Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Molecular dynamics simulation”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 703 records · Page 39
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

From Femtoseconds to Gigaseconds: The SolDeg Platform for the Performance Degradation Analysis of Silicon Heterojunction Solar Cells

Heterojunction Si solar cells exhibit notable performance degradation. Here, we modeled this degradation by electronic defects getting generated by thermal activation across energy barriers over time. To analyze the physics of this degradation, we developed the SolDeg platform to simulate the dynamics of electronic defect generation. First, femtosecond molecular dynamics simulations were performed to create a-Si/c-Si stacks, using the machine learning-based Gaussian approximation potential. Second, we created shocked clusters by a cluster blaster method. Third, the shocked clusters were analyzed to identify which of them supported electronic defects. Fourth, the distribution of energy barriers that control the generation of these electronic defects was determined. Fifth, an accelerated Monte Carlo method was developed to simulate the thermally activated time-dependent defect generation across the barriers. Our main conclusions are as follows. (1) The degradation of a-Si/c-Si heterojunction solar cells via defect generation is controlled by a broad distribution of energy barriers. (2) We developed the SolDeg platform to track the microscopic dynamics of defect generation across this wide barrier distribution and determined the time-dependent defect density N(t) from femtoseconds to gigaseconds, over 24 orders of magnitude in time. (3) We have shown that a stretched exponential analytical form can successfully describe the defect generation N(t) over at least 10 orders of magnitude in time. (4) We found that in relative terms, Voc degrades at a rate of 0.2%/year over the first year, slowing with advancing time. (5) We developed the time correspondence curve to calibrate and validate the accelerated testing of solar cells. We found a compellingly simple scaling relationship between accelerated and normal times t normal ∝ t accel T(accel)/T(normal) . (6) We also carried out experimental studies of defect generation in a-Si:H/c-Si stacks. We found a relatively high degradation rate at early times that slowed considerably at longer time scales.

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

Effect of Confinement of SIA Cluster Diffusion by Impurities on Radiation Defect Accumulation due to 14MeV neutrons in Tungsten

Impurities acting as traps, reduce the self-interstitial atom (SIA) cluster mobility, thereby increasing recombination and in turn enhancing radiation-resistance of polycrystalline materials. However, at elevated temperatures, depending on SIA-trap (impurity) binding energy, SIA clusters may trap and detrap (detach) numerous times. In tungsten, SIA clusters of all sizes glide one-dimensionally (1D) along their Burgers vector direction. Hence, detrapped SIAs would retrace their path, confining their 1D-glide between traps. However, small SIA clusters can change the direction of their 1D-glide by overcoming a rotation barrier. In addition, impurities or solutes are known to reduce this barrier. A lower rotation barrier can result in detrapped SIA clusters that diffuse in a random 1D direction, effectively leading to 3D (net-3D) diffusion. Here we investigate the effect of two cases of SIA diffusion, namely confined-1D diffusion and net-3D diffusion, on the damage accumulation in polycrystalline tungsten under 14 MeV neutron irradiation using the object kinetic Monte Carlo method. Simulations were performed using cascade debris obtained from molecular dynamics simulations with primary knock-on atom (PKA) energies corresponding to 14 MeV neutrons. In the simulations with net-3D diffusion, SIA clusters of all sizes diffuse in a random 1D direction after the clusters detrap. While for the confined 1D diffusion case, SIA clusters larger than size 5 retain their original direction of 1D-glide. In both types of simulations, trapped vacancies are assumed to be permanently immobilized. Unexpectedly, the damage accumulation was lower with confined 1D diffusion than that with net-3D. We present a systematic comparison of the influence of the two cases of SIA diffusion on the radiation damage accumulation as a function of dose rate, detrapping barrier, and impurity concentration at 1025 K.

