Comparison of molecular dynamics simulation methods for the study of grain boundary migration
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charge transport↗
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Recovering position-dependent diffusion from biased molecular dynamics simulations
All atom molecular dynamics (MD) models provide valuable insight into the dynamics of biophysical systems, but are limited in size or length by the high computational demands. The latter can be reduced by simulating long term diffusive dynamics (also known as Langevin dynamics or Brownian motion) of the most interesting and important user-defined parts of the studied system, termed collective variables (colvars). A few hundred nanosecond-long biased MD trajectory can therefore be extended to millisecond lengths in the colvars subspace at a very small additional computational cost. In this work, we develop a method for determining multidimensional anisotropic position- and timescale-dependent diffusion coefficients (D) by analysing the changes of colvars in an existing MD trajectory. As a test case, we obtained D for dihedral angles of the alanine dipeptide. An open source Mathematica{sup ®} package, capable of determining and visualizing D in one or two dimensions, is available at https://github.com/lbf-ijs/DiffusiveDynamics . Given known free energy and D, the package can also generate diffusive trajectories.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Molecular dynamics simulations of a hydrophilic MIL-160-based membrane demonstrate pressure-dependent selective uptake of industrially relevant greenhouse
Oral presentation for ACS Spring Meeting
Chapman, Jordan↗
Resolving the organization of CO 2 molecules confined in silica nanopores using in situ small-angle neutron scattering and molecular dynamics simulations
This work quantifies the core–shell structure of nano-confined CO 2 molecules under pressure in silica pores using in operando small-angle neutron scattering (SANS) measurements and molecular dynamics simulations.
Mohammed, Sohaib↗
Molecular Dynamics Simulations of the Interfacial Region between Boehmite and Gibbsite Basal Surfaces and High Ionic Strength Aqueous Solutions
Classical molecular dynamics (MD) simulations were used to study the interactions of up to 2 M NaCl and NaNO3 aqueous solutions with the presumed inert boehmite (010) and gibbsite (001) surfaces. The force field parameters used in these simulations were validated against density functional theory calculations of Na+ and Cl- hydrated complexes adsorbed at the boehmite (010) surface. In all the classical MD simulations and regardless of the ionic strength or the nature of the anion, Na+ ions were found to preferably form inner-sphere complexes over outer-sphere complexes at the aluminum (oxy)hydroxide surfaces, adsorbing closer to the surface than both water molecules and anions. In contrast, Cl- ions were distributed almost equally between inner- and outer-sphere positions. The resulting asymmetry in adsorption strengths offers molecular-scale evidence for the observed isoelectric point (IEP) shift to higher pH at high ionic strength for aluminum (oxy)hydroxides. As such, the MD simulations also provided clear evidence against the assumption that the basal surfaces of boehmite and gibbsite are inert to background electrolytes. Finally, the MD simulations indicated that, although the adsorption behavior of Na+ in NaNO3 and NaCl solutions was similar, the different affinities of NO3- and Cl- for the aluminum (oxy)hydroxide surfaces might have macroscopic consequences, such as difference in the sensitivity of the IEP to the electrolyte concentration.
Shen, Zhizhang↗
Effect of Cu2+ Activation on Interfacial Water Structure at the Sphalerite Surface as Studied by Molecular Dynamics Simulation
In the first part of this paper, an experimental contact angle study of the fresh and Cu2+ activated sphalerite-ZnS surface as well as the covellite-CuS (001) surface is reported describing the increased hydrophobic character of the surface during Cu2+ activation. In addition to these experimental results, the fresh sphalerite-ZnS (110), copper-zinc sulfide-CuZnS2 (110), villamaninite- CuS2 (100), and covellite-CuS (001) surfaces were examined using Molecular Dynamics Simulation (MDS). Our MDS results on the behavior of interfacial water at the fresh sphalerite-ZnS (110), copper-zinc sulfide-CuZnS2 (110), villamaninite-CuS2 (100), and covellite-CuS (001) surfaces include simulated contact angles, water number density distribution, water dipole orientation, water residence time, and hydrogen-bonding considerations. The copper content at the Cu2+ activated sphalerite surface seems to account for the increased hydrophobicity as revealed by both experimental and MD simulated contact angle measurements. The relatively greater hydrophobic character developed at the Cu2+ activated sphalerite surface and at the copper-zinc sulfide surface has been described by MDS, based on the structure of interfacial water and its dynamic properties. L.X.D. acknowledges funding from the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences.
