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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 793 records · Page 44
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

OpenAWSEM with Open3SPN2: A fast, flexible, and accessible framework for large-scale coarse-grained biomolecular simulations

We present OpenAWSEM and Open3SPN2, new cross-compatible implementations of coarse-grained models for protein (AWSEM) and DNA (3SPN2) molecular dynamics simulations within the OpenMM framework. These new implementations retain the chemical accuracy and intrinsic efficiency of the original models while adding GPU acceleration and the ease of forcefield modification provided by OpenMM’s Custom Forces software framework. By utilizing GPUs, we achieve around a 30-fold speedup in protein and protein-DNA simulations over the existing LAMMPS-based implementations running on a single CPU core. We showcase the benefits of OpenMM’s Custom Forces framework by devising and implementing two new potentials that allow us to address important aspects of protein folding and structure prediction and by testing the ability of the combined OpenAWSEM and Open3SPN2 to model protein-DNA binding. The first potential is used to describe the changes in effective interactions that occur as a protein becomes partially buried in a membrane. We also introduced an interaction to describe proteins with multiple disulfide bonds. Using simple pairwise disulfide bonding terms results in unphysical clustering of cysteine residues, posing a problem when simulating the folding of proteins with many cysteines. We now can computationally reproduce Anfinsen’s early Nobel prize winning experiments by using OpenMM’s Custom Forces framework to introduce a multi-body disulfide bonding term that prevents unphysical clustering. Our protein-DNA simulations show that the binding landscape is funneled towards structures that are quite similar to those found using experiments. In summary, this paper provides a simulation tool for the molecular biophysics community that is both easy to use and sufficiently efficient to simulate large proteins and large protein-DNA systems that are central to many cellular processes. These codes should facilitate the interplay between molecular simulations and cellular studies, which have been hampered by the large mismatch between the time and length scales accessible to molecular simulations and those relevant to cell biology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Molecular-resolution imaging of ice crystallized from liquid water by cryogenic liquid-cell TEM

Despite the ubiquity of ice, a molecular-resolution image of nanoscopic defects or microstructures in ice crystallized from liquid water has never been obtained. This is mainly due to the difficulties in preparing and preserving crystalline ice samples that can survive under high-resolution imaging conditions. Here, we report the stabilization and Å-resolution electron imaging of ice Ih crystallized from liquid water by developing cryogenic liquid-cell transmission electron microscopy (CRYOLIC-TEM). We combine lattice mapping with molecular dynamics simulations to reveal that ice formation is highly tolerant to nanoscale defects such as misoriented subdomains and trapped gas bubbles, which are stabilized by molecular-scale structural motifs. Importantly, bubble surfaces adopt low-energy nanofacets and create negligible strain fields in the surrounding crystal. These bubbles can dynamically nucleate, grow, migrate, dissolve, and coalesce under electron irradiation and be monitored in situ near a steady state. This work improves our understanding of water crystallization behaviors at a molecular spatial resolution.

Materials science↗
DOE OSTI2025

Reactivity of Carbonate Solvent Electrolytes on Lithium Silicon Anodes

Silicon (Si) is promising for lithium-ion battery (LIB) anodes due to their high theoretical capacity and low electrochemical potential. However, significant challenges remain, including severe volumetric expansion during cycling and the electrochemical instability of electrolytes, which leads to the formation of a nonuniform solid electrolyte interphase (SEI). To investigate SEI formation mechanisms, computational molecular dynamics simulations offer valuable insights. In this work, we examine the trajectories and charge transfer behavior of lithium hexafluorophosphate (LiPF 6 ) salt with various solvent compositions using density functional theory (DFT) and ab initio molecular dynamics (AIMD). Among the tested electrolyte systems, LiPF 6 with vinylene carbonate (VC) added to ethyl methyl carbonate (EMC) exhibits the lowest reactivity with the Si anode. In contrast, the effects of fluoroethylene carbonate (FEC) and VC depend on whether the primary solvent is EMC alone or a mixture of ethylene carbonate (EC) and EMC. Moreover, we show that electrolyte reactivity varies with the degree of lithiation of the Si anode (LiSi vs Li 15 Si 4 ) and under different charge states. To decouple electrolyte reactivity from surface effects, we analyze the dissociation and formation energies of individual species from solvated configurations. Overall, these first-principles-based findings provide a strategic foundation for electrolyte design to improve cycling stability and extend calendar life in LIBs using Si anodes.

