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Coarse grain

Noam Brown, Jiangtao Lei, Chendi Zhan, Linda J W Shimon, Lihi Adler-Abramovich, Guanghong Wei, Ehud Gazit
Self-assembly is a process of key importance in natural systems and in nanotechnology. Peptides are attractive building blocks due to their relative facile synthesis, biocompatibility and other unique properties. Diphenylalanine (FF) and its derivatives are known to form nanostructures of various architectures and remarkable characteristics. The larger triphenylalanine (FFF) was found to self-assemble as efficiently as FF, forming related but distinct architectures of plate-like and spherical nanostructures...
March 20, 2018: ACS Nano
Mark Dunscombe, Anne Robertson, Ignacio Peralta-Maraver, Peter Shaw
There is little understanding of the variability in the structure and function of metazoan hyporheic communities across streams draining geologies that weather to produce different pore sizes and, by extension, different hydrological conditions. In this study we selected two catchments in each of three geologies that had differing values of hydraulic conductivity and porosity, and sampled four riffles in each catchment at high and low water levels and at two depths. We found clear differences in the physical template of streams draining different geologies and in the composition and abundance of communities inhabiting the hyporheic zones of streams draining chalk/sandstone and limestone geologies...
February 28, 2018: Science of the Total Environment
Philipp S Orekhov, Ekaterina G Kholina, Marine E Bozdaganyan, Alexey M Nesterenko, Ilya B Kovalenko, Marina G Strakhovskaya
Phthalocyanines are aromatic macrocyclic compounds, which are structurally related to porphyrins. In clinical practice phthalocyanines are used in fluorescence imaging and photodynamic therapy of cancer and non-cancer lesions. Certain forms of the substituted polycationic metallophthalocyanines have been previously shown to be active in photodynamic inactivation of both Gram-negative and Gram-positive bacteria, one of them is zinc octakis(cholinyl)phthalocyanine (ZnPcChol8+ ). However, the molecular details of how these compounds translocate across bacterial membranes still remain unclear...
March 19, 2018: Journal of Physical Chemistry. B
Xing Chen, Detlef Wolf, Juliane Siebourg-Polster, Christian Czech, Ulrike Bonati, Dirk Fischer, Omar Khwaja, Martin Strahm
Progressive and irreversible muscle atrophy characterizes Spinal Muscular Atrophy (SMA) and other similar muscle disorder diseases. Objective assessment of muscle functions is an essential and important, although challenging, prerequisite for successful clinical trials. Current clinical rating scales restrain the movement abnormalities to certain predefined coarse-grained individual items. The Kinect 3-D sensor has emerged as a low-cost and portable motion sensing technology used to capture and track people's movement in many medical and research fields...
February 12, 2018: Journal of Visualized Experiments: JoVE
Nazar Ileri Ercan, Pieter Stroeve, Joseph W Tringe, Roland Faller
We present a coarse-grained MARTINI model for methylene blue (MB) and investigate the interactions of MB with dioleylphosphatidylcholine (DOPC) lipid bilayers by molecular dynamics simulations. Our results show that the charge state of MB and the oxidation degree of the DOPC bilayer play critical roles on membrane properties. Oxidation of the DOPC bilayer significantly increases permeability of water and MB molecules irrespective of the charge state of MB. The most significant changes in membrane properties are obtained for peroxidized lipid bilayers in the presence of cationic MB, with ~11% increase in membrane area per lipid head group and ~7% and 44% reduction in membrane thickness and lateral diffusivity, respectively...
March 19, 2018: Langmuir: the ACS Journal of Surfaces and Colloids
F Nasi, M C Nordström, E Bonsdorff, R Auriemma, T Cibic, P Del Negro
Biological Traits Analysis (BTA) was used to identify functional features of infaunal polychaete assemblages associated with contamination in two Italian coastal areas: the harbour of Trieste (Adriatic Sea) and the Mar Piccolo of Taranto (Ionian Sea). The analysis was performed on 103 taxa, collected at four stations in each area. The two areas differed in species composition. The low diversity and the presence of stress-tolerant species in more polluted sites were not reflected in functional diversity, due to species contributing little to community functions or being functionally redundant...
