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Coarse grain

Brandon L Peters, K Michael Salerno, Anupriya Agrawal, Dvora Perahia, Gary S Grest
The distinctive viscoelastic behavior of polymers results from a coupled interplay of motion on multiple length and time scales. Capturing the broad time and length scales of polymer motion remains a challenge. Using polyethylene (PE) as a model macromolecule, we construct coarse-grained (CG) models of PE with 3-6 methyl groups per CG bead and probe two critical aspects of the technique: pressure corrections required after iterative Boltzmann inversion (IBI) to generate CG potentials that match the pressure of reference fully-atomistic melt simulations and the transferability of CG potentials across temperatures...
May 23, 2017: Journal of Chemical Theory and Computation
David N Stelter, Tom Keyes
Freezing and melting of dipalmitoylphosphatidylcholine (DPPC) bilayers are simulated in both the explicit (Wet) and implicit solvent (Dry) coarse-grained MARTINI force fields with enhanced sampling, via the isobaric, molecular dynamics version of the generalized replica exchange method (gREM). Phase transitions are described with the entropic viewpoint, based upon the statistical temperature as a function of enthalpy, TS(H) = 1/(dS(H)/dH), where S is the configurational entropy. Bilayer thickness, area per lipid, and the second-rank order parameter (P2) are calculated vs temperature in the transition range...
May 22, 2017: Journal of Physical Chemistry. B
Jie Hu, Tao Chen, Moye Wang, Hue Sun Chan, Zhuqing Zhang
Structure-based coarse-grained Gō-like models have been used extensively in deciphering protein folding mechanisms because of their simplicity and tractability. Meanwhile, explicit-solvent molecular dynamics (MD) simulations with physics-based all-atom force fields have been applied successfully to simulate folding/unfolding transitions for several small, fast-folding proteins. To explore the degree to which coarse-grained Gō-like models and their extensions to incorporate nonnative interactions are capable of producing folding processes similar to those in all-atom MD simulations, here we systematically compare the computed unfolded states, transition states, and transition paths obtained using coarse-grained models and all-atom explicit-solvent MD simulations...
May 22, 2017: Physical Chemistry Chemical Physics: PCCP
R B Pandey, D J Jacobs, B L Farmer
The effect of preferential binding of solute molecules within an aqueous solution on the structure and dynamics of the histone H3.1 protein is examined by a coarse-grained Monte Carlo simulation. The knowledge-based residue-residue and hydropathy-index-based residue-solvent interactions are used as input to analyze a number of local and global physical quantities as a function of the residue-solvent interaction strength (f). Results from simulations that treat the aqueous solution as a homogeneous effective solvent medium are compared to when positional fluctuations of the solute molecules are explicitly considered...
May 21, 2017: Journal of Chemical Physics
Herre Jelger Risselada
Coarse-grained molecular dynamics simulations are applied to explore the experimentally observed ability of the liquid-ordered (lo)/liquid-disordered (ld) phase boundary to facilitate viral membrane fusion. Surprisingly, a formed fusion stalk can be both attracted (i.e., stalkophilic) and repelled (i.e., stalkophobic) by the lo/ld phase boundary. The phase boundary becomes stalkophilic if the lo phase constituents have the larger negative spontaneous curvature. In such a case, location of the highly curved stalk near the less-ordered and thus (relatively) softer boundary region becomes energetically favorable...
May 15, 2017: Biophysical Journal
Alberto Striolo, Brian Patrick Grady
Surfactant adsorption at solid-liquid interfaces is critical for a number of applications of vast industrial interest, and can also be used to seed surface-modification processes. Many of the surfaces of interest are nano-structured, as they might present surface roughness at the molecular scale, chemical heterogeneity, as well as a combination of both surface roughness and chemical heterogeneity. These effects provide 'lateral' confinement on the surfactant aggregates. It is of interest to quantify how much surfactant adsorbs on such nano-structured surfaces, and how the surfactant aggregates vary as the degree of lateral confinement changes...
May 18, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
Hwankyu Lee, Yong-Kul Lee
Asphaltene molecules, which consist of differently hydrogenated polyaromatic cores grafted with side alkyl chains of different sizes and grafting densities, were simulated with a solvent mixture of heptane and tetralin using coarse-grained force fields. Starting with the initial configuration of randomly distributed asphaltene molecules and solvents, the asphaltene molecules aggregate because of the attractive force between their polyaromatic cores, but their sizes and shapes differ. The average aggregate size decreases with an increase in the hydrogenated polycyclic core, side-chain length, and tetralin concentration, which agree with experimental observations in the hydrocracking process...
