MISTIQS: An open-source software for performing quantum dynamics simulations on quantum computers
Not Available
97 MATHEMATICS AND COMPUTING↗
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Machine-Learned Force Field for Molecular Dynamics Simulations of Nonequilibrium Ammonia Synthesis on Iron Catalysts
Ammonia (NH 3 ) is one of the most important industrial chemicals. The conventional NH 3 synthesis method-the Haber–Bosch process-converts atmospheric nitrogen (N 2 ) into NH 3 using H 2 with an iron (Fe) catalyst. However, this process requires high pressures (100–200 atm) and temperatures (700–800 K) near thermal equilibrium. Recently, Fe-based nanocatalysts have been reported to produce promising NH 3 yields under atmospheric pressures and temperature-modulated nonequilibrium conditions. Understanding the mechanism of nonequilibrium catalysis with programmed temperature variation could help to optimize this fully electrified and less energy-intensive process. Although reactive molecular dynamics (RMD) simulations can be a useful tool to model nonequilibrium catalytic processes, they require the development of accurate force fields (i.e., interatomic potentials). Here, we present a machine-learned (ML) force field within the Deep Potential MD (DPMD) framework, trained using periodic density functional theory (DFT) calculations, to model NH 3 synthesis on Fe catalysts with various surface adsorbates such as *N, *H, *N 2 , *H 2 , *NH, *NH 2 , and *NH 3 . Here, we generated the DFT data from static models of elementary reactions on the most stable (110) surface of body-centered cubic Fe, which then were augmented by data from constant number of particles–volume–temperature (NVT) DFT-MD trajectories at various temperatures. Finally, we utilized the fully optimized ML force field to investigate reaction dynamics at an Fe(110) surface at linearly increasing temperatures using NVT-DPMD simulations. Our simulations indicate that pulsed temperature ramping could prove favorable for NH3 synthesis. For example, we conducted ramping under multiple sets of conditions: (i) from 900 to 1200 K over periods of 0.1–0.3 ns for Fe surfaces precovered with N or NH along with H; and (ii) from 300 to 600 K over 0.1–0.3 ns for Fe surfaces precovered with NH 3 . While our simulations so far are limited to short time scales (very rapid heating), these observations shed light on the mechanism of the high NH 3 synthesis rate achieved in a novel temperature-modulated nonequilibrium catalytic reactor using pulsed heating and cooling.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Probing the Core–Shell Organization of Nanoconfined Methane in Cylindrical Silica Pores Using In Situ Small-Angle Neutron Scattering and Molecular Dynamics Simulations
Determining the structure of nanoconfined fluids is essential for predicting the fate of these fluids in subsurface geologic formations with nanoporous features and for engineering novel nanoporous materials for storing compressed gases. In this study, we probe the structure of nanoconfined methane at pressures in the range of 15–100 bar using in situ small-angle neutron scattering (SANS) measurements and molecular dynamics (MD) simulations. The structure of methane is probed in MCM-41 and SBA-15 with cylindrical pores and diameters of 3.3 and 6.8 nm, respectively. In situ SANS measurements and MD simulations showed that the confined methane molecules are organized in a core–shell structure, with the shell arising from the adsorption of methane molecules on the silica surface. The shell thicknesses of the adsorbed deuterated methane (CD4) molecules in MCM-41 obtained by SANS measurements are 1.4 ± 0.5, 2.1 ± 0.1, 3.2 ± 0.8, 4.0 ± 0.3, and 6.0 ± 0.7 Å at equilibrated pressures of 15.6, 35.6, 55.5, 73.3, and 95.7 bar, respectively. The shell thicknesses of the adsorbed CD4 layer in SBA-15 pores are 2.7 ± 0.5, 4.3 ± 0.7, 6.6 ± 0.7, 10.2 ± 0.3, and 14.6 ± 0.8 Å at equilibrated pressures of 15.5, 32.7, 52.4, 70, and 99.5 bar, respectively. These experimental results are in close agreement with the results predicted from MD simulations. Adsorption of methane molecules on the silica surfaces is primarily driven by van der Waals interactions between the methane molecules and the hydroxyl groups on the silica surface, while electrostatic interactions play a minor role. In conclusion, the experimental and simulation approaches described in this study provide fundamental insights into the organization of confined gases using methane as a specific example in the context of compressed fluid storage in natural and engineered materials for adaptive energy use.
