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Efficient creation of molecules from a cesium Bose-Einstein condensate: We report a new scheme to create weakly bound Cs$_2$ molecules from an atomic
Bose-Einstein condensate. The method is based on switching the magnetic field
to a narrow Feshbach resonance and yields a high atom-molecule conversion
efficiency of more than 30%, a factor of three higher than obtained with
conventional magnetic-field ramps. The Cs$_2$ molecules are created in a single
$g$-wave rotational quantum state. The observed dependence of the conversion
efficiency on the magnetic field and atom density shows scattering processes
beyond two-body coupling to occur in the vicinity of the Feshbach resonance. | cond-mat_soft |
Why monovalent salt reduces charge inversion of macroion by trivalent
counterions: A macroion with a strongly charged negative surface in 3:1 salt water
solution becomes net positive due to adsorption of an excessive number of
positive 3-ions. The widely accepted theory of such charge inversion is based
on the idea that adsorbed at the macroion surface 3-ions form a two-dimensional
strongly correlated liquid which attracts excessive 3-ions by their negative
images (correlation holes). In the absence of 1:1 salt this theory reasonably
agrees with experiments and numerical simulations. However, the same theory
predicts that adding a large concentration of 1:1 salt increases the net
positive charge, while experiments and simulations show that the charge
decreases. In this paper we argue that the theory was aiming at the case of a
very large macroion surface charge and ignored the effect of the competing
attraction of 3-ion to its screening atmosphere in the bulk of the solution. We
show that for parameters of experiments and simulations this effect makes
charge inversion weak and extremely sensitive to screening by large
concentration of 1:1 salt. As a result charge inversion decreases with addition
of 1:1 salt in agreement with experiments and simulations. | cond-mat_soft |
Shear hardening in frictionless amorphous solids near the jamming
transition: The jamming transition, generally manifested by a rapid increase of rigidity
under compression (i.e., compression hardening), is ubiquitous in amorphous
materials. Here we study shear hardening in deeply annealed frictionless
packings generated by numerical simulations, reporting critical scalings absent
in compression hardening. We demonstrate that hardening is a natural
consequence of shear-induced memory destruction. Based on an elasticity theory,
we reveal two independent microscopic origins of shear hardening: (i) the
increase of the interaction bond number and (ii) the emergence of anisotropy
and long-range correlations in the orientations of bonds, the latter highlights
the essential difference between compression and shear hardening. Through the
establishment of physical laws specific to anisotropy, our work completes the
criticality and universality of jamming transition, and the elasticity theory
of amorphous solids. | cond-mat_soft |
Complex Transport Phenomena in a Simple Lattice Gas System: The transport phenomena of a nonequilibrium lattice gas system are
investigated. We consider a simple system that consists of two particles
interacting repulsively and the potential forces acting on these particles.
Under an external driving field applied to only one particle, we found the
following relation between the mean velocity of the driven particle and the
coefficient of effective drag of this particle under certain conditions; With
the increase in the mean velocity, the coefficient of effective drag varies in
the form, increase $\to$ decrease $\to$ increase $\to$ decrease. Moreover,
under other conditions, we found the following relations between these values
which show changes similar to those between shear rate and shear viscosity
observed in the shear-thickening polymer or colloidal suspensions; With the
increase in the mean velocity, the coefficient of effective drag varies in the
form, increase $\to$ decrease or decrease $\to$ increase $\to$ decrease. We
explain the mechanisms of such phenomena by considering the transition
diagrams. | cond-mat_soft |
Geometric order parameters derived from the Voronoi tessellation show
signatures of the jamming transition: A jammed packing of frictionless spheres at zero temperature is perfectly
specified by the network of contact forces from which mechanical properties can
be derived. However, we can alternatively consider a packing as a geometric
structure, characterized by a Voronoi tessellation which encodes the local
environment around each particle. We find that this local environment
characterizes systems both above and below jamming and changes markedly at the
transition. A variety of order parameters derived from this tessellation carry
signatures of the jamming transition, complete with scaling exponents.
Furthermore, we define a real space geometric correlation function which also
displays a signature of jamming. Taken together, these results demonstrate the
validity and usefulness of a purely geometric approach to jamming. | cond-mat_soft |
Conservation laws of an electro-active polymer: Ionic electro-active polymers (E.A.P.) is an active material consisting in a
polyelectrolyte (for example Nafion). Such material is usually used as thin
film sandwiched between two platinum electrodes. The polymer undergoes large
bending motions when an electric field is applied across the thickness.
Conversely, a voltage can be detected between both electrodes when the polymer
is suddenly bent. The solvent-saturated polymer is fully dissociated, releasing
cations of small size. We used a continuous medium approach. The material is
modelled by the coexistence of two phases; it can be considered as a porous
medium where the deformable solid phase is the polymer backbone with fixed
anions; the electrolyte phase is made of a solvent (usually water) with free
cations. The microscale conservation laws of mass, linear momentum and energy
and the Maxwell's equations are first written for each phase. The physical
quantities linked to the interfaces are deduced. The use of an average
technique applied to the two-phase medium finally leads to an Eulerian
formulation of the conservation laws of the complete material. Macroscale
equations relative to each phase provides exchanges through the interfaces. An
analysis of the balance equations of kinetic, potential and internal energy
highlights the 2 Mireille Tixier, Jo{\"e}l Pouget phenomena responsible of the
conversion of one kind of energy into another, especially the dissipative ones
: viscous frictions and Joule effect. | cond-mat_soft |
Speckle-visibility spectroscopy: A tool to study time-varying dynamics: We describe a multispeckle dynamic light scattering technique capable of
resolving the motion of scattering sites in cases that this motion changes
systematically with time. The method is based on the visibility of the speckle
pattern formed by the scattered light as detected by a single exposure of a
digital camera. Whereas previous multispeckle methods rely on correlations
between images, here the connection with scattering site dynamics is made more
simply in terms of the variance of intensity among the pixels of the camera for
the specified exposure duration. The essence is that the speckle pattern is
more visible, i.e. the variance of detected intensity levels is greater, when
the dynamics of the scattering site motion is slow compared to the exposure
time of the camera. The theory for analyzing the moments of the spatial
intensity distribution in terms of the electric field autocorrelation is
presented. It is demonstrated for two well-understood samples, a colloidal
suspension of Brownian particles and a coarsening foam, where the dynamics can
be treated as stationary. However, the method is particularly appropriate for
samples in which the dynamics vary with time, either slowly or rapidly, limited
only by the exposure time fidelity of the camera. Potential applications range
from soft-glassy materials, to granular avalanches, to flowmetry of living
tissue. | cond-mat_soft |
Effects of static and temporally fluctuating tensions on semiflexible
polymer looping: Biopolymer looping is a dynamic process that occurs ubiquitously in cells for
gene regulation, protein folding, etc. In cellular environments, biopolymers
are often subject to tensions which are either static, or temporally
fluctuating far away from equilibrium. We study the dynamics of semiflexible
polymer looping in the presence of such tensions by using Brownian dynamics
simulation combined with an analytical theory. We show a minute tension
dramatically changes the looping time, especially for long chains. Considering
a dichotomically flipping noise as a simple example of the nonequilibrium
tension, we find the phenomenon of resonant activation, where the looping time
can be the minimum at an optimal flipping time. We discuss our results in
connection with recent experiments. | cond-mat_soft |
Morphology Formation in Binary Mixtures upon Gradual Destabilisation: Spontaneous liquid-liquid phase separation is commonly understood in terms of
phenomenological mean-field theories. These theories correctly predict the
structural features of the fluid at sufficiently long time scales and
wavelengths. However, these conditions are not met in various examples in
biology and materials science where the mixture is slowly destabilised, and
phase separation takes place close to the critical point. Using kinetic Monte
Carlo and molecular dynamics simulations of a binary surface fluid under these
conditions, we show that the characteristic length scale of the emerging
structure decreases, in 2D, with the 4/15 dynamic critical exponent of the
quench rate rather than the mean-field 1/6th power. Hence, the dynamics of
cluster formation governed by thermodynamically undriven Brownian motion is
much more sensitive on the rate of destabilisation than expected from
mean-field theory. We discuss the expected implications of this finding to 3D
systems with ordering liquid crystals, as well as phase-separating passive or
active particles. | cond-mat_soft |
A Transition State Theory for Calculating Hopping Times and Diffusion in
Highly Confined Fluids: Monte Carlo simulation is used to study the dynamical crossover from single
file diffusion to normal diffusion in fluids confined to narrow channels. We
show that the long time diffusion coefficients for a series of systems
involving hard and soft interaction potentials can be described in terms of a
hopping time that measures the time it takes for a particle to escape the cage
formed by its neighbors in the pore. Free energy barriers for the particle
hopping process are calculated and used to show that transition state theory
effectively describes the hopping time for all the systems studied, over a
range of pore diameters. Our work suggests that the combination of hopping
times and transition state theory offers a useful and general framework to
describe the dynamics of these highly confined fluids. | cond-mat_soft |
There and back again: bridging meso- and nanoscales to understand lipid
vesicle patterning: We describe a complete methodology to bridge the scales between nanoscale
Molecular Dynamics and (micrometer) mesoscale Monte Carlo simulations in lipid
membranes and vesicles undergoing phase separation, in which curving molecular
species are furthermore embedded. To go from the molecular to the mesoscale, we
notably appeal to physical renormalization arguments enabling us to rigorously
infer the mesoscale interaction parameters from its molecular counterpart. We
also explain how to deal with the physical timescales at stake at the
mesoscale. Simulating the so-obtained mesoscale system enables us to
equilibrate the long wavelengths of the vesicles of interest, up to the vesicle
size. Conversely, we then backmap from the meso- to the nano- scale, which
enables us to equilibrate in turn the short wavelengths down to the molecular
length-scales. By applying our approach to the specific situation of the
patterning of a vesicle membrane, we show that macroscopic membranes can thus
be equilibrated at all length-scales in achievable computational time offering
an original strategy to address the fundamental challenge of time scale in
simulations of large bio-membrane systems. | cond-mat_soft |
Velocity profile of granular flows down a heap described by dimensional
analysis: Gravity-driven thick granular flows are relevant to many industrial and
geophysical processes. In particular, it is important to know and understand
the particle velocity distributions as we get deeper into the flow from the
free surface. In this paper, we use dimensional analysis as a tool to reproduce
the velocity profile experimentally reported for granular flows down a confined
heap for the so-called flowing layer and the creep layer underneath: the grains
velocity first decrease linearly from the free surface, and then exponentially. | cond-mat_soft |
Dipole-dipole correlations in the nematic phases of symmetric
cyanobiphenyl dimers and their binary mixtures with 5CB: We report on the temperature dependence of birefringence and of the static
dielectric permittivity tensor in a series of binary mixtures between the
symmetric, bent-shaped, 1",9"-bis(4-cyanobiphenyl-4'-yl) nonane (CB9CB) dimer
and the monomeric nematogen 5CB. In the studied composition range the mixtures
exhibit two nematic phases with distinct birefringence and dielectric features.
