Long Time Scale Ensemble Methods in Molecular Dynamics: Ligand–Protein Interactions and Allostery in SARS-CoV-2 Targets
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37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
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Evaluation of Methods for Molecular Dynamics Simulation of Ionic Liquid Electric Double Layers
We investigate how systematically increasing the accuracy of various molecular dynamics modeling techniques influences the structure and capacitance of ionic liquid electric double layers (EDLs). The techniques probed concern long-range electrostatic interactions, electrode charging (constant charge versus constant potential conditions), and electrolyte polarizability. Our simulations are performed on a quasi-two-dimensional, or slab-like, model capacitor, which is composed of a polarizable ionic liquid electrolyte, [EMIM][BF4], interfaced between two graphite electrodes. To ensure an accurate representation of EDL differential capacitance, we derive new fluctuation formulas that resolve the differential capacitance as a function of electrode charge or electrode potential. The magnitude of differential capacitance shows sensitivity to different long-range electrostatic summation techniques, while the shape of differential capacitance is affected by charging technique and the polarizability of the electrolyte. For long-range summation techniques, errors in magnitude can be mitigated by employing two-dimensional or corrected three dimensional electrostatic summations, which lead to electric fields that conform to those of a classical electrostatic parallel plate capacitor. With respect to charging, the changes in shape are a result of ions in the Stern layer (i.e. ions at the electrode surface) having a higher electrostatic affinity to constant potential electrodes than to constant charge electrodes. For electrolyte polarizability, shape changes originate from induced dipoles that soften the interaction of Stern layer ions with the electrode. The softening is traced to ion correlations vertical to the electrode surface that induce dipoles that oppose double layer formation. In general, our analysis indicates an accuracy dependent differential capacitance profile that transitions from the characteristic camel shape with coarser representations to a more diffuse profile with finer representations.
Haskins, Justin B.↗
Ultrafast charge transfer coupled to quantum proton motion at molecule/metal oxide interface
Understanding how the nuclear quantum effects (NQEs) in the hydrogen bond (H-bond) network influence the photoexcited charge transfer at semiconductor/molecule interface is a challenging problem. By combining two kinds of emerging molecular dynamics methods at the ab initio level, the path integral–based molecular dynamics and time-dependent nonadiabatic molecular dynamics, and choosing CH 3 OH/TiO 2 as a prototypical system to study, we find that the quantum proton motion in the H-bond network is strongly coupled with the ultrafast photoexcited charge dynamics at the interface. The hole trapping ability of the adsorbed methanol molecule is notably enhanced by the NQEs, and thus, it behaves as a hole scavenger on titanium dioxide. The critical role of the H-bond network is confirmed by in situ scanning tunneling microscope measurements with ultraviolet light illumination. It is concluded the quantum proton motion in the H-bond network plays a critical role in influencing the energy conversion efficiency based on photoexcitation.
74 ATOMIC AND MOLECULAR PHYSICS↗
Roadmap on multiscale materials modeling
Modeling and simulation is transforming modern materials science, becoming an important tool for the discovery of new materials and material phenomena, for gaining insight into the processes that govern materials behavior, and, increasingly, for quantitative predictions that can be used as part of a design tool in full partnership with experimental synthesis and characterization. Modeling and simulation is the essential bridge from good science to good engineering, spanning from fundamental understanding of materials behavior to deliberate design of new materials technologies leveraging new properties and processes. This Roadmap presents a broad overview of the extensive impact computational modeling has had in materials science in the past few decades, and offers focused perspectives on where the path forward lies as this rapidly expanding field evolves to meet the challenges of the next few decades. The Roadmap offers perspectives on advances within disciplines as diverse as phase field methods to model mesoscale behavior and molecular dynamics methods to deduce the fundamental atomic-scale dynamical processes governing materials response, to the challenges involved in the interdisciplinary research that tackles complex materials problems where the governing phenomena span different scales of materials behavior requiring multiscale approaches. The shift from understanding fundamental materials behavior to development of quantitative approaches to explain and predict experimental observations requires advances in the methods and practice in simulations for reproducibility and reliability, and interacting with a computational ecosystem that integrates new theory development, innovative applications, and an increasingly integrated software and computational infrastructure that takes advantage of the increasingly powerful computational methods and computing hardware.