03 NATURAL GAS↗
Solvent-induced membrane stress in biofuel production: molecular insights from small-angle scattering and all-atom molecular dynamics simulations
The disruptive effect of organic solvents on microbial membranes represents a significant challenge to the economical production of green fuels and value-added chemicals from lignocellulosic feedstocks. One route to overcoming this challenge is to engineer microbes with membranes capable of resisting organic solvent stresses. In this regard, it is useful to understand the mechanisms by which organic solvents disrupt typical biomembranes. In this study, molecular dynamics (MD) simulation, complemented by small-angle X-ray and neutron scattering (SANS/SAXS), provide a molecular-scale view of the disruption of a microbial model membrane by 1-butanol and tetrahydrofuran (THF), two common water–organic cosolvent mixtures of importance in biofuel production. Solvent interactions at the interface between the head-group and fatty acid tail regions lead to more dramatic membrane changes than interactions solely at the head-groups or tails. Although both organic solvents are found to partition into the membrane, the depth of solvent penetration into the membrane is quite different. Specifically, 1-butanol localizes near the interface between the lipid heads and tails at low concentrations, but partitions into both the head and tail regions at high concentrations. In contrast, THF, overall, partitions less than 1-butanol and prefers the lipid tail regions. Importantly, the presence of 1-butanol near the head/tail interface introduces drastic membrane changes not seen with THF. The organic solvent interactions with the lipids lead to membrane thinning and fluidization, but more so for 1-butanol than for THF. These results suggest that an aim for the future engineering of robust membranes could be to design lipid head groups that reduce the accumulation of organic solvents at the head–tail interface and that rational designs need also be cognizant of the different solvent-specific mechanisms responsible for membrane disruption.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Reorganization of Water at Aqueous Aluminum Chloride (AlCl 3 ) Interfaces: Vibrational Sum Frequency Generation and Molecular Dynamics Simulations
AlCl 3 hydration states and complexation are not well understood both in solutions and at the air–aqueous interface despite their potential significance in natural waters and their industrial and energy-related applications. Here, we investigated Al 3+ and Cl – ion behaviors in an AlCl 3 aqueous bulk solution and at the air–aqueous interface using interface-selective vibrational sum frequency generation (SFG), Raman and infrared spectroscopies, molecular dynamics (MD) simulation, as well as molecular-informed reduced modeling. Our reduced modeling reveals relatively long-range effects for Al 3+ as compared to monovalent ions such as Na + indicating that the interfacial depth of trivalent ions can be significantly larger than that of monovalent ions at the air–water interface. MD simulations reveal interfacial stratification and multiple layering of the ions. Compression of the Al 3+ and Cl – distributions with increasing concentrations from 0.5 to 2.5 m is also observed in the subsurface regions. Significant SSP- and PPP-polarized SFG OH spectral intensity increases are observed from 0.5 to 1.5 m and 0.5 to 2.5 m, respectively, indicative of interfacial depth increases and a change in average orientation above 1.5 m. Extensive evaluation of SFG spectra, Fresnel-corrected using several approaches, shows the same trends. The nonmonotonic trend points to a changing structure in surface and subsurface water orientation and hydrogen bonding environment generally consistent with the MD simulation of stratification and water orientation changes. Furthermore, solvent-shared ion pairing is implicated with MD simulation radial distribution analysis and consistent with infrared spectral identification of the hexaaqua aluminum ion in the solution phase. Spectral evidence of a strong Al 3+ hydration shell and the acidic behavior of the Al 3+ ions is obvious in the Raman and infrared spectra of the bulk solution. In conclusion, we show that the MD dipole potential is directly related to the MD second-order susceptibility of the interface, χ SFG–MD (2) , both of which correlate up to ∼35 Å with the spectral observations of increasing and then saturating intensities, suggesting that both ion stratification and interfacial depth determine the water orientations at an air–water interface of 1-3 electrolyte solutions.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Effect of point defects on the thermal conductivity of UO 2 : molecular dynamics simulations
The thermal conductivity of uranium dioxide (UO 2 ) fuel is an important materials property that affects fuel performance since it is a key parameter determining the temperature distribution in the fuel, thus governing, e.g., dimensional changes due to thermal expansion, fission gas release rates, etc. The thermal conductivity of UO 2 nuclear fuel is also affected by fission gas, fission products, defects, and microstructural features such as grain boundaries. Here, molecular dynamics (MD) simulations are carried out to determine quantitatively, the effect of irradiation induced point defects on the thermal conductivity of UO 2 , as a function of defect concentrations, for a range of temperatures, 300 – 1500 K. The results will be used to develop enhanced continuum thermal conductivity models for MARMOT and BISON by INL. These models express the thermal conductivity as a function of microstructure state-variables, thus enabling thermal conductivity models with closer connection to the physical state of the fuel.
