The role of surfactant force field on the properties of liquid/liquid interfaces
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Servis, Michael J.↗
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Semi-Automated Creation of Density Functional Tight Binding Models through Leveraging Chebyshev Polynomial-Based Force Fields
Density functional tight binding (DFTB) is an attractive method for accelerated quantum simulations of condensed matter due to its enhanced computational efficiency over standard density functional theory (DFT) approaches. However, DFTB models can be challenging to determine for individual systems of interest, especially for metallic and interfacial systems where different bonding arrangements can lead to significant changes in electronic states. In this regard, we have created a rapid-screening approach for determining systematically improvable DFTB interaction potentials that can yield transferable models for a variety of conditions. Our method leverages a recent reactive molecular dynamics force field where many-body interactions are represented by linear combinations of Chebyshev polynomials. This allows for the efficient creation of multi-center representations with relative ease, requiring only a small investment in initial DFT calculations. Here, we have focused our workflow on TiH 2 as a model system and show that a relatively small training set based on unit-cell-sized calculations yields a model accurate for both bulk and surface properties. Our approach is easy to implement and can yield reliable DFTB models over a broad range of thermodynamic conditions, where physical and chemical properties can be difficult to interrogate directly and there is historically a significant reliance on theoretical approaches for interpretation and validation of experimental results.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Impact of Grafting Density on the Assembly and Mechanical Properties of Self-Assembled Metal–Organic Framework Monolayers
Polymer-grafted metal–organic frameworks (MOFs) can be used to form free-standing self-assembled MOF monolayers (SAMMs). Polymer chains can be introduced onto MOF surfaces through either the ligands or metal nodes using both grafting-to and grafting-from approaches. However, controlling the grafting density of polymer-grafted MOFs has not yet been achieved, because a means to control the density of grafting sites on the MOF surface has not been developed. In this study, the grafting density of polymer-grafted UiO-66 (UiO = University of Oslo) was controlled by functionalizing a portion of the Zr(IV) secondary building units (SBUs) on a UiO-66 surface with a so-called blocking agent. The remaining sites on the UiO-66 SBUs were functionalized with polymerization initiation groups, and polymers were grown from these sites to obtain particles with variable grafting densities and chain lengths that form SAMMs at an air–water interface. Even under conditions of low grafting density, these materials retain the ability to form SAMMs and their free-standing ability. Changes in particle arrangement within the monolayers were investigated using SEM imaging, and the toughness of the monolayers was evaluated using a film-on-water (FOW) method. Furthermore, coarse-grained molecular dynamics simulations were carried out to elucidate the morphology and mechanical properties of the monolayers. Findings from both experiments and simulations indicate that the toughness of SAMMs is more heavily influenced by the chain length of the grafted polymers than by the overall polymer content in the composite.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Selectivity of nitrate and chloride ions in microporous carbons: the role of anisotropic hydration and applied potentials
Understanding ion transport in porous carbons is critical for a wide range of technologies, including supercapacitors and capacitive deionization for water desalination, yet many details remain poorly understood. For instance, an atomistic understanding of how ion selectivity is influenced by the molecular shape of ions, morphology of the micropores and applied voltages is largely lacking. In this work, we combined molecular dynamics simulations with enhanced sampling methods to elucidate the mechanism of nitrate and chloride selectivity in subnanometer graphene slit-pores. We demonstrate that nitrate is preferentially adsorbed over chloride in the slit-like micropores. This preferential adsorption was found to stem from the weaker hydration energy and unique anisotropy of the ion solvation of nitrate. Beside the effects of ion dehydration, we found that applied potential plays an important role in determining the ion selectivity, leading to a lower selectivity of nitrate over chloride at a high applied potential. We conclude that the measured ion selectivity results from a complex interplay between voltage, confinement, and specific ion effects-including ion shape and local hydration structure.
