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Coarse grain

Amin Aramoon, Timothy D Breitzman, Christopher F Woodward, Jaafar A El-Awady
A new algorithm is developed to quantify the free-volume hole distribution and its evolution in coarse-grained molecular dynamics simulations of polymeric networks. This is achieved by analyzing the geometry of the network rather than a voxelized image of the structure to accurately and efficiently find and quantify free-volume hole distributions within large scale simulations of polymer networks. The free-volume holes are quantified by fitting the largest ellipsoids and spheres in the free-volumes between polymer chains...
August 16, 2017: Journal of Physical Chemistry. B
Chathuranga C De Silva, Porakrit Leophairatana, Takahiro Ohkuma, Jeffrey T Koberstein, Kurt Kremer, Debashish Mukherji
Polymer properties are inherently multi-scale in nature, where delicate local interaction details play a key role in describing their global conformational behavior. In this context, deriving coarse-grained (CG) multi-scale models for polymeric liquids is a non-trivial task. Further complexities arise when dealing with copolymer systems with varying microscopic sequences, especially when they are of amphiphilic nature. In this work, we derive a segment-based generic CG model for amphiphilic copolymers consisting of repeat units of hydrophobic (methylene) and hydrophilic (ethylene oxide) monomers...
August 14, 2017: Journal of Chemical Physics
Peter H Colberg, Raymond Kapral
The collective behavior of chemically propelled sphere-dimer motors made from linked catalytic and noncatalytic spheres in a quasi-two-dimensional confined geometry is studied using a coarse-grained microscopic dynamical model. Chemical reactions at the catalytic spheres that convert fuel to product generate forces that couple to solvent degrees of freedom as a consequence of momentum conservation in the microscopic dynamics. The collective behavior of the many-body system is influenced by direct intermolecular interactions among the motors, chemotactic effects due to chemical gradients, hydrodynamic coupling, and thermal noise...
August 14, 2017: Journal of Chemical Physics
Guojie Zhang, Marcus Müller
Membrane fission is a fundamental process in cells, involved inter alia in endocytosis, intracellular trafficking, and virus infection. Its underlying molecular mechanism, however, is only incompletely understood. Recently, experiments and computer simulation studies have revealed that dynamin-mediated membrane fission is a two-step process that proceeds via a metastable hemi-fission intermediate (or wormlike micelle) formed by dynamin's constriction. Importantly, this hemi-fission intermediate is remarkably metastable, i...
August 14, 2017: Journal of Chemical Physics
Pawel Krupa, Anna Halabis, Wioletta Zmudzinska, Stanislaw Oldziej, Harold Abraham Scheraga, Adam Liwo
By using the maximum likelihood method for force-field calibration recently developed in our laboratory, which is aimed at achieving the agreement between the simulated conformational ensembles of selected training proteins and the corresponding ensembles determined experimentally at various temperatures, the physics-based coarse-grained UNRES force field for simulations of protein structure and dynamics was optimized with seven small training proteins exhibiting a variety of secondary and tertiary structures...
August 15, 2017: Journal of Chemical Information and Modeling
Glen M Hocky, Thomas Dannenhoffer-Lafage, Gregory A Voth
Many free-energy sampling and quantum mechanics/molecular mechanics (QM/MM) computations on protein complexes have been performed where, by necessity, a single component is studied isolated in solution while its overall configuration is kept in the complex-like state by either rigid restraints or harmonic constraints. A drawback in these studies is that the system's native fluctuations are lost, both due to the change of environment and the imposition of the extra potential. Yet, we know that having both accurate structure and fluctuations is likely crucial to achieving correct simulation estimates for the subsystem within its native larger protein complex context...
August 11, 2017: Journal of Chemical Theory and Computation
Per Larsson, Linda Alskär, Christel A S Bergström
The internal molecular structure of lipid-based formulations (LBFs) is poorly understood. In this work we aimed at establishing coarse-grained molecular dynamics simulations as a tool for rapid screening and investigation of the internal environment of these formulations. In order to study complex LBFs composed of different kinds of lipids we simulated a number of systems containing either medium-chain or long-chain lipids with varying proportions of tri-, di- and monoglycerides. Structural and dynamic measurements and analyses identified that the internal environment in a mixture of lipids was locally ordered even in the absence of water, which might explain some of the previously reported effects on drug solubility in these systems...