May 17, 2017: Physical Chemistry Chemical Physics: PCCP
Mauro L Mugnai, D Thirumalai
Myosin VI (MVI) is the only known member of the myosin superfamily that, upon dimerization, walks processively toward the pointed end of the actin filament. The leading head of the dimer directs the trailing head forward with a power stroke, a conformational change of the motor domain exaggerated by the lever arm. Using a unique coarse-grained model for the power stroke of a single MVI, we provide the molecular basis for its motility. We show that the power stroke occurs in two major steps. First, the motor domain attains the poststroke conformation without directing the lever arm forward; and second, the lever arm reaches the poststroke orientation by undergoing a rotational diffusion...
May 16, 2017: Proceedings of the National Academy of Sciences of the United States of America
Hongbo Ma, Jeffrey A Nittrouer, Kensuke Naito, Xudong Fu, Yuanfeng Zhang, Andrew J Moodie, Yuanjian Wang, Baosheng Wu, Gary Parker
Sedimentary dispersal systems with fine-grained beds are common, yet the physics of sediment movement within them remains poorly constrained. We analyze sediment transport data for the best-documented, fine-grained river worldwide, the Huanghe (Yellow River) of China, where sediment flux is underpredicted by an order of magnitude according to well-accepted sediment transport relations. Our theoretical framework, bolstered by field observations, demonstrates that the Huanghe tends toward upper-stage plane bed, yielding minimal form drag, thus markedly enhancing sediment transport efficiency...
May 2017: Science Advances
Leto Peel, Daniel B Larremore, Aaron Clauset
Across many scientific domains, there is a common need to automatically extract a simplified view or coarse-graining of how a complex system's components interact. This general task is called community detection in networks and is analogous to searching for clusters in independent vector data. It is common to evaluate the performance of community detection algorithms by their ability to find so-called ground truth communities. This works well in synthetic networks with planted communities because these networks' links are formed explicitly based on those known communities...
May 2017: Science Advances
Seungyong You, Ling Wei, Sachin Shanbhag, David H Van Winkle
Two-dimensional electrophoresis was used to analyze the mobility of DNA fragments in micellar gels of pluronic F127 (EO_{100}PO_{70}EO_{100}) and pluronic P123 (EO_{20}PO_{70}EO_{20}). The 20-3500 base pair DNA fragments were separated by size first in agarose gels, and then in pluronic gels at room temperature. In agarose gels, the DNA mobility decreases monotonically with increasing DNA length. In pluronic gels, however, the mobility varies nonmonotonically according to fragment lengths that are strongly correlated with the diameter of the spherical micelles...
April 2017: Physical Review. E
Yu Takano, Hiroshi Koibuchi
We present Monte Carlo data of the stress-strain diagrams obtained using two different triangulated surface models. The first is the canonical surface model of Helfrich and Polyakov (HP), and the second is a Finsler geometry (FG) model. The shape of the experimentally observed stress-strain diagram is called J-shaped. Indeed, the diagram has a plateau for the small strain region and becomes linear in the relatively large strain region. Because of this highly nonlinear behavior, the J-shaped diagram is far beyond the scope of the ordinary theory of elasticity...
April 2017: Physical Review. E
Gerhard Jung, Martin Hanke, Friederike Schmid
In recent years it has become increasingly popular to construct coarse-grained models with non-Markovian dynamics in order to account for an incomplete separation of time scales. One challenge of a systematic coarse-graining procedure is the extraction of the dynamical properties, namely the memory kernel, from equilibrium all-atom simulations. In this paper we propose an iterative method for memory reconstruction from dynamical correlation functions. Compared to previously proposed non-iterative techniques, it ensures by construction that the target correlation functions of the original fine-grained systems are reproduced accurately by the coarse-grained system, regardless of time step and discretization effects...
May 15, 2017: Journal of Chemical Theory and Computation
Johannes Franz, Tristan Bereau, Stefanie Pannwitt, Veerappan Anbazhagan, Alexander Lehr, Udo Nubbemeyer, Ulrich Dietz, Mischa Bonn, Tobias Weidner, Dirk Schneider
Nitrated fatty acids (NO2-FAs) act as anti-inflammatory signal mediators, albeit the molecular mechanisms behind NO2-FAs' influence on diverse metabolic and signaling pathways in inflamed tissues are essentially elusive. Here, we combine fluorescence measurements with surface-specific sum frequency generation vibrational spectroscopy and coarse-grained computer simulations to demonstrate that NO2-FAs alter lipid organization by accumulation at the membrane-water interface. As the function of membrane proteins strongly depends on both, protein structure as well as membrane properties, we consecutively follow the structural dynamics of an integral membrane protein in presence of NO2-FAs...