36 MATERIALS SCIENCE↗
Multi-level parallelization of quantum-chemical calculations
Here, strategies for multiple-level parallelizations of quantum-mechanical calculations are discussed, with an emphasis on using groups of workers for performing parallel tasks. These parallel programming models can be used for a variety ab initio quantum chemistry approaches, including the fragment molecular orbital method and replica-exchange molecular dynamics. Strategies for efficient load balancing on problems of increasing granularity are introduced and discussed. A four-level parallelization is developed based on a multi-level hierarchical grouping, and a high parallel efficiency is achieved on the Theta supercomputer using 131 072 OpenMP threads.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
WISDOM project – XVIII. Molecular gas distributions and kinematics of three megamaser galaxies
ABSTRACT The co-evolution of galaxies and supermassive black holes (SMBHs) underpins our understanding of galaxy evolution, but different methods to measure SMBH masses have only infrequently been cross-checked. We attempt to identify targets to cross-check two of the most accurate methods, megamaser, and cold molecular gas dynamics. Three promising galaxies are selected from all those with existing megamaser SMBH mass measurements. We present Atacama Large Millimeter/sub-millimeter Array (ALMA) 12CO (2–1) and 230-GHz continuum observations with angular resolutions of ≈0${_{.}^{\prime\prime}}$5. Every galaxy has an extended rotating molecular gas disc and 230-GHz continuum source(s), but all also have irregularities and/or non-axisymmetric features: NGC 1194 is highly inclined and has disturbed and lopsided central 12CO (2–1) emission; NGC 3393 has a nuclear disc with fairly regular but patchy 12CO (2–1) emission with little gas near the kinematic major axis, faint emission in the very centre, and two brighter structures reminiscent of a nuclear ring and/or spiral; NGC 5765B has a strong bar and very bright 12CO (2–1) emission concentrated along two bisymmetric offset dust lanes and two bisymmetric nuclear spiral arms. 12CO (2–1) and 12CO (3–2) observations with the James Clerk Maxwell Telescope are compared with the ALMA observations. Because of the disturbed gas kinematics and the impractically long integration times required for higher angular resolution observations, none of the three galaxies is suitable for a future SMBH mass measurement. None the less, increasing the number of molecular gas observations of megamaser galaxies is valuable, and the ubiquitous disturbances suggest a link between large-scale gas properties and the existence of megamasers.
Liang, Fu-Heng (ORCID:0000000324961247)↗
Ab Initio Simulation of Amorphous Graphite
An amorphous graphite material has been predicted from molecular dynamics simulation using ab initio methods. Carbon materials reveal a strong proclivity to convert into a sp 2 network and then layer at temperatures near 3000 K within a density range of ca. 2.2–2.8 g/cm 3 . Each layer of amorphous graphite is a monolayer of amorphous graphene including pentagons and heptagons in addition to hexagons, and the planes are separated by about 3.1 Å. The layering transition has been studied using various structural and dynamical analyses. The transition is unique as one of partial ordering (long range order of planes and galleries, but topological disorder in the planes). The planes are quite flat, even though monolayer amorphous graphene puckers near pentagonal sites. Interplane cohesion is due partly to non-Van der Waals interactions. The structural disorder has been studied closely, especially the consequences of disorder to electronic transport. Finally, it is expected that the transition elucidated here may be salient to other layered materials.
42 ENGINEERING↗
Tunable Topological Phonon for Next-generation Quantum Transduction
This project aims to understand the critical factors that determine transduction performance of topological phonons across an oxide perovskite/tungsten diselenide heterojunction. We will investigate mechanisms of their propagation and interfacial coupling using modeling and machine learning approaches. Methods include density functional theory, molecular dynamics, numerical transport simulations, and active learning for building up a training dataset for force field development.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Boron adatom adsorption on graphene: A case study in computational chemistry methods for surface interactions
Though weak surface interactions and adsorption can play an important role in plasma processing and materials science, they are not necessarily simple to model. A boron adatom adsorbed on a graphene sheet serves as a case study for how carefully one must select the correct technique from a toolbox of computational chemistry methods. Using a variety of molecular dynamics potentials and density functional theory functionals, we evaluate the adsorption energy, investigate barriers to adsorption and migration, calculate corresponding reaction rates, and show that a surprisingly high level of theory may be necessary to verify that the system is described correctly.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Development of Masitinib Derivatives with Enhanced Mpro Ligand Efficiency and Reduced Cytotoxicity
Recently, a high-throughput screen of 1900 clinically used drugs identified masitinib, an orally bioavailable tyrosine kinase inhibitor, as a potential treatment for COVID-19. Masitinib acts as a broad-spectrum inhibitor for human coronaviruses, including SARS-CoV-2 and several of its variants. In this work, we rely on atomistic molecular dynamics simulations with advanced sampling methods to develop a deeper understanding of masitinib’s mechanism of M pro inhibition. To improve the inhibitory efficiency and to increase the ligand selectivity for the viral target, we determined the minimal portion of the molecule (fragment) that is responsible for most of the interactions that arise within the masitinib-Mpro complex. We found that masitinib forms highly stable and specific H-bond interactions with Mpro through its pyridine and aminothiazole rings. Importantly, the interaction with His 163 is a key anchoring point of the inhibitor, and its perturbation leads to ligand unbinding within nanoseconds. Based on these observations, a small library of rationally designed masitinib derivatives (M1–M5) was proposed. Our results show increased inhibitory efficiency and highly reduced cytotoxicity for the M3 and M4 derivatives compared to masitinib.
