scholarly journals Multiscale Modeling of Structure, Transport and Reactivity in Alkaline Fuel Cell Membranes: Combined Coarse-Grained, Atomistic and Reactive Molecular Dynamics Simulations

Polymers ◽  
2018 ◽  
Vol 10 (11) ◽  
pp. 1289 ◽  
Author(s):  
Dengpan Dong ◽  
Weiwei Zhang ◽  
Adam Barnett ◽  
Jibao Lu ◽  
Adri van Duin ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Md Simulations ◽  
Coarse Grained ◽  
Anion Exchange Membranes ◽  
Reactive Molecular Dynamics ◽  
Advantages And Disadvantages ◽  
Ionic Groups ◽  
Dynamics Simulations ◽  
Equilibrium Morphology ◽  
Hydrated Anion

In this study, molecular dynamics (MD) simulations of hydrated anion-exchange membranes (AEMs), comprised of poly(p-phenylene oxide) (PPO) polymers functionalized with quaternary ammonium cationic groups, were conducted using multiscale coupling between three different models: a high-resolution coarse-grained (CG) model; Atomistic Polarizable Potential for Liquids, Electrolytes and Polymers (APPLE&P); and ReaxFF. The advantages and disadvantages of each model are summarized and compared. The proposed multiscale coupling utilizes the strength of each model and allows sampling of a broad spectrum of properties, which is not possible to sample using any of the single modeling techniques. Within the proposed combined approach, the equilibrium morphology of hydrated AEM was prepared using the CG model. Then, the morphology was mapped to the APPLE&P model from equilibrated CG configuration of the AEM. Simulations using atomistic non-reactive force field allowed sampling of local hydration structure of ionic groups, vehicular transport mechanism of anion and water, and structure equilibration of water channels in the membrane. Subsequently, atomistic AEM configuration was mapped to ReaxFF reactive model to investigate the Grotthuss mechanism in the hydroxide transport, as well as the AEM chemical stability and degradation mechanisms. The proposed multiscale and multiphysics modeling approach provides valuable input for the materials-by-design of novel polymeric structures for AEMs.

Effective interaction between small unilamellar vesicles as probed by coarse-grained molecular dynamics simulations

2014 ◽  
Vol 86 (2) ◽  
pp. 215-222 ◽  
Author(s):  
Wataru Shinoda ◽  
Michael L. Klein
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Effective Interaction ◽  
Md Simulations ◽  
Coarse Grained ◽  
Repulsive Interaction ◽  
Spontaneous Curvature ◽  
Unilamellar Vesicles ◽  
Small Unilamellar Vesicles ◽  
Dynamics Simulations

Abstract A series of molecular dynamics (MD) simulations has been undertaken to investigate the effective interaction between vesicles including PC (phosphatidylcholine) and PE (phosphatidylethanolamine) lipids using the Shinoda–DeVane–Klein coarse-grained force field. No signatures of fusion were detected during MD simulations employing two apposed unilamellar vesicles, each composed of 1512 lipid molecules. Association free energy of the two stable vesicles depends on the lipid composition. The two PC vesicles exhibit a purely repulsive interaction with each other, whereas two PE vesicles show a free energy gain at the contact. A mixed PC/PE (1:1) vesicle shows a higher flexibility having a lower energy barrier on the deformation, which is caused by lipid sorting within each leaflet of the membranes. With a preformed channel or stalk between proximal membranes, PE molecules contribute to stabilize the stalk. The results suggest that the lipid components forming the membrane with a negative spontaneous curvature contribute to stabilize the stalk between two vesicles in contact.

scholarly journals Coupling all-atom molecular dynamics simulations of ions in water with Brownian dynamics

2016 ◽  
Vol 472 (2186) ◽  
pp. 20150556 ◽  
Author(s):  
Radek Erban
Keyword(s):  
Molecular Dynamics ◽  
Differential Equations ◽  
Aqueous Solutions ◽  
Molecular Dynamics Simulations ◽  
Brownian Dynamics ◽  
Md Simulations ◽  
Coarse Grained ◽  
Computational Domain ◽  
Coarse Grained Model ◽  
Dynamics Simulations

Molecular dynamics (MD) simulations of ions (K + , Na + , Ca 2+ and Cl − ) in aqueous solutions are investigated. Water is described using the SPC/E model. A stochastic coarse-grained description for ion behaviour is presented and parametrized using MD simulations. It is given as a system of coupled stochastic and ordinary differential equations, describing the ion position, velocity and acceleration. The stochastic coarse-grained model provides an intermediate description between all-atom MD simulations and Brownian dynamics (BD) models. It is used to develop a multiscale method which uses all-atom MD simulations in parts of the computational domain and (less detailed) BD simulations in the remainder of the domain.

