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European Physical Journal. E, Soft Matter

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https://www.readbyqxmd.com/read/29774472/uncooked-spaghetti-in-a-colander-injection-of-semiflexible-polymers-in-a-nanopore
#1
Thomas Auger, Loïc Auvray, Jean-Marc Di Meglio, Fabien Montel
We study the flow injection of semiflexible polymers in a nanopore with a diameter smaller than the persistence length of the macromolecules. The suction model from de Gennes and Brochard is modified to take into account the effect of the rigidity of the polymer in the Odijk regime. We show that in this case of extreme confinement the flow threshold vanishes slowly and that in the limit of infinitely small nanopore the free energy barrier eventually disappears.
May 17, 2018: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29774433/dynamic-and-thermodynamic-crossover-scenarios-in-the-kob-andersen-mixture-insights-from-multi-cpu-and-multi-gpu-simulations
#2
Daniele Coslovich, Misaki Ozawa, Walter Kob
The physical behavior of glass-forming liquids presents complex features of both dynamic and thermodynamic nature. Some studies indicate the presence of thermodynamic anomalies and of crossovers in the dynamic properties, but their origin and degree of universality is difficult to assess. Moreover, conventional simulations are barely able to cover the range of temperatures at which these crossovers usually occur. To address these issues, we simulate the Kob-Andersen Lennard-Jones mixture using efficient protocols based on multi-CPU and multi-GPU parallel tempering...
May 17, 2018: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29766348/simulating-squirmers-with-multiparticle-collision-dynamics
#3
Andreas Zöttl, Holger Stark
Multiparticle collision dynamics is a modern coarse-grained simulation technique to treat the hydrodynamics of Newtonian fluids by solving the Navier-Stokes equations. Naturally, it also includes thermal noise. Initially it has been applied extensively to spherical colloids or bead-spring polymers immersed in a fluid. Here, we review and discuss the use of multiparticle collision dynamics for studying the motion of spherical model microswimmers called squirmers moving in viscous fluids.
May 15, 2018: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29748868/how-to-simulate-patchy-particles-%C3%A2
#4
Lorenzo Rovigatti, John Russo, Flavio Romano
Patchy particles is the name given to a large class of systems of mesoscopic particles characterized by a repulsive core and a discrete number of short-range and highly directional interaction sites. Numerical simulations have contributed significantly to our understanding of the behaviour of patchy particles, but, although simple in principle, advanced simulation techniques are often required to sample the low temperatures and long time-scales associated with their self-assembly behaviour. In this work we review the most popular simulation techniques that have been used to study patchy particles, with a special focus on Monte Carlo methods...
May 14, 2018: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29748867/time-delay-induced-dynamical-behaviors-for-an-ecological-vegetation-growth-system-driven-by-cross-correlated-multiplicative-and-additive-noises
#5
Kang-Kang Wang, Hui Ye, Ya-Jun Wang, Sheng-Hong Li
In this paper, the modified potential function, the stationary probability distribution function (SPDF), the mean growth time and the mean degeneration time for a vegetation growth system with time delay are investigated, where the vegetation system is assumed to be disturbed by cross-correlated multiplicative and additive noises. The results reveal some fact that the multiplicative and additive noises can both reduce the stability and speed up the decline of the vegetation system, while the strength of the noise correlation and time delay can both enhance the stability of the vegetation and slow down the depression process of the ecological system...
May 14, 2018: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29748865/dynamics-of-a-polyelectrolyte-through-aerolysin-channel-as-a-function-of-applied-voltage-and-concentration-%C3%A2
#6
Manuela Pastoriza-Gallego, Bénédicte Thiébot, Laurent Bacri, Loïc Auvray, Juan Pelta
We describe the behaviour of a polyelectrolyte in confined geometry. The transport of a polyelectrolyte, dextran sulfate, through a recombinant protein channel, aerolysin, inserted into a planar lipid bilayer is studied as a function of applied voltage and polyelectrolyte concentration and chain length. The aerolysin pore has a weak geometry asymmetry, a high number of charged residues and the polyelectrolyte is strongly negatively charged. The resulting current blockades were characterized by short and long dwelling times...
May 11, 2018: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29748779/coarse-grained-simulation-of-dna-using-lammps-an-implementation-of-the-oxdna-model-and-its-applications
#7
Oliver Henrich, Yair Augusto Gutiérrez Fosado, Tine Curk, Thomas E Ouldridge
During the last decade coarse-grained nucleotide models have emerged that allow us to study DNA and RNA on unprecedented time and length scales. Among them is oxDNA, a coarse-grained, sequence-specific model that captures the hybridisation transition of DNA and many structural properties of single- and double-stranded DNA. oxDNA was previously only available as standalone software, but has now been implemented into the popular LAMMPS molecular dynamics code. This article describes the new implementation and analyses its parallel performance...