Birefringence measurements are used to estimate the temperature dependence of
the tilt between the axis defining the nanoscale helical modulation of the low
temperature nematic phase with the (local) direction of the maximal alignment
of the cyanobiphenyl units. Planar as well as magnetically and/or electrically
aligned samples are used to measure the perpendicular and parallel components
of the dielectric permittivity in both nematic phases. A self-consistent
molecular field theory that takes into account flexibility and symmetry of the
constituent mesogens is introduced for the calculation of order parameters and
intra-molecular orientational dipolar correlations of the flexible dimers as a
function of temperature/concentration. Utilising the tilt angle, as calculated
from the birefringence measurements, and the predictions of the molecular
theory, dielectric permittivity is modelled in the framework of the anisotropic
version of the Kirkwood-Frohlich theory. Using the inter-molecular Kirkwood
correlation factors as adjustable parameters, excellent agreement between
theory and permittivity measurements across the whole temperature range and
composition of the mixtures is obtained. The importance of the orientational,
intra- and inter-molecular, dipolar correlations, their relative impact on the
static dielectric properties, as well as their connection with the local
structure of the nematic phases of bent-shaped bimesogens, is discussed. | cond-mat_soft |
Asymmetric crystallization during cooling and heating in model
glass-forming systems: We perform molecular dynamics (MD) simulations of the crystallization process
in binary Lennard-Jones systems during heating and cooling to investigate
atomic-scale crystallization kinetics in glass-forming materials. For the
cooling protocol, we prepared equilibrated liquids above the liquidus
temperature $T_l$ and cooled each sample to zero temperature at rate $R_c$. For
the heating protocol, we first cooled equilibrated liquids to zero temperature
at rate $R_p$ and then heated the samples to temperature $T > T_l$ at rate
$R_h$. We measured the critical heating and cooling rates $R_h^*$ and $R_c^*$,
below which the systems begin to form a substantial fraction of crystalline
clusters during the heating and cooling protocols. We show that $R_h^* >
R_c^*$, and that the asymmetry ratio $R_h^*/R_c^*$ includes an intrinsic
contribution that increases with the glass-forming ability (GFA) of the system
and a preparation-rate dependent contribution that increases strongly as $R_p
\rightarrow R_c^*$ from above. We also show that the predictions from classical
nucleation theory (CNT) can qualitatively describe the dependence of the
asymmetry ratio on the GFA and preparation rate $R_p$ from the MD simulations
and results for the asymmetry ratio measured in Zr- and Au-based bulk metallic
glasses (BMG). This work emphasizes the need for and benefits of an improved
understanding of crystallization processes in BMGs and other glass-forming
systems. | cond-mat_soft |
Hydroanalysis of Animal Lysozymes c and Human Defensins a: Proteins appear to be the most dramatic natural example of self-organized
criticality (SOC), a concept that explains many otherwise apparently unlikely
phenomena. Protein functionality is dominated by long range
hydro(phobic/philic) interactions which both drive protein compaction and
mediate protein-protein interactions. In contrast to previous reductionist
short range hydrophobicity scales, the holistic Moret-Zebende hydrophobicity
scale represents a hydroanalytic tool that bioinformatically quantifies SOC in
a way fully compatible with evolution. Hydroprofiling identifies chemical
trends in the activities and substrate binding abilities of model enzymes and
antibiotic animal lysozymes c and antibiotic human defensins, which have been
the subject of tens of thousands of experimental studies. The analysis is
simple and easily performed, and immediately yields insights not obtainable by
traditional methods based on short-range real-space interactions, as described
either by classical force fields (CFF) used in molecular dynamics simulations
(MDS), or hydrophobicity scales based on transference energies from water to
organic solvents. | cond-mat_soft |
Capillary fracture of ultrasoft gels: heterogeneity and delayed
nucleation: A droplet of surfactant spreading on an ultrasoft ($E \lesssim 100$ Pa) gel
substrate will produce capillary fractures at the gel surface; these fractures
originate at the contact-line and propagate outwards in a starburst pattern.
There is an inherent variability in both the number of fractures formed and the
time delay before fractures form. In the regime where single fractures form, we
observe a Weibull-like distribution of delay times, consistent with a
thermally-activated process. The shape parameter is close to 1 for softer gels
(a Poisson process), and larger for stiffer gels (indicative of aging). For
single fractures, the characteristic delay time is primarily set by the
elastocapillary length of the system, calculated from the differential in
surface tension between the droplet and the substrate, rather than the elastic
modulus as for stiffer systems. For multiple fractures, all fractures appear
simultaneously and long delay times are suppressed. The delay time distribution
provides a new technique for probing the energy landscape and fracture
toughness of ultrasoft materials. | cond-mat_soft |
Velocity-driven frictional sliding: Coarsening and steady-state pulse
trains: Frictional sliding is an intrinsically complex phenomenon, emerging from the
interplay between driving forces, elasto-frictional instabilities, interfacial
nonlinearity and dissipation, material inertia and bulk geometry. We show that
homogeneous rate-and-state dependent frictional systems, driven at a prescribed
boundary velocity -- as opposed to a prescribed stress -- in a range where the
frictional interface is rate-weakening, generically host self-healing slip
pulses, a sliding mode not yet fully understood. Such velocity-driven
frictional systems are then shown to exhibit coarsening dynamics saturated at
the system length in the sliding direction, independently of the system's
height, leading to steadily propagating pulse trains. The latter may be viewed
as a propagating phase-separated state, where slip and stick characterize the
two phases. While pulse trains' periodicity is coarsening-limited by the
system's length, the single pulse width, characteristic slip velocity and
propagation speed exhibit rich properties, which are comprehensively understood
using theory and extensive numerics. Finally, we show that for sufficiently
small system heights, pulse trains are accompanied by periodic
elasto-frictional instabilities. | cond-mat_soft |
Water and Ice Dielectric Spectra Scaling at 0 °C: Dielectric spectra (10^4-10^11 Hz) of water and ice at 0 {\deg}C are
considered in terms of proton conductivity and compared to each other. In this
picture, the Debye relaxations, centered at 1/{\tau}_W ~ 20 GHz (in water) and
1/{\tau}_I ~ 5 kHz (in ice), are seen as manifestations of diffusion of
separated charges in the form of H3O+ and OH- ions. The charge separation
results from the self-dissociation of H2O molecules, and is accompanied by
recombination in order to maintain the equilibrium concentration, N. The charge
recombination is a diffusion-controlled process with characteristic lifetimes
of {\tau}_W and {\tau}_I, for water and ice respectively. The static
permittivity, {\epsilon}(0), is solely determined by N. Both, N and
{\epsilon}(0), are roughly constant at the water-ice phase transition, and both
increase, due to a slowing down of the diffusion rate, as the temperature is
lowered. The transformation of the broadband dielectric spectra at 0 {\deg}C
with the drastic change from {\tau}_W to {\tau}_I is mainly due to an abrupt
(by 0.4 eV) change of the activation energy of the charge diffusion. | cond-mat_soft |
Dynamics of collapsing and exploding Bose-Einstein condensed vortex
state: Using the time-dependent mean-field Gross-Pitaevskii equation we study the
dynamics of small repulsive Bose-Einstein condensed vortex states of ^{85}Rb
atoms in a cylindrical trap with low angular momentum hbar L per atom (L <= 6),
when the atomic interaction is suddenly turned attractive by manipulating the
external magnetic field near a Feshbach resonance. Consequently, the condensate
collapses and ejects atoms via explosion and a remnant condensate with a
smaller number of atoms emerges that survives for a long time. Detail of this
collapse and explosion is compared critically with a similar experiment
performed with zero angular momentum (L=0). Suggestion for future experiment
with vortex state is made. | cond-mat_soft |
Multiphase coexistence in polydisperse colloidal mixtures: We study the phase behavior of mixtures of monodisperse colloidal spheres
with a depletion agent which can have arbitrary shape and can possess a
polydisperse size or shape distribution. In the low concentration limit,
considered here, we can employ the free-volume theory and take the geometry of
particles of the depletion agent into account within the framework of
fundamental measure theory. We apply our approach to study the phase diagram of
a mixture of (monodisperse) colloidal spheres and two polydisperse polymer
components. By fine tuning the distribution of the polymer it is possible to
construct a complex phase diagram which exhibits two stable critical points. | cond-mat_soft |
Percolation in binary mixtures of linkers and particles: chaining {\it
{vs}} branching: Equilibrium gels of colloidal particles can be realized through the
introduction of a second species, a linker that mediates the bonds between the
colloids. A gel forming binary mixture whose linkers can self-assemble into
linear chains while still promoting the aggregation of particles is considered
in this work. The particles are patchy particles with $f_C$ patches of type $C$
and the linkers are patchy particles with $2$ patches of type $A$ and $f_B$
patches of type B. The bonds between patches of type $A$ ($AA$ bonds) promote
the formation of linear chains of linkers. Two different ways (model A and
model B) of bonding the linkers to the particles - or inducing branching - are
studied. In model A, there is a competition between chaining and branching,
since the bonding between linkers and particles is done through $AC$ bonds
only. In model B linkers aggregate to particles through bonds $BC$ only, making
chaining and branching independent. The percolation behaviour of these two
models is studied in detail, employing a generalized Flory-Stockmayer theory
and Monte Carlo simulations. The self-assembly of linkers into chains reduces
the fraction of particles needed for percolation to occur (models A and B) and
induces percolation when the fraction of particles is high (model B).
