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Results for “Classical molecular dynamic simulations”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 325 records · Page 18
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Inherent-state melting and the onset of glassy dynamics in two-dimensional supercooled liquids

Below the onset temperature T o , the equilibrium relaxation time of most glass-forming liquids exhibits glassy dynamics characterized by a super-Arrhenius temperature dependence. In this supercooled regime, the relaxation dynamics also proceeds through localized elastic excitations corresponding to hopping events between inherent states, i.e., potential-energy-minimizing configurations of the liquid. Despite its importance in distinguishing the supercooled regime from the high-temperature regime, the microscopic origin of T o is not yet known. Here, we construct a theory for the onset temperature in two dimensions and find that an inherent-state melting transition, described by the binding–unbinding transition of dipolar elastic excitations, delineates the supercooled regime from the high-temperature regime. The corresponding melting transition temperature is in good agreement with the onset temperature found in various two-dimensional (2D) atomistic models of glass formers and an experimental binary colloidal system confined to a water–air interface. Additionally, we find the predictions for the renormalized elastic moduli to agree with the experimentally observed values for the latter 2D colloidal system. We further discuss the predictions of our theory on the displacement and density correlations at supercooled conditions, which are consistent with observations of the Mermin–Wagner fluctuations in experiments and molecular simulations.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Practical guide to replica exchange transition interface sampling and forward flux sampling

Path sampling approaches have become invaluable tools to explore the mechanisms and dynamics of the so-called rare events that are characterized by transitions between metastable states separated by sizable free energy barriers. Their practical application, in particular to ever more complex molecular systems, is, however, not entirely trivial. Here, focusing on replica exchange transition interface sampling (RETIS) and forward flux sampling (FFS), we discuss a range of analysis tools that can be used to assess the quality and convergence of such simulations, which is crucial to obtain reliable results. The basic ideas of a step-wise evaluation are exemplified for the study of nucleation in several systems with different complexities, providing a general guide for the critical assessment of RETIS and FFS simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Improved Kelbg Potentials for Z > 1 and Application to Carbon Plasmas

In this work, we present a general form for the electron‐ion diffractive potential derived from the quantum pair density matrix and fit to the improved Kelbg potential for atomic numbers up to $Z = 54$. We apply classical molecular dynamics using the improved Kelbg potential for carbon with various forms of the Pauli potential to compute internal energies and pressures for hot, dense plasma conditions. Our results are compared to an equation of state model based on path integral Monte Carlo and density functional theory simulations to examine the extent to which the improved Kelbg potential reproduces the internal energy and pressure of carbon plasmas. The regions of validity for carbon agree generally with those derived previously for hydrogen once pressure ionization effects are incorporated. Based on our carbon results and previously published hydrogen studies, we discuss the general applicability and limitations of these potentials for equation of state studies in warm dense matter and high energy density plasmas.

general physics↗
DOE OSTI2022

Fock-Space Schrieffer–Wolff Transformation: Classically-Assisted Rank-Reduced Quantum Phase Estimation Algorithm

We present an extension of many-body downfolding methods to reduce the resources required in the quantum phase estimation (QPE) algorithm. In this paper, we focus on the Schrieffer–Wolff (SW) transformation of the electronic Hamiltonians for molecular systems that provides significant simplifications of quantum circuits for simulations of quantum dynamics. We demonstrate that by employing Fock-space variants of the SW transformation (or rank-reducing similarity transformations (RRST)) one can significantly increase the locality of the qubit-mapped similarity-transformed Hamiltonians. The practical utilization of the SW-RRST formalism is associated with a series of approximations discussed in the manuscript. In particular, amplitudes that define RRST can be evaluated using conventional computers and then encoded on quantum computers. The SW-RRST QPE quantum algorithms can also be viewed as an extension of the standard state-specific coupled-cluster downfolding methods to provide a robust alternative to the traditional QPE algorithms to identify the ground and excited states for systems with various numbers of electrons using the same Fock-space representations of the downfolded Hamiltonian. The RRST formalism serves as a design principle for developing new classes of approximate schemes that reduce the complexity of quantum circuits.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Investigation of fracture in porous materials: a phase-field fracture study informed by ReaxFF

