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At least 109 records · Page 6

Advanced Potential Energy Surfaces for Molecular Simulation

Advanced potential energy surfaces are defined as theoretical models that explicitly include many-body effects that transcend the standard fixed-charge, pairwise-additive paradigm typically used in molecular simulation. However, several factors relating to their software implementation have precluded their widespread use in condensed-phase simulations: the computational cost of the theoretical models, a paucity of approximate models and algorithmic improvements that can ameliorate their cost, underdeveloped interfaces and limited dissemination in computational code bases that are widely used in the computational chemistry community, and software implementations that have not kept pace with modern high-performance computing (HPC) architectures, such as multicore CPUs and modern graphics processing units (GPUs). Here in this Feature Article we review recent progress made in these areas, including well-defined polarization approximations and new multipole electrostatic formulations, novel methods for solving the mutual polarization equations and increasing the MD time step, combining linear-scaling electronic structure methods with new QM/MM methods that account for mutual polarization between the two regions, and the greatly improved software deployment of these models and methods onto GPU and CPU hardware platforms. Finally, we have now approached an era where multipole-based polarizable force fields can be routinely used to obtain computational results comparable to state-of-the-art density functional theory while reaching sampling statistics that are acceptable when compared to that obtained from simpler fixed partial charge force fields.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Atomic Movies of Laser-Induced Structural and Phase Transformations from Molecular Dynamics Simulations

Molecular dynamics (MD) simulations of laser-materials interactions are playing an important role in investigation of complex and highly non-equilibrium processes involved in short pulse laser processing and surface modification. This role is defined by the ability of MD simulations to reveal in-depth information on the structural and phase transformations induced by the laser excitation and, at the same time, to provide clear visual representations, or “atomic movies,” of laser-induced dynamic processes. This chapter provides a brief overview of recent progress in the description of laser coupling and relaxation of photo-excited states in metals, semiconductors, insulators and molecular systems within the general framework of the classical MD technique and presents several examples of MD simulations of laser melting, generation of crystal defects, photomechanical spallation, explosive boiling and molecular entrainment in laser ablation. Possible directions of future progress in atomistic modeling of laser-materials interactions and the potential role of MD simulations in the design of an integrated multiscale computational model capable of accounting for interrelations between processes occurring at different time- and length-scales are discussed.

Classical Molecular Dynamic↗

Predicting the Macroscopic Fracture Energy of Epoxy Resins from Atomistic Molecular Simulations

Predicting the macroscopic fracture energy of highly crosslinked glassy polymers from atomistic simulations is challenging due to the size of the process zone being large in these systems. Here, we present a scale-bridging approach that links atomistic molecular dynamics simulations to macroscopic fracture properties on the basis of a continuum fracture mechanics model for two different epoxy materials. Our approach reveals that the fracture energy of epoxy resins strongly depends on the functionality of epoxy resin and the component ratio between the curing agent (amine) and epoxide. The most intriguing part of our study is that we demonstrate that the fracture energy exhibits a maximum value within the range of conversion degrees considered (from 65% to 95%), which can be attributed to the combined effects of structural rigidity and post-yield deformability. Our study provides physical insight into the molecular mechanisms that govern the fracture characteristics of epoxy resins and demonstrates the success of utilizing atomistic molecular simulations towards predicting macroscopic material properties.

42 ENGINEERING↗

A novel energy conversion based method for velocity correction in molecular dynamics simulations

Molecular dynamics (MD) simulation has become an important tool for studying micro- or nano-scale dynamics and the statistical properties of fluids and solids. In MD simulations, there are mainly two approaches: equilibrium and non-equilibrium molecular dynamics (EMD and NEMD). In this paper, a new energy conversion based correction (ECBC) method for MD is developed. Unlike the traditional systematic correction based on macroscopic parameters, the ECBC method is developed strictly based on the physical interaction processes between the pair of molecules or atoms. The developed ECBC method can apply to EMD and NEMD directly. While using MD with this method, the difference between the EMD and NEMD is eliminated, and no macroscopic parameters such as external imposed potentials or coefficients are needed. With this method, many limits of using MD are lifted. The application scope of MD is greatly extended.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Molecular simulation of homogeneous nucleation of crystals of an ionic liquid from the melt