Jin, Jiaqi↗
Cytosolic expression, solution structures, and molecular dynamics simulation of genetically encodable disulfide‐rich de novo designed peptides
Abstract Disulfide‐rich peptides represent an important protein family with broad pharmacological potential. Recent advances in computational methods have made it possible to design new peptides which adopt a stable conformation de novo. Here, we describe a system to produce disulfide‐rich de novo peptides using Escherichia coli as the expression host. The advantage of this system is that it enables production of uniformly 13 C‐ and 15 N‐labeled peptides for solution nuclear magnetic resonance (NMR) studies. This expression system was used to isotopically label two previously reported de novo designed peptides, and to determine their solution structures using NMR. The ensemble of NMR structures calculated for both peptides agreed well with the design models, further confirming the accuracy of the design protocol. Collection of NMR data on the peptides under reducing conditions revealed a dependency on disulfide bonds to maintain stability. Furthermore, we performed long‐time molecular dynamics (MD) simulations with tempering to assess the stability of two families of de novo designed peptides. Initial designs which exhibited a stable structure during simulations were more likely to adopt a stable structure in vitro , but attempts to utilize this method to redesign unstable peptides to fold into a stable state were unsuccessful. Further work is therefore needed to assess the utility of MD simulation techniques for de novo protein design.
Buchko, Garry W.↗
High-Performance Molecular Dynamics Simulation for Biological and Materials Sciences: Challenges of Performance Portability, Dallas, TX, November 2018.
Highly-optimized parallel molecular dynamics programs have allowed researchers to achieve ground-breaking results in biological and materials sciences. This type of performance has come at the expense of portability: a significant effort is required for performance optimization on each new architecture. Using a metric that emphasizes speedup, we assess key accelerating programming components of four different best-performing molecular dynamics programs - GROMACS, NAMD, LAMMPS and CP2K-- each having a particular scope of application, for contribution to performance and for portability. We use builds with and without these components, tested on HPC systems. We also analyze the code-bases to determine compliance with portability recommendations. We find that for all four programs, the contributions of the non-portable components to speed are essential to the programs' performances; without them we see a reduction in time-to-solution of a magnitude that is insufferable to domain scientists. This characterizes the performance efficiency that must be approached for good performance portability on a programmatic level, suggesting solutions to this difficult problem, which should come from developers, industry and funding institutions, and possibly new research in programming languages.
Computer Science↗
Insights into Spontaneous Solid Electrolyte Interphase Formation at Magnesium Metal Anode Surface from Ab Initio Molecular Dynamics Simulations
Spontaneous chemical reactivity at multivalent (Mg, Ca, Zn, Al) electrode surfaces is critical to solid electrolyte interphase (SEI) formation, and hence, directly affects the longevity of batteries. Here, we report an investigation of the reactivity of 0.5 M Mg(TFSI)2 in 1,2-dimethoxyethane (DME) solvent at a Mg(0001) surface using ab initio molecular dynamics (AIMD) simulations and detailed Bader charge analysis. Based on the simulations, the initial degradation reactions of the electrolyte strongly depend on the structure of the Mg(TFSI)2 species near the anode surface. At the surface, the dissociation of Mg(TFSI)2 species occurs via cleavage of the N-S bond for the solvent separated ion pair (SSIP) and via cleavage of the C-S bond for the contact ion pair (CIP) configuration. In the case of the CIP, both TFSI anions undergo spontaneous bond dissociation reactions to form atomic O, C, S, F, and N species adsorbed on the surface of the Mg anode. These products indicate that the initial SEI layer formed on the surface of the pristine Mg anode consists of a complex mixture of multiple components such as oxides, carbides, sulfides, fluorides, and nitrides. We believe that the atomic level insights gained from these simulations will lay the groundwork for the rational design of tailored and functional interphases that are critical for the success of multivalent battery technology.
Agarwal, Garvit↗
Polarization as a field variable from molecular dynamics simulations: Applications to Electrical Double Layers.
Abstract not provided.
Mandadapu, Kranthi Kiran↗
Atomic and micro-structure features of nanoporous aluminosilicate glasses from reactive molecular dynamics simulations
Not provided.