May 10, 2018: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29730809/effect-of-an-insoluble-surfactant-on-the-dynamics-of-a-thin-liquid-film-flowing-over-a-non-uniformly-heated-substrate
#8
Ashna Srivastava, Naveen Tiwari
The stability analysis of a gravity-driven thin liquid film with an insoluble surfactant flowing over a surface with embedded, regularly spaced heaters is investigated. At the leading edge of a heater, the presence of a temperature gradient induces an opposing Marangoni stress at the interface leading to the formation of a capillary ridge. This ridge has been shown to be susceptible to thermocapillary (oscillating in the flow direction) and rivulet (spanwise periodic pattern) instabilities. The presence of an insoluble surfactant is shown to have a stabilizing effect on this system...
May 7, 2018: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29700690/structural-dynamical-transition-in-the-wahnstr%C3%A3-m-mixture
#9
Francesco Turci, Thomas Speck, C Patrick Royall
In trajectory space, dynamical heterogeneities in glass-forming liquids correspond to the emergence of a dynamical phase transition between an active phase poor in local structure and an inactive phase which is rich in local structure. We support this scenario with the study of a model additive mixture of Lennard-Jones particles, quantifying how the choice of the relevant structural and dynamical observable affects the transition in trajectory space. We find that the low mobility, structure-rich phase is dominated by icosahedral order...
April 26, 2018: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29700630/tumorcode-a-framework-to-simulate-vascularized-tumors
#10
Thierry Fredrich, Michael Welter, Heiko Rieger
During the past years our group published several articles using computer simulations to address the complex interaction of tumors and the vasculature as underlying transport network. Advances in imaging and lab techniques pushed in vitro research of tumor spheroids forward and animal models as well as clinical studies provided more insights to single processes taking part in tumor growth, however, an overall picture is still missing. Computer simulations are a non-invasive option to cumulate current knowledge and form a quasi in vivo system...
April 26, 2018: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29679175/numerical-simulation-of-wind-sand-movement-in-the-reversed-flow-region-of-a-sand-dune-with-a-bridge-built-downstream
#11
Wei He, Ning Huang, Bin Xu, Wenbo Wang
A bridge built inside the reversed flow region of a sand dune will change the characteristics of wind-sand movement in this region. The Reynolds-averaged Navier-Stokes simulation and discrete particle tracing are used to simulate the wind-sand movement around a sand dune with a bridge built inside the reversed region. Three cases with different bridge positions are studied. The results show that 1) compared with the isolated dune case, a tall bridge built at the leeward toe leads to an increase in the deposition rate on the leeward slope and a longer reversed flow region downstream of the sand dune; meanwhile, the high speed of crosswind on the bridge indicates that some measures should be taken to protect trains from strong crosswind; 2) a low bridge at the leeward toe has little effect on the sand deposition and reversed flow region of the dune; however, low sand transport rate and crosswind speed on the bridge show that anti-crosswind/sand measures should be taken according to the actual situation and 3) a low bridge on the leeward slope has little effect on the length of reversed flow region, however, high crosswind speed and sand flux on the bridge reveal the need of anti-crosswind/sand measures on the bridge...
April 23, 2018: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29675633/vapor-nucleation-paths-in-lyophobic-nanopores
#12
Antonio Tinti, Alberto Giacomello, Carlo Massimo Casciola
In recent years, technologies revolving around the use of lyophobic nanopores gained considerable attention in both fundamental and applied research. Owing to the enormous internal surface area, heterogeneous lyophobic systems (HLS), constituted by a nanoporous lyophobic material and a non-wetting liquid, are promising candidates for the efficient storage or dissipation of mechanical energy. These diverse applications both rely on the forced intrusion and extrusion of the non-wetting liquid inside the pores; the behavior of HLS for storage or dissipation depends on the hysteresis between these two processes, which, in turn, are determined by the microscopic details of the system...
April 19, 2018: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29651630/speeding-up-monte-carlo-simulation-of-patchy-hard-cylinders
#13
Alberto Giacomo Orellana, Emanuele Romani, Cristiano De Michele
The hard cylinder model decorated with attractive patches proved to be very useful recently in studying physical properties of several colloidal systems. Phase diagram, elastic constants and cholesteric properties obtained from computer simulations based on a simple hard cylinder model have been all successfully and quantitatively compared to experimental results. Key to these simulations is an efficient algorithm to check the overlap between hard cylinders. Here, we propose two algorithms to check the hard cylinder overlap and we assess their efficiency through a comparison with an existing method available in the literature and with the well-established algorithm for simulating hard spherocylinders...
