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https://www.readbyqxmd.com/read/28653074/parameterization-of-a-coarse-grained-model-with-short-ranged-interactions-for-modeling-fuel-cell-membranes-with-controlled-water-uptake
#1
Jibao Lu, Chance Miller, Valeria Molinero
The design of polymer electrolyte membranes with controlled water uptake is of high importance for high-performance fuel cells, because the water content of the membranes modulates their conductivity, chemical stability and mechanical strength. The water activity aw controls the equilibrium water uptake of a system. Predicting aw of materials is currently a daunting challenge for molecular simulations, because calculations of water activity require grand canonical simulations that are extremely expensive even with classical non-polarizable force fields...
June 27, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28651901/benchmarking-numerical-codes-for-tracer-transport-with-the-aid-of-laboratory-scale-experiments-in-2d-heterogeneous-porous-media
#2
Fadji Hassane Maina, Philippe Ackerer, Anis Younes, Alberto Guadagnini, Brian Berkowitz
We present a combined experimental and numerical modeling study that addresses two principal questions: (i) is any particular Eulerian-based method used to solve the classical advection-dispersion equation (ADE) clearly superior (relative to the others), in terms of yielding solutions that reproduce BTCs of the kind that are typically sampled at the outlet of a laboratory cell? and (ii) in the presence of matches of comparable quality against such BTCs, do any of these methods render different (or similar) numerical BTCs at locations within the domain? To address these questions, we obtained measurements from carefully controlled laboratory experiments, and employ them as a reference against which numerical results are benchmarked and compared...
June 7, 2017: Journal of Contaminant Hydrology
https://www.readbyqxmd.com/read/28650048/cooperative-wrapping-of-nanoparticles-of-various-sizes-and-shapes-by-lipid-membranes
#3
Kai Xiong, Jiayin Zhao, Daowen Yang, Qingwen Cheng, Jiuling Wang, Hongbing Ji
Understanding the interaction between nanoparticles (NPs) and cell membranes is crucial for the design of NP-based drug delivery systems and for the assessment of the risks exerted by the NPs. Recent experimental and theoretical studies have shown that cell membranes can mediate attraction between NPs and form tubular structures to wrap multiple NPs. However, the cooperative wrapping process is still not well understood, and the shape effect of NPs is not considered. In this article, we use large-scale coarse-grained molecular dynamics (CGMD) simulations to study the cooperative wrapping of NPs when a varying number of NPs adhered to the membrane...
June 26, 2017: Soft Matter
https://www.readbyqxmd.com/read/28649721/role-of-dynamic-heterogeneities-in-ionic-liquids-insights-from-all-atom-and-coarse-grained-molecular-dynamics-simulation-studies
#4
Tamisra Pal, Michael Vogel
We performed molecular dynamics simulations for the room-temperature ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate ([Bmim][PF6 ]). By employing all-atom (AA) and coarse-grained (CG) models, we compared the characteristic times of various dynamical modes, from vibration to diffusion, and the importance of dynamical heterogeneities at different levels of chemical resolution and over broad temperature ranges. It was shown that coarse graining leads to a substantial speedup in molecular dynamics, whereas it weakly affects the strength of dynamical heterogeneities...
June 26, 2017: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
https://www.readbyqxmd.com/read/28648754/what-can-human-guided-simulations-bring-to-rna-folding
#5
Liuba Mazzanti, Sébastien Doutreligne, Cedric Gageat, Philippe Derreumaux, Antoine Taly, Marc Baaden, Samuela Pasquali
Inspired by the recent success of scientific-discovery games for predicting protein tertiary and RNA secondary structures, we have developed an open software for coarse-grained RNA folding simulations, guided by human intuition. To determine the extent to which interactive simulations can accurately predict 3D RNA structures of increasing complexity and lengths (four RNAs with 22-47 nucleotides), an interactive experiment was conducted with 141 participants who had very little knowledge of nucleic acids systems and computer simulations, and had received only a brief description of the important forces stabilizing RNA structures...
June 22, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28646778/the-hydrological-functioning-of-a-constructed-fen-wetland-watershed
#6
Scott J Ketcheson, Jonathan S Price, Owen Sutton, George Sutherland, Eric Kessel, Richard M Petrone
Mine reclamation requires the reconstruction of entire landforms and drainage systems. The hydrological regime of reclaimed landscapes will be a manifestation of the processes operating within the individual landforms that comprise it. Hydrology is the most important process regulating wetland function and development, via strong controls on chemical and biotic processes. Accordingly, this research addresses the growing and immediate need to understand the hydrological processes that operate within reconstructed landscapes following resource extraction...
June 21, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28643001/prediction-of-self-assemblies-of-sodium-dodecyl-sulfate-and-fragrance-additives-using-coarse-grained-force-fields
#7
Chunwei Yang, Zhe Shen, Liang Wu, Haiqiu Tang, Lifeng Zhao, FengLei Cao, Huai Sun
Coarse-grained force field (CGFF) methods were applied to study the self-assembly of sodium dodecyl sulfate with fragrance additives. The CGFF parameters were parameterized and validated using experimental and all-atom simulation data. Direct molecular dynamics simulations were carried out to characterize the initial aggregation, partitioning of fragrances, and chemical potentials of the surfactant and fragrance molecules in aggregates of different sizes. The equilibrium critical micelle concentrations (CMCs) and micelle size distributions, which could not be obtained by direct simulation, were predicted using the calculated chemical potentials in combination with a thermodynamic model...
