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https://www.readbyqxmd.com/read/28448145/coarse-grained-molecular-dynamics-model-of-double-stranded-dna-for-dna-nanostructure-design
#1
Hiromasa Yagyu, Jae-Young Lee, Do-Nyun Kim, Osamu Tabata
A new coarse-grained molecular dynamics double-stranded DNA model (nCG-dsDNA model) using an improved beads-spring model was proposed. In this model, nucleotide comprising phosphate, sugar, and base group were replaced by a single bead. The double stranded model with 202 base pairs was created to tune the parameters of the bond, the non-bond, stack, angle bending, and electrostatic interaction. The average twisted angle and the persistence length of the model without electrostatic interaction were calculated at 35...
April 27, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28447640/abrasion-set-limits-on-himalayan-gravel-flux
#2
Elizabeth H Dingle, Mikaël Attal, Hugh D Sinclair
Rivers sourced in the Himalayan mountain range carry some of the largest sediment loads on the planet, yet coarse gravel in these rivers vanishes within approximately 10-40 kilometres on entering the Ganga Plain (the part of the North Indian River Plain containing the Ganges River). Understanding the fate of gravel is important for forecasting the response of rivers to large influxes of sediment triggered by earthquakes or storms. Rapid increase in gravel flux and subsequent channel bed aggradation (that is, sediment deposition by a river) following the 1999 Chi-Chi and 2008 Wenchuan earthquakes reduced channel capacity and increased flood inundation...
April 26, 2017: Nature
https://www.readbyqxmd.com/read/28445748/directional-force-originating-from-atp-hydrolysis-drives-the-groel-conformational-change
#3
Jie Liu, Kannan Sankar, Yuan Wang, Kejue Jia, Robert L Jernigan
Protein functional mechanisms usually require conformational changes, and often there are known structures for the different conformational states. However, usually neither the origin of the driving force nor the underlying pathways for these conformational transitions is known. Exothermic chemical reactions may be an important source of forces that drive conformational changes. Here we investigate this type of force originating from ATP hydrolysis in the chaperonin GroEL, by applying forces originating from the chemical reaction...
April 25, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28440374/electrotunable-lubricity-with-ionic-liquids-the-influence-of-nanoscale-roughness
#4
Alessio David, Oscar Y Fajardo, Alexei A Kornyshev, Michael Urbakh, Fernando Bresme
The properties of ionic liquids can be modified by applying an external electrostatic potential, providing a route to control their performance in nanolubrication applications. Most computational studies to date have focused on the investigation of smooth surfaces. Real surfaces are generally inhomogeneous and feature roughness of different length scales. We report here a study of the possible effects that surface roughness may have on electrotunable lubricity with ionic liquids, performed here by means of non-equilibrium molecular dynamics simulations...
April 25, 2017: Faraday Discussions
https://www.readbyqxmd.com/read/28439230/from-anxious-to-reckless-a-control-systems-approach-unifies-prefrontal-limbic-regulation-across-the-spectrum-of-threat-detection
#5
REVIEW
Lilianne R Mujica-Parodi, Jiook Cha, Jonathan Gao
Here we provide an integrative review of basic control circuits, and introduce techniques by which their regulation can be quantitatively measured using human neuroimaging. We illustrate the utility of the control systems approach using four human neuroimaging threat detection studies (N = 226), to which we applied circuit-wide analyses in order to identify the key mechanism underlying individual variation. In so doing, we build upon the canonical prefrontal-limbic control system to integrate circuit-wide influence from the inferior frontal gyrus (IFG)...
2017: Frontiers in Systems Neuroscience
https://www.readbyqxmd.com/read/28435877/design-and-function-of-biomimetic-multilayer-water-purification-membranes
#6
Shengjie Ling, Zhao Qin, Wenwen Huang, Sufeng Cao, David L Kaplan, Markus J Buehler
Multilayer architectures in water purification membranes enable increased water throughput, high filter efficiency, and high molecular loading capacity. However, the preparation of membranes with well-organized multilayer structures, starting from the nanoscale to maximize filtration efficiency, remains a challenge. We report a complete strategy to fully realize a novel biomaterial-based multilayer nanoporous membrane via the integration of computational simulation and experimental fabrication. Our comparative computational simulations, based on coarse-grained models of protein nanofibrils and mineral plates, reveal that the multilayer structure can only form with weak interactions between nanofibrils and mineral plates...
April 2017: Science Advances
https://www.readbyqxmd.com/read/28433029/early-stages-of-clathrin-aggregation-at-a-membrane-in-coarse-grained-simulations
#7
M Giani, W K den Otter, W J Briels
The self-assembly process of clathrin coated pits during endocytosis has been simulated by combining and extending coarse grained models of the clathrin triskelion, the adaptor protein AP2, and a flexible network membrane. The AP2's core, upon binding to membrane and cargo, releases a motif that can bind clathrin. In conditions where the core-membrane-cargo binding is weak, the binding of this motif to clathrin can result in a stable complex. We characterize the conditions and mechanisms resulting in the formation of clathrin lattices that curve the membrane, i...