The homogeneous nucleation of crystals of the ionic liquid [dmim{sup +}][Cl{sup −}] from its supercooled liquid phase in the bulk (P = 1 bar, T = 340 K, representing a supercooling of 58 K) was studied using molecular simulations. The string method in collective variables [Maragliano et al., J. Chem. Phys. 125, 024106 (2006)] was used in combination with Markovian milestoning with Voronoi tessellations [Maragliano et al., J. Chem. Theory Comput. 5, 2589–2594 (2009)] and order parameters for molecular crystals [E. E. Santiso and B. L. Trout, J. Chem. Phys. 134, 064109 (2011)] to sketch a minimum free energy path connecting the supercooled liquid and the monoclinic crystal phases, and to determine the free energy and the rates involved in the homogeneous nucleation process. The physical significance of the configurations found along this minimum free energy path is discussed with the help of calculations based on classical nucleation theory and with additional simulation results obtained for a larger system. Our results indicate that, at a supercooling of 58 K, the liquid has to overcome a free energy barrier of the order of 60 kcal/mol and to form a critical nucleus with an average size of about 3.6 nm, before it reaches the thermodynamically stable crystal phase. A simulated homogeneous nucleation rate of 5.0 × 10{sup 10} cm{sup −3} s{sup −1} was obtained for our system, which is in reasonable agreement with experimental and simulation rates for homogeneous nucleation of ice at similar degrees of supercooling. This study represents our first step in a series of studies aimed at understanding the nucleation and growth of crystals of organic salts near surfaces and inside nanopores.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Assessing the Impact of Point Defects on Molecular Diffusion in ZIF-8 Using Molecular Simulations

Because defects are ubiquitous in materials, they may play an important role in affecting the performance of materials in practical applications. In this paper, we investigate the influence of point defects on the diffusion of molecules including water, hydrocarbons, and acid gases in zeolitic imidazolate framework-8 (ZIF-8) using molecular simulations. To make these simulations possible, we introduce a force field that extends previous descriptions of pristine ZIF-8 to include experimentally relevant point defects. In general, the point defects we examined increase the local hopping rate for molecular diffusion, suggesting that low concentrations of these defects will not dominate long-range molecular diffusion in ZIF-8.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Molecular simulations of hydrated phyllomanganates

Hydrated phyllomanganates are layered Mn-oxide minerals with interlayers that can possess variable water contents and react strongly with trace metals due to octahedral vacancies in the layer. The unique properties of phyllomanganates afford them a significant role in many environmental phenomena that affect soil and water composition mainly via cation exchange and adsorption of trace metals. Slight variations in the structural and chemical composition often result in a dramatic difference in the chemical reactivity of the minerals. Molecular simulations at the classical mechanical level of theory, which uses a simplified description of the interatomic potential energies, can provide an atomistic perspective of the relationship between the chemical composition and the bulk and interlayer structures. Here, we introduce a set of interatomic potentials for hydrated phyllomanganates with variable vacancy and Mn 3+ content and report the classical mechanical simulation results performed at standard temperature and pressure. The potentials we introduce provide not only a reasonable reproduction of the experimentally determined atomic structures of the chalcophanite group, but also new insights on similar phyllomanganate minerals with hexagonal symmetry and a range of vacancy contents. When a vacancy is protonated, Mn 3+ is unstable in the hexagonal birnessite layer and occupies the interlayer as a cap on the associated vacancy. When a vacancy was charge-balanced by Mn 3+ and Na + , considerable amounts of Mn 3+ were incorporated into the hexagonal birnessite layer, but only at total Mn(III) contents greater than ~10% and with disordered layer stacking. The potentials also predicted a vacancy-free, triclinic Na-birnessite structure with Mn(III)-rich rows in the layer which were arranged parallel to the b-axis and separated by two rows of Mn(IV) octahedra. The dominant interlayer Na complex at a water content ≥0.7 H 2 O/MnO 2 was an octahedrally-coordinated, split interlayer site with two birnessite O atoms in the axial positions and four interlayer H 2 O in the equatorial positions. Other interlayer Na complexes including some edge- and face-sharing complexes existed in trace amounts (<10%). These classical mechanical simulations represent a successful first test of the introduced interatomic potentials, which can be used to further explore the interlayer and surface complexes of phyllomanganate and birnessite-group minerals.