Microscopic features (e.g, pore shapes, sizes, and distribution) in porous material substantially affect the overall mechanical properties such as stiffness and strength. In turn, these material properties determine the macroscopic behaviors of fracture in the porous material. In certain cases, macroscopic properties can be derived from the porous skeleton and void ratio (i.e., porosity), but in many other cases, such derivation is a challenging task. This paper presents a numerical investigation of microporosity and micropore shapes effect on the macrofracture behavior in porous amorphous silica. For this study, we extend the recently-proposed combined molecular dynamic (MD) and phase-field (PF) fracture modeling approach by including different pore shapes in the atomistic domain. In the MD simulations, we adopt ReaxFF to evaluate the material properties, where four different micropore cases are considered. Based on the material properties derived from MD simulations, the macrofracture propagation of porous media is studied using hybrid PF simulation. In the characterization of the pore structure, the concept of pore ligament is proposed to relate the pore shape and the critical energy release rate. Two classical fracture problems were used to evaluate the effect of pore shape on the macrofracture behavior. The results of the case study show that although the micropore shapes change the macrofracture behaviors, these effects vary with the geometry and loading conditions of macroscopic boundary value problems. Furthermore, the case study also shows that the influence of micropore structure can be captured at the macroscopic level through the material properties derived from the MD simulations.

42 ENGINEERING↗
DOE OSTI2021

Clarifying the definition of ‘transonic’ screw dislocations

We report a number of recent Molecular Dynamics (MD) simulations have demonstrated that screw dislocations in face centred cubic (fcc) metals can achieve stable steady state motion above the lowest shear wave speed (v shear ) which is parallel to their direction of motion (often referred to as transonic motion). This is in direct contrast to classical continuum analyses which predict a divergence in the elastic energy of the host material at a crystal geometry dependent ‘critical’ velocity v crit . Within this work, we first demonstrate through analytic analyses that the elastic energy of the host material diverges at a dislocation velocity (v crit ) which is greater than v shear , i.e. v crit >v shear . We argue that it is this latter derived velocity (v crit ) which separates ‘subsonic’ and ‘supersonic’ regimes of dislocation motion in the analytic solution. In addition to our analyses, we also present a comprehensive suite of MD simulation results of steady state screw dislocation motion for a range of stresses and several cubic metals at both cryogenic and room temperatures. At room temperature, both our independent MD simulations and the earlier works find stable screw dislocation motion only below our derived v crit . Nonetheless, in real-world polycrystalline materials v crit cannot be interpreted as a hard limit for subsonic dislocation motion. In fact, at very low temperatures our MD simulations of Cu at 10 Kelvin confirm a recent claim in the literature that true ‘supersonic’ screw dislocations with dislocation velocities v>v crit are possible at very low temperatures.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2025

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

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

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Exceptionally high spallation strength for a high-entropy alloy demonstrated by experiments and simulations

High-entropy alloys are materials with an increasing number of technological applications. Amongst them, the Cantor alloy, FeMnCoCrNi, shows desirable mechanical properties at normal loading conditions. In this study we focus on the performance of the Cantor alloy at the ultra-high deformation rates of shock waves. We study shock-induced spallation using both experiments and atomistic simulations. Experimental loading is achieved using high power laser, with VISAR to obtain velocity profiles and spall strength, followed by transmission electron microscopy of the recovered samples. Molecular Dynamics (MD) simulations of shock-induced spallation are compared with experiments. Both experiments and simulations show a high spall strength which would be beneficial for certain applications, with experiments giving ~8 GPa at ~10 7 s -1 and MD giving almost ~30 GPa at ~10 9 s -1 . The difference between experiments and simulations can be explained by the difference in strain rate. Post-mortem analysis of the experimental samples shows nanotwins near the spall plane, while MD simulations show a highly disordered region giving rise to void nucleation and spall during loading.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Role of Dynamic Polarization Interactions in the Electrical Double Layer at Calcite (104) Interfaces with Aqueous Solutions