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

Structural and Dynamic Heterogeneity of Deep Eutectic Solvents Composed of Choline Chloride and Ortho-Phenol Derivatives

Structural, thermal, and dynamic properties of four deep eutectic solvents comprising choline chloride paired with ortho-phenolic derivative hydrogen-bond donors were probed using experiments and molecular simulations. The hydrogen-bond donors include phenol, catechol, o-chlorophenol, and o-cresol, in a 3:1 mixture with the hydrogen-bond acceptor choline chloride. Density, viscosity, and pulsed-field gradient NMR diffusivity measurements were conducted over a range of temperatures. Classical and ab initio molecular dynamics simulation results match experimental data reasonably well. Furthermore, the simulation results were then used to perform a more detailed analysis of the local structure and dynamics of these systems.

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

SynopFrame: Multiscale time-dependent visual abstraction framework for analyzing DNA nanotechnology simulations

We present an open-source framework, SynopFrame, that allows DNA nanotechnology (DNA-nano) experts to analyze and understand molecular dynamics simulation trajectories of their designs. We use a multiscale multi-dimensional abstraction space, connect the representations to a projected conformational space plot of the structure’s temporal sequence, and thus enable experts to analyze the dynamics of their structural designs and, specifically, failure cases of the assembly. In addition, our time-dependent abstraction representation allows the biologists, for the first time in a smooth and structurally clear way, to identify and observe temporal transitions of a DNA-nano design from one configuration to another, and to highlight important periods of the simulation for further analysis. We realize SynopFrame as a dashboard of the different synchronized 3D spatial and 2D schematic visual representations, with a color overlay to show essential properties such as the status of hydrogen bonds. The linking of the spatial, schematic, and abstract views ensures that users can effectively analyze the high-frequency motion. We also categorize the status of the hydrogen bonds into a new format to allow us to color-encode it and overlay it on the representations. To demonstrate the utility of SynopFrame, we describe example usage scenarios and report user feedback.

Abstraction space↗
DOE OSTI2020

PDADMAC/PSS Oligoelectrolyte Multilayers: Internal Structure and Hydration Properties at Early Growth Stages from Atomistic Simulations

We analyze the internal structure and hydration properties of poly(diallyl dimethyl ammonium chloride)/poly(styrene sulfonate sodium salt) oligoelectrolyte multilayers at early stages of their layer-by-layer growth process. Our study is based on large-scale molecular dynamics simulations with atomistic resolution that we presented recently [Sánchez et al., Soft Matter 2019, 15, 9437], in which we produced the first four deposition cycles of a multilayer obtained by alternate exposure of a flat silica substrate to aqueous electrolyte solutions of such polymers at 0.1M of NaCl. In contrast to any previous work, here we perform a local structural analysis that allows us to determine the dependence of the multilayer properties on the distance to the substrate. We prove that the large accumulation of water and ions next to the substrate observed in previous overall measurements actually decreases the degree of intrinsic charge compensation, but this remains as the main mechanism within the interface region. We show that the range of influence of the substrate reaches approximately 3 nm, whereas the structure of the outer region is rather independent from the position. This detailed characterization is essential for the development of accurate mesoscale models able to reach length and time scales of technological interest.

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

Elastic strain engineering of lattice thermal conductivity of silicon: An ab-initio study

Silicon (Si) is the most essential material in the semiconductor industry. It is important to manage the thermal properties of crystalline Si. Elastic strain engineering (ESE) has proven to be an effective tool in controlling the electrical conductivity of Si in strained-silicon technology; its effects on the thermal conductivity of silicon, therefore, warrants careful investigation. The ESE effect is much more pronounced for nanostructured materials due to the ultralarge elastic strains (on the order of 10%) achievable at the nanoscale. In this work, the lattice thermal conductivity (κ L ) of Si under hydrostatic, biaxial, and uniaxial strain states is studied with ab-initio simulations, and the values of strain-dependent κ L compare well with experimental results and existing molecular dynamics simulations. To understand the mechanisms of strain-modulated κ L , the phonon bands, scattering rate, and Grüneisen parameters of phonon modes are computed. It is shown that strain can significantly change the anharmonicity of the crystal system, thus changing phonon scattering rates and κ L . Our results demonstrate that ESE can reduce silicon κ L by up to approximately 90%. Furthermore, uniaxial and biaxial strains can induce highly anisotropic thermal conductivity in Si, with relative variations up to 58.5% and 14.5%, respectively.