July 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28642368/the-influence-of-disulfide-bonds-on-the-mechanical-stability-of-proteins-is-context-dependent
#8
Aitor Manteca, Álvaro Alonso-Caballero, Marie Fertin, Simon Poly, David De Sancho, Raul Perez-Jimenez
Disulfide bonds play a crucial role in proteins, modulating their stability and constraining their conformational dynamics. A particularly important case is that of proteins that need to withstand forces arising from their normal biological function and that are often disulfide bonded. However, the influence of disulfides on the overall mechanical stability of proteins is poorly understood. Here, we used single-molecule force spectroscopy (smFS) to study the role of disulfide bonds in different mechanical proteins in terms of their unfolding forces...
June 22, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28639287/exploration-of-conformational-changes-in-lactose-permease-upon-sugar-binding-and-proton-transfer-through-coarse-grained-simulations
#9
Yead Jewel, Prashanta Dutta, Jin Liu
Escherichia coli lactose permease (LacY) actively transports lactose and other galactosides across cell membranes through lactose/H(+) symport process. Lactose/H(+) symport is a highly complex process that involves sugar translocation, H(+) transfer, as well as large-scale protein conformational changes. The complete picture of lactose/H(+) symport is largely unclear due to the complexity and multiscale nature of the process. In this work, we develop the force field for sugar molecules compatible with PACE, a hybrid and coarse-grained force field that couples the united-atom protein models with the coarse-grained MARTINI water/lipid...
June 22, 2017: Proteins
https://www.readbyqxmd.com/read/28636915/probing-the-structural-dynamics-of-the-nmda-receptor-activation-by-coarse-grained-modeling
#10
Wenjun Zheng, Han Wen, Gary J Iacobucci, Gabriela K Popescu
N-Methyl-D-aspartate (NMDA) receptors are glutamate-gated excitatory channels that play essential roles in brain functions. High-resolution structures have been solved for an allosterically inhibited and agonist-bound form of a functional NMDA receptor; however, other key functional states (particularly the active open-channel state) were only resolved at moderate resolutions by cryo-electron microscopy (cryo-EM). To decrypt the mechanism of the NMDA receptor activation, structural modeling is essential to provide presently missing information about structural dynamics...
June 20, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28636825/a-new-mixed-all-atom-coarse-grained-model-application-to-melittin-aggregation-in-aqueous-solution
#11
Mee Y Shelley, Myvizhi Esai Selvan, Jun Zhao, Volodymyr Babin, Chenyi Liao, Jianing Li, John Clarence Shelley
We introduce a new mixed resolution, all-atom/coarse-grained approach (AACG) for modeling peptides in aqueous solution and apply it to characterizing the aggregation of melittin. All of the atoms in peptidic components are represented while a single site is used for each water molecule. With the full flexibility of the peptide retained, our AACG method achieves speedups by a factor of 3-4 for CPU time reduction and another factor of roughly 7 for diffusion. An Ewald treatment permits the inclusion of long-range electrostatic interactions...
June 21, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28635295/coarse-grained-models-of-aqueous-and-pure-liquid-alkanes
#12
Gaurav Gyawali, Samuel Sternfield, Revati Kumar, Steven W Rick
A model for linear alkanes is presented in which interaction sites are only on the carbon atoms and the range of the potential is reduced using the Stillinger-Weber potential. The model is optimized for aqueous and liquid alkane properties and can match thermodynamic and structural properties, including solvation free energies, liquid densities, and liquid/vapor and liquid/water surface tensions for alkanes over a range of lengths.The results for long alkanes indicates that such models can be useful as accurate, yet efficient, coarse-grained potentials for macromolecules in water and other environments...
June 21, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28634293/intrinsic-map-dynamics-exploration-for-uncharted-effective-free-energy-landscapes
#13
Eliodoro Chiavazzo, Roberto Covino, Ronald R Coifman, C William Gear, Anastasia S Georgiou, Gerhard Hummer, Ioannis G Kevrekidis
We describe and implement a computer-assisted approach for accelerating the exploration of uncharted effective free-energy surfaces (FESs). More generally, the aim is the extraction of coarse-grained, macroscopic information from stochastic or atomistic simulations, such as molecular dynamics (MD). The approach functionally links the MD simulator with nonlinear manifold learning techniques. The added value comes from biasing the simulator toward unexplored phase-space regions by exploiting the smoothness of the gradually revealed intrinsic low-dimensional geometry of the FES...