60 APPLIED LIFE SCIENCES↗
Evolution of Metastable Structures at Bimetallic Surfaces from Microscopy and Machine-Learning Molecular Dynamics
The restructuring of interfaces plays a crucial role in materials science and heterogeneous catalysis. Bimetallic systems, in particular, often adopt very different compositions and morphologies at surfaces compared to the bulk. For the first time, we reveal a detailed atomistic picture of long-time scale restructuring of Pd deposited on Ag using microscopy, spectroscopy, and novel simulation methods. By developing and performing accelerated machine-learning molecular dynamics followed by an automated analysis method, we discover and characterize previously unidentified surface restructuring mechanisms in an unbiased fashion, including Pd-Ag place exchange and Ag pop-out as well as step ascent and descent. Remarkably, layer-by-layer dissolution of Pd into Ag is always preceded by an encapsulation of Pd islands by Ag, resulting in a significant migration of Ag out of the surface and a formation of extensive vacancy pits within a period of microseconds. These metastable structures are of vital catalytic importance, as Ag-encapsulated Pd remains much more accessible to reactants than bulk-dissolved Pd. We report our approach is broadly applicable to complex multimetallic systems and enables the previously intractable mechanistic investigation of restructuring dynamics at atomic resolution.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Zero-cost corrections to influence functional coefficients from bath response functions
Recent work has shown that it is possible to circumvent the calculation of the spectral density and directly generate the coefficients of the discretized influence functionals using data from classical trajectory simulations. However, the accuracy of this procedure depends on the validity of the high temperature approximation. In this work, an alternative derivation based on the Kubo formalism is provided. This enables the calculation of additional correction terms that increases the range of applicability of the procedure to lower temperatures. Because it is based on the Kubo-transformed correlation function, this approach allows the direct use of correlation functions obtained from methods such as ring-polymer molecular dynamics and centroid molecular dynamics in determining the influence functional coefficients for subsequent system-solvent simulations. The accuracy of the original procedure and the corrected procedure is investigated across a range of parameters. It is interesting that the correction term comes at zero additional cost. Furthermore, it is possible to improve upon the correction using zero-cost physical intuition and heuristics making the method even more accurate.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Efficacy of the radial pair potential approximation for molecular dynamics simulations of dense plasmas
Macroscopic simulations of dense plasmas rely on detailed microscopic information that can be computationally expensive and is difficult to verify experimentally. In this work, we delineate the accuracy boundary between microscale simulation methods by comparing Kohn–Sham density functional theory molecular dynamics (KS-MD) and radial pair potential molecular dynamics (RPP-MD) for a range of elements, temperature, and density. By extracting the optimal RPP from KS-MD data using force matching, we constrain its functional form and dismiss classes of potentials that assume a constant power law for small interparticle distances. Our results show excellent agreement between RPP-MD and KS-MD for multiple metrics of accuracy at temperatures of only a few electron volts. The use of RPPs offers orders of magnitude decrease in computational cost and indicates that three-body potentials are not required beyond temperatures of a few eV. Due to its efficiency, the validated RPP-MD provides an avenue for reducing errors due to finite-size effects that can be on the order of ∼20%.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Fast predictions of liquid-phase acid-catalyzed reaction rates using molecular dynamics simulations and convolutional neural networks