Percolation by heating and percolation loops in temperature composition
diagrams are obtained when the formation of chains is energetically favourable,
by increasing the entropic gain of branching (model A). Chaining and branching
are found to follow a model dependent relation at percolation, which shows
that, for the same composition, longer chains require less branching for
percolation to occur. | cond-mat_soft |
Grain refinement and partitioning of impurities in the grain boundaries
of a colloidal polycrystal: We study the crystallization of a colloidal model system in presence of
secondary nanoparticles acting as impurities. Using confocal microscopy, we
show that the nanoparticles segregate in the grain boundaries of the colloidal
polycrystal. We demonstrate that the texture of the polycrystal can be tuned by
varying independently the nanoparticle volume fraction and the crystallization
rate, and quantify our findings using standard models for the nucleation and
growth of crystalline materials. Remarkably, we find that the efficiency of the
segregation of the nanoparticles in the grain-boundaries is determined solely
by the typical size of the crystalline grains. | cond-mat_soft |
Morphological Transitions during Melting of Small Cylindrical Aggregates: Most studies on melting under confinement focus only on the solid and liquid
melt phases. Despite of its ubiquity, contributions from the capillary
interface (liquid / vapor interface) are often neglected. In this study the
melting behavior of small cylindrical aggregates in vapor attached to planar
surfaces is analyzed. For the assumed boundary conditions (cylindrical solid
with a non wetting top plane and a wettable side wall) solid and the liquid
phases can coexist within a certain temperature range. Due to capillary
instability, the liquid phase can form either an axisymmetric rouloid
morphology or, above a certain threshold liquid volume fraction, a bulge
coexisting with a rouloid-like section. The corresponding melting points are
different. The analysis explicitly describes the behavior of a real system of
small aggregates of long chain alkanes on planar substrates. It also gives
qualitative insights into the melting behavior of small aggregates with
anisotropic wetting behaviors in general. It reveals in particular how melting
points and melting pathways depend on the energetic respectively morphological
pathways leading to complete melting. | cond-mat_soft |
Local orientational mobility in regular hyperbranched polymers: We study the dynamics of local bond orientation in regular hyperbranched
polymers modeled by Vicsek fractals. The local dynamics is investigated through
the temporal autocorrelation functions of single bonds and the corresponding
relaxation forms of the complex dielectric susceptibility. We show that the
dynamic behavior of single segments depends on their remoteness from the
periphery rather than on the size of the whole macromolecule. Remarkably, the
dynamics of the core segments (which are most remote from the periphery) shows
a scaling behavior that differs from the dynamics obtained after structural
average. We analyze the most relevant processes of single segment motion and
provide an analytic approximation for the corresponding relaxation times.
Furthermore, we describe an iterative method to calculate the orientational
dynamics in the case of very large macromolecular sizes. | cond-mat_soft |
Surface Roughness and Hydrodynamic Boundary Conditions: We report results of investigations of a high-speed drainage of thin aqueous
films squeezed between randomly nanorough surfaces. A significant decrease in
hydrodynamic resistance force as compared with predicted by Taylor's equation
is observed. However, this reduction in force does not represents the slippage.
The measured force is exactly the same as that between equivalent smooth
surfaces obeying no-slip boundary conditions, but located at the intermediate
position between peaks and valleys of asperities. The shift in hydrodynamic
thickness is shown to be independent on the separation and/or shear rate. Our
results disagree with previous literature data reporting very large and
shear-dependent boundary slip for similar systems. | cond-mat_soft |
The role of correlations in the collective behaviour of microswimmer
suspensions: In this Letter, we study the collective behaviour of a large number of
self-propelled microswimmers immersed in a fluid. Using unprecedently
large-scale lattice Boltzmann simulations, we reproduce the transition to
bacterial turbulence. We show that, even well below the transition, swimmers
move in a correlated fashion that cannot be described by a mean-field approach.
We develop a novel kinetic theory that captures these correlations and is
non-perturbative in the swimmer density. To provide an experimentally
accessible measure of correlations, we calculate the diffusivity of passive
tracers and reveal its non-trivial density dependence. The theory is in
quantitative agreement with the lattice Boltzmann simulations and captures the
asymmetry between pusher and puller swimmers below the transition to
turbulence. | cond-mat_soft |
Molecular simulations of sliding on SDS surfactant films: We use molecular dynamics simulations to study the frictional response of the
anionic surfactant sodium dodecyl sulfate (SDS) monolayers and hemicylindrical
aggregates physisorbed on gold. Our simulations of a sliding spherical asperity
reveals two friction regimes: At low loads, the films show Amontons' friction
with a friction force that rises linearly with normal load. At high loads, the
friction force is independent of load as long as no direct solid-solid contact
occurs. The transition between these two regimes happens when only a single
molecular layer is confined in the gap between the sliding bodies. The friction
force at high loads on a monolayer rises monotonically with film density and
drops slightly with the transition to hemicylindrical aggregates. This
monotonous increase of friction force is compatible with a traditional plowing
model of sliding friction. At low loads, the friction coefficient reaches a
minimum at intermediate surface concentrations. We attribute this behavior to a
competition between adhesive forces, repulsion of the compressed film, and the
onset of plowing. | cond-mat_soft |
Characterization of the sub-micrometer hierarchy levels in the
twist-bend nematic phase with nanometric helices via photopolymerization.
Explanation for the sign reversal in the polar response: Photo-polymerization of a reactive mesogen mixed with a mesogenic dimer,
shown to exhibit the twist-bend nematic phase ($N_{TB}$), reveals the complex
structure of the self-deformation patterns observed in planar cells. The
polymerized reactive mesogen retains the structure formed by liquid crystalline
molecules in the twist bend phase, thus enabling observation by Scanning
Electron Microscope (SEM). Hierarchical ordering scales from tens of nanometers
to micrometers are imaged in detail. Submicron features, anticipated from
earlier X-ray experiments, are visualized directly. In the self-deformation
stripes formed in the $N_{TB}$ phase, the average director field is found
tilted in the cell plane by an angle of up to 45$^{\circ}$ from the cell
rubbing direction. This tilting explains the sign inversion being observed in
the electro-optical studies. | cond-mat_soft |
Condensed states of a semiflexible copolymer in poor solvent: Figures of
eight and discrete size torii: We examine the condensed states of a simple semiflexible copolymer in which
there are two monomer types that are immiscible with each other and with the
solvent. Although this is similar to the well known problem of collapse for a
semiflexible homopolymer we find that it gives rise to a much richer variety of
condensed states. We predict the existence of these states using simple
analytic arguments and also observe them directly using Brownian dynamics
simulations. | cond-mat_soft |
Topology mediated organization of E.coli chromosome in fast growth
conditions: Recent experiments have been able to visualise chromosome organization in
fast-growing E.coli cells. However, the mechanism underlying the
spatio-temporal organization remains poorly understood. We propose that the DNA
adopts a specific polymer topology as it goes through its cell cycle. We
establish that the emergent entropic forces between polymer segments of the
DNA-polymer with modified topology, leads to chromosome organization as seen
in-vivo. We employ computer simulations of a replicating bead spring model of a
polymer in a cylinder to investigate the problem. Our simulation of the
overlapping cell cycles not only show successful segregation, but also
reproduces the evolution of the spatial organization of the chromosomes as
observed in experiments. This manuscript in addition to our previous work on
slowly growing bacterial cells, shows that our topology-based model can explain
the organization of chromosomes in all growth conditions. | cond-mat_soft |
Gel-state nucleation in multilamellar vesicles of
dimyristoylphosphatidylcholine and its relation to the critical temperature:
A lattice model and microcalorimetry: Differential microcalorimetric measurements have been performed in aqueous
dispersions of dimyristoylphosphatidylcholine (DMPC) multilamellar vesicles in
a wide range of temperatures covering the whole transition between the lamellar
gel and lamellar fluid states (the chain-melting/ordering transition). The
shape of calorimetric curves was analyzed in a temperature range some distance
away but close to the chain-ordering transition point where small nuclei of gel
(solid state) are formed. In this range, where the fraction of the "new-state"
lipid is small, the nucleation process can be considered independent of the
interlayer interactions and determined mainly by the lateral interactions. The
small-scale nucleation was analyzed in terms of a two-dimensional Ising-like
lattice model. The gel-fluid contact energy related to the critical temperature
(in terms of Ising model) was estimated for DMPC studied here and
dipalmitoylphosphatidylcholine studied earlier. The contact energy was found to
be not high enough to provide the discontinuous, first-order character of
transition. Therefore, the signs of first-order character observed in the
vesicles made of these lipids are not due to lateral but rather interlayer
3D-interactions. The extrapolation to longer lipids shows that the transition
discontinuity inherent to a lipid layer (i.e., determined by the lateral
interactions themselves) is expected for the saturated phosphatidylcholines
having more than 16-18 C-atoms per chain. Interestingly, it is the saturated
chains of this length that are the most abundant in biological membranes.
Probably, the biological membrane "prefers" to be near the critical state where
the system is the most responsive to physical actions. | cond-mat_soft |
Controlling polymer translocation with crowded medium and polymer length
asymmetry: Polymer translocation in crowded environments is a ubiquitous phenomenon in
biological systems. We studied polymer translocation through a pore in free,
one-sided (asymmetric), and two-sided (symmetric) crowded environments.
Extensive Langevin dynamics simulation is employed to model the dynamics of the
flexible polymer and crowding particles. We studied how crowding size and
packing fraction play a crucial role in the translocation process. After
determining the standard scaling properties of the translocation probability,
time, and MSD, we observed that the translocation rate and bead velocities are
location-dependent as we move along the polymer backbone, even in a crowd-free
environment. Counter-intuitively, translocation rate and bead velocities showed
the opposite behavior; for example, middle monomers near the pore exhibit
maximum bead velocity and minimum translocation rate. Free energy calculation
for asymmetrically placed polymer indicates there exists a critical number of
segments that make the polymer to prefer the receiver side for translocation.