58 GEOSCIENCES↗

Visual Analytics for Deep Embeddings of Large Scale Molecular Dynamics Simulations

Molecular Dynamics (MD) simulation have been emerging as an excellent candidate for understanding complex atomic and molecular scale mechanism of bio-molecules that control essential bio-physical phenomenon in a living organism. But this MD technique produces large-size and long-timescale data that are inherently high-dimensional and occupies many terabytes of data. Processing this immense amount of data in a meaningful way is becoming increasingly difficult. Therefore, specific dimensionality reduction algorithm using deep learning technique has been employed here to embed the high-dimensional data in a lower-dimension latent space that still preserves the inherent molecular characteristics i.e. retains biologically meaningful information. Subsequently, the results of the embedding models are visualized for model evaluation and analysis of the extracted underlying features. However, most of the existing visualizations for embeddings have limitations in evaluating the embedding models and understanding the complex simulation data. We propose an interactive visual analytics system for embeddings of MD simulations to not only evaluate and explain an embedding model but also analyze various characteristics of the simulations. Our system enables exploration and discovery of meaningful and semantic embedding results and supports the understanding and evaluation of results by the quantitatively described features of the MD simulations (even without specific labels).

Chae, Junghoon↗

Characterizing Surface Ice-Philicity Using Molecular Simulations and Enhanced Sampling

The formation of ice, which plays an important role in diverse contexts ranging from cryopreservation to atmospheric science, is often mediated by solid surfaces. Although surfaces that interact favorably with ice (relative to liquid water) can facilitate ice formation by lowering nucleation barriers, the molecular characteristics that confer ice-philicity to a surface are complex and incompletely understood. To address this challenge, here we introduce a robust and computationally efficient method for characterizing surface ice-philicity that combines molecular simulations and enhanced sampling techniques to quantify the free energetic cost of increasing surface–ice contact at the expense of surface–water contact. Using this method to characterize the ice-philicity of a family of model surfaces that are lattice matched with ice but vary in their polarity, we find that the nonpolar surfaces are moderately ice-phobic, whereas the polar surfaces are highly ice-philic. In contrast, for surfaces that display no complementarity to the ice lattice, we find that ice-philicity is independent of surface polarity and that both nonpolar and polar surfaces are moderately ice-phobic. Furthermore, our work thus provides a prescription for quantitatively characterizing surface ice-philicity and sheds light on how ice-philicity is influenced by lattice matching and polarity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

LongBondEliminator: A Molecular Simulation Tool to Remove Ring Penetrations in Biomolecular Simulation Systems

We develop a workflow, implemented as a plugin to the molecular visualization program VMD, that can fix ring penetrations with minimal user input. LongBondEliminator, detects ring piercing artifacts by the long, strained bonds that are the local minimum energy conformation during minimization for some assembled simulation system. The LongBondEliminator tool then automatically treats regions near these long bonds using multiple biases applied through NAMD. By combining biases implemented through the collective variables module, density-based forces, and alchemical techniques in NAMD, LongBondEliminator will iteratively alleviate long bonds found within molecular simulation systems. Through three concrete examples with increasing complexity, a lignin polymer, an viral capsid assembly, and a large, highly glycosylated protein aggrecan, we demonstrate the utility for this method in eliminating ring penetrations from classical MD simulation systems. The tool is available via gitlab as a VMD plugin, and has been developed to be generically useful across a variety of biomolecular simulations.

59 BASIC BIOLOGICAL SCIENCES↗

Density of States–Based Molecular Simulations

One of the central problems in statistical mechanics is that of finding the density of states of a system. Knowledge of the density of states of a system is equivalent to knowledge of its fundamental equation, from which all thermodynamic quantities can be obtained. Over the past several years molecular simulations have made considerable strides in their ability to determine the density of states of complex fluids and materials. Here we report on some of the more promising approaches proposed in the recent literature along with their advantages and limitations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Molecular Simulations of the Thermophysical Properties of Polyethylene Glycol Siloxane (PEGS) Solvent for Precombustion CO 2 Capture

Here, the thermophysical properties for neat polyethylene glycol siloxane solvent (PEGS) along with CO 2 , H 2 , H 2 O, and H 2 S gas absorption in PEGS at 298–373 K were investigated via molecular simulations. The predicted neat PEGS density, heat capacity, surface tension, and CO 2 and H 2 solubilities in PEGS solvent agree reasonably well with the experimental data, with typical differences of 0.8–20%, while the predicted PEGS solvent viscosity is 1.7–2.5 times larger than the experimental data. Gas solubility in PEGS at 298 K decreases in the following order, H 2 O (31000) > H 2 S (230) > CO 2 (33) > H 2 (1), which follows the same order as the gas–PEGS interaction. In contrast, gas diffusivity in PEGS at 298 K decreases in an opposite way, H 2 (1) > CO 2 (0.22) ≈ H 2 S (0.12) > H 2 O (0.018). The numbers in parentheses are the corresponding values relative to H 2 . Compared to the widely studied poly(dimethylsiloxane) (PDMS) solvent, PEGS is more hydrophilic due to its stronger interaction with H 2 O and fewer branched –CH 3 groups, which in turn leads to fewer hydrophobic pockets. The CO 2 /H 2 solubility selectivity in PEGS is larger than that in PDMS due to a stronger interaction with CO 2 in PEGS. Finally, it was found that CO 2 absorption in PEGS could significantly improve the CO 2 –PEGS solution dynamics by 5–6 times, resulting in a decrease in solution viscosity and increase in diffusivity. These CO 2 absorption effects are due to solution volume expansion upon CO 2 absorption compared to the neat PEGS solvent volume and the possibility that CO 2 acts as a “lubricant” to decrease the solvent–solvent interaction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Parallel continuous simulated tempering and its applications in large-scale molecular simulations