The rates of liquid-phase, acid-catalyzed reactions relevant to the upgrading of biomass into high-value chemicals are highly sensitive to solvent composition and identifying suitable solvent mixtures is theoretically and experimentally challenging. We show that the complex atomistic configurations of reactant–solvent environments generated by classical molecular dynamics simulations can be exploited by 3D convolutional neural networks to enable accurate predictions of Brønsted acid-catalyzed reaction rates for model biomass compounds. We develop a 3D convolutional neural network, which we call SolventNet, and train it to predict acid-catalyzed reaction rates using experimental reaction data and corresponding molecular dynamics simulation data for seven biomass-derived oxygenates in water–cosolvent mixtures. We show that SolventNet can predict reaction rates for additional reactants and solvent systems an order of magnitude faster than prior simulation methods. This combination of machine learning with molecular dynamics enables the rapid, high-throughput screening of solvent systems and identification of improved biomass conversion conditions.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Simulations of classical three-body thermalization in one dimension
One-dimensional systems, such as nanowires or electrons moving along strong magnetic field lines, have peculiar thermalization physics. The binary collision of pointlike particles, typically the dominant process for reaching thermal equilibrium in higher-dimensional systems, cannot thermalize a 1D system. We study how dilute classical 1D gases thermalize through three-body collisions. We consider a system of identical classical point particles with pairwise repulsive inverse power-law potential V ij ∝ 1/|x i –x j | n or the pairwise Lennard-Jones potential. Using Monte Carlo methods, we compute a collision kernel and use it in the Boltzmann equation to evolve a perturbed thermal state with temperature T toward equilibrium. We explain the shape of the kernel and its dependence on the system parameters. Additionally, we implement molecular dynamics simulations of a many-body gas and show agreement with the Boltzmann evolution in the low-density limit. For the inverse power-law potential, the rate of thermalization is proportional to ρ 2 T$\frac{1}{2}$ – $\frac{1}{n}$, where ρ is the number density. Furthermore, the corresponding proportionality constant decreases with increasing n.
1-dimensional systems↗
Exploring Li-Ion Transport Properties of Li 3 TiCl 6 : A Machine Learning Molecular Dynamics Study
We performed large-scale molecular dynamics simulations based on a machine-learning force field (MLFF) to investigate the Li-ion transport mechanism in cation-disordered Li 3 TiCl 6 cathode at six different temperatures, ranging from 25°C to 100°C. In this work, deep neural network method and data generated by ab − initio molecular dynamics (AIMD) simulations were deployed to build a high-fidelity MLFF. Radial distribution functions, Li-ion mean square displacements (MSD), diffusion coefficients, ionic conductivity, activation energy, and crystallographic direction-dependent migration barriers were calculated and compared with corresponding AIMD and experimental data to benchmark the accuracy of the MLFF. From MSD analysis, we captured both the self and distinct parts of Li-ion dynamics. The latter reveals that the Li-ions are involved in anti-correlation motion that was rarely reported for solid-state materials. Similarly, the self and distinct parts of Li-ion dynamics were used to determine Haven’s ratio to describe the Li-ion transport mechanism in Li 3 TiCl 6 . Obtained trajectory from molecular dynamics infers that the Li-ion transportation is mainly through interstitial hopping which was confirmed by intra- and inter-layer Li-ion displacement with respect to simulation time. Ionic conductivity (1.06 mS/cm) and activation energy (0.29eV) calculated by our simulation are highly comparable with that of experimental values. Overall, the combination of machine-learning methods and AIMD simulations explains the intricate electrochemical properties of the Li 3 TiCl 6 cathode with remarkably reduced computational time. Thus, our work strongly suggests that the deep neural network-based MLFF could be a promising method for large-scale complex materials.
