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Coarse grain

Federico Elias-Wolff, Martin Lindén, Alexander P Lyubartsev, Erik G Brandt
Membrane curvature sensing, where the binding free energies of membrane-associated molecules depend on the local membrane curvature, is a key factor to modulate and maintain the shape and organization of cell membranes. However, the microscopic mechanisms are not well understood, partly due to absence of efficient simulation methods. Here, we describe a method to compute the curvature dependence of the binding free energy of a membrane-associated probe molecule that interacts with a buckled membrane, which has been created by lateral compression of a flat bilayer patch...
January 19, 2018: Journal of Chemical Theory and Computation
Patrick D Ellis Fisher, Qi Shen, Bernice Akpinar, Luke K Davis, Kenny Kwok Hin Chung, David Baddeley, Andela Saric, Thomas J Melia, Bart W Hoogenboom, Chenxiang Lin, C Patrick Lusk
Nuclear pore complexes (NPCs) form gateways that control molecular exchange between the nucleus and the cytoplasm. They impose a diffusion barrier to macromolecules and enable the selective transport of nuclear transport receptors with bound cargo. The underlying mechanisms that establish these permeability properties remain to be fully elucidated, but require unstructured nuclear pore proteins rich in Phe-Gly (FG)-repeat domains of different types, such as FxFG and GLFG. While physical modeling and in vitro approaches have provided a framework for explaining how the FG network contributes to the barrier and transport properties of the NPC, it remains unknown whether the number and/or the spatial positioning of different FG-domains along a cylindrical, ~40 nm diameter transport channel contributes to their collective properties and function...
January 19, 2018: ACS Nano
Zhengying Tan, Senlin Lu, Hui Zhao, Xiao Kai, Peng Jiaxian, Myat Sandar Win, Shang Yu, Shinich Yonemochi, Qingyue Wang
As an accumulation of solid organic and inorganic pollutant particles on outdoor ground surfaces, road dust is an important carrier of heavy metal contaminants and can be a valuable medium for characterizing urban environmental quality. Because the dusts can be an important source of atmospheric particles and take impact on human health, the aim of this study described in detail the mineralogical characteristics, morphology, and heavy metal content of road dust from Xuanwei and Fuyuan, locations with high lung cancer incidence...
January 19, 2018: Environmental Geochemistry and Health
Shun Okushima, Toshihiro Kawakatsu
We perform a series of Monte Carlo simulations on an interface between a liquid crystal (LC) material in isotropic phase in its bulk and a surfactant membrane. These two objects are simulated using coarse-grained molecular models. We estimate physical properties of the membrane such as the interfacial tension and the bending rigidity, focusing on the anchoring effects of the membrane on the LC. According to our simulation results, when the strength of the homeotropic anchoring denoted by the anchoring parameter ξ is increased, the interfacial tension decreases and the bending rigidity first increases in ξ<ξ_{m}, and it then decreases in ξ_{m}<ξ...
November 2017: Physical Review. E
Martijn Zuiddam, Ralf Everaers, Helmut Schiessel
The positions along DNA molecules of nucleosomes, the most abundant DNA-protein complexes in cells, are influenced by the sequence-dependent DNA mechanics and geometry. This leads to the "nucleosome positioning code", a preference of nucleosomes for certain sequence motives. Here we introduce a simplified model of the nucleosome where a coarse-grained DNA molecule is frozen into an idealized superhelical shape. We calculate the exact sequence preferences of our nucleosome model and find it to reproduce qualitatively all the main features known to influence nucleosome positions...
November 2017: Physical Review. E
Marc Lämmel, Klaus Kroy
The mesoscale structure of aeolian sand transport determines a variety of natural phenomena studied in planetary and Earth science. We analyze it theoretically beyond the mean-field level, based on the grain-scale transport kinetics and splash statistics. A coarse-grained analytical model is proposed and verified by numerical simulations resolving individual grain trajectories. The predicted height-resolved sand flux and other important characteristics of the aeolian transport layer agree remarkably well with a comprehensive compilation of field and wind-tunnel data, suggesting that the model robustly captures the essential mesoscale physics...