April 16, 2018: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29644548/rheology-of-granular-materials-composed-of-crushable-particles
#14
Duc-Hanh Nguyen, Émilien Azéma, Philippe Sornay, Farhang Radjaï
We investigate sheared granular materials composed of crushable particles by means of contact dynamics simulations and the bonded-cell model for particle breakage. Each particle is paved by irregular cells interacting via cohesive forces. In each simulation, the ratio of the internal cohesion of particles to the confining pressure, the relative cohesion, is kept constant and the packing is subjected to biaxial shearing. The particles can break into two or more fragments when the internal cohesive forces are overcome by the action of compressive force chains between particles...
April 11, 2018: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29626264/active-particle-condensation-by-non-reciprocal-and-time-delayed-interactions
#15
Mihir Durve, Arnab Saha, Ahmed Sayeed
We consider the flocking of self-propelling agents in two dimensions, each of which communicates with its neighbors within a limited vision-cone. Also, the communication occurs with some time-delay. The communication among the agents are modeled by Vicsek rules. In this study we explore the combined effect of non-reciprocal interaction (induced by limited vision-cone) among the agents and the presence of delay in the interactions on the dynamical pattern formation within the flock. We find that under these two influences, without any position-based attractive interactions or confining boundaries, the agents can spontaneously condense into "drops"...
April 9, 2018: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29619671/time-irreversibility-in-reversible-shell-models-of-turbulence
#16
Massimo De Pietro, Luca Biferale, Guido Boffetta, Massimo Cencini
Turbulent flows governed by the Navier-Stokes equations (NSE) generate an out-of-equilibrium time irreversible energy cascade from large to small scales. In the NSE, the energy transfer is due to the nonlinear terms that are formally symmetric under time reversal. As for the dissipative term: first, it explicitly breaks time reversibility; second, it produces a small-scale sink for the energy transfer that remains effective even in the limit of vanishing viscosity. As a result, it is not clear how to disentangle the time irreversibility originating from the non-equilibrium energy cascade from the explicit time-reversal symmetry breaking due to the viscous term...
April 6, 2018: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29616416/jurin-s-law-revisited-exact-meniscus-shape-and-column-height
#17
Sai Liu, Shanpeng Li, Jianlin Liu
Capillary rise of a liquid column is a historical problem, which has normally been formulated by Jurin's law. In the present study, we investigate the exact solutions of the column height, considering the real shape of the meniscus according to the Young-Laplace equation. The analytical solution in the planar model and the numerical solution in the axisymmetric model on the meniscus shape are both given, which are compared with the results from Jurin's law, modified Jurin's law and Surface Evolver simulation...
March 30, 2018: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29616355/vertical-structure-of-the-velocity-field-induced-by-mode-i-and-mode-ii-solitary-waves-in-a-stratified-fluid
#18
Oxana Kurkina, Ekaterina Rouvinskaya, Andrey Kurkin, Ayrat Giniyatullin, Efim Pelinovsky
The structure of the velocity field induced by internal solitary waves of the first and second modes is determined. The contribution from second-order terms in asymptotic expansion into the horizontal velocity is estimated for the models of almost two- and three-layer fluid for solitons of positive and negative polarity. The influence of the nonlinear correction manifests itself firstly in the shape of the lines of zero horizontal velocity: they are curved and the shape depends on the soliton amplitude and polarity, while for the leading-order wave field they are horizontal...
March 30, 2018: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29589210/the-effect-of-flow-on-viscoelastic-emulsion-microstructure
#19
Valentina Preziosi, Antonio Perazzo, Giovanna Tomaiuolo, Stefano Guido
Emulsions made of oil, water and surfactants are widespread soft materials with complex structures depending on composition and temperature. Emulsion phase behavior at rest has been widely investigated but flow-induced effects, which are very relevant in many applications, can still be further explored towards improved emulsion microstructural design. In this work, we use low energy emulsification processing to create small-sized emulsions. In a previous report, we showed the emulsion morphology development and the effect of flow on the microstructure of a highly viscoelastic attractive emulsion which result in a concentrated nanoemulsion after viscoelastic droplet filaments are disrupted...
March 29, 2018: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29589130/the-tension-of-framed-membranes-from-computer-simulations
#20
Daniel Hamkens, Claus Jeppesen, John H Ipsen
We have analyzed the behavior of a randomly triangulated, self-avoiding surface model of a flexible, fluid membrane subject to a circular boundary by Wang-Landau Monte Carlo computer simulation techniques. The dependence of the canonical free energy and frame tension on the frame area is obtained for flexible membranes. It is shown that for low bending rigidities the framed membrane is only stable above a threshold tension, suggesting a discontinuous transition from the collapsed (branched polymer) state to a finite tension extended state...
March 28, 2018: European Physical Journal. E, Soft Matter
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