36 MATERIALS SCIENCE↗
An accurate, non-empirical method for incorporating decoherence into Ehrenfest dynamics
In mixed quantum-classical nonadiabatic molecular dynamics methods, the anchoring of the electronic wave function to a single nuclear geometry results in both quantitative and qualitative errors in the dynamics. In the context of both Ehrenfest and trajectory surface hopping methods, methods for incorporating decoherence are widely used to eliminate these errors. However, the accuracy of these methods often depends strongly on the parameterization of the decoherence time and/or other related quantities. Here, we present a refinement of the recently introduced collapse to a block (TAB) scheme for incorporating decoherence into Ehrenfest dynamics. The proposed approach incorporates an approximation to the history of the population dynamics and treats the coherence decay as Gaussian, rather than exponential. This method uses parameters that can be obtained from first principles, rather than empirical fitting. Application to one-dimensional models indicates excellent agreement with numerically exact simulations. We also introduce a second refinement to the TAB method: a robust linear least-squares algorithm for determining collapse probabilities.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
The interpenetration polymer network in a cement paste–waterborne epoxy system
The formation of the interpenetrating polymer network (IPN) structure within the cement-polymer system has been revealed by experiments from 2 dimensional to 3-dimensional scales. However, the microstructure design and performance prediction of IPN as a function of specific C-S-H/polymer components or ingredients' parameters e.g. water to cement ratios (w/c), polymer to cement ratios (p/c), monomer components, degree of polymerization (DP), etc. is by far not available. Here we developed a mesoscale model for IPN visualization based on the Flory-Huggins interaction theory which was applied to cement science for the first time. All the ingredients in the micro-structure were considered as soluble beads with rational sizes based on their properties obtained by molecular dynamic methods. The interaction parameters of each bead were then determined based on their element ratios and chemical backbones. The model was validated with the waterborne epoxy-cement material (WECM) in which a novel waterborne epoxy resin (WEP) was prepared and impregnated. The verification results on the 2D-3D scale show that the developed model predicts the WECM's IPN structures by rule and line concerning DP, w/c, and p/c in the mixture. The C-S-H beads were progressively scaled in size which alters the C-S-H texture to have completely different dissolution characteristics. Beads of diameter ~6 Å are more unstable and soluble which enable them to form a continuous phase in water or a composite structure with WEP. In contrast, beads with diameters larger than 10 Å have different properties with stronger nucleation effects. The results also suggest the impregnation content of WEP in cement-based material should be limited to 10% vol. to prevent the polymer IPN from decomposing into discrete clusters. The application of Flory-Huggins theory in cement-based composites demonstrates great potential in performance prediction and microstructure design.
36 MATERIALS SCIENCE↗
Overcoming time and complexity limitations in molecular dynamics investigations of equilibrium melting
Abstract A hybrid Monte-Carlo molecular-dynamics method for determining solidus and liquidus compositions in multicomponent systems is presented that overcomes both the time limitations in conventional molecular dynamics that prevent the evolution of distinct solid and liquid compositions via diffusion and the complexity challenge that prevents use of thermodynamic assessment in systems of many components. This hybrid method is validated in the Cu–Ni system against an independent assessment of solidus and liquidus compositions based on the regular solution model. Strategies for efficient mapping of different phase diagrams, based on the thermodynamic parameter T 0 , the temperature at which two phases of the composition X 0 have equal free energies, are presented and then demonstrated for the copper-nickel fully miscible system and the gold–silicon eutectic system. A calculation of the solidus and liquidus sampled during the equilibrium melting of equiatomic CrMnFeCoNi is performed, indicating that this method has potential to be extended to the study of many component alloys.
Au-Si↗
Building an extensible cell wall
Abstract This article recounts, from my perspective of four decades in this field, evolving paradigms of primary cell wall structure and the mechanism of surface enlargement of growing cell walls. Updates of the structures, physical interactions, and roles of cellulose, xyloglucan, and pectins are presented. This leads to an example of how a conceptual depiction of wall structure can be translated into an explicit quantitative model based on molecular dynamics methods. Comparison of the model’s mechanical behavior with experimental results provides insights into the molecular basis of complex mechanical behaviors of primary cell wall and uncovers the dominant role of cellulose–cellulose interactions in forming a strong yet extensible network.