Accumulation and recovery of lattice damage, tungs↗
DOE OSTI2022

Solvation Thermodynamics of Solutes in Water and Ionic Liquids Using the Multiscale Solvation-Layer Interface Condition Continuum Model

We report molecular assembly processes are generally driven by thermodynamic properties in solutions. Atomistic modeling can be very helpful in designing and understanding complex systems, except that bulk solvent is very inefficient to treat explicitly as discrete molecules. The SLIC/CDC multiscale model combines continuum solvent electrostatics based on the solvent layer interface condition (SLIC) with statistical thermodynamic models for hydrogen bonding and nonpolar modes: cavity formation, dispersion interactions, combinatorial mixing (CDC). The SLIC/CDC model predicts Gibbs energies of solvation for a database of 500 solutes in water with average accuracy better than 1 kcal/mol both for experimental measurements and for explicit-solvent molecular dynamics simulations. The separate SLIC/CDC energy mode values agree quantitatively with those computed from explicit-solvent molecular dynamics. The SLIC/SASA multiscale model combines the SLIC continuum electrostatic model with the solvent accessible surface area (SASA) nonpolar energy mode. The SLIC/SASA model predicts Gibbs energies of solvation with better than 1.4 kcal/mol average accuracy in aqueous systems and better than 1.6 kcal/mol average accuracy in ionic liquids. Both models predict solvation entropies, and are the first implicit-solvation models capable of predicting solvation heat capacities.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Relationships between Water’s Structure and Solute Affinity at Polypeptoid Brush Surfaces

Excellent antifouling surfaces are generally thought to create a tightly bound layer of water that resists solute adsorption, and highly hydrophilic surfaces such as those with zwitterionic functionalities are of significant current interest as antifoulant strategies. Furthermore, despite significant proofs-of-concept, we still lack a fundamental understanding of how the nanoscopic structure of this hydration layer translates to reduced fouling, how surface chemistry can be tuned to achieve antifouling through hydration water, and why, in particular, zwitterionic surfaces seem so promising. Here, we use molecular dynamics simulations and free energy calculations to investigate the molecular relationships among surface chemistry, hydration water structure, and surface–solute affinity across a variety of surface-decorated chemistries. Specifically, we consider polypeptoid-decorated surfaces that display well-known experimental antifouling capabilities and that can be synthesized sequence specifically, with precise backbone positioning of, e.g., charged groups. Through simulations, we calculate the affinities of a range of small solutes to polypeptoid brush surfaces of varied side-chain chemistries. We then demonstrate that measures of the structure of surface hydration water in response to a particular surface chemistry signal solute–surface affinity; specifically, we find that zwitterionic chemistries produce solute–surface repulsion through highly coordinated hydration water while suppressing tetrahedral structuring around the solute, in contrast to uncharged surfaces that show solute–surface affinity. Based on the relationship of this structural perturbation to the affinity of small-molecule solutes, we propose a molecular mechanism by which zwitterionic surface chemistries enhance solute repulsion, with broader implications for the design of antifouling surfaces.

36 MATERIALS SCIENCE↗
DOE OSTI2024

On the role of asymmetric molecular geometry in high-performance organic solar cells

Although asymmetric molecular design has been widely demonstrated effective for organic photovoltaics (OPVs), the correlation between asymmetric molecular geometry and their optoelectronic properties is still unclear. To access this issue, we have designed and synthesized several symmetric-asymmetric non-fullerene acceptors (NFAs) pairs with identical physical and optoelectronic properties. Interestingly, we found that the asymmetric NFAs universally exhibited increased open-circuit voltage compared to their symmetric counterparts, due to the reduced non-radiative charge recombination. From our molecular-dynamic simulations, the asymmetric NFA naturally exhibits more diverse molecular interaction patterns at the donor (D):acceptor (A) interface as compared to the symmetric ones, as well as higher D:A interfacial charge-transfer state energy. Moreover, it is observed that the asymmetric structure can effectively suppress triplet state formation. These advantages enable a best efficiency of 18.80%, which is one of the champion results among binary OPVs. Therefore, this work unambiguously demonstrates the unique advantage of asymmetric molecular geometry, unveils the underlying mechanism, and highlights the manipulation of D:A interface as an important consideration for future molecular design.

14 SOLAR ENERGY↗
DOE OSTI2020

Multiscale computational understanding and growth of 2D materials: a review

Abstract The successful discovery and isolation of graphene in 2004, and the subsequent synthesis of layered semiconductors and heterostructures beyond graphene have led to the exploding field of two-dimensional (2D) materials that explore their growth, new atomic-scale physics, and potential device applications. This review aims to provide an overview of theoretical, computational, and machine learning methods and tools at multiple length and time scales, and discuss how they can be utilized to assist/guide the design and synthesis of 2D materials beyond graphene. We focus on three methods at different length and time scales as follows: (i) nanoscale atomistic simulations including density functional theory (DFT) calculations and molecular dynamics simulations employing empirical and reactive interatomic potentials; (ii) mesoscale methods such as phase-field method; and (iii) macroscale continuum approaches by coupling thermal and chemical transport equations. We discuss how machine learning can be combined with computation and experiments to understand the correlations between structures and properties of 2D materials, and to guide the discovery of new 2D materials. We will also provide an outlook for the applications of computational approaches to 2D materials synthesis and growth in general.

