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European Physical Journal. E, Soft Matter

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https://www.readbyqxmd.com/read/29349724/analyzing-similarities-in-genome-sequences
#1
I C Fonseca, E Nogueira, P H Figueirêdo, S Coutinho
This article investigates aspects of similarity between complete sequences of mitochondrial DNA by determining the distribution of the relative frequencies of words with different lengths and the characteristics of their relevance throughout the sequences. The degree of similarity is obtained by comparing the distances between words contained within these sequences. Our results indicate that the best groupings among different species depend on the lengths of words and their respective relative frequencies. We also observed that the longer the word the more consistent the grouping between the sequences becomes...
January 19, 2018: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29340874/lattice-boltzmann-simulations-of-droplet-dynamics-in-time-dependent-flows
#2
F Milan, M Sbragaglia, L Biferale, F Toschi
We study the deformation and dynamics of droplets in time-dependent flows using 3D numerical simulations of two immiscible fluids based on the lattice Boltzmann model (LBM). Analytical models are available in the literature, which assume the droplet shape to be an ellipsoid at all times (P.L. Maffettone, M. Minale, J. Non-Newton. Fluid Mech 78, 227 (1998); M. Minale, Rheol. Acta 47, 667 (2008)). Beyond the practical importance of using a mesoscale simulation to assess "ab initio" the robustness and limitations of such theoretical models, our simulations are also key to discuss --in controlled situations-- some relevant phenomenology related to the interplay between the flow time scales and the droplet time scales regarding the "transparency" transition for high enough shear frequencies for an external oscillating flow...
January 16, 2018: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29340794/a-unified-description-of-colloidal-thermophoresis
#3
REVIEW
Jérôme Burelbach, Daan Frenkel, Ignacio Pagonabarraga, Erika Eiser
We use the dynamic length and time scale separation in suspensions to formulate a general description of colloidal thermophoresis. Our approach allows an unambiguous definition of separate contributions to the colloidal flux and clarifies the physical mechanisms behind non-equilibrium motion of colloids. In particular, we derive an expression for the interfacial force density that drives single-particle thermophoresis in non-ideal fluids. The issuing relations for the transport coefficients explicitly show that interfacial thermophoresis has a hydrodynamic character that cannot be explained by a purely thermodynamic consideration...
January 16, 2018: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29330740/3d-reconstruction-of-dynamic-liquid-film-shape-by-optical-grid-deflection-method
#4
L Fourgeaud, E Ercolani, J Duplat, P Gully, V S Nikolayev
In this paper, we describe the optical grid deflection method used to reconstruct the 3D profile of liquid films deposited by a receding liquid meniscus. This technique uses the refractive properties of the film surface and is suitable for liquid thickness from several microns to millimeter. This method works well for strong interface slopes and changing in time film shape; it applies when the substrate and fluid media are transparent. The refraction is assumed to be locally unidirectional. The method is particularly appropriate to follow the evolution of parameters such as dynamic contact angle, triple liquid-gas-solid contact line velocity or dewetting ridge thickness...
January 15, 2018: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29330621/nonuniversal-behaviour-of-helical-two-dimensional-three-component-turbulence
#5
Moritz Linkmann, Michele Buzzicotti, Luca Biferale
The dynamics of two-dimensional three-component (2D3C) flows is relevant to describe the long-time evolution of strongly rotating flows and/or of conducting fluids with a strong mean magnetic field. We show that in the presence of a strong helical forcing, the out-of-plane component ceases to behave as a passive advected quantity and develops a nontrivial dynamics which deeply changes its large-scale properties. We show that a small-scale helicity injection correlates the input on the 2D component with the one on the out-of-plane component...
January 15, 2018: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29327242/self-assembly-of-magnetically-functionalized-star-polymer-nano-colloids
#6
Ronald Blaak, Christos N Likos
We explore the potential of star-polymers that carry super-paramagnetic nano-particles as end-groups with respect to the single-molecule self-assembly process. With the aid of molecular dynamics simulation, the configurations of these macromolecules are analyzed as a function of functionality, magnetic interaction strength, and the length of the polymeric arms. By means of an external magnetic field the nano-particles can be controlled to form static or dynamic dipolar chains, resulting in conformations of isolated stars that can be characterized by the average number of chains and length...
January 12, 2018: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29299703/membrane-undulations-in-a-structured-fluid-universal-dynamics-at-intermediate-length-and-time-scales
#7
Rony Granek, Haim Diamant
The dynamics of membrane undulations inside a viscous solvent is governed by distinctive, anomalous, power laws. Inside a viscoelastic continuous medium these universal behaviors are modified by the specific bulk viscoelastic spectrum. Yet, in structured fluids the continuum limit is reached only beyond a characteristic correlation length. We study the crossover to this asymptotic bulk dynamics. The analysis relies on a recent generalization of the hydrodynamic interaction in structured fluids, which shows a slow spatial decay of the interaction toward the bulk limit...