In this paper, we introduce a parallel continuous simulated tempering (PCST) method for enhanced sampling in studying large complex systems. It mainly inherits the continuous simulated tempering (CST) method in our previous studies [C. Zhang and J. Ma, J. Chem. Phys. 130, 194112 (2009); C. Zhang and J. Ma, J. Chem. Phys. 132, 244101 (2010)], while adopts the spirit of parallel tempering (PT), or replica exchange method, by employing multiple copies with different temperature distributions. Differing from conventional PT methods, despite the large stride of total temperature range, the PCST method requires very few copies of simulations, typically 2–3 copies, yet it is still capable of maintaining a high rate of exchange between neighboring copies. Furthermore, in PCST method, the size of the system does not dramatically affect the number of copy needed because the exchange rate is independent of total potential energy, thus providing an enormous advantage over conventional PT methods in studying very large systems. The sampling efficiency of PCST was tested in two-dimensional Ising model, Lennard-Jones liquid and all-atom folding simulation of a small globular protein trp-cage in explicit solvent. The results demonstrate that the PCST method significantly improves sampling efficiency compared with other methods and it is particularly effective in simulating systems with long relaxation time or correlation time. We expect the PCST method to be a good alternative to parallel tempering methods in simulating large systems such as phase transition and dynamics of macromolecules in explicit solvent.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Molecular-Level Insights into the NMR Relaxivity of Gadobutrol Using Quantum and Classical Molecular Simulations

MRI is an indispensable diagnostic tool in modern medicine; however, understanding the molecular-level processes governing NMR relaxation of water in the presence of MRI contrast agents remains a challenge, hindering the molecular-guided development of more effective contrast agents. By using quantum-based polarizable force fields, the first-of-its-kind molecular dynamics (MD) simulations of Gadobutrol are reported where the 1 H NMR longitudinal relaxivity r 1 of the aqueous phase is determined without any adjustable parameters. The MD simulations of r 1 dispersion (i.e., frequency dependence) show good agreement with measurements at frequencies of interest in clinical MRI. Importantly, the simulations reveal key insights into the molecular level processes leading to r 1 dispersion by decomposing the NMR dipole–dipole autocorrelation function G(t) into a discrete set of molecular modes, analogous to the eigenmodes of a quantum harmonic oscillator. The molecular modes reveal important aspects of the underlying mechanisms governing r 1 , such as its multiexponential nature and the importance of the second eigenmodal decay. By simply analyzing the MD trajectories on a parameter-free approach, the Gadobutrol simulations show that the outer-shell water contributes ∼50% of the total relaxivity r 1 compared to the inner-shell water, in contrast to simulations of (nonchelated) gadolinium-aqua where the outer shell contributes only ∼15% of r 1 . The deviation between simulations and measurements of r 1 below clinical MRI frequencies is used to determine the low-frequency electron-spin relaxation time for Gadobutrol, in good agreement with independent studies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Molecular Simulations of CO 2 and H 2 Solubility, CO 2 Diffusivity, and Solvent Viscosity at 298 K for 27 Commercially Available Physical Solvents