For one-sided crowding, we have identified a critical crowding size above which
there exists a non-zero probability to translocate into the crowding side
instead of the free side. Moreover, we have observed that shifting the polymer
towards the crowded side compensates for one-sided crowding, yielding an equal
probability akin to a crowder-free system. Under two-sided crowding, the
mechanism of how a slight variation in crowder size and packing fraction can
force a polymer to switch its translocation direction is proposed, which has
not been explored before. Using this control we achieved an equal translocation
probability like a crowd-free scenario. These conspicuous yet counter-intuitive
phenomena are rationalized by simple theoretical arguments based on osmotic
pressure and radial entropic forces. | cond-mat_soft |
Dynamic model and stationary shapes of fluid vesicles: A phase-field model that takes into account the bending energy of fluid
vesicles is presented. The Canham-Helfrich model is derived in the
sharp-interface limit. A dynamic equation for the phase-field has been solved
numerically to find stationary shapes of vesicles with different topologies and
the dynamic evolution towards them. The results are in agreement with those
found by minimization of the Canham-Helfrich free energy. This fact shows that
our phase-field model could be applied to more complex problems of
instabilities. | cond-mat_soft |
Contact-line pinning controls how quickly colloidal particles
equilibrate with liquid interfaces: Previous experiments have shown that spherical colloidal particles relax to
equilibrium slowly after they adsorb to a liquid-liquid interface, despite the
large interfacial energy gradient driving the adsorption. The slow relaxation
has been explained in terms of transient pinning and depinning of the contact
line on the surface of the particles. However, the nature of the pinning sites
has not been investigated in detail. We use digital holographic microscopy to
track a variety of colloidal spheres---inorganic and organic, charge-stabilized
and sterically stabilized, aqueous and non-aqueous---as they breach liquid
interfaces. We find that nearly all of these particles relax logarithmically in
time over timescales much larger than those expected from viscous dissipation
alone. By comparing our results to theoretical models of the pinning dynamics,
we infer the area per defect to be on the order of a few square nanometers for
each of the colloids we examine, whereas the energy per defect can vary from a
few $kT$ for non-aqueous and inorganic spheres to tens of $kT$ for aqueous
polymer particles. The results suggest that the likely pinning sites are
topographical features inherent to colloidal particles---surface roughness in
the case of silica particles and grafted polymer "hairs" in the case of polymer
particles. We conclude that the slow relaxation must be taken into account in
experiments and applications, such as Pickering emulsions, that involve
colloids attaching to interfaces. The effect is particularly important for
aqueous polymer particles, which pin the contact line strongly. | cond-mat_soft |
Shear induced drainage in foamy yield-stress fluids: Shear induced drainage of a foamy yield stress fluid is investigated using
MRI techniques. Whereas the yield stress of the interstitial fluid stabilizes
the system at rest, a fast drainage is observed when a horizontal shear is
imposed. It is shown that the sheared interstitial material behaves as a
viscous fluid in the direction of gravity, the effective viscosity of which is
controlled by shear in transient foam films between bubbles. Results provided
for several bubble sizes are not captured by the R^2 scaling classically
observed for liquid flow in particulate systems, such as foams and thus
constitute a remarkable demonstration of the strong coupling of drainage flow
and shear induced interstitial flow. Furthermore, foam films are found to be
responsible for the unexpected arrest of drainage, thus trapping irreversibly a
significant amount of interstitial liquid. | cond-mat_soft |
Local dielectric spectroscopy of near-surface glassy polymer dynamics: A non-contact scanning-probe-microscopy method was used to probe local
near-surface dielectric susceptibility and dielectric relaxation in
poly-vinyl-acetate (PVAc) near the glass transition. Dielectric spectra were
measured from 10-4 Hz to 102 Hz as a function of temperature. The measurements
probed a 20 nm thick layer below the free-surface of a bulk film. A small (4 K)
reduction in glass transition temperature and moderate narrowing of the
distribution of relaxation times was found. In contrast to results for
ultra-thin-films confined on or between metallic electrodes, no reduction in
the dielectric strength was found, inconsistent with the immobilization of
slower modes. | cond-mat_soft |
Second harmonic light scattering induced by defects in the twist-bend
nematic phase of liquid crystal dimers: The nematic twist-bend ($\mathrm{N_{TB}}$) phase, exhibited by certain
thermotropic liquid crystalline (LC) dimers, represents a new orientationally
ordered mesophase -- the first distinct nematic variant discovered in many
years. The $\mathrm{N_{TB}}$ phase is distinguished by a heliconical winding of
the average molecular long axis (director) with a remarkably short (nanoscale)
pitch and, in systems of achiral dimers, with an equal probability to form
right- and left-handed domains. The $\mathrm{N_{TB}}$ structure thus provides
another fascinating example of spontaneous chiral symmetry breaking in nature.
The order parameter driving the formation of the heliconical state has been
theoretically conjectured to be a polarization field, deriving from the bent
conformation of the dimers, that rotates helically with the same nanoscale
pitch as the director field. It therefore presents a significant challenge for
experimental detection. Here we report a second harmonic light scattering
(SHLS) study on two achiral, $\mathrm{N_{TB}}$-forming LCs, which is sensitive
to the polarization field due to micron-scale distortion of the helical
structure associated with naturally-occurring textural defects. These defects
are parabolic focal conics of smectic-like "pseudo-layers", defined by planes
of equivalent phase in a coarse-grained description of the $\mathrm{N_{TB}}$
state. Our SHLS data are explained by a coarse-grained free energy density that
combines a Landau-deGennes expansion of the polarization field, the elastic
energy of a nematic, and a linear coupling between the two. | cond-mat_soft |
Formation of molecules near a Feshbach resonance in a 1D optical lattice: We calculate the binding energy of two atoms interacting near a Feshbach
resonance in the presence of a 1D periodic potential. The critical value of the
scattering length needed to produce a molecule as well as the value of the
molecular binding energy in the unitarity limit of infinite scattering length
are calculated as a function of the intensity of the laser field generating the
periodic potential. The Bloch bandwidth and the effective mass of molecules are
shown to depend strongly on the value of the scattering length due to the
correlated motion of the two atoms. | cond-mat_soft |
Spontaneous Patterning of Confined Granular Rods: Vertically vibrated rod-shaped granular materials confined to quasi-2D
containers self organize into distinct patterns. We find, consistent with
theory and simulation, a density dependent isotropic-nematic transition. Along
the walls, rods interact sterically to form a wetting layer. For high rod
densities, complex patterns emerge as a result of competition between bulk and
boundary alignment. A continuum elastic energy accounting for nematic
distortion and local wall anchoring reproduces the structures seen
experimentally. | cond-mat_soft |
Physical processes causing the formation of penitentes: Snow penitentes form in sublimation conditions by differential ablation. Here
we investigate the physical processes at the initial stage of penitente growth
and perform the linear stability analysis of a flat surface submitted to the
solar heat flux. We show that these patterns do not simply result from the
self-illumination of the surface --a scale-free process-- but are primarily
controlled by vapor diffusion and heat conduction. The wavelength at which snow
penitentes emerge is derived and discussed. We found that it is controlled by
aerodynamic mixing of vapor above the ice surface. | cond-mat_soft |
Role of solvation in pressure-induced helix stabilization: In contrast to the well-known destabilization of globular proteins by high
pressure, re- cent work has shown that pressure stabilizes the formation of
isolated {\alpha}-helices. However all simulations to date have obtained a
qualitatively opposite result within the experimen- tal pressure range. We show
that using a protein force field (Amber03w) parametrized in conjunction with an
accurate water model (TIP4P/2005) recovers the correct pressure- dependence and
an overall stability diagram for helix formation similar to that from experi-
ment; on the other hand, we confirm that using TIP3P water results in a very
weak pressure destabilization of helices. By carefully analyzing the
contributing factors, we show that this is not merely a consequence of
different peptide conformations sampled using TIP3P. Rather, there is a
critical role for the solvent itself in determining the dependence of total
system volume (peptide and solvent) on helix content. Helical peptide
structures exclude a smaller volume to water, relative to non-helical
structures with both the water models, but the total system volume for helical
conformations is higher than non-helical conformations with TIP3P water at low
to intermediate pressures, in contrast to TIP4P/2005 water. Our results further
emphasize the importance of using an accurate water model to study protein
folding under conditions away from standard temperature and pressure. | cond-mat_soft |
Monte Carlo Simulation of a Model of Water: We simulate TIP3P water using a constrained Monte Carlo algorithm to generate
electrostatic interactions eliminating the need to sum over long ranged Coulomb
interactions. We study discretization errors when interpolating charges using
splines and Gaussians. We compare our implementation to molecular dynamics and
Brownian dynamics codes. | cond-mat_soft |
Microparticle transport networks with holographic optical tweezers and
cavitation bubbles: Optical transport networks for active absorbing microparticles are made with
holographic optical tweezers. The particles are powered by the optical
potentials that make the network and transport themselves via random vapor
propelled hops to different traps without the requirement for external forces
or microfabricated barriers. The geometries explored for the optical traps are
square lattices, circular arrays and random arrays. The degree distribution for
the connections or possible paths between the traps are localized like in the
case of random networks. The commute times to travel across $n$ different traps
scale as $n^2$, in agreement with random walks on connected networks. Once a
particle travels the network, others are attracted as a result of the vapor
explosions. | cond-mat_soft |
Dynamics of short polymer chains in solution: We present numerical and analytical results describing the effect of
hydrodynamic interactions on the dynamics of a short polymer chain in solution.
A molecular dynamics algorithm for the polymer is coupled to a direct
simulation Monte Carlo algorithm for the solvent. We give an explicit
expression for the velocity autocorrelation function of the centre of mass of
the polymer which agrees well with numerical results if Brownian dynamics,
hydrodynamic correlations and sound wave scattering are included. | cond-mat_soft |
Lees-Edwards boundary conditions for lattice Boltzmann: Lees Edwards boundary conditions (LEbc) for Molecular Dynamics simulations
are an extension of the well known periodic boundary conditions and allow the
simulation of bulk systems in a simple shear flow. We show how the idea of LEbc
can be implemented in lattice Boltzmann simulations and how LEbc can be used to
overcome the problem of a maxinum shear rate that is limited to less than 1/Ly
(with Ly the transverse system size) in traditional lattice Boltzmann
implementations of shear flow. | cond-mat_soft |
Probing the degree of heterogeneity within a shear band of a model glass: Recent experiments provide evidence for density variations along shear bands
(SB) in metallic glasses with a length scale of a few hundreds nanometers. Via
molecular dynamics simulations of a generic binary glass model, here we show
that this is strongly correlated with variations of composition, coordination
number, viscosity and heat generation. Individual shear events along the
SB-path show a mean distance of a few nanometers, comparable to recent
experimental findings on medium range order. The aforementioned variations
result from these localized perturbations, mediated by elasticity. | cond-mat_soft |
Magnetoelastic instability in soft thin films: Ferromagnetic particles are incorporated in a thin soft elastic matrix. A
lamella, made of this smart material, is studied experimentally and modeled. We
show herein that thin films can be actuated using an external magnetic field
applied through the system. The system is found to be switchable since
subcritical pitchfork bifurcation is discovered in the beam shape when the
magnetic field orientation is modified. Strong magnetoelastic effects can be
obtained depending on both field strength and orientation. Our results provide
versatile ways to contribute to many applications from the microfabrication of
actuators to soft robotics. As an example, we created a small synthetic octopus
piloted by an external magnetic field. | cond-mat_soft |
Relaxation times, rheology, and finite size effects: We carry out overdamped simulations in a simple model of jamming - a
collection of bi-disperse soft core frictionless disks in two dimensions - with
the aim to explore the finite size dependence of different quantities, both the
relaxation time obtained from the relaxation of the energy and the
pressure-equivalent of the shear viscosity. The motivation for the paper is the
observation [Nishikawa et al., J. Stat. Phys, 182, 37 (2021)] that there are
finite size effects in the relaxation time, $\tau$, that give problems in the
determination of the critical divergence, and the claim that this is due to a
finite size dependence, $\tau\sim\ln N$, which makes $\tau$ an ill-defined
quantity. Beside analyses to determine the relaxation time for the whole system
we determine particle relaxation times which allow us to determine both
histograms of particle relaxation times and the average particle relaxation
times - two quantities that are very useful for the analyses. The starting
configurations for the relaxation simulations are of two different kinds:
completely random or taken from steady shearing simulations, and we find that
the difference between these two cases are bigger than previously noted and
that the observed problems in the determination of the critical divergence
obtained when starting from random configurations are not present when instead
starting the relaxations from shearing configurations. We also argue that the
the effect that causes the $\ln N$-dependence is not as problematic as
asserted. When it comes to the finite size dependence of the
pressure-equivalent of the shear viscosity we find that our data don't give
support for the claimed strong finite size dependence, but also that it is at
odds with what one would normally expect for a system with a diverging
correlation length, and that this calls for a novel understanding of the
phenomenon of shear-driven jamming. | cond-mat_soft |
Sorting and separation of microparticles by surface properties using
liquid crystal-enabled electro-osmosis: Sorting and separation of microparticles is a challenging problem of
interdisciplinary nature. Existing technologies can differentiate
microparticles by their bulk properties, such as size, density, electric
polarizability, etc. The next level of challenge is to separate particles that
show identical bulk properties and differ only in subtle surface features, such
as functionalization with ligands. In this work, we propose a technique to sort
and separate particles and fluid droplets that differ in surface properties. As
a dispersive medium, we use a nematic liquid crystal (LC) rather than an
isotropic fluid, which allows us to amplify the difference in surface
properties through distinct perturbations of LC order around the dispersed
particles. The particles are placed in a LC cell with spatially distorted
molecular orientation subject to an alternating current electric field. The
gradients of the molecular orientation perform two functions. First, elastic
interactions between these pre-imposed gradients and distortions around the
particles separate the particles with different surface properties in space.