May 15, 2017: Chemistry: a European Journal
Ivana Dimić, Ivana Cvijović-Alagić, Anton Hohenwarter, Reinhard Pippan, Vesna Kojić, Jelena Bajat, Marko Rakin
The purpose of this study was to estimate the electrochemical behavior and biocompatibility of ultrafine-grained (UFG) commercially pure titanium (CPTi) and Ti-13Nb-13Zr (TNZ) alloy obtained by high-pressure torsion process. Electrochemical behavior of materials in artificial saliva at 37°C was evaluated by potentiodynamic polarization tests and electrochemical impedance spectroscopy (EIS), and the obtained results indicated that UFG TNZ alloy showed corrosion current density (jcorr  = 53 ± 5 nA cm(-2) ) which was 2 times lower compared to coarse-grained (CG) TNZ alloy (jcorr  = 110 ± 12 nA cm(-2) ) and higher corrosion resistance, while UFG CPTi and CPTi showed approximately the same corrosion rate (mean jcorr ∼ 38-40 nA cm(-2) )...
May 15, 2017: Journal of Biomedical Materials Research. Part B, Applied Biomaterials
Nathalie Colloc'h, Sophie Sacquin-Mora, Giovanna Avella, Anne-Claire Dhaussy, Thierry Prangé, Beatrice Vallone, Eric Girard
Investigating the effect of pressure sheds light on the dynamics and plasticity of proteins, intrinsically correlated to functional efficiency. Here we detail the structural response to pressure of neuroglobin (Ngb), a hexacoordinate globin likely to be involved in neuroprotection. In murine Ngb, reversible coordination is achieved by repositioning the heme more deeply into a large internal cavity, the "heme sliding mechanism". Combining high pressure crystallography and coarse-grain simulations on wild type Ngb as well as two mutants, one (V101F) with unaffected and another (F106W) with decreased affinity for CO, we show that Ngb hinges around a rigid mechanical nucleus of five hydrophobic residues (V68, I72, V109, L113, Y137) during its conformational transition induced by gaseous ligand, that the intrinsic flexibility of the F-G loop appears essential to drive the heme sliding mechanism, and that residue Val 101 may act as a sensor of the interaction disruption between the heme and the distal histidine...
May 12, 2017: Scientific Reports
Duccio Malinverni, Alfredo Jost Lopez, Paolo De Los Rios, Gerhard Hummer, Alessandro Barducci
The interaction between the Heat Shock Proteins 70 and 40 is at the core of the ATPase regulation of the chaperone machinery that maintains protein homeostasis. However, the structural details of the interaction are still elusive and contrasting models have been proposed for the transient Hsp70/Hsp40 complexes. Here we combine molecular simulations based on both coarse-grained and atomistic models with co-evolutionary sequence analysis to shed light on this problem by focusing on the bacterial DnaK/DnaJ system...
May 12, 2017: ELife
Tobias Rau, Florian Weik, Christian Holm
We present a coarse-grained (CG) model of a charged double-stranded DNA immersed in an electrolyte solution that can be used for a variety of electrokinetic applications. The model is based on an earlier rigid and immobile model of Weik et al. and includes now semi-flexibility and mobility, so that DNA dynamics can be sufficiently captured to simulate a full nanopore translocation process. To this end we couple the DNA hydrodynamically via a raspberry approach to a lattice-Boltzmann fluid and parametrize the counterions with a distant dependent friction...
May 12, 2017: Soft Matter
Zackary N Scholl, Weitao Yang, Piotr E Marszalek
Proteins obtain their final functional configuration through incremental folding with many intermediate steps in the folding pathway. If known, these intermediate steps could be valuable new targets for designing therapeutics and the sequence of events could elucidate the mechanism of refolding. However, determining these intermediate steps is hardly an easy feat, and has been elusive for most proteins, especially large, multidomain proteins. Here, we effectively map part of the folding pathway for the model large multidomain protein, Luciferase, by combining single-molecule force-spectroscopy experiments and coarse-grained simulation...
May 9, 2017: Biophysical Journal
Fabio Trovato, Edward P O'Brien
Chemical kinetic modeling has previously been used to predict that fast-translating codons can enhance cotranslational protein folding by helping to avoid misfolded intermediates. Consistent with this prediction, protein aggregation in yeast and worms was observed to increase when translation was globally slowed down, possibly due to increased cotranslational misfolding. Observation of similar behavior in molecular simulations would confirm predictions from the simpler chemical kinetic model and provide a molecular perspective on cotranslational folding, misfolding, and the impact of translation speed on these processes...
May 9, 2017: Biophysical Journal
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