Momeni, Kasra↗
DOE OSTI2023

Critical behavior in a chiral molecular model

Understanding the condensed-phase behavior of chiral molecules is important in biology as well as in a range of technological applications, such as the manufacture of pharmaceuticals. Here, we use molecular dynamics simulations to study a chiral four-site molecular model that exhibits a second-order symmetry-breaking phase transition from a supercritical racemic liquid into subcritical D-rich and L-rich liquids. We determine the infinite-size critical temperature using the fourth-order Binder cumulant, and we show that the finite-size scaling behavior of the order parameter is compatible with the 3D Ising universality class. We also study the spontaneous D-rich to L-rich transition at a slightly subcritical temperature of T = 0.985Tc, and our findings indicate that the free energy barrier for this transformation increases with system size as N2/3, where N is the number of molecules, consistent with a surface-dominated phenomenon. The critical behavior observed herein suggests a mechanism for chirality selection in which a liquid of chiral molecules spontaneously forms a phase enriched in one of the two enantiomers as the temperature is lowered below the critical point. Furthermore, the increasing free energy barrier with system size indicates that fluctuations between the L-rich and D-rich phases are suppressed as the size of the system increases, trapping it in one of the two enantiomerically enriched phases. Such a process could provide the basis for an alternative explanation for the origin of biological homochirality. We also conjecture the possibility of observing nucleation at subcritical temperatures under the action of a suitable chiral external field.

Chemistry↗
DOE OSTI2020

CephFS experiments on stria.sandia.gov

This report is an institutional record of experiments conducted to explore performance of a vendor installation of CephFS on the SNL stria cluster. Comparisons between CephFS, the Lustre parallel file system, and NFS were done using the IOR and MDTEST benchmarking tools, a test program which uses the SEACAS/Trilinos IOSS library, and the checkpointing activity performed by the LAMMPS molecular dynamics simulation.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2021

First-Principles Grand-Canonical Simulations of Water Adsorption in Proton-Exchanged Zeolites

Water appears by design or as impurities in many important reactive systems. For those catalyzed by porous solid acids, such as widely used zeolites, experimentally quantifying the amount or elucidating the structure of adsorbed water clusters at reaction conditions is challenging, while computational studies (e.g., first-principles molecular dynamics simulations) often need to assume the loading to examine solvation effects. Furthermore, we perform first-principles grand-canonical simulations to predict water adsorption to H-ZSM-5 zeolites under specified experimental conditions. Presampling with inexpensive force fields and a pool-based parallelization algorithm are used to improve simulation efficiency, while molecular dynamics is used to sample configurations involving hydronium species. We observe that H + exchange dramatically increases the hydrophilicity of zeolite MFI and an appreciable amount of water is present at very low relative humidities. At all conditions examined, the zeolitic protons are found to dissociate readily from the surface basic sites and become mobile by participating in the hydrogen-bonded chains of adsorbed water molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1996

Mechanism of unassisted ion transport across membrane bilayers

To establish how charged species move from water to the nonpolar membrane interior and to determine the energetic and structural effects accompanying this process, we performed molecular dynamics simulations of the transport of Na+ and Cl- across a lipid bilayer located between two water lamellae. The total length of molecular dynamics trajectories generated for each ion was 10 ns. Our simulations demonstrate that permeation of ions into the membrane is accompanied by the formation of deep, asymmetric thinning defects in the bilayer, whereby polar lipid head groups and water penetrate the nonpolar membrane interior. Once the ion crosses the midplane of the bilayer the deformation "switches sides"; the initial defect slowly relaxes, and a defect forms in the outgoing side of the bilayer. As a result, the ion remains well solvated during the process; the total number of oxygen atoms from water and lipid head groups in the first solvation shell remains constant. A similar membrane deformation is formed when the ion is instantaneously inserted into the interior of the bilayer. The formation of defects considerably lowers the free energy barrier to transfer of the ion across the bilayer and, consequently, increases the permeabilities of the membrane to ions, compared to the rigid, planar structure, by approximately 14 orders of magnitude. Our results have implications for drug delivery using liposomes and peptide insertion into membranes.