Second, these pre-imposed patterns create electro-osmotic flows powered by the
electric field that transport the sorted particles to different locations thus
separating them. The demonstrated unique sorting and separation capability
opens opportunities in lab-on-a-chip, cell sorting and bio-sensing
applications. | cond-mat_soft |
Observation of a uniaxial ferroelectric smectic A phase: We report the smectic $A_F$, a new liquid crystal phase of the ferroelectric
nematic realm. The smectic $A_F$ is a phase of small polar, rod-shaped
molecules which form two-dimensional fluid layers spaced by approximately the
mean molecular length. The phase is uniaxial, with the molecular director, the
local average long-axis orientation, normal to the layer planes, and
ferroelectric, with a spontaneous electric polarization parallel to the
director. Polarization measurements indicate almost complete polar ordering of
the $\sim 10$ Debye longitudinal molecular dipoles, and hysteretic polarization
reversal with a coercive field of about $2 \times 10^5$ V/m is observed. The
smectic $A_F$ phase appears upon cooling in two binary mixtures of partially
fluorinated mesogens: 2N/DIO, exhibiting a nematic ($N$) -- smectic $Z_A$
(Sm$Z_A$) -- ferroelectric nematic ($N_F$) -- smectic $A_F$ (Sm$A_F$) phase
sequence; and 7N/DIO, exhibiting an $N$ -- Sm$Z_A$ -- Sm$A_F$ phase sequence.
The latter presents an opportunity to study a transition between two smectic
phases having orthogonal systems of layers. | cond-mat_soft |
Complex coacervation: A field theoretic simulation study of
polyelectrolyte complexation: Using the complex Langevin sampling strategy, field theoretic simulations are
performed to study the equilibrium phase behavior and structure of symmetric
polycation-polyanion mixtures without salt in good solvents. Static structure
factors for the segment density and charge density are calculated and used to
study the role of fluctuations in the electrostatic and chemical potential
fields beyond the random phase approximation. We specifically focus on the role
of charge density and molecular weight on the structure and complexation
behavior of polycation-polyanion solutions. A demixing phase transition to form
a ``complex coacervate'' is observed in strongly charged systems, and the
corresponding spinodal and binodal boundaries of the phase diagram are
investigated. | cond-mat_soft |
Softly Constrained Films: The shape of materials is often subject to a number of geometric constraints
that limit the size of the system or fix the structure of its boundary. In soft
and biological materials, however, these constraints are not always hard, but
are due to other physical mechanisms that affect the overall force balance. A
capillary film spanning a flexible piece of wire or a cell anchored to a
compliant substrate by mean of adhesive contacts are examples of these softly
constrained systems in the macroscopic and microscopic world. In this article I
review some of the important mathematical and physical developments that
contributed to our understanding of shape formation in softly constrained films
and their recent application to the mechanics of adherent cells. | cond-mat_soft |
Casimir force between two substrates within three different layers using
the scattering approach: We compute the Casimir force for a system composed of two layers as
substrates within three different homogenous layers. We use the scattering
approach along with the Matsubara formalism in order to calculate the Casimir
force at finite temperature. We impose the appropriate boundary condition on
the tangential components of the electric and magnetic fields to construct the
reflection matrices. Our calculation is simple such that one can extend it to
systems containing inhomogeneous layers as good candidates for designing
nanomachines. We find that the Casimir force is proportional to L^(-5) where L
is the thickness of the inner layer. | cond-mat_soft |
Steady-State Homogeneous Nucleation and Growth of Water Droplets:
Extended Numerical Treatment: The steady-state homogeneous vapor-to-liquid nucleation and the succeeding
liquid droplet growth process are studied for water system by means of the
coarse-grained molecular dynamics simulations with the mW-model suggested
originally in [Molinero, V.; Moore, E. B. \textit{J. Phys. Chem. B}
\textbf{2009}, \textit{113}, 4008-4016]. The investigation covers the
temperature range $273 \leq T/K \leq 363$ and the system's pressure $p\simeq 1$
atm. The thermodynamic integration scheme and the extended mean first passage
time method as a tool to find the nucleation and cluster growth characteristics
are applied. The surface tension is numerically estimated and is compared with
the experimental data for the considered temperature range. We extract the
nucleation characteristics such as the steady-state nucleation rate, the
critical cluster size, the nucleation barrier, the Zeldovich factor; perform
the comparison with the other simulation results and test the treatment of the
simulation results within the classical nucleation theory. We found that the
liquid droplet growth is unsteady and follows the power law. At that, the
growth laws exhibit the features unified for all the considered temperatures.
The geometry of the nucleated droplets is also studied. | cond-mat_soft |
Polymer packaging and ejection in viral capsids: shape matters: We use a mesoscale simulation approach to explore the impact of different
capsid geometries on the packaging and ejection dynamics of polymers of
different flexibility. We find that both packing and ejection times are faster
for flexible polymers. For such polymers a sphere packs more quickly and ejects
more slowly than an ellipsoid. For semiflexible polymers, however, the case
relevant to DNA, a sphere both packs and ejects more easily. We interpret our
results by considering both the thermodynamics and the relaxational dynamics of
the polymers. The predictions could be tested with bio-mimetic experiments with
synthetic polymers inside artificial vesicles. Our results suggest that phages
may have evolved to be roughly spherical in shape to optimise the speed of
genome ejection, which is the first stage in infection. | cond-mat_soft |
Adsorption of a random heteropolymer with self-interactions onto an
interface: We consider the adsorption of a random heteropolymer onto an interface within
the model by Garel et al. [1] by taking into account self-interactions between
the monomers. Within the replica trick and by using a self-consistent
preaveraging procedure we map the adsorption problem onto the problem of
binding state of a quantum mechanical Hamiltonian. The analysis of the latter
is treated within the variational method based on the 2-nd Legendre transform.
We have found that self-interactions favor the localization. The effect is
intensified with decrease of the temperature. Within a model without taking
into account the repulsive ternary monomer-monomer interactions we predict a
reentrant localization transition for large values of the asymmetry of the
heteropolymer and at low enough temperatures. | cond-mat_soft |
Cavity nucleation in single-component homogeneous amorphous solids under
negative pressure: Understanding the cavity formation and cavity growth mechanisms in solids has
fundamental and applied importance for the correct determination of their
exploitation capabilities and mechanical characteristics. In this work, we
present the molecular dynamics simulation results for the process of
homogeneous formation of nanosized cavities in a single-component amorphous
metallic alloy. To identify cavities of various shapes and sizes, an original
method has been developed, which is based on filling cavities by virtual
particles (balls) of the same diameter. By means of the mean first-passage time
analysis, it was shown that the cavity formation in an amorphous metallic melt
is the activation-type process. This process can be described in terms of the
classical nucleation theory, which is usually applied to the case of first
order phase transitions. Activation energy, critical size and nucleation rate
of cavities are calculated, the values of which are comparable with those for
the case of crystal nucleation in amorphous systems. | cond-mat_soft |
Propagating Density Spikes in Light-Powered Motility-Ratchets: Combining experiments and computer simulations, we use a spatially periodic
and flashing light-field to direct the motion of phototactic active colloids.
Here, the colloids self-organize into a density spike pattern, which resembles
a shock wave and propagates over long distances, almost without dispersing. The
underlying mechanism involves a synchronization of the colloids with the
light-field, so that particles see the same intensity gradient each time the
light-pattern is switched on, but no gradient in between (for example). This
creates a pulsating transport whose strength and direction can be controlled
via the flashing protocol and the self-propulsion speed of the colloids. Our
results might be useful for drug delivery applications and can be used to
segregate active colloids by their speed. | cond-mat_soft |
Magic angles and cross-hatching instability in hydrogel fracture: The full 2D analysis of roughness profiles of fracture surfaces resulting
from quasi-static crack propagation in gelatin gels reveals an original
behavior characterized by (i) strong anisotropy with maximum roughness at
$V$-independent symmetry-preserving angles, (ii) a sub-critical instability
leading, below a critical velocity, to a cross-hatched regime due to straight
macrosteps drifting at the same magic angles and nucleated on crack-pinning
network inhomogeneities. Step height values are determined by the width of the
strain-hardened zone, governed by the elastic crack blunting characteristic of
soft solids with breaking stresses much larger that low strain moduli. | cond-mat_soft |
Collective dynamics of soft active particles: We present a model of soft active particles that leads to a rich array of
collective behavior found also in dense biological swarms of bacteria and other
unicellular organisms. Our model uses only local interactions, such as
Vicsek-type nearest neighbor alignment, short-range repulsion, and a local
boundary term. Changing the relative strength of these interactions leads to
migrating swarms, rotating swarms and jammed swarms, as well as swarms that
exhibit run-and-tumble motion, alternating between migration and either
rotating or jammed states. Interestingly, although a migrating swarm moves
slower than an individual particle, the diffusion constant can be up to three
orders of magnitude larger, suggesting that collective motion can be highly
advantageous, for example, when searching for food. | cond-mat_soft |
Craters Formed in Granular Beds by Impinging Jets of Gas: When a jet of gas impinges vertically on a granular bed and forms a crater,
the grains may be moved by several different mechanisms: viscous erosion,
diffused gas eruption, bearing capacity failure, and/or diffusion-driven
shearing. The relative importance of these mechanisms depends upon the flow
regime of the gas, the mechanical state of the granular material, and other
physical parameters. Here we report research in two specific regimes: viscous
erosion forming scour holes as a function of particle size and gravity; and
bearing capacity failure forming deep transient craters as a function of soil
compaction. | cond-mat_soft |
Crack Formation in the Presence of an Electric Field in Droplets of
Laponite Gel: When a colloidal gel dries through evaporation, cracks are usually formed,
which often reveal underlying processes at work during desiccation. Desiccating
colloid droplets of few hundred $\mu l$ size show interesting effects of
pattern formation and cracking which makes this an active subject of current
research. Since aqueous gels of clay are known to be strongly affected by an
electric field, one may expect crack patterns to exhibit a field effect. In the
present study we allow droplets of laponite gel to dry under a radial electric
field. This gives rise to highly reproducible patterns of cracks, which depend
on the strength, direction and time of exposure to the electric field. For a
continuously applied DC voltage, cracks always appear on dissipation of a
certain constant amount of energy. If the field is switched off before cracks
appear, the observed results are shown to obey a number of empirical scaling
relations, which enable us to predict the time of appearance and the number of
cracks under specified conditions. | cond-mat_soft |
Investigating the influence of particle size and shape on froth
flotation based benefication of lithium-rich minerals in slags: The demand for lithium, as well as other critical resources, needed for
electrochemical energy storage is expected to grow significantly in the future.