April 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28433024/perspective-dissipative-particle-dynamics
#8
Pep Español, Patrick B Warren
Dissipative particle dynamics (DPD) belongs to a class of models and computational algorithms developed to address mesoscale problems in complex fluids and soft matter in general. It is based on the notion of particles that represent coarse-grained portions of the system under study and allow, therefore, reaching time and length scales that would be otherwise unreachable from microscopic simulations. The method has been conceptually refined since its introduction almost twenty five years ago. This perspective surveys the major conceptual improvements in the original DPD model, along with its microscopic foundation, and discusses outstanding challenges in the field...
April 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28433020/introducing-the-mean-field-approximation-to-cdft-mmpol-method-statistically-converged-equilibrium-and-nonequilibrium-free-energy-calculation-for-electron-transfer-reactions-in-condensed-phases
#9
Hiroshi Nakano, Hirofumi Sato
A new theoretical method to study electron transfer reactions in condensed phases is proposed by introducing the mean-field approximation into the constrained density functional theory/molecular mechanical method with a polarizable force field (CDFT/MMpol). The method enables us to efficiently calculate the statistically converged equilibrium and nonequilibrium free energies for diabatic states in an electron transfer reaction by virtue of the mean field approximation that drastically reduces the number of CDFT calculations...
April 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28433015/probing-the-effects-of-surface-hydrophobicity-and-tether-orientation-on-antibody-antigen-binding
#10
Derek B Bush, Thomas A Knotts
Antibody microarrays have the potential to revolutionize molecular detection for many applications, but their current use is limited by poor reliability, and efforts to change this have not yielded fruitful results. One difficulty which limits the rational engineering of next-generation devices is that little is known, at the molecular level, about the antibody-antigen binding process near solid surfaces. Atomic-level structural information is scant because typical experimental techniques (X-ray crystallography and NMR) cannot be used to image proteins bound to surfaces...
April 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28433014/phase-behavior-of-supported-lipid-bilayers-a-systematic-study-by-coarse-grained-molecular-dynamics-simulations
#11
Asma Poursoroush, Maria Maddalena Sperotto, Mohamed Laradji
Solid-supported lipid bilayers are utilized by experimental scientists as models for biological membranes because of their stability. However, compared to free standing bilayers, their close proximity to the substrate may affect their phase behavior. As this is still poorly understood, and few computational studies have been performed on such systems thus far, here we present the results from a systematic study based on molecular dynamics simulations of an implicit-solvent model for solid-supported lipid bilayers with varying lipid-substrate interactions...
April 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28430446/piecing-together-the-allosteric-patterns-of-chaperonin-groel
#12
Jin Chen, Qian Zhang, Weitong Ren, Wenfei Li
Despite considerable effort, elucidating allostery of large macromolecular assemblies at a molecular level in solution remains technically challenging due to its structural complexity. Here we have employed an approach combining amide backbone hydrogen/deuterium exchange coupled with mass spectrometry, fluorescence spectroscopy and molecular simulations to characterize allosteric patterns of chaperonin GroEL, a ~800 kDa tetradecamer from E. coli. Using available crystal structures of GroEL, we quantitatively map out GroEL allosteric changes in solution by resolving exchange behaviors of 133 overlapping proteolytic peptides with more than 95% sequence coverage...
April 21, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28429759/dual-mechanisms-of-grain-refinement-in-a-fecocrni-high-entropy-alloy-processed-by-high-pressure-torsion
#13
Wenqian Wu, Min Song, Song Ni, Jingshi Wang, Yong Liu, Bin Liu, Xiaozhou Liao
An equiatomic FeCoCrNi high-entropy alloy with a face-centered cubic structure was fabricated by a powder metallurgy route, and then processed by high-pressure torsion. Detailed microscopy investigations revealed that grain refinement from coarse grains to nanocrystalline grains occurred mainly via concurrent nanoband (NB) subdivision and deformation twinning. NB-NB, twin-NB and twin-twin interactions contributed to the deformation process. The twin-twin interactions resulted in severe lattice distortion and accumulation of high densities of dislocations in the interaction areas...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28429276/enhancing-thermal-stability-of-a-highly-concentrated-insulin-formulation-with-pluronic-f-127-for-long-term-use-in-microfabricated-implantable-devices
#14
Jason Li, Michael K Chu, Brian Lu, Sako Mirzaie, Kuan Chen, Claudia R Gordijo, Oliver Plettenburg, Adria Giacca, Xiao Yu Wu
Development of highly concentrated formulations of protein and peptide drugs is a major challenge due to increased susceptibility to aggregation and precipitation. Numerous drug delivery systems including implantable and wearable controlled-release devices require thermally stable formulations with high concentrations due to limited device sizes and long-term use. Herein we report a highly concentrated insulin gel formulation (up to 80 mg/mL, corresponding to 2200 IU/mL), stabilized with a non-ionic amphiphilic triblock copolymer (i...