November 2017: Physical Review. E
Martin Girard, Trung Dac Nguyen, Monica Olvera de la Cruz
Coarse-grained potentials are ubiquitous in mesoscale simulations. While various methods to compute effective interactions for spherically symmetric particles exist, anisotropic interactions are seldom used, due to their complexity. Here we describe a general formulation, based on a spatial decomposition of the density fields around the particles, akin to atomic orbitals. We show that anisotropic potentials can be efficiently computed in numerical simulations using Fourier-based methods. We validate the field formulation and characterize its computational efficiency with a system of colloids that have Gaussian surface charge distributions...
November 2017: Physical Review. E
Konark Bisht, Stefan Klumpp, Varsha Banerjee, Rahul Marathe
A human pathogen, Neisseria gonorrhoeae (NG), moves on surfaces by attaching and retracting polymeric structures called Type IV pili. The tug-of-war between the pili results in a two-dimensional stochastic motion called twitching motility. In this paper, with the help of real-time NG trajectories, we develop coarse-grained models for their description. The fractal properties of these trajectories are determined and their influence on first passage time and formation of bacterial microcolonies is studied. Our main observations are as follows: (i) NG performs a fast ballistic walk on small time scales and a slow diffusive walk over long time scales with a long crossover region; (ii) there exists a characteristic persistent length l_{p}^{*}, which yields the fastest growth of bacterial aggregates or biofilms...
November 2017: Physical Review. E
Julien Morthomas, Claudio Fusco, Zengqiang Zhai, Olivier Lame, Michel Perez
The ability of a simple coarse-grained finite-extensible nonlinear elastic (FENE) Lennard-Jones (LJ) polymer model to be crystallized is investigated by molecular dynamics simulations. The optimal FENE Lennard-Jones parameter combinations (ratio between FENE and LJ equilibrium distances) and the optimal lattice parameters are calculated for five different perfect crystallite structures: simple tetragonal, body-centered tetragonal, body-centered orthorhombic, hexagonal primitive, and hexagonal close packed. It was found that the most energetically favorable structure is the body-centered orthorhombic...
November 2017: Physical Review. E
Matthew Smart, Aruna Rajagopal, Wing-Ki Liu, Bae-Yeun Ha
The permeability of the bacterial outer membrane, enclosing Gram-negative bacteria, depends on the interactions of the outer, lipopolysaccharide (LPS) layer, with surrounding ions and molecules. We present a coarse-grained model for describing how cationic amphiphilic molecules (e.g., antimicrobial peptides) interact with and perturb the LPS layer in a biologically relevant medium, containing monovalent and divalent salt ions (e.g., Mg^{2+}). In our approach, peptide binding is driven by electrostatic and hydrophobic interactions and is assumed to expand the LPS layer, eventually priming it for disruption...
October 2017: Physical Review. E
Yuta Yoshimoto, Takuma Hori, Ikuya Kinefuchi, Shu Takagi
We investigate the effect of capillary condensation on gas diffusivity in porous media composed of randomly packed spheres with moderate wettability. To simulate capillary phenomena at the pore scale while retaining complex pore networks of the porous media, we employ density functional theory (DFT) for coarse-grained lattice gas models. The lattice DFT simulations reveal that capillary condensations preferentially occur at confined pores surrounded by solid walls, leading to the occlusion of narrow pores. Consequently, the characteristic lengths of the partially wet structures are larger than those of the corresponding dry structures with the same porosities...
October 2017: Physical Review. E
D B Abraham, A Maciołek, A Squarcini, O Vasilyev
We examine in detail the theoretical foundations of striking long-range couplings emerging in arrays of fluid cells connected by narrow channels by using a lattice gas (Ising model) description of a system. We present a reexamination of the well known exact determination of the two-point correlation function along the edge of a channel using the transfer matrix technique and a different interpretation is provided. The explicit form of the correlation length is found to grow exponentially with the cross section of the channels at the bulk two-phase coexistence...
October 2017: Physical Review. E
Joerg Noetel, Igor M Sokolov, Lutz Schimansky-Geier
We consider a microswimmer that moves in two dimensions at a constant speed and changes the direction of its motion due to a torque consisting of a constant and a fluctuating component. The latter will be modeled by a symmetric Lévy-stable (α-stable) noise. The purpose is to develop a kinetic approach to eliminate the angular component of the dynamics to find a coarse-grained description in the coordinate space. By defining the joint probability density function of the position and of the orientation of the particle through the Fokker-Planck equation, we derive transport equations for the position-dependent marginal density, the particle's mean velocity, and the velocity's variance...