CO 2 and H 2 solubilities, CO 2 /H 2 solubility selectivities, CO 2 diffusivities, and solvent viscosities in 27 commercially available physical solvents at 298 K were calculated from molecular simulations using the CHARMM36 all-atom force field for most solvents, and the simulation results were compared with available experimental data in this report. The van der Waals radius parameters for solvents were slightly tuned to reproduce the experimental solvent density. The simulated CO 2 solubilities are comparable with the experimental data, with an average absolute difference of 28%. For the homologous compounds containing the –(OCH 2 CH 2 )– repeat unit, both simulated and experimental data show that CO 2 solubility decreases when the number of repeat units is increased; CO 2 solubilities in these homologous compounds exhibit almost a perfect positive linear correlation with the solvent free-volume fractions. The simulated H 2 solubilities and CO 2 /H 2 solubility selectivities are also comparable with the experimental data, with differences of 22% and 17%, respectively. The H 2 solubilities in all solvents researched here correlate very well with the solvent free-volume fractions, exhibiting a positive linear correlation coefficient of 0.84. Additionally, simulations show that CO 2 solubility decreases when the temperature is increased. In contrast, H 2 solubility increases at elevated temperature, which is partly due to the increased solvent free-volume fraction at elevated temperature. Lastly, although the viscosity difference tends to be large (30%–246%) between simulation and experiment, both simulated and experimental data exhibit a similar solvent viscosity trend. Furthermore, simulations show that CO 2 diffusivities in solvents are very strongly correlated with the solvent viscosities and the relationship between them is given by D$_{CO_{2}}$ = (2.6 ± 0.3) × 10 –9 /η solvent 0.59 ± 0.03.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Membrane Permeability of Fatty Acyl Compounds Studied via Molecular Simulation

Interest in fatty acid-derived products as fuel and chemical precursors has grown substantially. Microbes can be genetically engineered to produce fatty acid-derived products that are able to cross host membranes and can be extracted into an applied organic overlay. This process is thought to be passive, with a rate dependent on the chemistry of the crossing compound. The relationship between the chemical composition and the energetics and kinetics of product accumulation within the overlay is not well understood. Through biased and unbiased molecular simulation, we compute the membrane permeability coefficients from production to extraction for different fatty acyl products, including fatty acids, fatty alcohols, fatty aldehydes, alkanes, and alkenes. These simulations identify specific interactions that accelerate the transit of aldehydes across the membrane bilayer relative to other oxidized products, specifically the lack of hydrogen bonds to the surrounding membrane environment. However, since extraction from the outer membrane leaflet into the organic phase is found to be rate limiting for the entire process, we find that fatty alcohols and fatty aldehydes would both manifest similar fluxes into a dodecane overlay under equivalent conditions, outpacing the accumulation of acids or alkanes into the organic phase. Since aldehydes are known to be highly reactive as well as toxic in high quantities, the findings suggest that indeed fatty alcohols are the optimal long-tail fatty acyl product for extraction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Molecular Interactions at the Cellulose-Lignin Interface Explored via Molecular Simulation

Lignin and cellulose are found ubiquitously in plant cell walls, making them two of the most abundant biopolymers on Earth. In spite of their ubiquity, comparatively little is known quantitatively about their interactions within native biomass, and by extension how their interaction may play a role in biomaterials. The possible binding faces for lignin on crystalline cellulose I-ss and the heterogeneous chemistries found in native lignin typically preclude the isolation of specific interactions for quantitative comparison in the laboratory. In this study, we use molecular simulation to examine individual combinations of binding face and lignin chemistry to quantify lignin-cellulose interactions, including contributions from both specific hydrogen bonds and nonspecific van der Waals interactions. For all lignin chemistries simulated, the hydrophobic 200 face is the preferred for cellulose interactions. For hydrophilic crystalline faces, lignin is found to bind most effectively to the 110 face. The affinity between lignin and cellulose increases as additional lignin methoxy groups are added. These groups increase the lignin-cellulose contact area, increasing the binding affinity. These trends are extended to larger lignin polymers, where the relationships between lignin polymer size and binding affinity are quantified through biased simulation. In this case, the binding surface area between the lignin polymer and the cellulose surface dictates the interaction strength.

09 BIOMASS FUELS↗

Early Experiences Porting the NAMD and VMD Molecular Simulation and Analysis Software to GPU-Accelerated OpenPOWER Platforms, In: ISC High Performance 2016: High Performance Computing

All-atom molecular dynamics simulations of biomolecules provide a powerful tool for exploring the structure and dynamics of large protein complexes within realistic cellular environments. Unfortunately, such simulations are extremely demanding in terms of their computational requirements, and they present many challenges in terms of preparation, simulation methodology, and analysis and visualization of results. We describe our early experiences porting the popular molecular dynamics simulation program NAMD and the simulation preparation, analysis, and visualization tool VMD to GPU-accelerated OpenPOWER hardware platforms. We report our experiences with compiler-provided autovectorization and compare with hand-coded vector intrinsics for the POWER8 CPU. We explore the performance benefits obtained from unique POWER8 architectural features such as 8-way SMT and its value for particular molecular modeling tasks. Finally, we evaluate the performance of several GPU-accelerated molecular modeling kernels and relate them to other hardware platforms.

Computer Science↗