Reactions at mineral interfaces with aqueous solutions control many geochemical and biogeochemical processes in the Earth’s critical zone. At the molecular level, insights into important properties such as the structure of the electrical double layer (EDL) at specific mineral interfaces continue to improve due to the increasing fidelity of laboratory instrumentation and computational approaches. However, molecular simulation approaches suffer from limited reach into relevant scales of time, length, and system complexity. To span this gap, a novel hybrid approach that couples first principle plane-wave density functional theory (DFT) with classical DFT (cDFT) is demonstrated and applied to calcite (104) interfaces with various electrolytes. In this approach, a region of interest described using DFT interacts with the surrounding medium described using cDFT to arrive at a self-consistent ground state. Benchmarking against experimental observations and entirely first principle DFT simulations demonstrates that this hybrid model efficiently encompasses the key short-range and collective interactions in the EDL. Simulations of calcite (104)/solution interfaces reveal the key static and dynamic polarization interactions that give rise to structuring of ions and water. Ion hydration interactions have the strongest effect on the depth of the first minimum in the density distribution of counterions at the surface, and the position and width of the first density peak is largely determined by the strength of ion-correlation forces. Finer details of ion distributions are controlled by mutual polarization of the calcite surface and interfacial electrolyte. Finally, this new ability to efficiently and rigorously predict EDL structure at mineral surfaces in contact with complex solutions paves the way to accurately modeling sorption, nucleation, dissolution, and growth in realistic systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Accelerating Ab Initio Simulation via Nested Monte Carlo and Machine Learned Reference Potentials

As a corollary of the rapid advances in computing, ab initio simulation is playing an increasingly important role in modeling materials at the atomic scale. Two strategies are possible, ab initio Monte Carlo (AIMC) and molecular dynamics (AIMD) simulation. The former benefits from exact sampling from the correct thermodynamic distribution, while the latter is typically more efficient with its collective all-atom coordinate updates. In this study, using a relatively simple test model comprised of helium and argon, we show that AIMC can be brought up to, and even above, the performance levels of AIMD via a hybrid nested sampling/machine learning (ML) strategy. Here, ML provides an accurate classical reference potential (up to three-body explicit interactions) that can pilot long collective Monte Carlo moves that are accepted or rejected in toto à la nested Monte Carlo (NMC); this is in contrast to the single move nature of a naive implementation. Our proposed method only requires a small up front expense from evaluating the ab initio energies and forces of (100) random configurations for training. Importantly, our method does not totally rely on the trained, assuredly imperfect, interaction. We show that high performance and exact sampling at the desired level of theory can be realized even when the trained interaction has appreciable differences from the ab initio potential. Remarkably, at the highest levels of performance realized via our approach, a pair of statistically uncorrelated atomic configurations can be generated with (1) ab initio calculations.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2024

Two-Dimensional Projected-Momentum Covariance Mapping for Coulomb Explosion Imaging

We introduce projected-momentum covariance mapping, an extension of recoil-frame covariance mapping for 2D ion imaging studies. By considering the two-dimensional projection of the ion momenta as recorded by the detector, one opens the door to a complex suite of analysis tools adapted from three-dimensional momentum imaging studies. This includes the use of different frames of reference to unravel the dynamics of fragmentation and the application of fragment momentum constraints to isolate specific fragmentation channels. The technique is demonstrated on data from a two-dimensional ion imaging study of the Coulomb explosion of the cis and trans isomers of 1,2-dichloroethene, following strong-field ionization by an intense near-infrared femtosecond laser pulse. Classical simulations are used to guide the interpretation of projected-momentum covariance maps. The results offer a detailed insight into the distinct Coulomb explosion dynamics for this pair of isomers and lay the groundwork for future time-resolved studies of photoisomerization dynamics in this molecular system.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Onset of cavitation and vapor bubble development over hydrophilic and hydrophobic surfaces