scholarly journals Coarse-grained molecular dynamics simulations of nanoplastics interacting with a hydrophobic environment in aqueous solution

RSC Advances ◽  
2021 ◽  
Vol 11 (44) ◽  
pp. 27734-27744
Author(s):  
Lorenz F. Dettmann ◽  
Oliver Kühn ◽  
Ashour A. Ahmed
Keyword(s):  
Carbon Nanotubes ◽  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Water Treatment ◽  
Md Simulations ◽  
Coarse Grained ◽  
Treatment Technologies ◽  
Dynamics Simulations ◽  
Binding Mechanisms ◽  
Soil And Water

The binding mechanisms of nanoplastics (NPs) to carbon nanotubes as hydrophobic environmental systems have been explored by coarse-grained MD simulations. The results could be closely connected to fate of NPs in soil and water treatment technologies.

Revisiting stress–strain behavior and mechanical reinforcement of polymer nanocomposites from molecular dynamics simulations

2020 ◽  
Vol 22 (29) ◽  
pp. 16760-16771 ◽  
Author(s):  
Jianxiang Shen ◽  
Xiangsong Lin ◽  
Jun Liu ◽  
Xue Li
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Polymer Nanocomposites ◽  
Md Simulations ◽  
Coarse Grained ◽  
Stress Strain ◽  
Mechanical Reinforcement ◽  
Strain Behavior ◽  
Nanoparticle Interactions ◽  
Dynamics Simulations

Through coarse-grained MD simulations, the effects of nanoparticle properties, polymer–nanoparticle interactions, chain crosslinks and temperature on the stress–strain behavior and mechanical reinforcement of PNCs are comprehensively investigated.

MOLECULAR DYNAMICS SIMULATIONS OF HELIX BUNDLE PROTEINS USING UNRES FORCE FIELD AND ALL-ATOM FORCE FIELD

2012 ◽  
Vol 11 (06) ◽  
pp. 1201-1215 ◽  
Author(s):  
KAIFU GAO ◽  
MINGHUI YANG
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Protein A ◽  
Md Simulations ◽  
Time Frame ◽  
Coarse Grained ◽  
Staphylococcal Protein A ◽  
Villin Headpiece ◽  
Helix Bundle ◽  
Dynamics Simulations

We have investigated the folding of two helix-bundle proteins, 36-residue Villin headpiece and 56-residue E-domain of Staphylococcal protein A, by combining molecular dynamics (MD) simulations with Coarse-Grained United-Residue (UNRES) Force Field and all-atom force field. Starting from extended structures, each of the proteins was folded to a stable structure within a short time frame using the UNRES model. However, the secondary structures of helices were not well formed. Further refinement using MD simulations with the all-atom force field was able to fold the protein structure into the native-like state with the smallest main-chain root-mean-square deviation of around 3 Å. Detailed analysis of the folding trajectories was presented and the performance of GPU-based MD simulations was also discussed.

scholarly journals Perspectives on High-Throughput Ligand/Protein Docking With Martini MD Simulations

2021 ◽  
Vol 8 ◽  
Author(s):  
Paulo C. T. Souza ◽  
Vittorio Limongelli ◽  
Sangwook Wu ◽  
Siewert J. Marrink ◽  
Luca Monticelli
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
High Throughput ◽  
Protein Flexibility ◽  
Md Simulations ◽  
Protein Docking ◽  
Rational Drug Design ◽  
Coarse Grained ◽  
Scoring Functions ◽  
Dynamics Simulations

Molecular docking is central to rational drug design. Current docking techniques suffer, however, from limitations in protein flexibility and solvation models and by the use of simplified scoring functions. All-atom molecular dynamics simulations, on the other hand, feature a realistic representation of protein flexibility and solvent, but require knowledge of the binding site. Recently we showed that coarse-grained molecular dynamics simulations, based on the most recent version of the Martini force field, can be used to predict protein/ligand binding sites and pathways, without requiring any a priori information, and offer a level of accuracy approaching all-atom simulations. Given the excellent computational efficiency of Martini, this opens the way to high-throughput drug screening based on dynamic docking pipelines. In this opinion article, we sketch the roadmap to achieve this goal.

scholarly journals The Assembly Switch Mechanism of FtsZ Filament Revealed by All-Atom Molecular Dynamics Simulations and Coarse-Grained Models