11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
Atomic scale etching of diamond: insights from molecular dynamics simulations
Diamond is a promising material for multiple applications in quantum information processing and sensing as well as applications in microelectronics. However, diamond devices can be limited by surface defects that compromise charge stability and spin coherence, among others. Improved strategies in plasma etching of diamond could play an important role in minimizing or eliminating these defects. In this work, we explore plasma-assisted atomic scale etching of diamond using argon ions (Ar + ), hydrogen ions (H + ) and hydrogen atoms (H). We employ classical molecular dynamics (MD) simulations and test several interatomic potentials based on the Reactive Empirical Bond Order (REBO) form with comparisons to a variety of published experimental results. We performed MD simulations of low-energy hydrogen ($\leqslant$50 eV) and argon ( $\leqslant$200 eV) ion bombardment of diamond surfaces. Ar + bombardment can be used to locally smooth initially rough diamond surfaces via the formation of an amorphous C layer, the thickness of which increases with argon ion energy. Subsequent exposure with hydrogen ions (or fast neutrals) will selectively etch this amorphous C layer, leaving the underlying diamond layer mostly intact if the H energy is maintained below about 10 eV. The simulations suggest that combining Ar + smoothing with selective, near threshold energy H removal of amorphous C can be an effective strategy for diamond surface engineering, leading to more reliable and sensitive diamond color center devices.
74 ATOMIC AND MOLECULAR PHYSICS↗
Predicting the preferred morphology of hexagonal boron nitride domain structure on nickel from ReaxFF-based molecular dynamics simulations
An understanding of the nucleation and growth of hexagonal boron nitride (hBN) on nickel substrates is essential to its development as a functional material. In particular, fundamental insights into the formation of the hexagonal lattices with alternating boron (B) and nitrogen (N) atoms could be exploited to control hBN lattice morphologies for targeted applications. Here, the preferred shapes and edge configurations of atomically smooth hBN on Ni(111) were investigated using molecular dynamics (MD) simulations, along with reactive force field (ReaxFF) developed to represent the Ni/B/N system and the lattice-building B–N bond formation. The obtained hBN lattices, from different B : N feed ratios, are able to confirm that hBN domain geometries can indeed be tuned by varying thermodynamic parameters (i.e., chemical potentials of N and B) – a finding that has only been predicted using quantum mechanical theories. Here, we also showed that the nitrogen fed to the system plays a more crucial role in dictating the size of hBN lattices. With an increase of the relative N content, the simulated hBN domain shapes also transition from equilateral triangles to hexagons, again, consistent with the anticipation based on Density Functional Theory (DFT) calculations. Hence, a plausible approach to acquire a desired hBN nanostructure depends on careful control over the synthesis conditions, which now can benefit from reliable molecular simulations.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Molecular dynamics simulations of dislocations in TlBr crystals under an electrical field
TlBr crystals have superior radiation detection properties; however, their properties degrade in the range of hours to weeks when an operating electrical field is applied. To account for this rapid degradation using the widely-accepted vacancy migration mechanism, the vacancy concentration must be orders of magnitude higher than any conventional estimates. The present work has incorporated a new analytical variable charge model in molecular dynamics (MD) simulations to examine the structural changes of materials under electrical fields. Our simulations indicate that dislocations in TlBr move under electrical fields. As a result, this discovery can lead to new understanding of TlBr aging mechanisms under external fields.
