single parametric. The information can
explain the selection of specific folding pathways from an infinite number of
possible ways as well as other folding characteristics observed in computer
simulation studies. | cond-mat_soft |
Superposition of macroscopic numbers of atoms and molecules: We theoretically examine photoassociation of a non-ideal Bose-Einstein
condensate, focusing on evidence for a macroscopic superposition of atoms and
molecules. This problem raises an interest because, rather than two states of a
given object, an atom-molecule system is a seemingly impossible macroscopic
superposition of different objects. Nevertheless, photoassociation enables
coherent intraparticle conversion, and we thereby propose a viable scheme for
creating a superposition of a macroscopic number of atoms with a macroscopic
number of molecules. | cond-mat_soft |
Shear-induced reinforcement in boehmite gels: a rheo-X-ray-scattering
study: Boehmite, an aluminum oxide hydroxide $\gamma$-AlO(OH), is broadly used in
the form of particulate dispersions in industrial applications, e.g., for the
fabrication of ceramics and catalyst supports or as a binder for extrusion
processes. Under acidic conditions, colloidal boehmite dispersions at rest form
gels, i.e., space-spanning percolated networks that behave as soft solids at
rest, and yet yield and flow like liquids under large enough deformations. Like
many other colloidal gels, the solid-like properties of boehmite gels at rest
are very sensitive to their previous mechanical history. Our recent work
[Sudreau et al., J. Rheol. 66, 91-104 (2022), and Phys. Rev. Material 6,
L042601 (2022)] has revealed such \textit{memory effects}, where the shear
experienced prior to flow cessation drives the elasticity of boehmite gels:
while gels formed following application of a shear rate $\dot\gamma_{\rm p}$
larger than a critical value $\dot\gamma_{\rm c}$ are insensitive to shear
history, gels formed after application of $\dot\gamma_{\rm p}<\dot\gamma_{\rm
c}$ display reinforced viscoelastic properties and non-negligible residual
stresses. Here, we provide a microstructural scenario for these striking
observations by coupling rheometry and small-angle X-ray scattering.
Time-resolved measurements for $\dot\gamma_{\rm p} <\dot\gamma_{\rm c}$ show
that scattering patterns develop an anisotropic shape that persists upon flow
cessation, whereas gels exposed to $\dot\gamma_{\rm p}>\dot\gamma_{\rm c}$
display isotropic scattering patterns upon flow cessation. Moreover, as the
shear rate applied prior to flow cessation is decreased below $\dot\gamma_{\rm
c}$, the level of anisotropy frozen in the sample microstructure grows
similarly to the viscoelastic properties, thus providing a direct link between
mechanical reinforcement and flow-induced microstructural anisotropy. | cond-mat_soft |
Free energy of alternating two-component polymer brushes on cylindrical
templates: We use computer simulations to investigate the stability of a two-component
polymer brush de-mixing on a curved template into phases of different
morphological properties. It has been previously shown via molecular dynamics
simulations that immiscible chains having different length and anchored to a
cylindrical template will phase separate into striped phases of different
widths oriented perpendicularly to the cylindrical axis. We calculate free
energy differences for a variety of stripe widths, and extract simple
relationships between the sizes of the two polymers, N_1 and N_2, and the free
energy dependence on the stripe width. We explain these relationships using
simple physical arguments based upon previous theoretical work on the free
energy of polymer brushes. | cond-mat_soft |
First-principles molecular dynamics study of deuterium diffusion in
liquid tin: Understanding the retention of hydrogen isotopes in liquid metals, such as
lithium and tin, is of great importance in designing a liquid plasma-facing
component in fusion reactors. However, experimental diffusivity data of
hydrogen isotopes in liquid metals are still limited or controversial. We
employ first-principles molecular dynamics simulations to predict diffusion
coefficients of deuterium in liquid tin at temperatures ranging from 573 to
1673 K. Our simulations indicate faster diffusion of deuterium in liquid tin
than the self-diffusivity of tin. In addition, we find that the structural and
dynamic properties of tin are insensitive to the inserted deuterium at
temperatures and concentrations considered. We also observe that tin and
deuterium do not form stable solid compounds. These predicted results from
simulations enable us to have a better understanding of the retention of
hydrogen isotopes in liquid tin. | cond-mat_soft |
A kinetic perspective of charge transfer reactions: the downfall of
hard/soft acid/base interactions: We show how to incorporate the possibility of kinetic control in the
conceptual Density Functional Theory formalism. This allow us to prove that the
hard/soft acid/base principle will likely fail when the reactions are not
thermodynamically-driven. | cond-mat_soft |
Statistical mechanics of two-dimensional foams: Physical foundations of
the model: In a recent series of papers [1--3], a statistical model that accounts for
correlations between topological and geometrical properties of a
two-dimensional shuffled foam has been proposed and compared with experimental
and numerical data. Here, the various assumptions on which the model is based
are exposed and justified: the equiprobability hypothesis of the foam
configurations is argued. The range of correlations between bubbles is
discussed, and the mean field approximation that is used in the model is
detailed. The two self-consistency equations associated with this mean field
description can be interpreted as the conservation laws of number of sides and
bubble curvature, respectively. Finally, the use of a '' Grand-Canonical ''
description, in which the foam constitutes a reservoir of sides and curvature,
is justified. | cond-mat_soft |
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