April 20, 2017: Drug Delivery and Translational Research
https://www.readbyqxmd.com/read/28426204/parameter-optimization-for-interaction-between-c-terminal-domains-of-hiv-1-capsid-protein
#15
Hao Sha, Fangqiang Zhu
HIV-1 capsid proteins (CAs) assemble into a capsid that encloses the viral RNA. The binding between a pair of C-terminal domains (CTDs) constitutes a major interface in both the CA dimers and the large CA assemblies. Here we attempt to use a general residue-level coarse-grained model to describe the interaction between two isolated CTDs in Monte Carlo simulations. With the standard parameters that depend only on the residue types, the model predicts a much weaker binding in comparison to the experiments. Detailed analysis reveals that some Lennard-Jones parameters are not compatible with the experimental CTD dimer structure, thus resulting in an unfavorable interaction energy...
April 20, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28425718/testing-high-concentrations-of-membrane-active-antibiotic-chlorhexidine-via-computational-titration-and-calorimetry
#16
Brad Van Oosten, Drew Marquardt, Thad A Harroun
Coarse grained strategies for membrane simulations are designed to increase the time and length scales of molecular dynamics simulations. For membrane active antibiotics, the concentration dependence of their action presents a tremendous challenge in simulation scale. In this study we examine the effects of concentration for the popular membrane active antibacterial drug chlorhexidine. It presents an interesting biophysical modelling test, where from experimental experience we know that model membranes of DMPC can absorb very high quantities of the drug without disruption...
April 20, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28423273/conformational-dynamics-of-mechanically-compliant-dna-nanostructures-from-coarse-grained-molecular-dynamics-simulations
#17
Ze Shi, Carlos E Castro, Gaurav Arya
Structural DNA nanotechnology, the assembly of rigid 3D structures of complex yet precise geometries, has recently been used to design dynamic, mechanically compliant nanostructures with tunable equilibrium conformations and conformational distributions. Here we use coarse-grained molecular dynamics simulations to provide insights into the conformational dynamics of a set of mechanically compliant DNA nanostructures-DNA hinges that use single-stranded DNA "springs" to tune the equilibrium conformation of a layered double-stranded DNA "joint" connecting two stiff "arms" constructed from DNA helix bundles...
April 24, 2017: ACS Nano
https://www.readbyqxmd.com/read/28422503/predicting-protein-interactions-of-concentrated-globular-protein-solutions-using-colloidal-models
#18
Mahlet Asfaw Woldeyes, Cesar Calero-Rubio, Eric M Furst, Christopher J Roberts
Protein interactions of α-chymotrypsinogen A (aCgn) were quantified using light scattering from low to high protein concentrations. Static light scattering (SLS) was used to determine the excess Rayleigh ratio (R(ex)) and osmotic second virial coefficients (B22) as a function of pH and total ionic strength (TIS). Repulsive (attractive) protein-protein interactions (PPI) were observed at pH 5 (pH 7), with decreasing repulsions (attractions) upon increasing TIS. Simple colloidal potential-of-mean force models (PMF) that account for short-range non-electrostatic attractions and screened electrostatic interactions were used to fit model parameters from data for B22 vs TIS at both pH values...
April 19, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28422265/nanoporous-poly-3-hexylthiophene-thin-film-structures-from-self-organization-of-a-tunable-molecular-bottlebrush-scaffold
#19
Suk-Kyun Ahn, Jan-Michael Y Carrillo, Jong K Keum, Jihua Chen, David Uhrig, Bradley S Lokitz, Bobby G Sumpter, S Michael Kilbey
The ability to widely tune the design of macromolecular bottlebrushes provides access to self-assembled nanostructures formed by microphase segregation in melt, thin film and solution that depart from structures adopted by simple linear copolymers. A series of random bottlebrush copolymers containing poly(3-hexylthiophene) (P3HT) and poly(d,l-lactide) (PLA) side chains grafted on a poly(norbornene) backbone were synthesized via ring-opening metathesis polymerization (ROMP) using the grafting through approach...
April 19, 2017: Nanoscale
https://www.readbyqxmd.com/read/28419507/a-rapid-solvent-accessible-surface-area-estimator-for-coarse-grained-molecular-simulations
#20
Shuai Wei, Charles L Brooks, Aaron T Frank
The rapid and accurate calculation of solvent accessible surface area (SASA) is extremely useful in the energetic analysis of biomolecules. For example, SASA models can be used to estimate the transfer free energy associated with biophysical processes, and when combined with coarse-grained simulations, can be particularly useful for accounting for solvation effects within the framework of implicit solvent models. In such cases, a fast and accurate, residue-wise SASA predictor is highly desirable. Here, we develop a predictive model that estimates SASAs based on Cα-only protein structures...
June 5, 2017: Journal of Computational Chemistry
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