2021 ◽  
Vol 12 ◽  
Author(s):  
Dashuai Lv ◽  
Jingyuan Li ◽  
Sheng Ye
Keyword(s):  
Molecular Dynamics ◽  
Bound States ◽  
Conformational Dynamics ◽  
Md Simulations ◽  
Coarse Grained ◽  
Multi Scale ◽  
Switch Mechanism ◽  
Dynamics Simulations ◽  
Cooperative Assembly ◽  
Computational Strategy

Bacterial cytoskeletal protein FtsZ binds and hydrolyzes GTP, and assembles into dynamic filaments that are essential for cell division. Here, we used a multi-scale computational strategy that combined all-atom molecular dynamics (MD) simulations and coarse-grained models to reveal the conformational dynamics of assembled FtsZ. We found that the top end of a filament is highly dynamic and can undergo T-to-R transitions in both GTP- and GDP-bound states. We observed several subcategories of nucleation related dimer species, which leading to a feasible nucleation pathway. In addition, we observed that FtsZ filament exhibits noticeable amounts of twisting, indicating a substantial helicity of the FtsZ filament. These results agree with the previously models and experimental data. Anisotropy network model (ANM) analysis revealed a polymerization enhanced assembly cooperativity, and indicated that the cooperative motions in FtsZ are encoded in the structure. Taken together, our study provides a molecular-level understanding of the diversity of the structural states of FtsZ and the relationships among polymerization, hydrolysis, and cooperative assembly, which should shed new light on the molecular basis of FtsZ’s cooperativity.

scholarly journals Lipid-Uptake Pathways and Lipid-Protein interactions in P-glycoprotein Revealed by Coarse-Grained Molecular Dynamics Simulations

2017 ◽  
Author(s):  
E. Barreto-Ojeda ◽  
V. Corradi ◽  
R.-X. Gu ◽  
D.P. Tieleman
Keyword(s):  
Molecular Dynamics ◽  
Protein Interactions ◽  
Experimental Studies ◽  
Md Simulations ◽  
Lipid Binding ◽  
Coarse Grained ◽  
Substrate Uptake ◽  
Lipid Uptake ◽  
P Glycoprotein ◽  
Dynamics Simulations

AbstractP-glycoprotein (P-gp) exports a broad range of dissimilar compounds, including drugs, lipids and lipid-like molecules. Due to its substrate promiscuity, P-gp is a key player in the development of cancer multidrug resistance (MDR). Although P-gp is one of the most studied members of ABC-transporters, the mechanism of how its substrates access the cavity remains unclear. In this work, we performed coarse-grained (CG) molecular dynamics (MD) simulations to explore possible pathways of lipid-uptake in the inward-facing conformation of P-gp embedded in bilayers with different PC:PE lipid ratios. Our results show that in the inward facing orientation only lipids from the lower leaflet are taken up by the transporter. We identify positively charged residues at the portals of P-gp that favor lipid entrance to the cavity, as well as lipid binding sites, in good agreement with previous experimental studies. Our results show no selectivity for PC vs. PE lipids. We offer several examples of lipid uptake-pathways for PC and PE lipids that help to elucidate the molecular mechanism of substrate-uptake in P-gp.

scholarly journals Reactive Molecular Dynamics Simulations On Thermal Decomposition of 3-Methyl-2,6-Dinitrophenol

2021 ◽  
Author(s):  
Jiaxiang Zhao ◽  
Yun Xiao ◽  
Jiayuan He ◽  
Jianlong Wang
Keyword(s):  
Molecular Dynamics ◽  
Thermal Decomposition ◽  
Intermediate Product ◽  
Md Simulations ◽  
Heating Rates ◽  
Intermediate Products ◽  
Reactive Molecular Dynamics ◽  
Reaxff Force Field ◽  
Dynamics Simulations ◽  
Time Required

Abstract The decomposition mechanism of 3-methyl-2,6-dinitrophenol (MDNP) was simulated by reaction molecular dynamics using ReaxFF force field. The evolution of some main products with time at different heating rates (10, 15 and 20 K·ps-1) were obtained as well. The simulation outcomes reveal that with the elevation of the heating rate, the shorter the time required for the system to reach equilibrium, and the more products are produced. At three heating rates, the main intermediate products are C7H7O5N2, C7H6O4N2, C7H5O5N2, C7H5O4N2, HON, NO, NO2 and the primary final products are N2, CO2, H2O, H2, NH3, amongst which C7H5O5N2 is the first produced intermediate product and H2O is the first produced final product with the biggest abundance. The intermediate products first increase and then decrease to zero. Moreover, the primary chemistry reactions in the MDNP pyrolysis are acquired by ReaxFF MD simulations.

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