36 MATERIALS SCIENCE↗
Probing the limits of metal plasticity with molecular dynamics simulations
Ordinarily, the strength and plasticity properties of a metal are defined by dislocations—line defects in the crystal lattice whose motion results in material slippage along lattice planes. Dislocation dynamics models are usually used as mesoscale proxies for true atomistic dynamics, which are computationally expensive to perform routinely. However, atomistic simulations accurately capture every possible mechanism of material response, resolving every “jiggle and wiggle” of atomic motion, whereas dislocation dynamics models do not. We present fully dynamic atomistic simulations of bulk single-crystal plasticity in the body-centred-cubic metal tantalum. Our goal is to quantify the conditions under which the limits of dislocation-mediated plasticity are reached and to understand what happens to the metal beyond any such limit. In our simulations, the metal is compressed at ultrahigh strain rates along its [001] crystal axis under conditions of constant pressure, temperature and strain rate. To address the complexity of crystal plasticity processes on the length scales (85–340 nm) and timescales (1 ns–1μs) that we examine, we use recently developed methods of in situ computational microscopy to recast the enormous amount of transient trajectory data generated in our simulations into a form that can be analysed by a human. Our simulations predict that, on reaching certain limiting conditions of strain, dislocations alone can no longer relieve mechanical loads; instead, another mechanism, known as deformation twinning (the sudden re-orientation of the crystal lattice), takes over as the dominant mode of dynamic response. Below this limit, the metal assumes a strain-path-independent steady state of plastic flow in which the flow stress and the dislocation density remain constant as long as the conditions of straining thereafter remain unchanged. In this distinct state, tantalum flows like a viscous fluid while retaining its crystal lattice and remaining a strong and stiff metal.
36 MATERIALS SCIENCE↗
Distribution and Transport of CO 2 in Hyperbranched Poly(ethylenimine)-Loaded MCM-41: A Molecular Dynamics Simulation Approach
Not Available
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
SurGBSA: Learning Representations from Molecular Dynamics Simulations
Source code implementation for "SurgGBSA: Learning Representations From Molecular Dynamics Trajectories".
Jones, WilliamD↗
Stress effects on the initial lithiation of crystalline silicon nanowires: Reactive molecular dynamics simulations using ReaxFF
Silicon (Si) has been recognized as a promising anode material for the next-generation high-capacity lithium (Li)-ion batteries because of its high theoretical energy density. Recent in situ transmission electron microscopy (TEM) revealed that the electrochemical lithiation of crystalline Si nanowires (c-SiNWs) proceeds by the migration of the interface between the lithiated Si (LixSi) shell and the pristine unlithiated core, accompanied by solid-state amorphization. The underlying atomic mechanisms of Li insertion into c-Si remain poorly understood. In this research, we perform molecular dynamics (MD) simulations using the reactive force field (ReaxFF) to characterize the lithiation process of c-SiNWs. Our calculations show that ReaxFF can accurately reproduce the energy barriers of Li migration from DFT calculations in both crystalline (c-Si) and amorphous Si (a-Si). The ReaxFF-based MD simulations reveal that Li insertion into interlayer spacing between two adjacent (111) planes results in the peeling-off of the (111) facets and subsequent amorphization, in agreement with experimental observations. We find that breaking of the Si–Si bonds between (111)-bilayers requires a rather high local Li concentration, which explains the atomically sharp amorphous–crystalline interface (ACI). Our stress analysis shows that lithiation induces compressive stress at the ACI layer, causing retardation or even the stagnation of the reaction front, also in good agreement with TEM observations. Lithiation at high temperatures (e.g. 1200 K) shows that Li insertion into c-SiNW results in an amorphous to crystalline phase transformation at Li : Si composition of ~4.2:1. In conclusion, our modeling results provide a comprehensive picture of the effects of reaction and diffusion-induced stress on the interfacial dynamics and mechanical degradation of SiNW anodes under chemo-mechanical lithiation.