Selvaraj, Selva Chandrasekaran (ORCID:000000029023↗
A First Principles Approach to Spectral Phonon Transport in Heterostructures
Understanding thermal transport across interfaces which give rise to a thermal resistance (also known as Kapitza resistance) is a critical issue affecting the development of nanotechnologies. Much modern and emergent nanotechnology consist of adjacent materials, and phonon mediated heat transfer governs thermal behavior across internal interfaces in these devices. The physics of thermal transport in solids are governed both by phenomena occurring at the atomic scale and interactions with the material's microstructure. The forecasting of fundamental quantities such as temperature, heat flux and thermal conductivity typically employs the semi-classical Boltzmann transport equation to predict the macroscopic behavior of materials in terms of the microscopic dynamics of its heat carriers. Kapitza resistance was first discovered in liquid helium experiments and has led to a fundamental research thrust in micro and nano-scale heat transport, the behavior of thermal carriers across internal interfaces. Thermal interfacial resistance (TIR) is a widely studied phenomenon, first engaged by Swartz and Pohl through their development of the acoustic and diffuse mismatch methods, then continued through myriad efforts with varying methods and approaches in an attempt to resolve carrier behavior at thermal interfaces. Many of the fundamental approaches to TIR have been at the nanoscale, and research is conducted with molecular dynamics (MD) and density functional theory (DFT) methods. The limitations of these methods is system size; atomistic methods tend to be limited to system sizes of 100,000 atoms or less. Larger length-scale methods have also been pursued, based on the principles of acoustic or diffuse mismatch, but not all include simulation of TIR using a full phonon band spectrum, or temperature dependent methods. Our approach to enabling phonon transport in layered materials draws upon our previous work of demonstrating spectrally coupled phonon transport in homogeneous and heterogeneous materials. We use a semi-analytical approach in which the Bose-Einstein (B-E) statistics set the strength of the phonon radiance in a frequency group, but the B-E statistics are informed with information from the transport system. The B-E statistics in a single frequency group feels the influence of all the groups through the spatial temperature. We also include a new field term which is an indicator of the amount of non-equilibrium behavior of the phonon spectrum---this is added to the phonon source term in all groups to ensure closure and conservation of energy, as the phonon groups in the transport system and the analytical systems are coupled. This work builds upon our previous approach by adding a phonon coupling term at an internal interface, using the principles of the DMM through transmission and reflection coefficients. In this work, the coefficients are determined through computing a common temperature at the interface, influenced by the phonon band structure of both materials, in effect, providing mixing between the two material systems and using the common temperature to set the strength of the phonon radiance at the boundaries on either side of the interface. Our approach uses material properties computed along various crystallographic orientations, and while some isotropy is built into the interface condition, the material properties weight the phonon distributions in the proper crystalline direction. Greater resolution of phonon behavior in proximity to an interface, and more accurate predictions of TIR are obtained. While it is true the assumption of diffuse mismatch can yield inconsistent results compared to experiment especially at low temperatures, this work focuses on room temperature and beyond effects, for future applications in nuclear fuel, or thermoelectric devices; a modified mismatch approach may be feasible if applied properly. Additionally, our methods focus on bridging mesoscale to engineering scale
36 MATERIALS SCIENCE↗
Effect of slip on vortex shedding from a circular cylinder in a gas flow
Most studies of vortex shedding from a circular cylinder in a gas flow have explicitly or implicitly assumed that the no-slip condition applies on the cylinder surface. To investigate the effect of slip, vortex shedding is simulated using molecular gas dynamics (the direct simulation Monte Carlo method) and computational fluid dynamics (the incompressible Navier-Stokes equations with a slip boundary condition). A Reynolds number of 100, a Mach number of 0.3, and a corresponding Knudsen number of 0.0048 are examined. For these conditions, compressibility effects are small, and periodic laminar vortex shedding is obtained. Slip on the cylinder is varied using combinations of diffuse and specular molecular reflections with accommodation coefficients from zero (maximum slip) to unity (minimum slip). Although unrealistic, bounce-back molecular reflections are also examined because they approximate the no-slip boundary condition (zero slip). The results from both methods are in reasonable agreement. The shedding frequency increases slightly as the accommodation coefficient is decreased, and shedding ceases at low accommodation coefficients (large slip). The streamwise and transverse forces decrease as the accommodation coefficient is decreased. Based on the good agreement between the two methods, computational fluid dynamics is used to determine the critical accommodation coefficient below which vortex shedding ceases for Reynolds numbers of 60–100 at a Mach number of 0.3. Finally, conditions to observe the effect of slip on vortex shedding appear to be experimentally realizable, although challenging.
42 ENGINEERING↗