Slags obtained from pyrometallurgical recycling represent a promising resource
of valuable materials, among them lithium and rare earth elements found in
artificial minerals particulate phases. This study investigates the flotation
separation of engineered artificial minerals (EnAMs) in slags, such as lithium
aluminate and gehlenite as valuable and gangue phases, respectively. Flotation
experiments are carried out in a Partridge-Smith cell using oleic acid (OA) as
a benchmark surfactant. Particle characterization is performed using SEM-based
Mineral Liberation Analysis (MLA), which provides particle discrete
information. From this information, bivariate Tromp functions based on
non-parametric kernel density estimation are computed to characterize the
separation behavior with respect to particle descriptors. This approach enables
investigating the influence of particle size and shape on separation behavior
of EnAMs. Furthermore, these results allow for the optimization of flotation
experiments for enriching Li-bearing EnAMs. | cond-mat_soft |
Casimir Torques between Anisotropic Boundaries in Nematic Liquid
Crystals: Fluctuation-induced interactions between anisotropic objects immersed in a
nematic liquid crystal are shown to depend on the relative orientation of these
objects. The resulting long-range ``Casimir'' torques are explicitely
calculated for a simple geometry where elastic effects are absent. Our study
generalizes previous discussions restricted to the case of isotropic walls, and
leads to new proposals for experimental tests of Casimir forces and torques in
nematics. | cond-mat_soft |
Active interaction switching controls the dynamic heterogeneity of soft
colloidal dispersions: We employ Reactive Dynamical Density Functional Theory (R-DDFT) and Reactive
Brownian Dynamics (R-BD) simulations to investigate the dynamics of a
suspension of active soft Gaussian colloids with binary interaction switching,
i.e., a one-component colloidal system in which every particle stochastically
switches at predefined rates between two interaction states with different
mobility. Using R-DDFT we extend a theory previously developed to access the
dynamics of inhomogeneous liquids to study the influence of the switching
activity on the self and distinct part of the Van Hove function in bulk
solution, and determine the corresponding mean squared displacement of the
switching particles. Our results demonstrate that, even though the average
diffusion coefficient is not affected by the switching activity, it
significantly modifies the non-equilibrium dynamics and diffusion coefficients
of the individual particles, leading to a crossover from short to long times,
with a regime for intermediate times showing anomalous diffusion. In addition,
the self-part of the van Hove function has a Gaussian form at short and long
times, but becomes non-Gaussian at intermediates ones, having a crossover
between short and large displacements. The corresponding self-intermediate
scattering function shows the two-step relaxation patters typically observed in
soft materials with heterogeneous dynamics such as glasses and gels. We also
introduce a phenomenological Continuous Time Random Walk (CTRW) theory to
understand the heterogeneous diffusion of this system. R-DDFT results are in
excellent agreement with R-BD simulations and the analytical predictions of
CTRW theory, thus confirming that R-DDFT constitutes a powerful method to
investigate not only the structure and phase behavior, but also the dynamical
properties of non-equilibrium active switching colloidal suspensions. | cond-mat_soft |
Network evolution controlling strain-induced damage and self-healing of
elastomers with dynamic bonds: Highly stretchable and self-healable supramolecular elastomers are promising
materials for future soft electronics, biomimetic systems, and smart textiles,
due to their dynamic cross-linking bonds. The dynamic or reversible nature of
the cross-links gives rise to interesting macroscopic responses in these
materials such as self-healing and rapid stress-relaxation. However, the
relationship between bond activity and macroscopic mechanical response, and the
self-healing properties of these dynamic polymer networks (DPNs) remains poorly
understood. Using coarse-grained molecular dynamics (CGMD) simulations, we
reveal a fundamental connection between the macroscopic behaviors of DPNs and
the shortest paths between distant nodes in the polymer network. Notably, the
trajectories of the material on the shortest path-strain map provide key
insights into understanding the stress-strain hysteresis, anisotropy, stress
relaxation, and self-healing of DPNs. Based on CGMD simulations under various
loading histories, we formulate a set of empirical rules that dictate how the
shortest path interacts with stress and strain. This lays the foundation for
the development of a physics-based theory centered around the non-local
microstructural feature of shortest paths to predict the mechanical behavior of
DPNs. | cond-mat_soft |
Packing of softly repulsive particles in a spherical box - a generalised
Thomson problem: We study the (near or close to) ground state distribution of N softly
repelling particles trapped in the interior of a spherical box. The charges
mutually interact via an inverse power law potential of the form $1/r^\gamma$.
We study three regimes in which the charges form an single spherical shell at
the edge of the box ($\gamma=1$), a series of concentric shells of increasing
density ($\gamma=2$) and $\gamma=12$ for which the charges form shells with a
more uniform charge distribution. We conduct numerical simulations for clusters
containing up to 5000 charges and compare charge density across the system with
continuum limit results. The agreement between numerical (discrete) results and
the continuum limit is found to improve with increasing N. | cond-mat_soft |
Computational Pipeline to probe NaV1.7 gain-of-functions variants in
neuropathic painful syndromes: Applications of machine learning and graph theory techniques to neuroscience
have witnessed an increased interest in the last decade due to the large data
availability and unprecedented technology developments. Their employment to
investigate the effect of mutational changes in genes encoding for proteins
modulating the membrane of excitable cells, whose biological correlates are
assessed at electrophysiological level, could provide useful predictive clues.
We apply this concept to the analysis of variants in sodium channel NaV1.7
subunit found in patients with chronic painful syndromes, by the implementation
of a dedicated computational pipeline empowering different and complementary
techniques including homology modeling, network theory, and machine learning.
By testing three templates of different origin and sequence identities, we
provide an optimal condition for its use. Our findings reveal the usefulness of
our computational pipeline in supporting the selection of candidates for cell
electrophysiology assay and with potential clinical applications. | cond-mat_soft |
Morphology Selection of Nanoparticle Dispersions by Polymer Media: Designable media can control properties of nanocomposite materials by
spatially organizing nanoparticles. Here we theoretically study particle
organization by ultrathin polymer films of grafted chains (``brushes'').
Polymer-soluble nanoparticles smaller than a brush-determined threshold
disperse in the film to a depth scaling inversely with particle volume. In the
polymer-insoluble case, aggregation is directed: provided particles are
non-wetting at the film surface, the brush stabilizes the dispersion and
selects its final morphology of giant elongated aggregates with a
brush-selected width. | cond-mat_soft |
Arrest of three-dimensional gravity-confined shear flow of wet granular
matter: We study the arrest of three-dimensional flow in wet granular matter subject
to a sinusoidal external force and a gravitational field confining the flow in
the vertical direction. The minimal strength of the external force that is
required to keep the system in motion is determined by considering the balance
of injected and dissipated power. This provides a prediction whose excellent
quality is demonstrated by a data collapse for an extensive set of event-driven
molecular dynamics simulations where we varied the system size, particle
number, the energy dissipated upon rupturing capillary bridges, and the bridge
length where rupture occurs. The three parameters of the theoretical prediction
all lie within narrow margins of theoretical estimates. | cond-mat_soft |
Distinct signature of two local structural motifs of liquid water in the
scattering function: Liquids generally become more ordered upon cooling. However, it has been a
long-standing debate on whether such structural ordering in liquid water takes
place continuously or discontinuosly: continuum vs. mixture models. Here, by
computer simulations of three popular water models and analysis of recent
scattering experiment data, we show that, in the structure factor of water,
there are two overlapped peaks hidden in the apparent "first diffraction peak",
one of which corresponds to the neighboring O-O distance as in ordinary liquids
and the other to the longest periodicity of density waves in a tetrahedral
structure. This unambiguously proves the coexistence of two local structural
motifs. Our findings not only provide key clues to settle long-standing
controversy on the water structure but also allow experimental access to the
degree and range of structural ordering in liquid water. | cond-mat_soft |
Lateral depletion effect on two-dimensional ordering of
bacteriorhodopsins in a lipid bilayer: A theoretical study based on a binary
hard-disk model: The two-dimensional ordering of bacteriorhodopsins in a lipid bilayer was
studied using a binary hard-disk model. The phase diagrams were calculated,
taking into account the lateral depletion effects. The critical concentrations
of the protein ordering for the monomers and the trimers were obtained from the
phase diagrams. The critical concentration ratio agreed well with the
experiment when the repulsive core interaction between the depletants, namely
the lipids, was taken into account. The results suggest that the depletion
effect plays an important role in the association behaviors of transmembrane
proteins. | cond-mat_soft |
Role of interfacial elasticity for the rheological properties of
saponin-stabilized emulsions: Hypothesis Saponins are natural surfactants which can provide highly
viscoelastic interfaces. This property can be used to quantify precisely the
effect of interfacial dilatational elasticity on the various rheological
properties of bulk emulsions. Experiments We measured the interfacial
dilatational elasticity of adsorption layers from four saponins (Quillaja,
Escin, Berry, Tea) adsorbed on hexadecane-water and sunflower oil-water
interfaces. In parallel, the rheological properties under steady and
oscillatory shear deformations were measured for bulk emulsions, stabilized by
the same saponins (oil volume fraction between 75 and 85 %). Findings Quillaja
saponin and Berry saponin formed solid adsorption layers (shells) on the
SFO-water interface. As a consequence, the respective emulsions contained
non-spherical drops. For the other systems, the interfacial elasticities varied
between 2 mN/m and 500 mN/m. We found that this interfacial elasticity has very
significant impact on the emulsion shear elasticity, moderate effect on the
dynamic yield stress, and no effect on the viscous stress of the respective
steadily sheared emulsions. The last conclusion is not trivial, because the
dilatational surface elasticity is known to have strong impact on the viscous
stress of steadily sheared foams. Mechanistic explanations of all observed
effects are described. | cond-mat_soft |
Capillary Forces on a Small Particle at a Liquid-Vapor Interface: Theory
and Simulation: We study the meniscus on the outside of a small spherical particle with
radius $R$ at a liquid-vapor interface. The liquid is confined in a cylindrical
container with a finite radius $L$ and has a contact angle $\pi/2$ at the
container surface. The center of the particle is placed at various heights
along the central axis of the container. By varying $L$, we are able to
systematically study the crossover of the meniscus from nanometer to
macroscopic scales. The meniscus rise or depression on the particle is found to
grow as $\ln (2L/R)$ when $R\ll L\ll \kappa^{-1}$ with $\kappa^{-1}$ being the
capillary length and saturate to a value predicted by the Derjaguin-James
formula when $R \ll \kappa^{-1} \ll L$. The capillary force on the particle
exhibits a linear dependence on the particle's displacement from its
equilibrium position at the interface when the displacement is small. The
associated spring constant is found to be $2\pi\gamma\ln^{-1} (2L/R)$ for $L\ll
\kappa^{-1}$ and saturates to $2\pi\gamma\ln^{-1} (3.7\kappa^{-1}/R)$ for $L\gg
\kappa^{-1}$. At nanometer scales, we perform molecular dynamics simulations of
the described geometry and the results agree well with the predictions of the
macroscopic theory of capillarity. At micrometer to macroscopic scales,
comparison to experiments by Anachkov \textit{et al.} [Soft Matter {\bf 12},
7632 (2016)] shows that the finite span of a liquid-vapor or liquid-liquid
interface needs to be considered to interpret experimental data collected with
$L \sim \kappa^{-1}$. | cond-mat_soft |
Proposition of extension of models relating rheological quantities and