59 BASIC BIOLOGICAL SCIENCES↗
Calculation of the detonation state of HN 3 with quantum accuracy
HN 3 is a unique liquid energetic material that exhibits ultrafast detonation chemistry and a transition to metallic states during detonation. We combine the Chebyshev interaction model for efficient simulation (ChIMES) many-body reactive force field and the extended-Lagrangian multiscale shock technique molecular dynamics method to calculate the detonation properties of HN 3 with the accuracy of Kohn–Sham density-functional theory. ChIMES is based on a Chebyshev polynomial expansion and can accurately reproduce density-functional theory molecular dynamics (DFT-MD) simulations for a wide range of unreactive and decomposition conditions of liquid HN 3 . We show that addition of random displacement configurations and the energies of gas-phase equilibrium products in the training set allows ChIMES to efficiently explore the complex potential energy surface. Schemes for selecting force field parameters and the inclusion of stress tensor and energy data in the training set are examined. Structural and dynamical properties and chemistry predictions for the resulting models are benchmarked against DFT-MD. We demonstrate that the inclusion of explicit four-body energy terms is necessary to capture the potential energy surface across a wide range of conditions. Our results generally retain the accuracy of DFT-MD while yielding a high degree of computational efficiency, allowing simulations to approach orders of magnitude larger time and spatial scales. The techniques and recipes for MD model creation we present allow for direct simulation of nanosecond shock compression experiments and calculation of the detonation properties of materials with the accuracy of Kohn–Sham density-functional theory.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Structural evolution in Au- and Pd-based metallic glass forming liquids and the case for improved molecular dynamics force fields
The results of a combined experimental and computational investigation of the structural evolution of Au 81 Si 19 , Pd 82 Si 18 , and Pd 77 Cu 6 Si 17 metallic glass forming liquids are presented. Electrostatically levitated metallic liquids are prepared, and synchrotron x-ray scattering studies are combined with embedded atom method molecular dynamics simulations to probe the distribution of relevant structural units. Metal–metalloid based metallic glass forming systems are an extremely important class of materials with varied glass forming ability and mechanical processibility. High quality experimental x-ray scattering data are in poor agreement with the data from the molecular dynamics simulations, demonstrating the need for improved interatomic potentials. The first peak in the x-ray static structure factor in Pd 77 Cu 6 Si 17 displays evidence for a Curie–Weiss type behavior but also a peak in the effective Curie temperature. In conclusion, a proposed order parameter distinguishing glass forming ability, 1/(S(T,q 1 )−1, shows a peak in the effective Curie temperature near a crossover temperature established by the behavior of the viscosity, T A .
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Non-equilibrium molecular dynamics studies of thermal diffusion of hydrogen isotopes in low concentration zirconium hydrides
Tritium permeability in zirconium-based tritium getter critically impacts tritium storage and environmental safety during operation of tritium-producing burnable absorber rods (TPBARs). Previous experiments indicated that during irradiation operation, the hydrogen equilibrium pressured is increased. Further experimental and modeling studies suggested that the enhanced tritium release observed for reactor scale assemblies might be related to a thermal diffusion known as the Soret effect. A direct measurement of the Soret factor, however, has not been performed. To improve TPBAR and other nuclear applications, here we have applied two non-equilibrium molecular dynamics methods to study thermal diffusion of hydrogen isotopes in low-concentration zirconium hydrides. One of the methods produces sufficiently converged results to distinguish crystal orientation, isotope type, and concentration effects. In conclusion, with this method, crystal orientation, isotope type, and concentration effects are discussed.