Materials Science↗
Effect of ZrO 2 on the structure and properties of soda-lime silicate glasses from molecular dynamics simulations
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Lu, Xiaonan↗
Aggregation of cyclic polypeptoids bearing zwitterionic end-groups with attractive dipole–dipole and solvophobic interactions: a study by small-angle neutron scattering and molecular dynamics simulation
Aggregation behavior of cyclic polypeptoids bearing zwitterionic end-groups in methanol has been studied using a combination of experimental and simulation techniques. Here, the data from SANS and cryo-TEM indicate that the solution contains small clusters of these cyclic polypeptoids, ranging from a single polypeptoid chain to small oligomers, while the linear counterpart shows no cluster formation. Atomistic molecular dynamics simulations reveal that the driving force for this clustering behavior is due to the interplay between the effective repulsion due to the solvation of the dipoles formed by the charged end-groups in each polypeptoid chain and the attractive forces due to dipole–dipole interactions and the solvophobic effect.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Understanding nucleic acid structural changes by comparing wide-angle x-ray scattering (WAXS) experiments to molecular dynamics simulations
Wide-angle x-ray scattering (WAXS) is emerging as a powerful tool for increasing the resolution of solution structure measurements of biomolecules. Compared to its better known complement, small angle x-ray scattering (SAXS), WAXS targets higher scattering angles and can enhance structural studies of molecules by accessing finer details of solution structures. Although the extension from SAXS to WAXS is easy to implement experimentally, the computational tools required to fully harness the power of WAXS are still under development. Currently, WAXS is employed to study structural changes and ligand binding in proteins; however, the methods are not as fully developed for nucleic acids. Here, we show how WAXS can qualitatively characterize nucleic acid structures as well as the small but significant structural changes driven by the addition of multivalent ions. We show the potential of WAXS to test all-atom molecular dynamics (MD) simulations and to provide insight into understanding how the trivalent ion cobalt(III) hexammine (CoHex) affects the structure of RNA and DNA helices. We find that MD simulations capture the RNA structural change that occurs due to addition of CoHex.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Nanoparticle generation and transport resulting from femtosecond laser ablation of ultrathin metal films: Time-resolved measurements and molecular dynamics simulations
The synthesis of metal nanoparticles by ultrafast laser ablation of nanometers-thick metal films has been studied experimentally and computationally. Near-threshold backside laser ablation of 2–20 nm-thick Pt films deposited on fused silica substrates was found to produce nanoparticles with size distributions that were bimodal for the thicker films, but collapsed into a single mode distribution for the thinnest film. Time-resolved imaging of blackbody emission from the Pt nanoparticles was used to reveal the nanoparticle propagation dynamics and estimate their temperatures. The observed nanoparticle plume was compact and highly forward-directed with a well-defined collective velocity that permitted multiple rebounds with substrates to be revealed. Large-scale molecular dynamics simulations were used to understand the evolution of compressive and tensile stresses in the thicker melted liquid films that lead to their breakup and ejection of two groups of nanoparticles with different velocity and size distributions. Ultrafast laser irradiation of ultrathin (few nm) metal films avoids the splitting of the film and appears to be a method well-suited to cleanly synthesize and deposit nanoparticles from semitransparent thin film targets in highly directed beams.
77 NANOSCIENCE AND NANOTECHNOLOGY↗
Surface hopping molecular dynamics simulation of ultrafast methyl iodide photodissociation mapped by Coulomb explosion imaging
Our simulation demonstrates the robustness of the Coulomb explosion imaging technique in studying methyl iodide photodissociation, and shows that it can be effectively used for imaging non-adiabatic transitions in coordinate space.
Ding, Yijue↗
Structure and ionic diffusion of alkaline-earth ions in mixed cation glasses A 2 O–2MO–4SiO 2 with molecular dynamics simulations
Not Available
Konstantinou, Konstantinos↗
Local Elastic Constants for Epoxy-Nanotube Composites from Molecular Dynamics Simulation
A method from molecular dynamics simulation is developed for determining local elastic constants of an epoxy/nanotube composite. The local values of C11, C33, K12, and K13 elastic constants are calculated for an epoxy/nanotube composite as a function of radial distance from the nanotube. While the results possess a significant amount of statistical uncertainty resulting from both the numerical analysis and the molecular fluctuations during the simulation, the following observations can be made. If the size of the region around the nanotube is increased from shells of 1 to 6 in thickness, then the scatter in the data reduces enough to observe trends. All the elastic constants determined are at a minimum 20 from the center of the nanotube. The C11, C33, and K12 follow similar trends as a function of radial distance from the nanotube. The K13 decreases greater distances from the nanotube and becomes negative which may be a symptom of the statistical averaging.
Frankland, S. J. V.↗