March 9, 2018: Marine Environmental Research
A V Belyaev, J L Dunster, J M Gibbins, M A Panteleev, V Volpert
Hemostasis is a complex physiological mechanism that functions to maintain vascular integrity under any conditions. Its primary components are blood platelets and a coagulation network that interact to form the hemostatic plug, a combination of cell aggregate and gelatinous fibrin clot that stops bleeding upon vascular injury. Disorders of hemostasis result in bleeding or thrombosis, and are the major immediate cause of mortality and morbidity in the world. Regulation of hemostasis and thrombosis is immensely complex, as it depends on blood cell adhesion and mechanics, hydrodynamics and mass transport of various species, huge signal transduction networks in platelets, as well as spatiotemporal regulation of the blood coagulation network...
March 5, 2018: Physics of Life Reviews
Bruce Palmer
This paper will describe a formalism for using correlation functions between different grid cells as the basis for determining coarse-grained hydrodynamic equations for modeling the behavior of mesoscopic fluid systems. Configurations from a molecular dynamics simulation or other atomistic simulation are projected onto basis functions representing grid cells in a continuum hydrodynamic simulation. Equilibrium correlation functions between different grid cells are evaluated from the molecular simulation and used to determine the evolution operator for the coarse-grained hydrodynamic system...
February 2018: Physical Review. E
Shushan He, Lutz Maibaum
Understanding the (de)mixing behavior of multicomponent lipid bilayers is an important step towards unraveling the nature of spatial composition heterogeneities in cellular membranes and their role in biological function. We use coarse-grained molecular dynamics simulations to study the composition phase diagram of a quaternary mixture of phospholipids and cholesterol. This mixture is known to exhibit both uniform and coexisting phases. We compare and combine different statistical measures of membrane structure to identify the onset of phase coexistence in composition space...
March 16, 2018: Journal of Physical Chemistry. B
Yining Han, Jaehyeok Jin, Jacob W Wagner, Gregory A Voth
Coarse-grained (CG) models serve as a powerful tool to simulate molecular systems at much longer temporal and spatial scales. Previously, CG models and methods have been built upon classical statistical mechanics. The present paper develops a theory and numerical methodology for coarse-graining in quantum statistical mechanics, by generalizing the multiscale coarse-graining (MS-CG) method to quantum Boltzmann statistics. A rigorous derivation of the sufficient thermodynamic consistency condition is first presented via imaginary time Feynman path integrals...
March 14, 2018: Journal of Chemical Physics
Beatriz A Pazmiño Betancourt, Francis W Starr, Jack F Douglas
Relaxation in glass-forming liquids occurs as a multi-stage hierarchical process involving cooperative molecular motion. First, there is a "fast" relaxation process dominated by the inertial motion of the molecules whose amplitude grows upon heating, followed by a longer time α-relaxation process involving both large-scale diffusive molecular motion and momentum diffusion. Our molecular dynamics simulations of a coarse-grained glass-forming polymer melt indicate that the fast, collective motion becomes progressively suppressed upon cooling, necessitating large-scale collective motion by molecular diffusion for the material to relax approaching the glass-transition...
March 14, 2018: Journal of Chemical Physics
Andrea Torchi, Davide Bochicchio, Giovanni M Pavan
The rational design of supramolecular polymers that can adapt or respond in time to specific stimuli in controlled way is interesting for many applications, but this requires understanding the molecular factors that make the material faster or slower in responding to the stimulus. To this end, it is necessary to study the dynamic adaptive properties at submolecular resolution, which is difficult at experimental level. Here we show coarse-grained molecular dynamics simulations (<5Å resolution) demonstrating how the dynamic adaptivity and stimuli responsiveness of a supramolecular polymer is controlled by the intrinsic dynamics of the assembly, which is in turn determined by the structure of the monomers...
March 15, 2018: Journal of Physical Chemistry. B
Xiaoxiao Li, Jianning Liu, Zhuonan Liu, Mesfin Tsige, Shi-Qing Wang
New experiments show that tensile stress vanishes shortly after preyield deformation of polymer glasses while tensile stress after postyield deformation stays high and relaxes on much longer time scales, thus hinting at a specific molecular origin of stress in ductile cold drawing: chain tension rather than intersegmental interactions. Molecular dynamics simulation based on a coarse-grained model for polystyrene confirms the conclusion that the chain network plays an essential role, causing the glassy state to yield and to respond with a high level of intrachain retractive stress...
