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At least 469 records · Page 26

Bayesian force fields from active learning for simulation of inter-dimensional transformation of stanene

Abstract We present a way to dramatically accelerate Gaussian process models for interatomic force fields based on many-body kernels by mapping both forces and uncertainties onto functions of low-dimensional features. This allows for automated active learning of models combining near-quantum accuracy, built-in uncertainty, and constant cost of evaluation that is comparable to classical analytical models, capable of simulating millions of atoms. Using this approach, we perform large-scale molecular dynamics simulations of the stability of the stanene monolayer. We discover an unusual phase transformation mechanism of 2D stanene, where ripples lead to nucleation of bilayer defects, densification into a disordered multilayer structure, followed by formation of bulk liquid at high temperature or nucleation and growth of the 3D bcc crystal at low temperature. The presented method opens possibilities for rapid development of fast accurate uncertainty-aware models for simulating long-time large-scale dynamics of complex materials.

Chemistry↗

High-pressure phase transition in 3-D printed nanolamellar high-entropy alloy by imaging and simulation insights

Abstract We report on the high-resolution imaging and molecular dynamics simulations of a 3D-printed eutectic high-entropy alloy (EHEA) Ni 40 Co 20 Fe 10 Cr 10 Al 18 W 2 consisting of nanolamellar BCC and FCC phases. The direct lattice imaging of 3D-printed samples shows the Kurdjumov–Sachs (K–S) orientation relation {111} FCC parallel to {110} BCC planes in the dual-phase lamellae. Unlike traditional iron and steels, this alloy shows an irreversible BCC-to-FCC phase transformation under high pressures. The nanolamellar morphology is maintained after pressure cycling to 30 GPa, and nano-diffraction studies show both layers to be in the FCC phase. The chemical compositions of the dual-phase lamellae after pressure recovery remain unchanged, suggesting a diffusion-less BCC–FCC transformation in this EHEA. The lattice imaging of the pressure-recovered sample does not show any specific orientation relation between the two resulting FCC phases, indicating that many grain orientations are produced during the BCC–FCC phase transformation. Molecular dynamics simulations on phase transformation in a nanolamellar BCC/FCC in K–S orientation show that phase transformation from BCC to FCC is completed under high pressures, and the FCC phase is retained on decompression aided by the stable interfaces. Our work elucidates the irreversible phase transformation under static compression, providing an understanding of the orientation relationships in 3-D printed EHEA under high pressures.

3-D Printing↗

Equilibrium and Dynamics Properties of Poly(oxyethylene) Melts and Related Poly(alkylethers) from Simulations and Ab Initio Calculations

Molecular dynamics simulations of POE melts have been performed utilizing a potential force field parameterized to reproduce conformer energies and rotational energy barriers in dimethoxyethane as determined from ab initio electronic structure calculations. Chain conformations and dimensions of POE from the simulations were found to be in good agreement with predictions of a rotational isomeric state (RIS) model based upon the ab initio conformational. energies. The melt chains were found to be somewhat extended relative to chains at theta conditions. This effect will be discussed in light of neutron scattering experiments which indicate that POE chains are extended in the melt relative to theta solutions. The conformational characteristics of POE chains will also be compared with those of other poly (alkylethers), namely poly(oxymethylene), poly(oxytrimethylene) and poly(oxytetramethylene). Local conformational dynamics were found to be more rapid than in polymethylene. Calculated C-H vector correlation times were found to be in reasonable agreement with experimental values from C-13 NMR spin-lattice relaxation times. The influence of ionic salts on local conformations and dynamics will also be discussed.

