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At least 1,531 records · Page 85
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

PTM‐Psi : A python package to facilitate the computational investigation of p ost‐ t ranslational m odification on p rotein s tructures and their i mpacts on dynamics and functions

Abstract Post‐translational modification (PTM) of a protein occurs after it has been synthesized from its genetic template, and involves chemical modifications of the protein's specific amino acid residues. Despite of the central role played by PTM in regulating molecular interactions, particularly those driven by reversible redox reactions, it remains challenging to interpret PTMs in terms of protein dynamics and function because there are numerous combinatorially enormous means for modifying amino acids in response to changes in the protein environment. In this study, we provide a workflow that allows users to interpret how perturbations caused by PTMs affect a protein's properties, dynamics, and interactions with its binding partners based on inferred or experimentally determined protein structure. This Python‐based workflow, called PTM‐Psi , integrates several established open‐source software packages, thereby enabling the user to infer protein structure from sequence, develop force fields for non‐standard amino acids using quantum mechanics, calculate free energy perturbations through molecular dynamics simulations, and score the bound complexes via docking algorithms. Using the S ‐nitrosylation of several cysteines on the GAP2 protein as an example, we demonstrated the utility of PTM‐Psi for interpreting sequence–structure–function relationships derived from thiol redox proteomics data. We demonstrate that the S ‐nitrosylated cysteine that is exposed to the solvent indirectly affects the catalytic reaction of another buried cysteine over a distance in GAP2 protein through the movement of the two ligands. Our workflow tracks the PTMs on residues that are responsive to changes in the redox environment and lays the foundation for the automation of molecular and systems biology modeling.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Computational and Experimental Determination of the Properties, Structure, and Stability of Peptoid Nanosheets and Nanotubes

Peptoids (N-substituted glycines) are a group of highly controllable peptidomimetic polymers. Amphiphilic diblock peptoids have been engineered to assemble crystalline nanospheres, nanofibrils, nanosheets, and nanotubes with biochemical, biomedical, and bioengineering applications. The mechanical properties of peptoid nanoaggregates and their relationship to the emergent self-assembled morphologies have been relatively unexplored and are critical for the rational design of peptoid nanomaterials. In this work, we consider a family of amphiphilic diblock peptoids consisting of a prototypical tube-former (Nbrpm6Nc6, a NH 2 -capped hydrophobic block of six N-((4-bromophenyl)methyl)glycine residues conjugated to a polar NH 3 (CH 2 ) 5 CO tail), a prototypical sheet-former (Nbrpe6Nc6, where the hydrophobic block comprises six N-((4-bromophenyl)ethyl)glycine residues), and an intermediate sequence that forms mixed structures ((NbrpeNbrpm)3Nc6). We combine all-atom molecular dynamics simulations and atomic force microscopy to determine the mechanical properties of the self-assembled 2D crystalline nanosheets and relate these properties to the observed self-assembled morphologies. We find good agreement between our computational predictions and experimental measurements of Young’s modulus of crystalline nanosheets. A computational analysis of the bending modulus along the two axes of the planar crystalline nanosheets reveals bending to be more favorable along the axis in which the peptoids stack by interdigitation of the side chains compared to that in which they form columnar crystals with π-stacked side chains. Here, we construct molecular models of nanotubes of the Nbrpm6Nc6 tube-forming peptoid and predict a stability optimum in good agreement with experimental measurements. A theoretical model of nanotube stability suggests that this optimum is a free energy minimum corresponding to a “Goldilocks” tube radius at which capillary wave fluctuations in the tube wall are minimized.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Switching of Hybrid Improper Ferroelectricity in Oxide Double Perovskites