NASA Discipline Exobiology↗
DOE OSTI2021

Signatures of electronic and nuclear coherences in ultrafast molecular x-ray and electron diffraction

Femtosecond x-ray and electron diffraction hold promise to image the evolving structures of single molecules. We present a unified quantum-electrodynamical formulation of diffraction signals, based on the exact many-body nuclear + electronic wavefunction that can be extracted from quantum chemistry simulations. This gives a framework for analyzing various approximate molecular dynamics simulations. We show that the complete description of ultrafast diffraction signals contains interesting contributions involving mixed elastic and inelastic scattered photons that are usually masked by other larger contributions and are neglected. These terms include overlaps of nuclear wavepackets between different electronic states that provide an electronic decoherence mechanism and are important for the time-resolved imaging of conical intersections.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
NASA NTRS1998

Computer Simulation of the far Infrared Collision Induced Absorption Spectra of Gaseous CO2

Far infrared collision induced absorption spectra of gaseous CO2 were computed using molecular dynamics simulations. The quadrupole and hexadecapole multipolar induction, through the trace, and the anisotropy of the molecular polarizability were found to be insufficient to represent properly the dipole induction mechanism. For a detailed analysis of the induction process the spectra obtained were decomposed into components resulting from different terms of the induced dipole. Based on this decomposition, all additional overlap contribution for each term was proposed. When spectra were recomputed including such overlap, good agreement between experiment and simulation was achieved over the temperature range at which measurements exist (233-400 K). The use of an anisotropic intermolecular potential was found to be of critical importance for obtaining the right shape of the far wings of the spectra.

Gruszka, Marcin↗
DOE OSTI2024

Improved Precision Scaling for Simulating Coupled Quantum-Classical Dynamics

In this paper, we present a superpolynomial improvement in the precision scaling of quantum simulations for coupled quantum-classical systems. Such systems are found in, e.g., molecular-dynamics simulations within the Born-Oppenheimer approximation. By employing a framework based on the Koopman–von Neumann formulation of classical mechanics, we express the Liouville equation of motion as unitary dynamics and utilize phase kickback from a dynamical quantum simulation to calculate the quantum forces acting on classical particles. This approach allows us to simulate the dynamics of these classical particles without the overheads associated with measuring gradients and solving the equations of motion on a classical computer, resulting in a superpolynomial advantage at the price of increased space complexity. We demonstrate that these simulations can be performed in both microcanonical and canonical ensembles, enabling the estimation of thermodynamic properties from the prepared probability density. Published by the American Physical Society 2024

Simon, Sophia (ORCID:0000000332612338)↗
DOE OSTI2023

Multiscale simulations reveal TDP-43 molecular-level interactions driving condensation

The RNA-binding protein TDP-43 is associated with mRNA processing and transport from the nucleus to the cytoplasm. TDP-43 localizes in the nucleus as well as accumulating in cytoplasmic condensates such as stress granules. Aggregation and formation of amyloid-like fibrils of cytoplasmic TDP-43 are hallmarks of numerous neurodegenerative diseases, most strikingly present in >90% of amyotrophic lateral sclerosis (ALS) patients. If excessive accumulation of cytoplasmic TDP-43 causes, or is caused by, neurodegeneration is presently not known. In this work, we use molecular dynamics simulations at multiple resolutions to explore TDP-43 self- and cross-interaction dynamics. A full-length molecular model of TDP-43, all 414 amino acids, was constructed from select structures of the protein functional domains (N-terminal domain, and two RNA recognition motifs, RRM1 and RRM2) and modeling of disordered connecting loops and the low complexity glycine-rich C-terminus domain. All-atom CHARMM36m simulations of single TDP-43 proteins served as guides to construct a coarse-grained Martini 3 model of TDP-43. The Martini model and a coarser implicit solvent Cα model, optimized for disordered proteins, were subsequently used to probe TDP-43 interactions; self-interactions from single-chain full-length TDP-43 simulations, cross-interactions from simulations with two proteins and simulations with assemblies of dozens to hundreds of proteins. Our findings illustrate the utility of different modeling scales for accessing TDP-43 molecular-level interactions and suggest that TDP-43 has numerous interaction preferences or patterns, exhibiting an overall strong, but dynamic, association and driving the formation of biomolecular condensates.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Interfacial solvation and slow transport of hydrated excess protons in non-ionic reverse micelles