Smith, Grant D.↗

Developing reliable machine learning interatomic potential for Fe–Cr–Ni austenitic alloys

Gaining atomistic understanding of mechanical behavior of heat-resistant structural materials such as Fe–Cr–Ni-based alloys requires an approach with an accuracy close to density functional theory (DFT) that considers the intrinsic properties of the bulk lattice and important defects such as stacking faults, grain boundaries, and surfaces. This work aims to develop reliable machine learning interatomic potential (MLIAP) at cross-scale for Fe–Cr–Ni ternary alloys with a focus on the face-centered-cubic (fcc) solid solution structure. Leveraging the advantages of moment tensor potentials, which typically necessitate a relatively small training dataset and enable rapid calculations using the large-scale atomic/molecular massively parallel simulator package, we ensure the stability and accuracy of the trained potentials. Important defects such as stacking faults, grain boundaries, and surfaces for wide-range compositions are investigated. Structural, thermal, elastic, and defect properties are determined from molecular dynamics simulations comprising several thousand atoms, generated via canonical Monte Carlo simulations guided by the trained potential. The trained potential allows efficient atomic simulations of structural, thermal, and mechanical properties of fcc Fe–Cr–Ni solid solution alloys as a function of composition and temperature. Therefore, the MLIAP approach represents a major advancement from DFT calculations that are limited to small simulation sizes and traditional molecular dynamics simulations using relatively low accuracy potentials. Furthermore, this work outlines a practical foundation for further investigating the structural evolution and mechanical behavior of austenitic stainless steel and nickel-based alloys in a wide array of applications in extreme environments.

Crystal structure↗

Granular Flow

LIGGGHTS-INL is a capability-extended version of LIGGGHTS. LIGGGHTS is an Open Source Discrete Element Method Particle Simulation Software (https://www.cfdem.com/media/DEM/docu/Manual.html). LIGGGHTS stands for LAMMPS improved for general granular and granular heat transfer simulations. LAMMPS is a classical molecular dynamics simulator. It is widely used in the field of Molecular Dynamics (https://lammps.sandia.gov/doc/Manual.html). Thanks to physical and algorithmic analogies, LAMMPS is a very good platform for DEM simulations. LAMMPS offers a GRANULAR package to perform these kinds of simulations. LIGGGHTS aims to improve those capability with the goal to apply it to industrial applications.

Xia, Yidong↗

Machine Learning Enabled Atomistic Study of the Micro-Cold Spray Process [Poster]

Micro-cold spray is typically conducted by impacting 200-2000 nm particles at velocities of ~500 m/s. Molecular dynamics simulations have been used to study micro cold spray, but the particles that can be simulated using conventional potentials are much smaller than those used experimentally. The viewgraphs taken from molecular dynamics simulations and shown below are cross-sections of a 50 nm Ta particle with a 3 nm oxide layer impacting at 500 m/s using a machine learning enabled DeePMD potential. Using more expensive reactive interatomic potentials, the previous largest particle size for a metal/oxide impact simulation was 12 nm.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Simulating the Effects of Carbon Nanotube Continuity and Interfacial Bonding on Composite Strength and Stiffness

Molecular dynamics simulations of carbon nanotube (CNT) composites, in which the CNTs are continuous across the periodic boundary, overestimate the experimentally measured mechanical properties of CNT composites along the fiber direction. Since the CNTs in these composites are much shorter than the composite dimensions, load must be transferred either directly between CNTs or through the matrix, a mechanism that is absent in simulations of effectively continuous CNTs. In this study, the elastic and fracture properties of high volume fraction discontinuous carbon nanotube/amorphous carbon composite systems were compared to those of otherwise equivalent continuous CNT composites using ReaxFF reactive molecular dynamics simulations. These simulations were used to show how the number of nanotube-matrix interfacial covalent bonds affect composite mechanical properties. Furthermore, the mechanical impact of interfacial bonding was decomposed to reveal its effect on the properties of the CNTs, the interfacial layer of matrix, and the bulk matrix. For the composites with continuous reinforcement, it was found that any degree of interfacial bonding has a negative impact on axial tensile strength and stiffness. This is due to disruption of the structure of the CNTs and interfacial matrix layer by the interfacial bonds. For the discontinuous composites, the modulus was maximized between 4%-7% interfacial bonding and the strength continues to increase up to the highest levels of interfacial bonding studied. Areas of low stress and voids were observed in the simulated discontinuous composites at the ends of the tubes, from which fracture was observed to initiate. Experimental carbon nanotube yarn composites were fabricated and tested. The results were used to illustrate knockdown factors relative to the mechanical performance of the tubes themselves.