August 11, 2017: Molecular Pharmaceutics
A Filipponi, P Giammatteo
We implemented a kinetic Monte Carlo computer simulation of the nucleation process in the framework of the coarse grained scenario of the Classical Nucleation Theory (CNT). The computational approach is efficient for a wide range of temperatures and sample sizes and provides a reliable simulation of the stochastic process. The results for the nucleation rate are in agreement with the CNT predictions based on the stationary solution of the set of differential equations for the continuous variables representing the average population distribution of nuclei size...
December 7, 2016: Journal of Chemical Physics
Laura Lupi, Baron Peters, Valeria Molinero
According to Classical Nucleation Theory (CNT), the transition from liquid to crystal occurs in a single activated step with a transition state controlled by the size of the crystal embryo. This picture has been challenged in the last two decades by several reports of two-step crystallization processes in which the liquid first produces pre-ordered or dense domains, within which the crystal nucleates in a second step. Pre-ordering preceding crystal nucleation has been recently reported in simulations of ice crystallization, raising the question of whether the mechanism of ice nucleation involves two steps...
December 7, 2016: Journal of Chemical Physics
Brian J Sirovetz, Nicholas P Schafer, Peter G Wolynes
Protein sequences have evolved to fold into functional structures, resulting in families of diverse protein sequences that all share the same overall fold. One can harness protein family sequence data to infer likely contacts between pairs of residues. In the current study, we combine this kind of inference from coevolutionary information with a coarse-grained protein force field ordinarily used with single sequence input, the Associative memory, Water mediated, Structure and Energy Model (AWSEM), to achieve improved structure prediction...
August 11, 2017: Proteins
Exequiel E Barrera, Ezequiel N Frigini, Rodolfo D Porasso, Sergio Pantano
Coarse-grained simulation schemes are increasingly gaining popularity in the scientific community because of the significant speed up granted, allowing a considerable expansion of the accessible time and size scales accessible to molecular simulations. However, the number of compatible force fields capable of representing ensembles containing different molecular species (i.e., Protein, DNA, etc) is still limited. Here, we present a set of parameters and simplified representation for lipids compatible with the SIRAH force field for coarse-grained simulations ( http://www...
August 10, 2017: Journal of Molecular Modeling
Tamal Roy, Kai Szuttor, Jens Smiatek, Christian Holm, Steffen Hardt
We study the effect of pressure-driven flow on a single surface-tethered DNA molecule confined between parallel surfaces. The influence of flow and channel parameters as well as the length of the molecules on their extension and orientation is explored. In the experiments the chain conformations are imaged by laser scanning confocal microscopy. We find that the fractional extension of the tethered DNA molecules mainly depends on the wall shear stress, with effects of confinement being very weak. Experiments performed with molecules of different contour length show that the fractional extension is a universal function of the product of the wall shear stress and the contour length, a result that can be obtained from a simple scaling relation...
August 11, 2017: Soft Matter
Cheng-Yu Shih, Maxim V Shugaev, Chengping Wu, Leonid V Zhigilei
The ability of short pulse laser ablation in liquids to produce clean colloidal nanoparticles and unusual surface morphology has been employed in a broad range of practical applications. In this paper, we report the results of large-scale molecular dynamics simulations aimed at revealing the key processes that control the surface morphology and nanoparticle size distributions by pulsed laser ablation in liquids. The simulations of bulk Ag targets irradiated in water are performed with an advanced computational model combining a coarse-grained representation of liquid environment and an atomistic description of laser interaction with metal targets...
August 3, 2017: Journal of Physical Chemistry. C, Nanomaterials and Interfaces
Chanfei Su, Holger Merlitz, Hauke Rabbel, Jens Uwe Sommer
Using coarse-grained molecular dynamics simulations we study the passive translocation of nanoparticles with a size of about 1 nm and with tunable degrees of hydrophobicity through lipid bilayer membranes. We observe a window of translocation with a sharp maximum for nanoparticles having a hydrophobicity in between hydrophilic and hydrophobic. Passive translocation can be identified as diffusive motion of individual particles in a free energy landscape. By combining direct sampling with umbrella-sampling techniques we calculate the free energy landscape for nanoparticles covering a wide range of hydrophobicities...