25 ENERGY STORAGE↗
Large-Scale Molecular Dynamics Simulation of the Dehydration of a Suspension of Smectite Clay Nanoparticles
Fine-grained sediments and sedimentary rocks play important roles in a variety of modern energy technologies from petroleum geology to geological carbon sequestration and radioactive waste management. However, despite their utility and ubiquity, many of their properties remain poorly understood. In particular, the ability to predict the permeability and mechanics of these media remains a persistent fundamental challenge in the geosciences. In the present work, we show how large-scale classical molecular dynamics (MD) simulations can help interpret the properties of fine-grained sedimentary material. All-atom simulations containing 30 discrete clay particles are utilized to understand the evolution of a clay nanoparticle suspension during its progressive dehydration. Microstructural (pore size distribution, tortuosity, anisotropy), thermodynamic (enthalpy and free energy of hydration, anion exclusion), mechanical (total suction), and transport properties (diffusion coefficient tensors of water and sodium) are calculated and compared to the experiment. Overall, our results provide new insight into the coupled chemistry, mechanics, and transport properties of disordered nanoparticle assemblages and shed light upon the important role of water films in controlling these properties.
02 PETROLEUM↗
Manipulating molecular order in nematic liquid crystal capillary bridges via surfactant adsorption: guiding principles from dissipative particle dynamics simulations
The ability of liquid crystals (LCs) to change orientational order is used in applications, ranging from sensors to displays. The aim of this work is to computationally investigate how surfactant adsorption on cylindrical LC bridges can be used to control such orientational order. Building from classical fundamental lessons, understanding the ordering of mesogens along a preferred axis with the help of molecular modelling contributes to investigations of systems that could be a platform for LC-based sensing applications. The coarse-grained dissipative particle dynamics (DPD) simulation method is implemented here, because it allows us to quantify the effect of molecular features on the properties of meso-scopic systems containing LC bridges, an aqueous solvent, and surfactants at various concentrations. Three surfactant types are modelled with short, medium, and long tail lengths, respectively. All surfactants adsorb at the LC–water interface. It is found that the length of the surfactant hydrophobic tail determines the effectiveness by which the LC order is affected. Short tails are not as effective as long ones. Surfactants with long tails affect the LC order, but, in agreement with experiments, predominantly only within a short distance from the LC–water interface. For these surfactants, the surface density at the LC–water interface is an important knob that can be used to control the order of the LCs. As the effective LC–surfactant interactions change, so does the distribution of the surfactants at the interface. Consistent with theoretical expectations, the results presented here elucidate the effect of molecular features on the anchoring mechanism between surfactants and mesogens within cylindrical bridges dispersed in aqueous systems and could be helpful for designing novel surface-active compounds in the development of advanced sensing devices based on LCs.