Anisotropy in Thermal Conductivity↗
DOE OSTI2024

Surface molecular pump enables ultrahigh catalyst activity

The performance of electrocatalysts is critical for renewable energy technologies. While the electrocatalytic activity can be modulated through structural and compositional engineering following the Sabatier principle, the insufficiently explored catalyst-electrolyte interface is promising to promote microkinetic processes such as physisorption and desorption. By combining experimental designs and molecular dynamics simulations with explicit solvent in high accuracy, we demonstrated that dimethylformamide can work as an effective surface molecular pump to facilitate the entrapment of oxygen and outflux of water. Dimethylformamide disrupts the interfacial network of hydrogen bonds, leading to enhanced activity of the oxygen reduction reaction by a factor of 2 to 3. This strategy works generally for platinum-alloy catalysts, and we introduce an optimal model PtCuNi catalyst with an unprecedented specific activity of 21.8 ± 2.1 mA/cm 2 at 0.9 V versus the reversible hydrogen electrode, nearly double the previous record, and an ultrahigh mass activity of 10.7 ± 1.1 A/mg Pt .

Science & Technology - Other Topics↗
DOE OSTI2023

Data-driven prediction of α IIb β 3 integrin activation paths using manifold learning and deep generative modeling

The integrin heterodimer is a transmembrane protein critical for driving cellular process and is a therapeutic target in the treatment of multiple diseases linked to its malfunction. Activation of integrin involves conformational transitions between bent and extended states. Some of the conformations that are intermediate between bent and extended states of the heterodimer have been experimentally characterized, but the full activation pathways remain unresolved both experimentally due to their transient nature and computationally due to the challenges in simulating rare barrier crossing events in these large molecular systems. An understanding of the activation pathways can provide new fundamental understanding of the biophysical processes associated with the dynamic interconversions between bent and extended states and unveil new putative therapeutic targets. In this work, we apply nonlinear manifold learning to coarse-grained molecular dynamics simulations of bent, extended, and two intermediate states of αI I b β3 integrin to learn a low-dimensional embedding of the configurational phase space. We then train deep generative models to learn an inverse mapping between the low-dimensional embedding and high-dimensional molecular space and use these models to interpolate the molecular configurations constituting the activation pathways between the experimentally characterized states. Furthermore, this work furnishes plausible predictions of integrin activation pathways and reports a generic and transferable multi-scale technique to predict transition pathways for biomolecular systems.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Solvent–Solvent Correlations across Graphene: The Effect of Image Charges

Wetting experiments show pure graphene to be weakly hydrophilic, but its contact angle (CA) also reflects the character of the supporting material. Measurements and Molecular Dynamics simulations on suspended and supported graphene often reveal a CA reduction due to the presence of the supporting substrate. A similar reduction is consistently observed when graphene is wetted from both sides. The effect has been attributed to transparency to molecular interactions across the graphene sheet, however, the possibility of substrate-induced graphene polarization has also been considered. Computer simulations of CA on graphene have so far been determined by ignoring the material’s conducting properties. We improve the graphene model by incorporating its conductivity according to the Constant Applied Potential Molecular Dynamics. Using this method, we compare the wettabilities of suspended graphene and graphene supported by water by measuring the CA of cylindrical water drops on the sheets. The inclusion of graphene conductivity and concomitant polarization effects lead to a lower CA on suspended graphene but the CA reduction is significantly bigger when the sheets are also wetted from the opposite side. The stronger adhesion is accompanied by a profound change in the correlations among water molecules across the sheet. While partial charges on water molecules interacting across an insulator sheet attract charges of the opposite sign, apparent attraction among like charges is manifested across the conducting graphene. The change is associated with graphene polarization, as the image charges inside the conductor attract equally signed partial charges of water molecules on both sides of the sheet. Additionally, by using a non-polar liquid (diiodomethane), we affirm a detectable wetting translucency when liquid-liquid forces are dominated by dispersive interactions. Furthermore, our findings are important for predictive modeling toward a variety of applications including sensors, fuel cell membranes, water filtration, and graphene-based electrode materials in high-performance supercapacitors.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2024