January 5, 2018: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29299695/inertial-shear-flow-of-assemblies-of-frictionless-polygons-rheology-and-microstructure
#8
Émilien Azéma, Farhang Radjaï, Jean-Noël Roux
Motivated by the understanding of shape effects in granular materials, we numerically investigate the macroscopic and microstructural properties of anisotropic dense assemblies of frictionless polydisperse rigid pentagons in shear flow, and compare them with similar systems of disks. Once subjected to large cumulative shear strains their rheology and microstructure are investigated in uniform steady states, depending on inertial number I, which ranges from the quasistatic limit ([Formula: see text]) to 0.2...
January 5, 2018: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29274072/simulation-of-phase-separation-with-temperature-dependent-viscosity-using-lattice-boltzmann-method
#9
Heping Wang, Duyang Zang, Xiaoguang Li, Xingguo Geng
This paper presents an exploration of the phase separation behavior and pattern formation in a binary fluid with temperature-dependent viscosity via a coupled lattice Boltzmann method (LBM). By introducing a viscosity-temperature relation into the LBM, the coupling effects of the viscosity-temperature coefficient [Formula: see text] , initial viscosity [Formula: see text] and thermal diffusion coefficient [Formula: see text] , on the phase separation were successfully described. The calculated results indicated that an increase in initial viscosity and viscosity-temperature coefficient, or a decrease in the thermal diffusion coefficient, can lead to the orientation of isotropic growth fronts over a wide range of viscosity...
December 27, 2017: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29274066/dynamical-heterogeneities-and-mechanical-non-linearities-modeling-the-onset-of-plasticity-in-polymer-in-the-glass-transition
#10
R J Masurel, P Gelineau, F Lequeux, S Cantournet, H Montes
In this paper we focus on the role of dynamical heterogeneities on the non-linear response of polymers in the glass transition domain. We start from a simple coarse-grained model that assumes a random distribution of the initial local relaxation times and that quantitatively describes the linear viscoelasticity of a polymer in the glass transition regime. We extend this model to non-linear mechanics assuming a local Eyring stress dependence of the relaxation times. Implementing the model in a finite element mechanics code, we derive the mechanical properties and the local mechanical fields at the beginning of the non-linear regime...
December 27, 2017: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29273950/what-experiments-on-pinned-nanobubbles-can-tell-about-the-critical-nucleus-for-bubble-nucleation
#11
Qianxiang Xiao, Yawei Liu, Zhenjiang Guo, Zhiping Liu, Daan Frenkel, Jure Dobnikar, Xianren Zhang
The process of homogeneous bubble nucleation is almost impossible to probe experimentally, except near the critical point or for liquids under large negative tension. Elsewhere in the phase diagram, the bubble nucleation barrier is so high as to be effectively insurmountable. Consequently, there is a severe lack of experimental studies of homogenous bubble nucleation under conditions of practical importance (e.g., cavitation). Here we use a simple geometric relation to show that we can obtain information about the homogeneous nucleation process from Molecular Dynamics studies of bubble formation in solvophobic nanopores on a solid surface...
December 22, 2017: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29255973/reconsidering-the-clapeyron-equation-in-the-freezing-of-colloidal-suspensions-from-macroscale-to-the-microscale
#12
Lilin Wang, Zhijun Wang
A long controversy of ice lensing exists in the research of frost heave. By elucidating the mechanical and thermodynamic equilibria at the interface, the thermodynamics of the water/ice interface is revealed from macroscale to microscale for the freezing of colloidal suspensions. The application of the Clapeyron equation is confirmed both at macroscale to microscale via curvature effect. The origin of ice lensing/banding can be initialized from the growth of pore ice in the interpretation of thermodynamics at the interface, even without the traditional mechanical analyses...
December 20, 2017: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29256179/lattice-boltzmann-study-of-chemically-driven-self-propelled-droplets
#13
F Fadda, G Gonnella, A Lamura, A Tiribocchi
We numerically study the behavior of self-propelled liquid droplets whose motion is triggered by a Marangoni-like flow. This latter is generated by variations of surfactant concentration which affect the droplet surface tension promoting its motion. In the present paper a model for droplets with a third amphiphilic component is adopted. The dynamics is described by Navier-Stokes and convection-diffusion equations, solved by the lattice Boltzmann method coupled with finite-difference schemes. We focus on two cases...