microscopic structure through the use of a double fractal structure: Colloidal suspensions and the relation between their rheology and their
microstructure is investigated. The literature showed great evidence of the
relation between rheological quantities and particle volume fraction, ignoring
the influence of the cluster. We propose to extend previous models using a new
double fractal structure which allows, first, to recover the well-known models
on the case of percolated system and, second, to capture the influence of the
cluster size. This new model emphasises the necessity of such structure to
account for recent experimental results. Then, the model is compared with data
coming from the literature and shows close agreement. | cond-mat_soft |
Conformation of a Polyelectrolyte Complexed to a Like-Charged Colloid: We report results from a molecular dynamics (MD) simulation on the
conformations of a long flexible polyelectrolyte complexed to a charged sphere,
\textit{both negatively charged}, in the presence of neutralizing counterions
in the strong Coulomb coupling regime. The structure of this complex is very
sensitive to the charge density of the polyelectrolyte. For a fully charged
polyelectrolyte the polymer forms a dense two-dimensional "disk", whereas for a
partially charged polyelectrolyte the monomers are spread over the colloidal
surface. A mechanism involving the \textit{overcharging} of the polyelectrolyte
by counterions is proposed to explain the observed conformations. | cond-mat_soft |
Phase Separation of Rigid-Rod Suspensions in Shear Flow: We analyze the behavior of a suspension of rigid rod-like particles in shear
flow using a modified version of the Doi model, and construct diagrams for
phase coexistence under conditions of constant imposed stress and constant
imposed strain rate, among paranematic, flow-aligning nematic, and log-rolling
nematic states. We calculate the effective constitutive relations that would be
measured through the regime of phase separation into shear bands. We calculate
phase coexistence by examining the stability of interfacial steady states and
find a wide range of possible ``phase'' behaviors. | cond-mat_soft |
Lift and drag forces on an inclined plow moving over a granular surface: We studied the drag and lift forces acting on an inclined plate while it is
dragged on the surface of a granular media, both in experiment and numerical
simulation. In particular, we investigated the influence of the horizontal
velocity of the plate and its angle of attack. We show that a steady wedge of
grains is moved in front of the plow and that the lift and drag forces are
proportional to the weight of this wedge. These constants of proportionality
vary with the angle of attack but not (or only weakly) on the velocity. We
found a universal effective friction law which accounts for the dependence on
all the above-mentioned parameters. The stress and velocity fields are
calculated from the numerical simulations and show the existence of a shear
band under the wedge and that the pressure is non-hydrostatic. The strongest
gradients in stress and shear occur at the base of the plow where the
dissipation rate is therefore highest. | cond-mat_soft |
Shapes of Semiflexible Polymers in Confined Spaces: We investigate the conformations of a semiflexible polymer confined to a
square box. Results of Monte Carlo simulations show the existence of a shape
transition when the persistence length of the polymer becomes comparable to the
dimensions of box. An order parameter is introduced to quantify this behavior.
A simple mean-field model is constructed to study the effect of the shape
transition on the effective persistence length of the polymer. | cond-mat_soft |
Fluctuation-dissipation relations and energy landscape in an
out-of-equilibrium strong glass-forming liquid: We study the out-of-equilibrium dynamics following a temperature-jump in a
model for a strong liquid, BKS-silica, and compare it with the well known case
of fragile liquids. We calculate the fluctuation-dissipation relation, from
which it is possible to estimate an effective temperature $T_{eff}$ associated
to the slow out-of-equilibrium structural degrees of freedom. We find the
striking and unexplained result that, differently from the fragile liquid
cases, $T_{eff}$ is smaller than the bath temperature. | cond-mat_soft |
A soft-lithographed chaotic electrokinetic micromixer for efficient
chemical reactions in lab-on-chips: Mixing is one of the basic functions which automated lab-on-chips require for
the effective management of liquid samples. In this paper we report on the
working principle, design, fabrication and experimental characterization of a
soft-lithographed micromixer for microfluidic applications. The device
effectively mixes two liquids by means of chaotic advection obtained as an
implementation of a Linked Twisted Map (LTM). In this sense it is chaotic. The
liquids are electrokinetically displaced by generating rolls through AC
electroosmosis on co-planar electrodes. The device performance has been tested
on dyed DI-water for several voltages, frequencies and flow-rates, displaying
good mixing properties in the range of $10 \div 100$kHz, at low peak-to-peak
voltages ($\sim15 \div 20$ volts). Low voltage supply, small dimensions and
possibility of fabrication via standard lithographic techniques make the device
highly integrable in lab-on-a-chip platforms. | cond-mat_soft |
Anisotropic pair correlations in binary and multicomponent hard-sphere
mixtures in the vicinity of a hard wall: A combined density functional theory
and simulation study: The fundamental measure approach to classical density functional theory has
been shown to be a powerful tool to predict various thermodynamic properties of
hard-sphere systems. We employ this approach to determine not only one-particle
densities but also two-particle correlations in binary and six-component
mixtures of hard spheres in the vicinity of a hard wall. The broken isotropy
enables us to carefully test a large variety of theoretically predicted
two-particle features by quantitatively comparing them to the results of
Brownian dynamics simulations. Specifically, we determine and compare the
one-particle density, the total correlation functions, their contact values,
and the force distributions acting on a particle. For this purpose, we follow
the compressibility route and theoretically calculate the direct correlation
functions by taking functional derivatives. We usually observe an excellent
agreement between theory and simulations, except for small deviations in cases
where local crystal-like order sets in. Our results set the course for further
investigations on the consistency of functionals as well as for structural
analysis on, e.g., the primitive model. In addition, we demonstrate that due to
the suppression of local crystallization, the predictions of six-component
mixtures are better than those in bidisperse or monodisperse systems. Finally,
we are confident that our results of the structural modulations induced by the
wall lead to a deeper understanding of ordering in anisotropic systems in
general, the onset of heterogeneous crystallization, caging effects, and glassy
dynamics close to a wall, as well as structural properties in systems with
confinement. | 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 |
Theory of Ideal Four-Wave Mixing in Bose-Einstein Condensates: Starting from a second-quantized Hamiltonian of many-particle systems, we
derive the Gross-Pitaevskii (GP) equation in momentum space, which is suitable
for studying the multi-wave mixing processes of coherent matter waves. The
coupling equations are then applied to study ideal four-wave mixing (4WM), in
which only four waves with definite wavevectors are involved. Some interesting
problems of 4WM, such as the phase-matching condition, the collapse and revival
behaviour, the effects of relative phase difference, and the conversion
efficiency are discussed in detail. We also show that the main characters of
recent 4WM experiment [Deng et al, Nature 398, 218 (1999)] can be undersood in
the present simplified model. | cond-mat_soft |
Euler-Poincaré approaches to nematodynamics: Nematodynamics is the orientation dynamics of flowless liquid-crystals. We
show how Euler-Poincar\'e reduction produces a unifying framework for various
theories, including Ericksen-Leslie, Luhiller-Rey, and Eringen's micropolar
theory. In particular, we show that these theories are all compatible with each
other and some of them allow for more general configurations involving a non
vanishing discination density. All results are also extended to flowing liquid
crystals. | cond-mat_soft |
Wetting on Random Roughness: the Ubiquity of Wenzel Prewetting: The wetting properties of solid substrates with macroscopic random roughness
are considered as a function of the microscopic contact angle of the wetting
liquid and its partial pressure in the surrounding gas phase. It is shown that
Wenzel prewetting, which has been recently predicted for a rather wide class of
roughness profiles derived from Gaussian random processes by a general
distortion procedure, should in fact be ubiquitous and prevail under even much
milder conditions. The well-known transition occurring at Wenzel's angle is
accompanied by a prewetting transition, at which a jump in the adsorbed liquid
volume occurs. This should be present on most surfaces bearing homogeneous,
isotropic random roughness. | cond-mat_soft |
New criteria for cluster identification in continuum systems: Two new criteria, that involve the microscopic dynamics of the system, are
proposed for the identification of clusters in continuum systems. The first one
considers a residence time in the definition of the bond between pairs of
particles, whereas the second one uses a life time in the definition of an
aggregate. Because of the qualitative features of the clusters yielded by the
criteria we call them chemical and physical clusters, respectively. Molecular
dynamics results for a Lennard-Jones system and general connectivity theories
are presented. | cond-mat_soft |
Fermi level quantum numbers and secondary gap of conducting carbon
nanotubes: For the single-wall carbon nanotubes conducting in the simplest tight binding
model, the complete set of line group symmetry based quantum numbers for the
bands crossing at Fermi level are given. Besides linear (k), helical (k'} and
angular momenta, emerging from roto-translational symmetries, the parities of U
axis and (in the zig-zag and armchair cases only) mirror planes appear in the
assignation. The helical and angular momentum quantum numbers of the crossing
bands never vanishes, what supports proposed chirality of currents. Except for
the armchair tubes, the crossing bands have the same quantum numbers and,
according to the non-crossing rule, a secondary gap arises, as it is shown by
the accurate tight-binding calculation. In the armchair case the different
vertical mirror parity of the crossing bands provides substantial conductivity,
though kF is slightly decreased. | cond-mat_soft |
Aggregation and structural phase transitions of semiflexible polymer
bundles: a braided circuit topology approach: We present a braided circuit topology framework for investigating topology
and structural phase transitions in aggregates of semiflexible polymers. In the
conventional approach to circuit topology, which specifically applies to single
isolated folded linear chains, the number and arrangement of contacts within
the circuitry of a folded chain give rise to increasingly complex fold
topologies. Another avenue for achieving complexity is through the interaction
and entanglement of two or more folded linear chains. The braided circuit
topology approach describes the topology of such multiple-chain systems and
offers topological measures such as writhe, complexity, braid length, and
isotopy class. This extension of circuit topology to multichains reveals the
interplay between collapse, aggregation, and entanglement. In this work, we
show that circuit topological motif fractions are ideally suited order
parameters to characterise structural phase transitions in entangled systems
that can detect structural re-ordering other measures cannot. | cond-mat_soft |
Monitoring spatially heterogeneous dynamics in a drying colloidal thin
film: We report on a new type of experiment that enables us to monitor spatially
and temporally heterogeneous dynamic properties in complex fluids. Our approach
is based on the analysis of near-field speckles produced by light diffusely
reflected from the superficial volume of a strongly scattering medium. By
periodic modulation of an incident speckle beam we obtain pixel-wise ensemble
averages of the structure function coefficient, a measure of the dynamic
activity. To illustrate the application of our approach we follow the different
stages in the drying process of a colloidal thin film. We show that we can
access ensemble averaged dynamic properties on length scales as small as ten
micrometers over the full field of view. | cond-mat_soft |
Rubber friction on (apparently) smooth lubricated surfaces: We study rubber sliding friction on hard lubricated surfaces. We show that
even if the hard surface appears smooth to the naked eye, it may exhibit short
wavelength roughness, which may give the dominant contribution to rubber
friction. That is, the observed sliding friction is mainly due to the
viscoelastic deformations of the rubber by the substrate surface asperities.
