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.

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.

Molecular dynamics simulations of simple aromatic compounds adsorption on single-walled carbon nanotubes

RSC Advances ◽  
2016 ◽  
Vol 6 (84) ◽  
pp. 80972-80980 ◽  
Author(s):  
Han Ding ◽  
Xin Shen ◽  
Chao Chen ◽  
Xiaojian Zhang
Keyword(s):  
Carbon Nanotubes ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Aromatic Compounds ◽  
Single Walled Carbon Nanotubes ◽  
Md Simulations ◽  
Single Walled Carbon ◽  
Dynamics Simulations ◽  
Walled Carbon Nanotubes

We have conducted MD simulations and RDG calculations to reveal the mechanisms of simple aromatic compounds adsorption on SWCNTs.

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 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.

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 Diffusive-Ballistic Heat Conduction in Carbon Nanotubes

2007 ◽  
Vol 1022 ◽  
Author(s):  
Junichiro Shiomi ◽  
Shigeo Maruyama
Keyword(s):  
Thermal Conductivity ◽  
Carbon Nanotubes ◽  
Molecular Dynamics ◽  
Heat Conduction ◽  
Md Simulations ◽  
Gradual Transition ◽  
Length Dependence ◽  
Conductivity Profile ◽  
Non Equilibrium Molecular Dynamics ◽  
Dynamics Simulations

AbstractHeat conduction of finite-length single-walled carbon nanotubes (SWNTs) has been studied by means of non-equilibrium molecular dynamics (MD) simulations. The length-dependence of the thermal conductivity was quantified for a range of nanotube-lengths at room temperature. The length dependence of thermal conductivity exhibits a gradual transition from nearly pure ballistic heat conduction to diffusive-ballistic heat conduction. The results show that the thermal conductivity profile does not converge even beyond a micrometer nanotube-length. Furthermore, the diameter dependence suggests that the phonon diffusion is reduced with the diameter.

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.

Silver nitrate in aqueous solution and as molten salt: A molecular dynamics simulation and NMR relaxation study

1994 ◽  
Vol 72 (11) ◽  
pp. 2278-2285 ◽  
Author(s):  
Aatto Laaksonen ◽  
Helena Kovacs
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Silver Nitrate ◽  
Nmr Relaxation ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Correlation Times ◽  
Nitrate Ion ◽  
Relaxation Measurements ◽  
Dynamics Simulations

Using molecular dynamics simulations, the motion and intermolecular interactions of the ions of silver nitrate are studied in aqueous solution and compared to the results obtained from simulations of molten AgNO3. The particularly interesting and experimentally frequently studied modes of reorientational motion (in-plane and end-over-end) of the planar nitrate ion have been determined from the simulation results. In accordance with earlier experimental results, the correlation times for the end-over-end rotation in aqueous solution are longer than those for the in-plane rotation, while the opposite is found to hold in the melt. In addition, the rotational motion of the nitrate ion in aqueous solution is experimentally studied using 14N relaxation measurements. Good agreement is found between the reorientational correlation times obtained from MD simulations and from NMR relaxation measurements.

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 Lipid molecules can induce an opening of membrane-facing tunnels in cytochrome P450 1A2

2016 ◽  
Vol 18 (44) ◽  
pp. 30344-30356 ◽  
Author(s):  
Petr Jeřábek ◽  
Jan Florián ◽  
Václav Martínek
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Cytochrome P450 ◽  
Molecular Dynamics Simulations ◽  
Coarse Grained ◽  
Cytochrome P450 1A2 ◽  
Structure And Dynamics ◽  
Human Cytochrome ◽  
Membrane Bound ◽  
Dynamics Simulations

The structure and dynamics of the membrane-bound full-length human cytochrome P450 1A2 (CYP1A2) in aqueous solution determined by coarse-grained and all-atom molecular dynamics simulations.

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