Cavitation, the formation of vapor bubbles as the liquid pressure is reduced below the saturated vapor pressure, often requires a substantial negative relative pressure in a pure liquid. Classical nucleation theory (CNT) provides an estimate for the rate of cavitation but there is often a disconnect between the predictions at the molecular scale compared to observations at the macroscale. We report on mesoscale simulations of cavitation based on many-body dissipative particle dynamics (mDPD), a coarse-grained molecular dynamics (MD), which bridges the two scales. A liquid layer is confined between smooth planar walls at a constant temperature, while the pressure is reduced slowly by expanding the wall-bounded domain. The wetting properties of the liquid are determined by the parameters of the interaction potentials. With hydrophilic walls, homogeneous nucleation is observed in the liquid bulk. As a bubble forms and grows, it creates a strong pressure pulse and oscillations that cause other bubbles that may have formed slightly later to collapse. For a nearly neutral wall with a contact angle close to 90 ° , heterogeneous nucleation occurs at the walls at a smaller negative pressure and generates weaker pressure oscillations. With hydrophobic walls or seed particles, heterogeneous nucleation readily occurs, where fluctuations and the merger of transient surface bubbles are significant.

Science & Technology - Other Topics↗
DOE OSTI2021

Molecular Dynamics Driven by the Many-Body Expansion (MBE-MD)

Here, we present a protocol for classical and nuclear quantum dynamics, in which the energies and forces are generated by the many-body expansion (MBE), and apply it to water clusters using the TTM2.1-F and MB-Pol interaction potentials at various temperatures. We carry out MBE-MD classical and nuclear quantum dynamical simulations in which the energies and forces of the full system are approximated by the 2-, 3-, and 4-body terms of the MBE expansion and compare the average potential and the vibrational density of states (VDOS) with the full simulation, i.e., the one for which no MBE is used. Our results indicate that the thermally averaged potential energy from the MBE up to the 4-body term converges with near identical behavior to the one from the full simulation. The 3-body makes a substantial contribution (~20%) to the energy, whereas the 4- body is necessary for obtaining quantitatively accurate energetics and forces, albeit making a small contribution to each (~2%). We further show that the harmonic frequencies are reproduced to within a few wavenumbers (cm -1 ) at the 4-body level, and that the slowest modes to converge with the MBE rank are those involving the strongest hydrogen bonds. Anharmonicity exacerbates this effect, so that a 4-body description of the energies and forces is needed to achieve accurate anharmonic vibrational frequencies in the hydrogen-bonded OH-stretching region. We also discuss the asymptotic scaling of the MBE-MD protocol with respect to the cost of the underlying potential energy evaluation, suggesting that electronic structure methods that scale at least as N 4 ,N being the size of the system, are needed to result in savings over the traditional full MD simulation. We anticipate that MBE-MD protocol can evolve into a powerful and practical method, which will allow for highly accurate ab initio MD simulations on a much broader range of molecular systems than can be currently handled.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Crystal nucleation rates in one-component Yukawa systems

Nucleation in the supercooled Yukawa system is relevant for addressing current challenges in understanding a range of crystallizing systems including white dwarf (WD) stars. We use both brute force and seeded molecular dynamics simulations to study homogeneous nucleation of crystals from supercooled Yukawa liquids. With our improved approach to seeded simulations, we obtain quantitative predictions of the crystal nucleation rate and cluster size distributions as a function of temperature and screening length. These quantitative results show trends towards fast nucleation with short-ranged potentials. They also indicate that for temperatures T > 0.9⁢T m , where T m is the melt temperature, classical homogeneous nucleation is too slow to initiate crystallization but transient clusters of ~100 particles should be common. As a result, we apply these general results to a typical WD model and obtain a delay of ~0.6 Gyr in the onset of crystallization that may be observable.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Coalescence and splashing threshold for head-on collisions of liquid metal nanodroplets