October 2017: Physical Review. E
Zhenwei Yao
Various lattice gas automata have been proposed in the past decades to simulate physics and address a host of problems on collective dynamics arising in diverse fields. In this work, we employ the lattice gas model defined on the sphere to investigate the curvature-driven dynamic structures and analyze the statistical behaviors in equilibrium. Under the simple propagation and collision rules, we show that the uniform collective movement of the particles on the sphere is geometrically frustrated, leading to several nonequilibrium dynamic structures not found in the planar lattice, such as the emergent bubble and vortex structures...
December 2017: Physical Review. E
Alan R Denton
Interparticle interactions and bulk properties of colloidal suspensions can be substantially modified by the addition of nanoparticles. Extreme asymmetries in size and charge between colloidal particles and nanoparticles present severe computational challenges to molecular-scale modeling of such complex systems. We present a statistical mechanical theory of effective electrostatic interactions that can greatly ease large-scale modeling of charged colloid-nanoparticle mixtures. By applying a sequential coarse-graining procedure, we show that a multicomponent mixture of charged colloids, nanoparticles, counterions, and coions can be mapped first onto a binary mixture of colloids and nanoparticles and then onto a one-component model of colloids alone...
December 2017: Physical Review. E
Handan Arkin, Wolfhard Janke
The conformational behavior of a coarse-grained finite polymer chain near an attractive spherical surface was investigated by means of multicanonical Monte Carlo computer simulations. In a detailed analysis of canonical equilibrium data over a wide range of sphere radius and temperature, we have constructed entire phase diagrams both for nongrafted and end-grafted polymers. For the identification of the conformational phases, we have calculated several energetic and structural observables such as gyration tensor based shape parameters and their fluctuations by canonical statistical analysis...
December 2017: Physical Review. E
Yoshiki Hiruta, Sadayoshi Toh
We have found that in two-dimensional Kolmogorov flow a spatially localized turbulent state (SLT) exists stably and travels with a constant speed on average switching the moving direction randomly and intermittently for moderate values of the control parameters: Reynolds number and the flow rate. We define the coarse-grained position and velocity of an SLT and separate the motion of the SLT from its internal turbulent dynamics by introducing a co-moving frame. The switching process of an SLT represented by the coarse-grained velocity seems to be a random telegraph signal...
December 2017: Physical Review. E
Sebastian Leitmann, Felix Höfling, Thomas Franosch
We study the dynamics of solutions of infinitely thin needles up to densities deep in the semidilute regime by Brownian dynamics simulations. For high densities, these solutions become strongly entangled and the motion of a needle is essentially restricted to a one-dimensional sliding in a confining tube composed of neighboring needles. From the density-dependent behavior of the orientational and translational diffusion, we extract the long-time transport coefficients and the geometry of the confining tube...
July 2017: Physical Review. E
Yongxiang Huang, Lipo Wang, F G Schmitt, Xiaobo Zheng, Nan Jiang, Yulu Liu
In recent years several local extrema-based methodologies have been proposed to investigate either the nonlinear or the nonstationary time series for scaling analysis. In the present work, we study systematically the distribution of the local extrema for both synthesized scaling processes and turbulent velocity data from experiments. The results show that for the fractional Brownian motion (fBm) without intermittency correction the measured extremal-point-density (EPD) agrees well with a theoretical prediction...
July 2017: Physical Review. E
Andrea Pelissetto, Ettore Vicari
We investigate the dynamic behavior of finite-size systems close to a first-order transition (FOT). We develop a dynamic finite-size scaling (DFSS) theory for the dynamic behavior in the coexistence region where different phases coexist. This is characterized by an exponentially large time scale related to the tunneling between the two phases. We show that, when considering time scales of the order of the tunneling time, the dynamic behavior can be described by a two-state coarse-grained dynamics. This allows us to obtain exact predictions for the dynamical scaling functions...
July 2017: Physical Review. E
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