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Coarse grain

Adarsh K Chaurasia, Andrew M Rukangu, Michael K Philen, Gary D Seidel, Eric C Freeman
In the current paper, phospholipid bilayers are modeled using coarse-grained molecular dynamics simulations with the MARTINI force field. The extracted molecular trajectories are analyzed using Fourier analysis of the undulations and orientation vectors to establish the differences between the two approaches for evaluating the bending modulus. The current work evaluates and extends the implementation of the Fourier analysis for molecular trajectories using a weighted horizon-based averaging approach. The effect of numerical parameters in the analysis of these trajectories is explored by conducting parametric studies...
March 2018: Physical Review. E
Sunil Kumar Yadav, Shankar P Das
Starting from a microscopic model, the continuum field theoretic description of the dynamics of a system of active ingredients or "particles" is presented. The equations of motion for the respective collective densities of mass and momentum follow exactly from that of a single element in the flock. The single-particle dynamics has noise and anomalous momentum dependence in its frictional terms. The equations for the collective densities are averaged over a local equilibrium distribution to obtain the corresponding coarse grained equations of fluctuating nonlinear hydrodynamics (FNH)...
March 2018: Physical Review. E
Han Kheng Teoh, Ee Hou Yong
We study the phase transition from free flow to congested phases in the Nagel-Schreckenberg (NS) model by using the dynamically driven renormalization group (DDRG). The breaking probability p that governs the driving strategy is investigated. For the deterministic case p=0, the dynamics remain invariant in each renormalization-group (RG) transformation. Two fully attractive fixed points, ρ_{c}^{*}=0 and 1, and one unstable fixed point, ρ_{c}^{*}=1/(v_{max}+1), are obtained. The critical exponent ν which is related to the correlation length is calculated for various v_{max}...
March 2018: Physical Review. E
Taras Y Molotilin, Salim R Maduar, Olga I Vinogradova
Reducing the complexity of cross-linked polymer networks by preserving their main macroscale properties is key to understanding them, and a crucial issue is to relate individual properties of the polymer constituents to those of the reduced network. Here we study polymer networks in a good solvent, by considering star polymers as their unit elements, and first quantify the interaction between their centers of masses. We then reduce the complexity of a network by replacing sets of its bridged star polymers by equivalent effective soft particles with dense cores...
March 2018: Physical Review. E
Fabio C Zegarra, Dirar Homouz, Yossi Eliaz, Andrei G Gasic, Margaret S Cheung
We investigated the impact of hydrodynamic interactions (HI) on protein folding using a coarse-grained model. The extent of the impact of hydrodynamic interactions, whether it accelerates, retards, or has no effect on protein folding, has been controversial. Together with a theoretical framework of the energy landscape theory (ELT) for protein folding that describes the dynamics of the collective motion with a single reaction coordinate across a folding barrier, we compared the kinetic effects of HI on the folding rates of two protein models that use a chain of single beads with distinctive topologies: a 64-residue α/β chymotrypsin inhibitor 2 (CI2) protein, and a 57-residue β-barrel α-spectrin Src-homology 3 domain (SH3) protein...
March 2018: Physical Review. E
Jordi Baró, Jörn Davidsen
The hypothesis of critical failure relates the presence of an ultimate stability point in the structural constitutive equation of materials to a divergence of characteristic scales in the microscopic dynamics responsible for deformation. Avalanche models involving critical failure have determined common universality classes for stick-slip processes and fracture. However, not all empirical failure processes exhibit the trademarks of criticality. The rheological properties of materials introduce dissipation, usually reproduced in conceptual models as a hardening of the coarse grained elements of the system...
March 2018: Physical Review. E
Zhi-Cheng Yang, Stefanos Kourtis, Claudio Chamon, Eduardo R Mucciolo, Andrei E Ruckenstein
We develop a tensor network technique that can solve universal reversible classical computational problems, formulated as vertex models on a square lattice [Nat. Commun. 8, 15303 (2017)2041-172310.1038/ncomms15303]. By encoding the truth table of each vertex constraint in a tensor, the total number of solutions compatible with partial inputs and outputs at the boundary can be represented as the full contraction of a tensor network. We introduce an iterative compression-decimation (ICD) scheme that performs this contraction efficiently...