Benjamin D Jensen↗

Grain growth of nanocrystalline aluminum under tensile deformation: A combined in situ TEM and atomistic study

Nanocrystalline Al thin films have been strained in situ in a transmission electron microscope using two separate nanomechanical techniques involving a push-to-pull device and a microelectromechanical system (MEMS) device. Deformation-induced grain growth was observed to occur via stress-assisted grain boundary migration with extensive grain growth occurring in the necked region, indicating that the increase in local stress drives the boundary migration. Under applied tensile stresses close to the ultimate tensile strength of 450 MPa for a nanocrystalline Al specimen, measured boundary migration speeds are 0.2 – 0.7 nm s -1 for grains outside necked region and increases to 2.5 nm s -1 for grains within the necked region where the local estimated tensile stresses are elevated to around 630 MPa. By tracking grain boundary motion over time, molecular dynamics simulations showed qualitative agreement in terms of pronounced grain boundary migration with the experimental observations. The combined in situ observation and molecular dynamics simulation results underscore the important role of stress-driven grain growth in plastically deforming nanocrystalline metals, leading to intergranular fracture through predominant grain boundary sliding in regions with large localized deformation.

36 MATERIALS SCIENCE↗

Custom-trained Machine-learning Interatomic Potentials: ZnCl2 Aqueous Solution

This dataset was generated using an iterative active-learning strategy implemented in the ArcaNN software package (https://github.com/arcann-chem/arcann_training) to train machine-learning interatomic potentials for aqueous ZnCl2 solutions. Each active-learning cycle consisted of three stages: training, exploration, and labeling. The initial training set combined configurations generated in this work from enhanced-sampling ab initio molecular dynamics simulations with configurations from a previously reported neural-network-potential study of aqueous ZnCl2. The enhanced-sampling ab initio molecular dynamics simulations involved Zn–Cl separation and the chloride coordination number around Zn²? as collective variables. These configurations served as the seed dataset. Subsequent active-learning cycles expanded the training set by identifying and labeling configurations that were poorly represented by the current models, thereby improving coverage of ion-association states and changes in local coordination and charge-state environments relevant to the solution free-energy landscape. For all selected configurations, single-point calculations of the total energies and atomic forces were performed within density functional theory using the CP2K Quickstep module. Reference calculations employed the revPBE-D3 and r2SCAN exchange-correlation functionals. Motivated by recent work on aqueous Zn²?, the main revPBE calculations omitted D3 dispersion contributions involving Zn²?, while retaining the D3 correction for water and chloride. For comparison, fully dispersion-corrected revPBE-D3 reference calculations were also performed, with D3 applied to all species, including Zn²?. Valence electrons were treated explicitly, while core electrons were represented using norm-conserving Goedecker–Teter–Hutter pseudopotentials. The wave functions were expanded using the mixed Gaussian-and-plane-wave scheme with TZV2P-MOLOPT basis sets for all elements and a 600 Ry auxiliary plane-wave cutoff for the electron density. Self-consistent-field convergence was accelerated using the orbital-transformation and Direct Inversion in the Iterative Subspace algorithms, with a convergence threshold of 10?6. All single-point calculations were performed in periodic orthorhombic cells. The CELL_REF keyword in CP2K was used to define a fixed reference cell with a box length of 25 Å. This treatment ensured a consistent reference for configurations extracted from NpT trajectories with fluctuating cell dimensions. The resulting DFT energies and atomic forces constitute the ground-truth labels used to train the MLIPs. The resulting MLIP was trained for aqueous ZnCl2 solutions spanning concentrations from 0 to 30 molal and a broad pH range, from strongly acidic to strongly basic conditions. Representative examples of configurations included in the MLIP training dataset are provided below. These include 1) Representative configurations from the dataset labeled at the revPBE-D3 level, with D3 dispersion interactions involving Zn2+ excluded (revPBE-wo-D3). 2) Representative configurations from the dataset labeled at the fully dispersion-corrected revPBE-D3 level, with D3 interactions applied to all species, including Zn2+ (revPBE-D3). 3) Representative configurations from the dataset labeled at the r2SCAN level of theory (r2SCAN).