February 16, 2018: Physical Review Letters
Christian L Wennberg, Ali Narangifard, Magnus Lundborg, Lars Norlén, Erik Lindahl
The stratum corneum is the outermost layer of human skin and the primary barrier toward the environment. The barrier function is maintained by stacked layers of saturated long-chain ceramides, free fatty acids, and cholesterol. This structure is formed through a reorganization of glycosylceramide-based bilayers with cubic-like symmetry into ceramide-based bilayers with stacked lamellar symmetry. The process is accompanied by deglycosylation of glycosylceramides and dehydration of the skin barrier lipid structure...
March 13, 2018: Biophysical Journal
Anthony Banks, Sanbo Qin, Kevin L Weiss, Christopher B Stanley, Huan-Xiang Zhou
Conformational malleability allows intrinsically disordered proteins (IDPs) to respond agilely to their environments, such as nonspecifically interacting with in vivo bystander macromolecules (or crowders). Previous studies have emphasized conformational compaction of IDPs due to steric repulsion by macromolecular crowders, but effects of soft attraction are largely unexplored. Here we studied the conformational ensembles of the IDP FlgM in both polymer and protein crowders by small-angle neutron scattering...
March 13, 2018: Biophysical Journal
Amirhossein Mafi, Srinivas Abbina, Manu Thomas Kalathottukaren, James H Morrissey, Charles Haynes, Jayachandran N Kizhakkedathu, Jim Pfaendtner, Keng C Chou
Inorganic polyphosphate (polyP) released by human platelets has recently been shown to activate blood clotting and identified as a potential target for the development of novel antithrombotics. Recent studies have shown that polymers with cationic binding groups (CBGs) inhibit polyP and attenuate thrombosis. However, a good molecular-level understanding of the binding mechanism is lacking for further drug development. While molecular dynamics (MD) simulation can provide molecule-level information, the time scale required to simulate these large biomacromolecules makes classical MD simulation impractical...
March 14, 2018: Biomacromolecules
Takahiro Ohkuma, Kurt Kremer, Kostas Daoulas
Understanding properties of polymer alloys with computer simulations frequently requires equilibration of samples comprised of microscopically described long molecules. We present the extension of an efficient hierarchical backmapping strategy, initially developed for homopolymer melts, to equilibrate high-molecular-weight binary blends. These mixtures present significant interest for practical applications and fundamental polymer physics. In our approach, the blend is coarse-grained into models representing polymers as chains of soft blobs...
March 14, 2018: Journal of Physics. Condensed Matter: An Institute of Physics Journal
Yosadara Ruiz-Morales, Ascencion Romero-Martínez
The first critical micelle concentration (CMC) of the ionic surfactant sodium dodecyl sulfate (SDS), in diluted aqueous solution, has been determined at room temperature from the investigation of the bulk viscosity, at several concentrations of SDS, by means of coarse grain molecular dynamics simulations. The coarse-grained model molecules at the mesoscale level are adopted. The bulk viscosity of SDS was calculated at several millimolar concentrations of SDS in water using the MARTINI force field by means of NVT shear Mesocite molecular dynamics...
March 13, 2018: Journal of Physical Chemistry. B
Ronan M Keegan, Stuart J McNicholas, Jens M H Thomas, Adam J Simpkin, Felix Simkovic, Ville Uski, Charles C Ballard, Martyn D Winn, Keith S Wilson, Daniel J Rigden
Increasing sophistication in molecular-replacement (MR) software and the rapid expansion of the PDB in recent years have allowed the technique to become the dominant method for determining the phases of a target structure in macromolecular X-ray crystallography. In addition, improvements in bioinformatic techniques for finding suitable homologous structures for use as MR search models, combined with developments in refinement and model-building techniques, have pushed the applicability of MR to lower sequence identities and made weak MR solutions more amenable to refinement and improvement...
March 1, 2018: Acta Crystallographica. Section D, Structural Biology
K Michael Salerno, Noam Bernstein
Coarse-grained (CG) polymer simulations can access longer times and larger lengths than all-atom (AA) molecular dynamics simulations, however not all CG models correctly reproduce polymer properties on all length scales. Here we coarse grain atomistic position data from polyethylene (PE) and polytetrafluoroethylene (PTFE) melt simulations by combining λ backbone carbon atoms in a single CG bead. Resulting CG variables have correlations along the chain backbone that depend on the coarse-graining scale λ, and are generally not reproduced by independent bond-length, bond-angle and torsion-angle distributions...
March 12, 2018: Journal of Chemical Theory and Computation
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