March 2018: Physical Review. E
Hyun-Myung Chun, Xavier Durang, Jae Dong Noh
We investigate the low mass limit of Langevin dynamics for a charged Brownian particle driven by a magnetic Lorentz force. In the low mass limit, velocity variables relaxing quickly are coarse-grained out to yield effective dynamics for position variables. Without the Lorentz force, the low mass limit is equivalent to the high friction limit. Both cases share the same Langevin equation that is obtained by setting the mass to zero. The equivalence breaks down in the presence of the Lorentz force. The low mass limit cannot be achieved by setting the mass to zero...
March 2018: Physical Review. E
Kai Qi, Michael Bachmann
By means of the principle of minimal sensitivity we generalize the microcanonical inflection-point analysis method by probing derivatives of the microcanonical entropy for signals of transitions in complex systems. A strategy of systematically identifying and locating independent and dependent phase transitions of any order is proposed. The power of the generalized method is demonstrated in applications to the ferromagnetic Ising model and a coarse-grained model for polymer adsorption onto a substrate. The results shed new light on the intrinsic phase structure of systems with cooperative behavior...
May 4, 2018: Physical Review Letters
Urna Basu, Laurent Helden, Matthias Krüger
Nonlinear response theory, in contrast to linear cases, involves (dynamical) details, and this makes application to many-body systems challenging. From the microscopic starting point we obtain an exact response theory for a small number of coarse-grained degrees of freedom. With it, an extrapolation scheme uses near-equilibrium measurements to predict far-from-equilibrium properties (here, second order responses). Because it does not involve system details, this approach can be applied to many-body systems...
May 4, 2018: Physical Review Letters
Haridas Mundoor, Sungoh Park, Bohdan Senyuk, Henricus H Wensink, Ivan I Smalyukh
Order and fluidity often coexist, with examples ranging from biological membranes to liquid crystals, but the symmetry of these soft-matter systems is typically higher than that of the constituent building blocks. We dispersed micrometer-long inorganic colloidal rods in a nematic liquid crystalline fluid of molecular rods. Both types of uniaxial building blocks, while freely diffusing, interact to form an orthorhombic nematic fluid, in which like-sized rods are roughly parallel to each other and the molecular ordering direction is orthogonal to that of colloidal rods...
May 18, 2018: Science
Imtiaz Awan, Wajid Aziz, Imran Hussain Shah, Nazneen Habib, Jalal S Alowibdi, Sharjil Saeed, Malik Sajjad Ahmed Nadeem, Syed Ahsin Ali Shah
Considerable interest has been devoted for developing a deeper understanding of the dynamics of healthy biological systems and how these dynamics are affected due to aging and disease. Entropy based complexity measures have widely been used for quantifying the dynamics of physical and biological systems. These techniques have provided valuable information leading to a fuller understanding of the dynamics of these systems and underlying stimuli that are responsible for anomalous behavior. The single scale based traditional entropy measures yielded contradictory results about the dynamics of real world time series data of healthy and pathological subjects...
2018: PloS One
Timothy C Ricard, Cody Haycraft, Srinivasan Sesha Iyengar
We introduce a new coarse-graining technique for ab initio molecular dynamics that is based on the adaptive generation of connected geometric networks or graphs specific to a given molecular ge- ometry. The coarse-grained nodes depict a local chemical environment and are networked to create edges, triangles, tetrahedrons and higher order simplexes based on (a) a Delaunay triangulation procedure and (b) a method that is based on molecular, bonded and non-bonded, local interac- tions. The geometric sub-entities thus created, that is nodes, edges, triangles, and tetrahedrons, each represent an energetic measure for a specific portion of the molecular system, capturing a spe- cific set of interactions...