Evidence of short chains in liquid sulfur

High energy x-ray pair distribution function measurements show the average coordination number of the first shell in liquid sulfur is 1.86 ± 0.04 across the λ-transition, not precisely 2.0 as widely accepted. This indicates that upon melting, liquid sulfur does not comprise solely of S 8 rings but also possesses a significant number of short chains. Intensities of the pre-peak and first diffraction peak of the x-ray structure factor and third peak height of the pair distribution function all show deviations at the λ-transition temperature T λ , associated with the break-up of S 8 rings and the start of oligomer polymerization. A significant number of non-bonded or loosely bonded “interstitial atoms,” with an average coordination number of 0.20 ± 0.005, are also observed in the so-called “forbidden zone” between the first and second shells upon melting. The number of interstitial atoms is found to decrease to a minimum at the λ-transition, but the majority persist into the high temperature polymerized liquid. Furthermore, the existence of short chains and nearby interstitial atoms represent the two main factors required to initiate the S 8 -ring to chain transition, as proposed by recent molecular dynamics simulations.

Chemical bonding↗
DOE OSTI2023

Structures of elemental potassium at terapascal pressures

Here we investigate the pressure-temperature phase diagram of elemental potassium (K) up to multiterapascal (TPa) pressures using ab initio random structure searching (AIRSS), discovering eight structural phase transitions beyond the already known double hexagonal close-packed (dhcp) structure. Starting at 1.15 TPa, K transitions from the dhcp structure and passes through a variety of close-packed hexagonal and trigonal phases (dhcp → P6 3 /mmc → P3m1 → P$\bar{6}m2$), which differ only in their stacking sequence along the c axis. At 2.55 TPa, K adopts the hexagonal close-packed (hcp) structure, and at 7.21 TPa transitions into a complex orthorhombic phase of Fddd symmetry with 64 atoms in its (conventional) unit cell, before assuming an Ibam structure at 8.60 TPa, and, eventually, the face centered cubic (fcc) structure at 23.6 TPa, which persists well into the petapascal (PPa) regime. Further, we calculate the full pressure-temperature dependence of the melting line of K through extensive molecular dynamics simulations. We study the evolution of the bonding topology of K with pressure, finding that K passes through two quasi-molecular phases featuring diatomic pairs (the Fddd and Ibam structures), before ultimately becoming a high pressure electride (HPE) in the fcc phase. The electron-phonon and superconducting properties of K at these extreme pressures are also investigated, where we find the critical temperature T c rises to a maximum of between 7.65 K and 15.70 K in the hcp phase, before eventually decreasing to essentially zero in the fcc phase. Our results fully elucidate the structural and electronic behavior of K under the most extreme conditions, and provide new case studies for multi-TPa dynamic compression experiments.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Extemporaneous Mechanochemistry: Shock-Wave-Induced Ultrafast Chemical Reactions Due to Intramolecular Strain Energy

We report regions of energy localization referred to as hotspots are known to govern shock initiation and the run-to-detonation in energetic materials. Mounting computational evidence points to accelerated chemistry in hotspots from large intramolecular strains induced via the interactions between the shock wave and microstructure. However, definite evidence mapping intramolecular strain to accelerated or altered chemical reactions has so far been elusive. From a large-scale reactive molecular dynamics simulation of the energetic material 1,3,5-triamino-2,4,6-trinitrobenzene, we map decomposition kinetics to molecular temperature and intramolecular strain energy prior to reaction. Both temperature and intramolecular strain are shown to accelerate chemical kinetics. A detailed analysis of the atomistic trajectory shows that intramolecular strain can induce a mechanochemical alteration of decomposition mechanisms. The results in this paper could inform continuum-level chemistry models to account for a wide range of mechanochemical effects.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Species Separation and Hydrogen Streaming upon Shock Release from Polystyrene under Inertial Confinement Fusion Conditions

Shock release from inertial confinement fusion (ICF) shells poses a great challenge to single-fluid hydrodynamic equations, especially for describing materials composed of different ion species. This has been evidenced by a recent experiment [Haberberger et al., Phys. Rev. Lett. 123, 235001 (2019)], in which low-density plasmas ( 10 19 to 10 20 cm – 3 ) are measured to move far ahead of what radiation-hydrodynamic simulations predict. To understand such experimental observations, in this work we have performed large-scale nonequilibrium molecular-dynamics simulations of shock release in polystyrene (CH) at experimental conditions. These simulations revealed that upon shock releasing from the back surface of a CH foil, hydrogen can stream out of the bulk of the foil due to its mass being lighter than carbon. This released hydrogen, exhibiting a much broader velocity distribution than carbon, forms low-density plasmas moving in nearly constant velocities ahead of the in-flight shell, which is in quantitative agreement with the experimental measurements. Such kinetic effect of species separation is currently missing in single-fluid radiation-hydrodynamics codes for ICF simulations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