Dinpajooh, Mohammadhasan [Pacific Northwest Nation↗

Flow of long chain hydrocarbons through carbon nanotubes (CNTs)

The pressure-driven flow of long-chain hydrocarbons in nanosized pores is important in energy, environmental, biological, and pharmaceutical applications. This paper examines the flow of hexane, heptane, and decane in carbon nanotubes (CNTs) of pore diameters 1–8 nm using molecular dynamic simulations. Enhancement of water flow in CNTs in comparison to rates predicted by continuum models has been well established in the literature. Our work was intended to observe if molecular dynamic simulations of hydrocarbon flow in CNTs produced similar enhancements. We used the OPLS-AA force field to simulate the hydrocarbons and the CNTs. Our simulations predicted the bulk densities of the hydrocarbons to be within 3% of the literature values. Molecular sizes and shapes of the hydrocarbon molecules compared to the pore size create interesting density patterns for smaller sized CNTs. We observed moderate flow enhancements for all the hydrocarbons (1–100) flowing through small-sized CNTs. For very small CNTs the larger hydrocarbons were forced to flow in a cork-screw fashion. As a result of this flow orientation, the larger molecules flowed as effectively (similar enhancements) as the smaller hydrocarbons.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Failure of molecular dynamics to provide appropriate structures for quantum mechanical description of the aqueous chloride ion charge-transfer-to-solvent ultraviolet spectrum

The lowest band in the charge-transfer-to-solvent ultraviolet absorption spectrum of aqueous chloride ion is studied by experiment and computation. Interestingly, the experiments indicate that at concentrations up to at least 0.25 M, where calculations indicate ion pairing to be significant, there is no notable effect of ionic strength on the spectrum. The experimental spectra are fitted to aid comparison with computations. Classical molecular dynamic simulations are carried out on dilute aqueous Cl - , Na + , and NaCl, producing radial distribution functions in reasonable agreement with experiment and, for NaCl, clear evidence of ion pairing. Clusters are extracted from the simulations for quantum mechanical excited state calculations. Accurate ab initio coupled-cluster benchmark calculations on a small number of representative clusters are carried out and used to identify and validate an efficient protocol based on time-dependent density functional theory. The latter is used to carry out quantum mechanical calculations on thousands of clusters. The resulting computed spectrum is in excellent agreement with experiment for the peak position, with little influence from ion pairing, but is in qualitative disagreement on the width, being only about half as wide. It is concluded that simulation by classical molecular dynamics fails to provide an adequate variety of structures to explain the experimental CTTS spectrum of aqueous Cl - .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Melting point of iron at high pressure: An assessment of uncertainties and effect of electronic temperature

An accurate calculation of the melting point of iron at various pressures in the Earth's core is important for understanding the core structure, geodynamo, and the Earth's history. Previous studies have assessed the melt line of iron at these extreme conditions using various experimental measurement techniques as well as both ab initio and classic molecular dynamics simulations. However, experimental measurements have uncertainties up to several hundred Kelvin, and inconsistencies remain among simulation results. Here in this work, we propose an iterative framework that couples density functional theory (DFT) calculations and molecular dynamics simulations performed using an ensemble of interatomic potentials to assess the effect of electronic temperature on the melting point. We systematically validate the potentials by comparing lattice constants and phonon dispersion curves at 0 K and enthalpy differences between liquid and HCP, FCC, BCC phases of iron close to the melt line at 300 GPa with DFT. Our results show that HCP iron melts at 6144 K (at 300 GPa), BCC phase is thermodynamically unstable, and FCC is metastable at this temperature. The melting points of FCC and BCC phases at 300 GPa are 5858 and 5647 K, respectively.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Accurate and efficient parameterization of an atomic cluster expansion (ACE) potential for ammonia under extreme conditions