In ABO 3 -type perovskite oxides with Pnma symmetry, rotation (Q R+ , a 0 a 0 c + ) and tilt (Q T , a – a – c 0 ) of BO 6 octahedra are the two primary order parameters. These order parameters establish an inherent trilinear coupling with anti-ferroelectric A-site displacement (Q AFE ) to form the low-symmetry phase. The symmetry is further lowered in double perovskite oxides (DPOs) due to A/A' cation ordering. It in turn makes these systems polar via hybrid improper ferroelectric mechanism, primarily driven by Q R+ and Q T . Naturally, it has been believed that functionalities such as polarization can also be switched by tuning these primary order parameters. However, mystery around finding switching mechanism still remains. Our study based on density functional theory calculations combined with finite-temperature molecular dynamics simulations shows that the polarization switching is a two-step process, driven by out-of-phase rotation (Q R– , a 0 a 0 c – when Q T = 0 or, a – a – b – when Q T ≠ 0). A series of polar DPOs such as KLnFeOsO 6 [Ln = Sm, Gd, Dy, Tm (lanthanides) and Y (rare earth)], all belonging to P2 1 symmetry, are considered in this investigation. The polarization switching P ($\overrightarrow{P}$) occurs at a very high temperature of ~1150 K through a phase transition, from a polar (P2 1 ) phase with $\overrightarrow{P}$(+) to $\overrightarrow{P}$(-) via a non-polar P4/n phase. The switching itself is metastable in nature. The switching (both polarization and spin state) is only observed for a very short period of time (~23 ps) that poses limitation on using such a mechanism in memory device realization. We demonstrate a concurrent heating–cooling procedure to overcome such shortcoming. In conclusion, simulations conducted at 600 K further imply that long lasting switching can be achieved, at least for 1.2 ns for 600 K, and ideally for an infinite time, if the material is heated just above the T c followed by rapid cooling to a temperature below T c .

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

Defects vibrations engineering for enhancing interfacial thermal transport in polymer composites

To push upper boundaries of thermal conductivity in polymer composites, understanding of thermal transport mechanisms is crucial. Despite extensive simulations, systematic experimental investigation on thermal transport in polymer composites is limited. To better understand thermal transport processes, we design polymer composites with perfect fillers (graphite) and defective fillers (graphite oxide), using polyvinyl alcohol (PVA) as a matrix model. Measured thermal conductivities of ~1.38 ± 0.22 W m -1 K -1 in PVA/defective filler composites is higher than those of ~0.86 ± 0.21 W m -1 K -1 in PVA/perfect filler composites, while measured thermal conductivities in defective fillers are lower than those of perfect fillers. We identify how thermal transport occurs across heterogeneous interfaces. Thermal transport measurements, neutron scattering, quantum mechanical modeling, and molecular dynamics simulations reveal that vibrational coupling between PVA and defective fillers at PVA/filler interfaces enhances thermal conductivity, suggesting that defects in polymer composites improve thermal transport by promoting this vibrational coupling.

42 ENGINEERING↗
DOE OSTI2021

Three-state harmonic models for photoinduced charge transfer

A widely used strategy for simulating the charge transfer between donor and acceptor electronic states in an all-atom anharmonic condensedphase system is based on invoking linear response theory to describe the system in terms of an effective spin-boson model Hamiltonian. Extending this strategy to photoinduced charge transfer processes requires also taking into consideration the ground electronic state in addition to the excited donor and acceptor electronic states. In this paper, we revisit the problem of describing such nonequilibrium processes in terms of an effective three-state harmonic model. We do so within the framework of nonequilibrium Fermi’s golden rule (NE-FGR) in the context of photoinduced charge transfer in the carotenoid–porphyrin–C 60 (CPC 60 ) molecular triad dissolved in explicit tetrahydrofuran (THF). To this end, we consider different ways for obtaining a three-state harmonic model from the equilibrium autocorrelation functions of the donor–acceptor, donor–ground, and acceptor–ground energy gaps, as obtained from all-atom molecular dynamics simulations of the CPC 60 /THF system. The quantum-mechanically exact time-dependent NE-FGR rate coefficients for two different charge transfer processes in two different triad conformations are then calculated using the effective three-state model Hamiltonians as well as a hierarchy of more approximate expressions that lead to the instantaneous Marcus theory limit. Our results show that the photoinduced charge transfer in CPC 60 /THF can be described accurately by the effective harmonic three-state models and that nuclear quantum effects are small in this system.