May 17, 2018: Journal of Chemical Theory and Computation
Derya Meral, Davide Provasi, Diego Prada-Gracia, Jan Möller, Kristen Marino, Martin J Lohse, Marta Filizola
Various experimental and computational techniques have been employed over the past decade to provide structural and thermodynamic insights into G Protein-Coupled Receptor (GPCR) dimerization. Here, we use multiple microsecond-long, coarse-grained, biased and unbiased molecular dynamics simulations (a total of ~4 milliseconds) combined with multi-ensemble Markov state models to elucidate the kinetics of homodimerization of a prototypic GPCR, the µ-opioid receptor (MOR), embedded in a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)/cholesterol lipid bilayer...
May 16, 2018: Scientific Reports
Maria Aznar, Sergi Roca-Bonet, David Reguera
One of the most important components of a virus is the protein shell or capsid 
 that encloses its genetic material. The main role of the capsid is to protect 
 the viral genome against external aggressions, facilitating its safe and 
 efficient encapsulation and delivery. As a consequence, viral capsids have 
 developed astonishing mechanical properties that are crucial for viral function. 
 These remarkable properties have started to be unveiled in single-virus 
 nanoindentation experiments, and are opening the door to the use of 
 viral-derived artificial nanocages for promising bio- and nano-technological 
May 17, 2018: Journal of Physics. Condensed Matter: An Institute of Physics Journal
Weihong Gao, Zhenyou Wang, Jin Huang, Zihang Liu
Thermoelectric conversion from low-grade heat to electricity is regarded as the highly reliable and environmentally friendly technology in energy harvesting area. However, how to develop efficient thermoelectric materials using a simple fabrication method is still a critical challenge in thermoelectric community. Here we first fabricate the high thermoelectric performance of Ca doped AgSbSe2 with hierarchical microstructure using a facile approach, namely mechanical alloying (for only 30 minutes) and quick hot pressing method...
May 16, 2018: ACS Applied Materials & Interfaces
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
Jeremie S Kim, Damla Senol Cali, Hongyi Xin, Donghyuk Lee, Saugata Ghose, Mohammed Alser, Hasan Hassan, Oguz Ergin, Can Alkan, Onur Mutlu
BACKGROUND: Seed location filtering is critical in DNA read mapping, a process where billions of DNA fragments (reads) sampled from a donor are mapped onto a reference genome to identify genomic variants of the donor. State-of-the-art read mappers 1) quickly generate possible mapping locations for seeds (i.e., smaller segments) within each read, 2) extract reference sequences at each of the mapping locations, and 3) check similarity between each read and its associated reference sequences with a computationally-expensive algorithm (i...
May 9, 2018: BMC Genomics
E Couallier, A Riaublanc, E David Briand, B Rousseau
An artificial oil-in-water emulsion analogous to those found in bioresources or food matrices is simulated and studied experimentally. It is composed of one of the major natural free fatty acids (the oleic acid, OA) and the corresponding triacylglyceride (trioleic glyceride, or triolein, GTO). Because of the large time and length scales involved, the molecular simulations are done with the Martini force field, a coarse-grained model. This allowed us to study the water-OA-GTO system at different compositions with more than 20 000 molecules and up to 2 μs...
May 14, 2018: Journal of Chemical Physics
Lam-Kiu Fong, Ziwei Wang, George C Schatz, Erik Luijten, Chad A Mirkin
DNA hybridization onto DNA-functionalized nanoparticle surfaces (e.g., in the form of a spherical nucleic acid (SNA)) is known to be enhanced relative to hybridization free in solution. Surprisingly, via isothermal titration calorimetry, we reveal that this enhancement is enthalpically, as opposed to entropically, dominated by ∼20 kcal/mol. Coarse-grained molecular dynamics simulations suggest that the observed enthalpic enhancement results from structurally confining the DNA on the nanoparticle surface and preventing it from adopting enthalpically unfavorable conformations like those observed in the solution case...
May 15, 2018: Journal of the American Chemical Society
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