We present a machine learning interatomic potential for ammonia designed to capture its complex multiphase behavior, including both molecular and superionic phases. The potential is based on the atomic cluster expansion (ACE) formulation and has been parameterized to facilitate high-fidelity molecular dynamics simulations of ammonia under extreme conditions, for pressures up to 100 GPa and for temperatures above 500 K and up to 6000 K. A diverse range of configurations was generated through high-quality ab initio molecular dynamics simulations, covering insulating and superionic ice phases, liquid ammonia, molecular nitrogen (N 2 ) and hydrogen (H 2 ), and metastable compounds that form upon dissociation, including $NH^{+}_{4}$, $H^{+}_{3}$, N 2 H 4 , and N 3 H. We demonstrate that the ammonia ACE potential accurately reproduces experimental and density functional theory predicted isotherms and Hugoniots. Crucially, the potential is able to capture the intricate phase behavior of ammonia, including the transition from insulating molecular fluid to the superionic phase. This work provides a robust interatomic potential that can be used for large-scale, accurate simulations of ammonia under extreme thermodynamic conditions, offering a powerful tool for investigating its behavior in various phases and applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structure and Dynamics of CO 2 at the Air–Water Interface from Classical and Neural Network Potentials

The accurate description of the structure and dynamics of CO 2 at the instantaneous air–water interface, along with the effects of surface fluctuations on the CO 2 -transport processes, is essential for the development of negative emission technologies aimed at minimizing climate change. In this study, we performed molecular dynamics simulations of CO 2 at the air–water interface using neural network potentials (NNPs) trained on ab initio data generated through density-functional-theory-based molecular dynamics simulations. We compared these results with classical force fields to assess their performance in modeling interfacial CO 2 behavior. Our findings revealed that the asymmetric interactions, coupled with thermal surface fluctuations at the air–water interface, significantly influence CO 2 transport into the aqueous phase. The simulations demonstrate that classical force fields underestimate both the free energy of CO 2 transport and the strength of its interactions at the interface compared with the neural network potentials. In conclusion, the free energy and the interfacial dynamics of CO 2 are primarily influenced by the distribution of water within the instantaneous interfacial water layer, responsible for creating an asymmetric intermolecular interaction environment within the interfacial region.

Ab initio molecular dynamics↗

Functionalization of Electrodes with Tunable [EMIM] x [Cl] x +1 – Ionic Liquid Clusters for Electrochemical Separations

Functionalization of electrodes with clusters of hydrophobic molecules may improve the energy efficiency and selectivity of electrochemical separations by modulating the desolvation process occurring at the interface. Ionic liquids (IL), which have a broad range of compositions and properties, are potential candidates for controlling the transport, desolvation, and adsorption of target ions at electrochemical interfaces. We report a joint experimental and theoretical investigation of the structure, stability, and selective adsorption properties of the IL clusters 1-ethyl-3-methylimidazolium chloride [EMIM] x [Cl] x+1 - (x = 1 – 10) and demonstrate their ability to adsorb and separate ions from solution. The structure and stability of the IL clusters are determined experimentally using high-mass-resolution electrospray ionization mass spectrometry, collision-induced dissociation, and negative ion photoelectron spectroscopy. Global optimization theory and ab initio molecular dynamics simulations provide molecular-level insight into the bonding and structural fluxionality of these species. Ion soft landing is used to selectively functionalize the surface of highly oriented pyrolytic graphite (HOPG) working electrodes with [EMIM] 1 [Cl] 2 - , [EMIM] 3 [Cl] 4 - , and [EMIM] 5 [Cl] 6 - clusters. Kelvin probe microscopy provides insight into the relative stability of the clusters on HOPG and their effect on the work function of IL-functionalized electrodes. Cyclic voltammetry measurements reveal irreversible adsorption of Fe(CN) 6 4-/3- anions during redox cycling, while electrochemical impedance spectroscopy indicates a substantial decrease in the electron transfer resistance of the IL-functionalized electrodes due to adsorption of Fe(CN) 6 4-/3- . Overall, our findings demonstrate that IL clusters with different size and stoichiometry may be used to increase the efficiency of electrochemical separations, opening new horizons in selective electrode functionalization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Ion Pairing and Molecular Orientation at Liquid/Liquid Interfaces: Self-Assembly and Function