August 10, 2017: Journal of Physical Chemistry Letters
Daniel Corbett, Max Hebditch, Rose Keeling, Peng Ke, Sofia Ekizoglou, Prasad Srinivasan Sarangapani, Jai A Pathak, Christopher F van der Walle, Shahid Uddin, Clair Baldock, Carlos Avendano, Robin A Curtis
Predicting the concentrated solution behaviour for monoclonal antibodies requires developing and using minimal models to describe their shape and interaction potential. Towards this end, the small-angle X-ray scattering (SAXS) profiles for a monoclonal antibody (COE-03) have been measured under solution conditions chosen to produce weak self-association. The experiments are complemented with molecular simulations of a three-bead antibody model with and without inter-bead attraction. The scattering profile is extracted directly from the molecular simulation to avoid using the decoupling approximation...
August 10, 2017: Journal of Physical Chemistry. B
Holger Flechsig
Allosteric effects often underlie the activity of proteins, and elucidating generic design aspects and functional principles unique to allosteric phenomena represent a major challenge. Here an approach consisting of the in silico design of synthetic structures, which, as the principal element of allostery, encode dynamical long-range coupling among two sites, is presented. The structures are represented by elastic networks, similar to coarse-grained models of real proteins. A strategy of evolutionary optimization was implemented to iteratively improve allosteric coupling...
August 8, 2017: Biophysical Journal
Dingkun Hu, Wei Zhao, Yong Zhu, Hongqi Ai, Baotao Kang
A growing body of evidence shows that soluble Aβ aggregates, oligomers and even protofibrils, may be more neurotoxic than fibrils. Here we employ coarse grain model to investigate the aggregation of 75mer Aβ42 oligomers and salt effect, the cornerstone of fibril evolution. We find that the oligomer morphologies generated by 75 monomers or mixed by both 50 monomers and 5 preset pentameric nuclei are different (spherical vs bar-/disk-shaped) and characterize full of coil content (former) and >70% β-turn one (latter), respectively, indicating a novel role of the nuclei played in the early aggregation stage...
August 9, 2017: Chemistry: a European Journal
Hua Zhang, Tao Jiang, Guogen Shan, Shiqi Xu, Yujie Song
Gaussian network model (GNM), regarded as the simplest and most representative coarse-grained model, has been widely adopted to analyze and reveal protein dynamics and functions. Designing a variation of the classical GNM, by defining a new Kirchhoff matrix, is the way to improve the residue flexibility modeling. We combined information arising from local relative solvent accessibility (RSA) between two residues into the Kirchhoff matrix of the parameter-free GNM. The undetermined parameters in the new Kirchhoff matrix were estimated by using particle swarm optimization...
August 8, 2017: Scientific Reports
A Sahai, B Lopez, C O Johnston, M Panesi
A novel reduced-order method is presented for modeling reacting flows characterized by strong non-equilibrium of the internal energy level distribution of chemical species in the gas. The approach seeks for a reduced-order representation of the distribution function by grouping individual energy states into macroscopic bins, and then reconstructing state population using the maximum entropy principle. This work introduces an adaptive grouping methodology to identify and lump together groups of states that are likely to equilibrate faster with respect to each other...
August 7, 2017: Journal of Chemical Physics
Jiajian Jiang, Andrew Abi Mansour, Peter J Ortoleva
Plasmon properties are of significant interest in pure and applied nanoscience. While time-dependent density functional theory (TDDFT) can be used to study plasmons, it becomes impractical for elucidating the effect of size, geometric arrangement, and dimensionality in complex nanosystems. In this study, a new multiscale formalism that addresses this challenge is proposed. This formalism is based on Trotter factorization and the explicit introduction of a coarse-grained (CG) structure function constructed as the Weierstrass transform of the electron wavefunction...
August 7, 2017: Journal of Chemical Physics
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