This work employs molecular dynamics simulations to investigate the solvation and transport properties of hydrated excess protons (with a hydronium-like core structure) in non-ionic Igepal CO-520 reverse micelles of various sizes in a non-polar solvent. Multiscale Reactive Molecular Dynamics (MS-RMD) simulations were used to describe vehicular and hopping diffusion during the proton transport process. As detailed herein, an excess proton shows a marked tendency to localize in the interfacial region of micellar water pools. Slow proton transport was observed which becomes faster with increasing micellar size. Further analysis reveals that the slow diffusion of an excess proton is a combined result of slow water diffusion and the low proton hopping rate. This study also confirms that a low proton hopping rate in reverse micelles stems from the interfacial solvation of hydrated excess protons and the immobilization of interfacial water. The low water density in the interfacial region makes it difficult to form a complete hydrogen bond network near the hydrated excess proton, and therefore locks in the orientation of hydrated proton cations. The immobilization of the interfacial water also slows the relaxation of the overall hydrogen bond network.

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

A Hotspot’s Better Half: Non-Equilibrium Intra-Molecular Strain in Shock Physics

Shockwave interactions with a material’s microstructure localizes energy into hotspots, which act as nucleation sites for complex processes such as phase transformations and chemical reactions. To date, hotspots have been described via their temperature fields. Nonreactive, all-atom molecular dynamics simulations of shock-induced pore collapse in a molecular crystal show that more energy is localized as potential energy (PE) than can be inferred from the temperature field and that PE localization persists beyond thermal diffusion. Furthermore, the origin of the PE hotspot is traced to large intramolecular strains, storing energy in modes readily available for chemical decomposition.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Charged Biological Membranes Repel Large Neutral Molecules by Surface Dielectrophoresis and Counterion Pressure

Macromolecular crowding is the usual condition of cells. The implications of the crowded cellular environment for protein stability and folding, protein–protein interactions, and intracellular transport drive a growing interest in quantifying the effects of crowding. While the properties of crowded solutions have been extensively studied, less attention has been paid to the interaction of crowders with the cellular boundaries, i.e., membranes. However, membranes are key components of cells and most subcellular organelles, playing a central role in regulating protein channel and receptor functions by recruiting and binding charged and neutral solutes. While membrane interactions with charged solutes are dominated by electrostatic forces, here we show that significant charge-induced forces also exist between membranes and neutral solutes. Using neutron reflectometry measurements and molecular dynamics simulations of poly(ethylene glycol) (PEG) polymers of different molecular weights near charged and neutral membranes, we demonstrate the roles of surface dielectrophoresis and counterion pressure in repelling PEG from charged membrane surfaces. The resulting depletion zone is expected to have consequences for drug design and delivery, the activity of proteins near membrane surfaces, and the transport of small molecules along the membrane surface.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

A two-dimensional type I superionic conductor

Superionic conductors (SICs) possess liquid-like ionic diffusivity in the solid state, finding wide applicability from electrolytes in energy storage to materials for thermoelectric energy conversion. Type I SICs (e.g., AgI, Ag 2 Se, etc.) are defined by a first-order transition to the superionic state and have so far been found exclusively in three-dimensional crystal structures. Here, we reveal a two-dimensional type I SIC, α-KAg 3 Se 2 by scattering techniques and complementary simulations. Quasi-elastic neutron scattering and ab initio molecular dynamics simulations confirm that the superionic Ag + ions are confined to sub-nanometre sheets, with the simulated local structure validated by experimental X-ray powder pair-distribution-function analysis. Finally, we demonstrate that the phase transition temperature can be controlled by chemical substitution of the alkali metal ions that comprise the immobile charge-balancing layers. Our work thus extends the known classes of SICs and will facilitate the design of new materials with tailored ionic conductivities and phase transitions.

36 MATERIALS SCIENCE↗