We report that molecular orientation plays a pivotal role in defining the functionality and chemistry of interfaces, yet accurate measurements probing this important feature are few, due, in part, to technical and analytical limitations in extracting information from molecular monolayers. For example, buried liquid/liquid interfaces, where a complex and poorly understood balance of inter- and intramolecular interactions impart structural constraints that facilitate the formation of supramolecular assemblies capable of new functions, are difficult to probe experimentally. Here, we use vibrational sum-frequency generation spectroscopy, numerical polarization analysis, and atomistic molecular dynamics simulations to probe molecular orientations at buried oil/aqueous interfaces decorated with amphiphilic oligomers. We show that the orientation of self-assembled oligomers changes upon the addition of salts in the aqueous phase. The evolution of these structures can be described by competitive ion effects in the aqueous phase altering the orientations of the tails extending into the oil phase. These specific anionic effects occur via interfacial ion pairing and associated changes in interfacial solvation and hydrogen-bonding networks. These findings provide more quantitative insight into orientational changes encountered during self-assembly and pave the way for the design of functional interfaces for chemical separations, neuromorphic computing applications, and related biomimetic systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Release dynamics of nanodiamonds created by laser-driven shock-compression of polyethylene terephthalate

Laser-driven dynamic compression experiments of plastic materials have found surprisingly fast formation of nanodiamonds (ND) via X-ray probing. This mechanism is relevant for planetary models, but could also open efficient synthesis routes for tailored NDs. We investigate the release mechanics of compressed NDs by molecular dynamics simulation of the isotropic expansion of finite size diamond from different P-T states. Analysing the structural integrity along different release paths via molecular dynamic simulations, we found substantial disintegration rates upon shock release, increasing with the on-Hugnoiot shock temperature. We also find that recrystallization can occur after the expansion and hence during the release, depending on subsequent cooling mechanisms. Our study suggests higher ND recovery rates from off-Hugoniot states, e.g., via double-shocks, due to faster cooling. Laser-driven shock compression experiments of polyethylene terephthalate (PET) samples with in situ X-ray probing at the simulated conditions found diamond signal that persists up to 11 ns after breakout. In the diffraction pattern, we observed peak shifts, which we attribute to thermal expansion of the NDs and thus a total release of pressure, which indicates the stability of the released NDs.

36 MATERIALS SCIENCE↗

Cancer-associated somatic mutations in human phosphofructokinase-1 reveal a critical electrostatic interaction for allosteric regulation of enzyme activity

Metabolic reprogramming, including increased glucose uptake and lactic acid excretion, is a hallmark of cancer. The glycolytic ‘gatekeeper’ enzyme phosphofructokinase-1 (PFK1), which catalyzes the step committing glucose to breakdown, is dysregulated in cancers. While altered PFK1 activity and expression in tumors have been demonstrated, little is known about the effects of cancer-associated somatic mutations. Somatic mutations in PFK1 inform our understanding of allosteric regulation by identifying key amino acid residues involved in the regulation of enzyme activity. Here, we characterized mutations disrupting an evolutionarily conserved salt bridge between aspartic acid and arginine in human platelet (PFKP) and liver (PFKL) isoforms. Using purified recombinant proteins, we showed that disruption of the Asp–Arg pair in two PFK1 isoforms decreased enzyme activity and altered allosteric regulation. We determined the crystal structure of PFK1 to 3.6 Å resolution and used molecular dynamic simulations to understand molecular mechanisms of altered allosteric regulation. We showed that PFKP-D564N had a decreased total system energy and changes in the electrostatic surface potential of the effector site. Cells expressing PFKP-D564N demonstrated a decreased rate of glycolysis, while their ability to induce glycolytic flux under conditions of low cellular energy was enhanced compared with cells expressing wild-type PFKP. Taken together, these results suggest that mutations in Arg–Asp pair at the interface of the catalytic-regulatory domains stabilizes the t-state and presents novel mechanistic insight for therapeutic development in cancer.

59 BASIC BIOLOGICAL SCIENCES↗