Head-on collisions of liquid metal nanodroplets in a vacuum are investigated through molecular dynamics simulations in order to determine the transition threshold between the coalescing and splashing regimes for six different materials (aluminum, calcium, cerium, gold, platinum, and tin). Droplets of various sizes and initial speeds are simulated, and it is found that the Reynolds and Ohnesorge numbers are able to predict the transition between the coalescing and splashing regimes. An energy balance for coalescing droplets shows that the initial energy is mainly converted to thermal energy increasing the temperature of the combined droplets by several hundred to several thousand kelvin depending on the material, and this result is confirmed in the simulations. Furthermore, when splashing occurs, the number of smaller droplets formed and the spreading rate are found to be dependent on the initial size and initial speed of the original droplets.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Water transport in reverse osmosis membranes is governed by pore flow, not a solution-diffusion mechanism

We performed nonequilibrium molecular dynamics (NEMD) simulations and solvent permeation experiments to unravel the mechanism of water transport in reverse osmosis (RO) membranes. The NEMD simulations reveal that water transport is driven by a pressure gradient within the membranes, not by a water concentration gradient, in marked contrast to the classic solution-diffusion model. We further show that water molecules travel as clusters through a network of pores that are transiently connected. Permeation experiments with water and organic solvents using polyamide and cellulose triacetate RO membranes showed that solvent permeance depends on the membrane pore size, kinetic diameter of solvent molecules, and solvent viscosity. This observation is not consistent with the solution-diffusion model, where permeance depends on the solvent solubility. Motivated by these observations, we demonstrate that the solution-friction model, in which transport is driven by a pressure gradient, can describe water and solvent transport in RO membranes.

42 ENGINEERING↗
DOE OSTI2025

Quasiclassical sampling and Wigner sampling of initial vibrational coordinates and momenta for polyatomic molecules in Monte Carlo molecular dynamics simulations

In a quasiclassical trajectory simulation, the vibrational modes are initialised with quantised vibrational energies, but vibrational phases are sampled by Monte Carlo. This requires an algorithm to assign coordinates and momenta to the various atoms. In this work, we present two methods for implementing this for nonrotating polyatomic molecules, namely, fixed-energy vibrational-state-selected initial conditions and thermal initial conditions. We also present a method for initiating classical trajectories with a ground-state Wigner distribution. These vibrational treatments are sufficient to initialise trajectories for unimolecular processes, and we also show how they can be applied to simulate bimolecular collision processes. The treatments of unimolecular and bimolecular collision processes are available in two Python codes called wigner_state_selected.py and bimolecular_collision.py, respectively, which will generate initial condition files that are recognisable by the SHARC and SHARC-MN computer programs for dynamics calculations. Both codes are available as standalone programs, as well as being included in SHARC-MN, and they will be included in future versions of SHARC. Here, the methods implemented in these codes are mostly also available in the ANT computer program, and those that are not available in ANT will be incorporated in future versions of ANT.

Wigner distribution↗
DOE OSTI2024

How Rigid Are Anthranilamide Molecular Electrets?

As important as molecular electrets are for electronic materials and devices, conformational fluctuations strongly impact their macrodipoles and intrinsic properties. Herein, we employ molecular dynamics (MD) simulations with the polarizable charge equilibrium (PQEq) method to investigate the persistence length (L P ) of molecular electrets composed of anthranilamide (Aa) residues. The PQEq-MD dissipates the accepted static notions about Aa macromolecules, and L P represents the shortest Aa rigid segments. The classical model with a single L P value does not describe these oligomers. Introducing multiple L P values for the same macromolecule follows the observed trends and discerns the enhanced rigidity in their middle sections from the reduced stiffness at their terminal regions. Furthermore, L P distinctly depends on solvent polarity. The Aa oligomers maintain extended conformations in nonpolar solvents with L P exceeding 4 nm, while in polar media, increased conformational fluctuations reduce L P to about 2 nm. These characteristics set key guidelines about the utility of Aa conjugates for charge-transfer systems within organic electronics and energy engineering.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