Thermodynamics of high-pressure ice phases explored with atomistic simulations

Most experimentally known high-pressure ice phases have a body-centred cubic (bcc) oxygen lattice. Our large-scale molecular-dynamics simulations with a machine-learning potential indicate that, amongst these bcc ice phases, ices VII, VII' and X are the same thermodynamic phase under different conditions, whereas superionic ice VII" has a first-order phase boundary with ice VII'. Moreover, at about 300 GPa, the transformation between ice X and the Pbcm phase has a sharp structural change but no apparent activation barrier, whilst at higher pressures the barrier gradually increases. Our study thus clarifies the phase behaviour of the high-pressure ices and reveals peculiar solid–solid transition mechanisms not known in other systems.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Disorder-induced heating in molecular atmospheric pressure plasmas

Abstract Recent work has shown that ions are strongly coupled in atmospheric pressure plasmas when the ionization fraction is sufficiently large, leading to a temperature increase from disorder-induced heating (DIH) that is not accounted for in standard modelling techniques. Here, we extend this study to molecular plasmas. A main finding is that the energy gained by ions in DIH gets spread over both translational and rotational degrees of freedom on a nanosecond timescale, causing the final ion and neutral gas temperatures to be lower in the molecular case than in the atomic case. A model is developed for the equilibrium temperature that agrees well with molecular dynamics simulations. The model and simulations are also applied to pressures up to ten atmospheres. We conclude that DIH is a significant and predictable phenomena in molecular atmospheric pressure plasmas.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

Effect of an oxide layer on high velocity impact of tantalum particles characterized using molecular dynamics

Micro-cold spray, also commonly referred to as the aerosol deposition method or vacuum kinetic spraying, is a process for depositing nanostructured films of metals and ceramics by impacting solid nanoparticles at high velocity onto a substrate at room temperature and at low pressures. Tantalum films deposited by micro-cold spray are desirable because tantalum is non-reactive to certain molten metals and can therefore serve as a non-reactive barrier coating. However, unlike most other metals deposited by micro-cold spray, tantalum quickly forms an oxide layer when exposed to air. In the deposition of films using traditional cold spray with much larger particles, native oxides must fracture for particle–substrate bonding to occur. Furthermore, the fraction of the particle that is oxidized in micro-cold spray and the strain rates experienced by the particles upon impact are both much larger than in cold spray, suggesting that the role of the oxide on film deposition may be distinct. The effect of this oxide layer on particle deformation and adherence to a substrate under high strain rates is studied using molecular dynamics simulations. The effect of oxide layer thickness, particle diameter, and impact velocity are examined.

42 ENGINEERING↗
DOE OSTI2023

Crystal structure of dihydrofolate reductase from the filarial nematode W. bancrofti in complex with NADPH and folate

Lymphatic filariasis is a debilitating illness with an estimated 50 million cases as of 2018. The majority of cases are caused by the parasitic worm W. bancrofti and additional cases by the worms B. malayi and B. timori. Dihydrofolate reductase (DHFR) is an established target in the treatment of cancer, bacterial, and protozoal infections and may be a potential target for drugs targeting parasitic worm infections, including filariasis. Recent studies have shown that known antifolate compounds, including methotrexate, inhibit the activity of W. bancrofti DHFR (WbDHFR). However, the absence of structural information for filarial DHFRs has limited the study of more in-depth structure-function relationships. We report the structure of WbDHFR complexed with NADPH and folate using X-ray diffraction data measured to 2.47 Å resolution. The structure of WbDHFR reveals the usual DHFR fold and is currently only the second nematode DHFR structure in the Protein Data Bank. The equilibrium dissociation constants for NADPH (90 ± 29 nM) and folate (23 ± 4 nM) were determined by equilibrium titrations. The interactions of known antifolates with WbDHFR were analyzed using molecular docking programs and molecular dynamics simulations. Antifolates with a hydrophobic core and extended linker formed favorable interactions with WbDHFR. These combined data should now facilitate the rational design of filarial DHFR inhibitors, which in turn can be used to determine whether DHFR is a viable drug target for filariasis and whether existing antifolates may be repurposed for its treatment.

60 APPLIED LIFE SCIENCES↗