36 MATERIALS SCIENCE↗
Comparison of heavy-ion transport simulations: Mean-field dynamics in a box
Within the transport model evaluation project (TMEP) of simulations for heavy-ion collisions, the mean-field response is examined here. Specifically, zero-sound propagation is considered for neutron-proton symmetric matter enclosed in a periodic box, at zero temperature and around normal density. The results of several transport codes belonging to two families (BUU-like and QMD-like) are compared among each other and to exact calculations. For BUU-like codes, employing the test particle method, the results depend on the combination of the number of test particles and the spread of the profile functions that weight integration over space. These parameters can be properly adapted to give a good reproduction of the analytical zero-sound features. QMD-like codes, using molecular dynamics methods, are characterized by large damping effects, attributable to the fluctuations inherent in their phase-space representation. Moreover, for a given nuclear effective interaction, they generally lead to slower density oscillations, as compared to BUU-like codes. The latter problem is mitigated in the more recent lattice formulation of some of the QMD codes. Furthermore, the significance of these results for the description of real heavy-ion collisions is discussed.
73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
Accelerated molecular dynamics simulations of dislocation climb in nickel
We report the mechanical behavior of materials operating under high temperatures is strongly influenced by creep mechanisms such as dislocation climb, which is controlled by the diffusion of vacancies. However, atomistic simulations of these mechanisms have traditionally been impractical due to the long time scales required. To overcome these time scale challenges, we use Parallel Trajectory Splicing (ParSplice), an accelerated molecular dynamics method, to simulate dislocation climb in nickel. We focus on modeling the activity of a vacancy near a jog on an edge dislocation in order to observe vacancy pipe diffusion and vacancy absorption at the jog. From rigorously constructed trajectories encompassing more than 2000 vacancy absorption events over a simulation time of more than 4μs at 900 K, a comprehensive sampling of available atomistic mechanisms is collated and analyzed further with molecular statics calculations. We estimate average rates for pipe diffusion and vacancy absorption into the jog using data from the dynamic and static calculations, finding very good agreement. Our results strongly suggest that the dominant mechanism for vacancy absorption by jogs is via biased diffusion to the dislocation core followed by fast pipe diffusion to the jog.
36 MATERIALS SCIENCE↗
Computation of the Thermal Expansion Coefficient of Graphene with Gaussian Approximation Potentials
Direct experimental measurement of thermal expansion coefficient without substrate effects is a challenging task for two-dimensional (2D) materials, and its accurate estimation with large-scale ab initio molecular dynamics is computationally very expensive. Machine learning-based interatomic potentials trained with ab initio data have been successfully used in molecular dynamics simulations to decrease the computational cost without compromising the accuracy. In this work, we investigated using Gaussian approximation potentials to reproduce the density functional theory-level accuracy for graphene within both lattice dynamical and molecular dynamical methods, and to extend their applicability to larger length and time scales. Two such potentials are considered, GAP17 and GAP20. GAP17, which was trained with pristine graphene structures, is found to give closer results to density functional theory calculations at different scales. Further vibrational and structural analyses verify that the same conclusions can be deduced with density functional theory level in terms of the reasoning of the thermal expansion behavior, and the negative thermal expansion behavior is associated with long-range out-of-plane phonon vibrations. Thus, it is argued that the enabled larger system sizes by machine learning potentials may even enhance the accuracy compared to small-size-limited ab initio molecular dynamics.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Source of Processable Vitrimer Viscosities: Swap Frequencies and Steric Factors
Vitrimers exhibit high, processable viscosities, where other polymers do not, and are among the most promising polymers for closed-loop material circularity. We sought to investigate the underlying chemical kinetic factors that result in high viscosities for vitrimers, which are crucial to designing vitrimers with tunable viscosity. To interrogate these factors, we achieved the first simulated predictions of real vitrimer viscosities, using a novel kinetic Monte Carlo molecular dynamics method, overcoming the time and length scale gaps to predict experimental bulk viscosities. The vitrimer architecture investigated is based on poly(dimethylsiloxane) chains and vinylogous urethane bond swaps. We probed the effects of the extent of free swapping groups, %F, the activation energy, E A , and the steric factor, ρ. The steric factor is related to the intrinsic reaction probability for molecules with sufficient energy. All three factors were