74 ATOMIC AND MOLECULAR PHYSICS↗
Ab Initio Molecular Dynamics Simulation of Divalent Metal Cation Incorporation in Calcite: Implications for Interpreting X-ray Absorption Spectroscopy Data
Calcite (CaCO 3 ) is a ubiquitous mineral with the ability to accommodate a wide range of impurities. Determination of the coordination environment and incorporation modes of impurities in calcite has historically relied primarily on the interpretation of extended X-ray absorption fine structure (EXAFS) spectroscopy. However, lack of standards combined with the large number of degrees of freedom involved in shell-by-shell fits have made the interpretation of EXAFS spectra challenging. As such, in this work, ab initio molecular dynamics (AIMD) simulations were performed to investigate the incorporation of seven divalent metal cation impurities, namely, Ba 2+ , Pb 2+ , Sr 2+ , Cd 2+ , Mn 2+ , Co 2+ , and Zn 2+ , in calcite. These cations span a wide range of sizes: 30.7 to –22.8% change in ionic radius with respect to Ca 2+ . The atomic trajectories were then used to compute EXAFS spectra for direct comparison with published experimental spectra. The simulations confirmed that all seven metal cations incorporate in calcite via substitution in the calcium site. The AIMD–EXAFS approach allowed for overcoming limitations of the shell-by-shell fitting approach, such as the difficulties in resolving weak backscatterers beyond the first coordination shell. As a result, the AIMD–EXAFS approach was able to provide a detailed and comprehensive characterization of the structural relaxation around divalent metal cation impurities in calcite.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Molecular dynamics simulations for glass transition temperature predictions of polyhydroxyalkanoate biopolymers
Polyhydroxyalkanoates (PHAs) represent an emerging class of biosynthetic and biodegradable polyesters that exhibit considerable potential to replace petroleum-based plastics towards a sustainable future. Despite the promise, general structure–property mappings within this class of polymers remain largely unexplored. An efficient exploration of this vast chemical space calls for the development and validation of predictive methods for accurate estimation of a diverse range of properties for PHA-based polymers. Towards this aim, we present and validate in this work the results of our molecular dynamics (MD) simulation based approach aimed at predicting glass transition temperatures (T g ) of PHA-based polymers. Since generally available and widely used polymer forcefields exhibit a relatively poor performance for T g predictions, we have developed a new forcefield by modifying the polymer consistent force field (PCFF) via refining a selected set of torsion potentials of the polymer backbone using accurate density functional theory (DFT) computations. After carefully assessing the dependence of critical simulation parameters, such as, polymer chain length, number of polymer chains, supercell size, and thermal quenching rate used in the simulation, the applicability and transferability of the modified PCFF (mPCFF) is demonstrated by directly comparing the computed T g predictions of various polymers with different chemistries, polymer side chain lengths and functional groups forming the polymer side chains against the respective experimentally measured values. Furthermore, the transport properties such as self-diffusion coefficient and viscosity are computationally determined and their well-known correlation with the target properties is demonstrated. Lastly, we have employed the developed approach to predict T g values for a number of yet-to-be-synthesized PHA-based polymers with a diverse set of functional groups in the polymer side chains. The results are further rationalized by correlating the predicted T g values with the inter-chain H-bond formation tendencies of the different side chain functional groups. This work represents an important first step towards computationally guided design of PHA-based functional polymers and opens up new directions for a systematic investigation of composition- and configuration-dependent structure–property relationships in more complex binary and ternary copolymer systems.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Molecular dynamics simulations of the first charge of a Li-ion—Si-anode nanobattery
Rechargeable lithium-ion batteries are the most popular devices for energy storage but still a lot of research needs to be done to improve their cycling and storage capacity. Silicon has been proposed as an anode material because of its large theoretical capacity of ~3600 mAh/g. Therefore, focus is needed on the lithiation process of silicon anodes where it is known that the anode increases its volume more than 300%, producing cracking and other damages. In this study, we performed molecular dynamics atomistic simulations to study the swelling, alloying, and amorphization of a silicon nanocrystal anode in a full nanobattery model during the first charging cycle. A dissolved salt of lithium hexafluorophosphate in ethylene carbonate was chosen as the electrolyte solution and lithium cobalt oxide as cathode. External electric fields are applied to emulate the charging, causing the migration of the Li-ions from the cathode to the anode, by drifting through the electrolyte solution, thus converting pristine Si gradually into Li 14 Si 5 when fully lithiated. When the electric field is applied to the nanobattery, the temperature never exceeds 360 K due to a temperature control imposed resembling a cooling mechanism. The volume of the anode increases with the amorphization of the silicon as the external field is applied by creating a layer of LiSi alloy between the electrolyte and the silicon nanocrystal and then, at the arrival of more Li-ions changing to an alloy, where the drift velocity of Li-ions is greater than the velocity in the initial nanocrystal structure. Charge neutrality is maintained by concerted complementary reduction-oxidation reactions at the anode and cathode, respectively. Also, the nanobattery model developed here can be used to study charge mobility, current density, conductance and resistivity, among several other properties of several candidate materials for rechargeable batteries and constitutes the initial point for further studies on the formation of the solid electrolyte interphase in the anode.
25 ENERGY STORAGE↗