The presented results are of great importance for rubber sealing and other
rubber applications involving (apparently) smooth surfaces. | cond-mat_soft |
Mechanisms in the size segregation of a binary granular mixture: A granular mixture of particles of two sizes that is shaken vertically will
in most cases segregate. If the larger particles accumulate at the top of the
sample, this is called the Brazil-nut effect (BNE); if they accumulate at the
bottom, the reverse Brazil-nut effect (RBNE). While this process is of great
industrial importance in the handling of bulk solids, it is not well
understood. In recent years ten different mechanisms have been suggested to
explain when each type of segregation is observed. However, the dependence of
the mechanisms on driving conditions and material parameters and hence their
relative importance is largely unknown. In this paper we present experiments
and simulations where both types of particles are made from the same material
and shaken under low air pressure, which reduces the number of mechanisms to be
considered to seven. We observe both BNE and RBNE by varying systematically the
driving frequency and amplitude, diameter ratio, ratio of total volume of small
to large particles, and overall sample volume. All our results can be explained
by a combination of three mechanisms: a geometrical mechanism called void
filling, transport of particles in sidewall-driven convection rolls, and
thermal diffusion, a mechanism predicted by kinetic theory. | cond-mat_soft |
Importance of Metastable States in the Free Energy Landscapes of
Polypeptide Chains: We show that the interplay between excluded volume effects, hydrophobicity,
and hydrogen bonding of a tube-like representation of a polypeptide chain gives
rise to free energy landscapes that exhibit a small number of metastable minima
corresponding to common structural motifs observed in proteins. The complexity
of the landscape increases only moderately with the length of the chain.
Analysis of the temperature dependence of these landscapes reveals that the
stability of specific metastable states is maximal at a temperature close to
the mid-point of folding. These mestastable states are therefore likely to be
of particular significance in determining the generic tendency of proteins to
aggregate into potentially pathogenic agents. | cond-mat_soft |
Are granular materials simple? An experimental study of strain gradient
effects and localization: Experiments test the dependence of shearing stress on the first two gradients
of shear strain. The tests were conducted by direct numerical simulation using
the Discrete Element Method (DEM) on a large two-dimensional (2D) assembly of
circular disks. The assembly was coerced into non-uniformly deformed shapes by
applying body forces to the material region. The tests show that shearing
stress is affected by both the first and second gradients of shear strain, and
the measured responses to strain and its gradients are all incrementally
non-linear. The dilation rate is unaffected by strain gradients. Particle
rotations, although highly erratic, are, on average, consistent with the
mean-field rotation and unaffected by strain gradients. In independent
unconstrained tests, the material was sheared without body forces so that
localization could freely occur. Three localization patterns were observed:
microbands at very small strains; non-persistent shear bands at moderate
strains; and persistent bands at large strains. The observed features of
microbands and shear bands are consistent with the measured influences of
shearing strain and its first two derivatives. | cond-mat_soft |
Large-scale kinetic roughening behavior of coffee-ring fronts: We have studied the kinetic roughening behavior of the fronts of coffee-ring
aggregates via extensive numerical simulations of the off-lattice model
considered for this context in [C.\ S.\ Dias {\it et al.}, Soft Matter {\bf
14}, 1903 (2018)]. This model describes ballistic aggregation of patchy
colloids and depends on a parameter $r_\mathrm{AB}$ which controls the affinity
of the two patches, A and B. Suitable boundary conditions allow us to elucidate
a discontinuous pinning-depinning transition at $r_\mathrm{AB}=0$, with the
front displaying intrinsic anomalous scaling, but with unusual exponent values
$\alpha \simeq 1.2$, $\alpha_{\rm loc} \simeq 0.5$, $\beta\simeq 1$, and
$z\simeq 1.2$. For $0<r_\mathrm{AB}\le 1$, comparison with simulations of
standard off-lattice ballistic deposition indicates the occurrence of a
morphological instability induced by the patch structure. As a result, we find
that the asymptotic morphological behavior is dominated by macroscopic shapes.
The intermediate time regime exhibits one-dimensional KPZ exponents for
$r_\mathrm{AB}> 0.01$ and the system suffers a strong crossover dominated by
the $r_\mathrm{AB}=0$ behavior for $r_\mathrm{AB}\le 0.01$. A detailed analysis
of correlation functions shows that the aggregate fronts are always in the
moving phase for $0<r_\mathrm{AB}\le 1$ and that their kinetic roughening
behavior is intrinsically anomalous for $r_\mathrm{AB}\le 0.01$. | cond-mat_soft |
Supramolecule Structure for Amphiphilic Molecule by Dissipative Particle
Dynamics Simulation: Meso-scale simulation of structure formation for AB-dimers in solution W
monomers was performed by dissipative particle dynamics (DPD) algorithm. As a
simulation model, modified Jury Model was adopted Jury, S. et al. "Simulation
of amphiphilic mesophases using dissipative particle dynamics," Phys. Chem.
Chem. Phys. vol.1(1999) pp. 2051-2056, which represents mechanics of
self-assembly for surfactant hexaethylene glycol dodecyl ether (C12E6) and
water(H2 O). The same phase diagram as Jury's result was obtained. We also
found that it takes a longer time to form the hexagonal phase (H1) than to form
the lamellar phase (Lalpha). | cond-mat_soft |
The topological effect on the Mechanical properties of polymer knots: The mechanical properties of polymer knots under stretching in a bad or good
solvent are investigated by applying a given force $F$ to a point of the knot
while keeping another point fixed. The Monte Carlo sampling of the polymer
conformations on a simple cubic lattice is performed using a variant of the
Wang-Landau algorithm. The results of the calculations of the specific energy,
specific heat capacity and gyration radius for several knot topologies show a
general trend in the behavior of short polymer knots with lengths up to seventy
lattice units. At low tensile force $F$, knots can be found either in a compact
or an extended phase, depending if the temperature is low or high. At any
temperature, with increasing values of the force $F$, a polymer knot undergoes
a phase transition to a stretched state. This transition is characterized by a
strong peak in the heat capacity. There is also a minor peak, which corresponds
to a transition occurring at low temperatures when the conformations of
polymers in the stretched phase become swollen with increasing temperatures. It
is also shown that the behavior of short polymer rings is strongly influenced
by topological effects. The limitations in the number of accessible energy
states due to topological constraints is particularly evident in knots of small
size and such that their minimum number of crossing according to the Rolfsen
knot table is high. An example is provided by a cinquefoil knot $5_1$ with a
length of only fifty lattice units. The thermal and mechanical properties of
knots that can be represented with diagrams having the same minimum number of
crossings, are very similar. The size effects on the behavior of polymer knots
have been analyzed too. Surprisingly, it is found that topological effects fade
out very fast with increasing polymer length. | cond-mat_soft |
Tsallis Entropy and the transition to scaling in fragmentation: By using the maximum entropy principle with Tsallis entropy we obtain a
fragment size distribution function which undergoes a transition to scaling.
This distribution function reduces to those obtained by other authors using
Shannon entropy. The treatment is easily generalisable to any process of
fractioning with suitable constraints. | cond-mat_soft |
Energy Spectrum of Vortex Tangle: The energy spectrum of superfluid turbulence in the absence of the normal
fluid is studied numerically. In order to discuss the statistical properties,
we calculated the energy spectra of the 3D velocity field induced by dilute and
dense vortex tangles respectively, whose dynamics is calculated by the
Biot-Savart law. In the case of a dense tangle, the slope of the energy
spectrum is changed at $k=2\pi/l$, where $l$ is the intervortex spacing. For
$k>2\pi/l$, the energy spectrum has $k^{-1}$ behavior in the same manner as the
dilute vortex tangle, while otherwise the slope of the energy spectrum deviates
from $k^{-1}$ behavior. We compare the behavior for $k<2\pi/l$ with the
Kolmogorov law. | cond-mat_soft |
Properties of aqueous electrolyte solutions at carbon electrodes:
effects of concentration and surface charge on solution structure, ion
clustering and thermodynamics in the electric double layer: Surfaces are able to control physical-chemical processes in multi-component
solution systems and, as such, find application in a wide range of
technological devices. Understanding the structure, dynamics and thermodynamics
of non-ideal solutions at surfaces, however, is particularly challenging. Here,
we use Constant Chemical Potential Molecular Dynamics simulations to gain
insight into aqueous NaCl solutions in contact with graphite surfaces at high
concentrations and under the effect of applied surface charges: conditions
where mean-field theories describing interfaces cannot (typically) be reliably
applied. We discover an asymmetric effect of surface charge on the electric
double layer structure and resulting thermodynamic properties, which can be
explained by considering the affinity of the surface for cations and anions and
the cooperative adsorption of ions that occurs at higher concentrations. We
characterise how the sign of the surface charge affects ion densities and water
structure in the double layer and how the capacitance of the interface - a
function of the electric potential drop across the double layer - is largely
insensitive to the bulk solution concentration. Notably, we find that
negatively charged graphite surfaces induce an increase in the size and
concentration of extended liquid-like ion clusters confined to the double
layer. Finally, we discuss how concentration and surface charge affect the
activity coefficients of ions and water at the interface, demonstrating how
electric fields in this region should be explicitly considered when
characterising the thermodynamics of both solute and solvent at the
solid/liquid interface. | cond-mat_soft |
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