found to be significant, but the role of ρ was found to be the biggest and also the most underappreciated. The results show that the inclusion of accurate ρ is of critical importance for viscosity predictions, with the evidence suggesting that the typical assumption of ρ = 1 is not valid for vitrimers and that, indeed, very low steric factors are present in bond-swap vitrimers such that values of ρ < 10 –10 may be typical. This greatly influences the bond exchange rates and, ultimately, the viscosities. Recognition of this result is necessary for the prediction of vitrimer viscosities from molecular simulations and to make vitrimers by design from molecular dynamics. We also investigated the effects that E A , ρ, and the number of free swapping groups have upon vitreous range temperatures, TV, with respect to achieving a specific viscosity (η V = 1 × 10 8 Pa·s), as well as for a commonly reported higher viscosity extrapolation (η V = 1 × 10 12 Pa·s). The evidence suggests that vitrimers may follow universal curves for E A vs T V , as a function of ρ. Finally, this study achieves the first of these comparisons of molecular simulations to experiments and reveals critical insights toward creating vitrimers by design, while providing a route for the prediction of T V from kinetic Monte Carlo molecular dynamics simulations.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Efficient perturbation-tracking method for directly probing the spectral phonon properties from molecular dynamics simulations
Existing methods for directly extracting the spectral phonon properties from molecular dynamics (MD) simulations, like the normal mode analysis (NMA) and spectral energy density analysis, all require a very long simulation time to produce reliable results with good convergence. So far, these methods are mainly applied in studies using small systems and with empirical potentials, as the heavy computational load has greatly hindered their further applications. Here we propose a perturbation-tracking (PT) method for directly probing the mode-wise phonon anharmonic frequencies and lifetimes. We show that results obtained from our method are in excellent agreement with those from the conventional NMA approach, using Si as the model material system. Comparing with the NMA approach, the PT method offers a greater accuracy and significant improvement of efficiency. It takes an average of two orders of magnitude and up to three orders of magnitude less simulation time to obtain the same lifetime result of a phonon mode with intermediate to high accuracy. Meanwhile, our method preserves all the dynamics of probed phonon mode from a particular state, which means it is capable of studying the transient thermal transport processes in a nonequilibrium system. Besides the exceptional efficiency, our method also comes with freedom to choose to probe only those modes of interest. This makes it ideal for use with large systems and in computationally demanding applications, such as ab initio MD simulations. Moreover, the PT method we propose here is very straightforward and easy to implement.
74 ATOMIC AND MOLECULAR PHYSICS↗
Dislocation dynamics in polycrystalline materials
An extension of the dislocation dynamics method to polycrystalline materials is presented with emphasis on handling interactions between dislocations and grain boundaries. The key new features of the method include: (1) a grain boundary detection algorithm, (2) new dislocation emission criteria based on power dissipation and area growth, (3) mobility of dislocations at grain boundaries, and (4) extension of topological operations e.g. mesh adaption, collision, and dissociation to handle dislocations interacting with grain boundaries. Furthermore, verification and validation examples are executed to compare our calculations with existing analytic methods, molecular dynamics simulations, and experimental observations.
36 MATERIALS SCIENCE↗
Interplay between hydrogen, temperature, and character angle on dissociated dislocation energies in Fe–Ni–Cr austenitic stainless steels
Dislocation energy has an important role in the mechanical performance of structural metals. While dislocation energies cannot be fully obtained from continuum theories due to the contribution of the dislocation core, they have been calculated via atomistic simulations in elemental metals. However, constraints on the local atomic environments have prevented the use of such approaches in systems that incorporate alloying or interstitial solutes. In this work, we develop robust molecular dynamics methods to resolve these issues through a geometric construction of dislocation dipoles and the calculation of time-averaged energies. Furthermore, we apply these methods to calculate dislocation energies (including core energies) in an Fe 70 Ni 11 Cr 19 austenitic steel at a variety of character angles, hydrogen concentrations, temperatures, and dipole spacings. The resulting highly converged energies show an excellent agreement with continuum expressions. Overall, hydrogen concentrations up to 1.0 % do not have a significant effect on the elastic parameters and dislocation energy. The methods and insights derived in this work have the potential to facilitate the calculation of dislocation energies in a wide range of systems, and to guide our understanding of hydrogen embrittlement.
Alloyed systems↗