December 19, 2017: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29242998/contrasting-liquid-imbibition-into-uncoated-versus-pigment-coated-paper-enables-a-description-of-imbibition-into-new-generation-surface-filled-paper
#14
Guodong Liu, Sijia Fu, Zhaoqing Lu, Meiyun Zhang, Cathy Ridgway, Patrick Gane
The transport of print fluids into paper is directly dependent on the imbibition characteristic of the paper including both the z-, x- and y-directions. As the measurement of free liquid imbibition into the paper thickness (z-direction) is difficult experimentally, due to the thin nature of paper, in this paper we resort to imbibition along the y-direction of paper to analyse and explore the possibility of understanding the mechanistic differences between wicking into uncoated unfilled paper versus that of controllable pigment-filled paper and paper coating...
December 18, 2017: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29234967/finding-efficient-swimming-strategies-in-a-three-dimensional-chaotic-flow-by-reinforcement-learning
#15
K Gustavsson, L Biferale, A Celani, S Colabrese
We apply a reinforcement learning algorithm to show how smart particles can learn approximately optimal strategies to navigate in complex flows. In this paper we consider microswimmers in a paradigmatic three-dimensional case given by a stationary superposition of two Arnold-Beltrami-Childress flows with chaotic advection along streamlines. In such a flow, we study the evolution of point-like particles which can decide in which direction to swim, while keeping the velocity amplitude constant. We show that it is sufficient to endow the swimmers with a very restricted set of actions (six fixed swimming directions in our case) to have enough freedom to find efficient strategies to move upward and escape local fluid traps...
December 14, 2017: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29234907/rheotropism-of-the-dowser-texture
#16
Pawel Pieranski, Jean-Pierre Hulin, Maria Helena Godinho
In spite of its metastability, the pseudo-planar texture of a nematic layer confined between surfaces with homeotropic anchoring can be preserved indefinitely in certain conditions. The pseudo-planar texture, dubbed "the dowser texture", is degenerated and therefore sensitive to perturbations. It has been shown recently that the dowser texture is cuneitropic, that is to say, has a tendency to follow thickness gradients. Here, we point out that the dowser texture is also rheotropic or, in other words, has a weathercock behavior: it tends to follow the direction of Poiseuille flows...
December 14, 2017: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29230563/self-assembly-of-smart-mesoscopic-objects
#17
J Metzmacher, M Poty, G Lumay, N Vandewalle
Self-assembly due to capillary forces is a common method for generating 2D mesoscale structures made of identical particles floating at some liquid-air interface. We show herein how to create soft entities that deform or not the liquid interface as a function of the strength of some applied magnetic field. These smart floating objects self-assemble or not depending on the application of an external field. Moreover, we show that the self-assembling process can be reversed opening ways to rearrange structures...
December 12, 2017: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29188394/resonant-reshaping-of-colloidal-clusters-on-a-current-carrying-wire
#18
Lydiane Becu, Marc Basler, Miodrag L Kulić, Igor M Kulić
Colloids in confined geometries promise a path towards tailored microscopic superstructures. Yet, a major roadblock is posed by kinetically trapped states that prevent the assemblies from reaching their anticipated shapes. We investigate magnetic colloids trapped on a cylindrical surface of a current carrying wire. If kinetic traps could be avoided the wire's surface would act as an ideal mold for colloidal rings and helical fibers. We devise here a way to dynamically shake down the clusters and avoid kinetic traps in their energy landscape...
December 1, 2017: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29185124/the-role-of-dna-sequence-in-nucleosome-breathing
#19
Jamie Culkin, Lennart de Bruin, Marco Tompitak, Rob Phillips, Helmut Schiessel
Roughly 3/4 of human genomes are sequestered by nucleosomes, DNA spools with a protein core, dictating a broad range of biological processes, ranging from gene regulation, recombination, and replication, to chromosome condensation. Nucleosomes are dynamical structures and temporarily expose wrapped DNA through spontaneous unspooling from either end, a process called site exposure or nucleosome breathing. Here we ask how this process is influenced by the mechanical properties of the wrapped DNA, which is known to depend on the underlying base pair sequence...
November 30, 2017: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29178057/existence-of-the-passage-to-the-limit-of-an-inviscid-fluid
#20
Denis S Goldobin
In the dynamics of a viscous fluid, the case of vanishing kinematic viscosity is actually equivalent to the Reynolds number tending to infinity. Hence, in the limit of vanishing viscosity the fluid flow is essentially turbulent. On the other hand, the Euler equation, which is conventionally adopted for the description of the flow of an inviscid fluid, does not possess proper turbulent behaviour. This raises the question of the existence of the passage to the limit of an inviscid fluid for real low-viscosity fluids...
November 24, 2017: European Physical Journal. E, Soft Matter
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