June 20, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28633811/effects-and-mechanism-of-ultrasonic-irradiation-on-solidification-microstructure-and-mechanical-properties-of-binary-tial-alloys
#14
Ruirun Chen, Deshuang Zheng, Tengfei Ma, Hongsheng Ding, Yanqing Su, Jingjie Guo, Hengzhi Fu
In spite of their high temperature and reactivity, the binary TiAl alloys are successfully imposed by the ultrasonic irradiation and the microstructure evolution, solidification behaviors and mechanical properties are elaborately investigated. After ultrasonic irradiation, a high quality ingot without shrinkage defects and element segregation is obtained and the coarse dendrite structure is well modified into fine non-dendrite globular grains. The coarse lamellar colony and lamellar space of Ti44Al alloy is refined from 685μm to 52μm and 1185nm to 312nm, respectively (similarly, 819μm to 102μm and 2085nm to 565nm for Ti48Al alloy)...
September 2017: Ultrasonics Sonochemistry
https://www.readbyqxmd.com/read/28633759/martini-coarse-grained-force-field-extension-to-rna
#15
Jaakko J Uusitalo, Helgi I Ingólfsson, Siewert J Marrink, Ignacio Faustino
RNA has an important role not only as the messenger of genetic information but also as a regulator of gene expression. Given its central role in cell biology, there is significant interest in studying the structural and dynamic behavior of RNA in relation to other biomolecules. Coarse-grain molecular dynamics simulations are a key tool to that end. Here, we have extended the coarse-grain Martini force field to include RNA after our recent extension to DNA. In the same way DNA was modeled, the tertiary structure of RNA is constrained using an elastic network...
June 17, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28631928/free-energy-of-nanoparticle-binding-to-multivalent-polymeric-substrates
#16
Chad Gu, Rob D Coalson, David Jasnow, Anton Zilman
Characterization of the interactions between nanosize ligands and polymeric substrates is important for predictive design of nanomaterials and in biophysical applications. The multivalent nature of the polymer-nanoparticle interaction and the dynamics of multiple internal conformations of the polymer chains makes it difficult to infer microscopic interactions from macroscopic binding assays. Using coarse-grained simulations, we estimate the free energy of binding between a nanoparticle and a surface-grafted polymeric substrate as a function of pertinent parameters such as polymer chain length, nanoparticle size, and microscopic polymer-nanoparticle attraction...
June 20, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28630158/computational-studies-of-peptide-induced-membrane-pore-formation
#17
REVIEW
Richard Lipkin, Themis Lazaridis
A variety of peptides induce pores in biological membranes; the most common ones are naturally produced antimicrobial peptides (AMPs), which are small, usually cationic, and defend diverse organisms against biological threats. Because it is not possible to observe these pores directly on a molecular scale, the structure of AMP-induced pores and the exact sequence of steps leading to their formation remain uncertain. Hence, these questions have been investigated via molecular modelling. In this article, we review computational studies of AMP pore formation using all-atom, coarse-grained, and implicit solvent models; evaluate the results obtained and suggest future research directions to further elucidate the pore formation mechanism of AMPs...
August 5, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28629863/the-unfolding-mechanism-of-monomeric-mutant-sod1-by-simulated-force-spectroscopy
#18
Mona Habibi, Jörg Rottler, Steven S Plotkin
Mechanical unfolding of mutated apo, disulfide-reduced, monomeric superoxide dismutase 1 protein (SOD1) has been simulated via force spectroscopy techniques, using both an all-atom (AA), explicit solvent model and a coarse-grained heavy-atom Gō (HA-Gō) model. The HA-Gō model was implemented at two different pulling speeds for comparison. The most-common sequence of unfolding in the AA model agrees well with the most-common unfolding sequence of the HA-Gō model, when the same normalized pulling rate was used...
June 16, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28629720/exploring-connectivity-with-large-scale-granger-causality-on-resting-state-functional-mri
#19
Adora M DSouza, Anas Z Abidin, Lutz Leistritz, Axel Wismüller
BACKGROUND: Large-scale Granger causality (lsGC) is a recently developed, resting-state functional MRI (fMRI) connectivity analysis approach that estimates multivariate voxel-resolution connectivity. Unlike most commonly used multivariate approaches, which establish coarse-resolution connectivity by aggregating voxel time-series avoiding an underdetermined problem, lsGC estimates voxel-resolution, fine-grained connectivity by incorporating an embedded dimension reduction. NEW METHOD: We investigate application of lsGC on realistic fMRI simulations, modeling smoothing of neuronal activity by the hemodynamic response function and repetition time (TR), and empirical resting-state fMRI data...
June 16, 2017: Journal of Neuroscience Methods
https://www.readbyqxmd.com/read/28628337/buckling-under-pressure-curvature-based-lipid-segregation-and-stability-modulation-in-cardiolipin-containing-bilayers
#20
Kevin J Boyd, Nathan N Alder, Eric R May
Mitochondrial metabolic function is affected by the morphology and protein organization of the mitochondrial inner membrane (MIM). Cardiolipin (CL) is a unique tetra-acyl lipid that is involved in the maintenance of the highly-curved shape of the MIM as well as spatial organization of the proteins necessary for respiration and oxidative phosphorylation. Cardiolipin has been suggested to self-organize into lipid domains due to its inverted conical molecular geometry, though the driving forces for this organization are not fully understood...
June 19, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
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