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

Surface Segregation of Liquid Metal Plasma-Facing Component Alloys: A ReaxFF Investigation

Engineering liquid metal alloys offers a transformative pathway for plasma-facing components by enabling chemically tailored surfaces that can simultaneously optimize plasma-material interactions, reduce divertor heat flux, and enhance core plasma confinement, thereby advancing the commercial viability of nuclear fusion power plants. This study, employing an atomistic simulation approach, provides direct evidence that incorporating nonmetal surface-active agents (such as O and H, or their combination) enables strong surface segregation. This capability makes tin−aluminum (Sn−Al) and tin−lithium (Sn−Li) alloys, with suitable compositions, good candidates for PFC applications. Specifically, the presence of low-Z solutes (Li, Al) leads to preferential surface enrichment, which imparts low-Z sputtering characteristics, while the Sn solvent maintains thermophysical stability. To systematically examine this behavior, we developed a ReaxFF force field spanning the full Sn/Al/Li/O/H chemistry, validated it against formation energies and elastic constants, and applied it in reactive molecular dynamics simulations at fusion-relevant temperatures. We also introduced an overlapbased segregation index that captures interfacial compositional separation directly from atomistic density distributions. Here, this metric reveals a clear hierarchy of segregation regimes and provides a unified view across all systems studied. Together, these findings establish a mechanistic link between nonmetal chemistry and interfacial structure, providing a predictive framework for designing self-adaptive, low-sputtering liquid metal alloys for fusion applications.

Alloys↗
DOE OSTI2023

Cation–polymer interactions and local heterogeneity determine the relative order of alkali cation diffusion coefficients in PEGDA hydrogels

Current research efforts are focused on endowing polymer membranes with ion–ion selectivity by incorporating ion–polymer interactions into materials to bias the selective partitioning and or diffusivity of one species over another. However, little is known about the impact of such interactions on the mechanisms of ion transport. In this study, we probe the influence of cation–polymer interactions on cation, anion, and salt diffusivity in a model membrane material, poly(ethylene glycol) diacrylate (PEGDA) by modeling concentrated polyethylene oxide solutions via molecular dynamics simulations. These results are compared to published experimental data for LiCl, NaCl, and KCl diffusion in PEGDA. Experimentally, the order of salt and cation diffusion coefficients for LiCl, NaCl, and KCl deviate from the order in aqueous solutions. Here, simulations identify these deviations to arise from cation–polymer coordination in the membrane. Both the fraction of bound cations and the average binding lifetime increases with decreasing cation hydration free energy (moving down the alkali series), leading to different diffusivity trends in the membrane compared to solution. However, to recover the experimentally observed order of diffusivities cations and salt in our simulations, we needed to incorporate membrane heterogeneity explicitly via a polymer charge scaling procedure. Together, our results indicate that cation–polymer interactions, as well as spatial heterogeneity within the membrane, play a critical role in dictating the observed order of alkali cation and salt diffusion coefficients in membranes.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Anisotropic X-Ray Scattering of Transiently Oriented Water

We study the structural dynamics of liquid water by time-resolved anisotropic x-ray scattering under the optical Kerr effect condition. In this way, we can separate the anisotropic scattering decay of 160 fs from the delayed temperature increase of ~ 0.1 K occurring at 1 ps and quantify transient changes in the O-O pair distribution function. Polarizable molecular dynamics simulations reproduce well the experiment, indicating transient alignment of molecules along the electric field, which shortens the nearest-neighbor distances. In addition, analysis of the simulated water local structure provides evidence that two hypothesized fluctuating water configurations exhibit different polarizability.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Probing the electronic properties of the electrified silicon/water interface by combining simulations and experiments.

Silicon (Si) is broadly used in electrochemical and photoelectrochemical devices, where the capacitive and Faradaic reactions at the Si/water interfaces are critical for signal transduction or noise generation. However, probing the electrified Si/water interface at the microscopic level remains a challenging task. Here we focus on hydrogenated Si surfaces in contact with water, relevant to transient electronics and photoelectrochemical modulation of biological cells and tissues. We show that by carrying out first principles molecular dynamics simulations of the Si(100)/water interface in the presence of an electric field we can realistically correlate the computed flat-band potential and tunneling current images at the interface with experimentally measured capacitive and Faradaic currents. Specifically, we validate our simulations in the presence of bias by performing pulsed chronoamperometry measurements on Si wafers in solution. Consistent with prior experiments, our measurements and simulations indicate the presence of voltage-dependent capacitive currents at the interface. We also find that Faradaic currents are weakly dependent on the applied bias, which we relate to surface defects present in newly prepared samples.

Ye, Zifan↗
DOE OSTI2022

Demonstrate Improved Ag Diffusion and Describe the Basis for Pd Penetration Modeling in SiC

In past work, an effective diffusivity coefficient was determined for Ag transport through the silicon carbide layer of a tristructural isotropic fuel particle. The effective diffusivity coefficient accounts for the microstructure of the silicon carbide and includes both bulk diffusion and grain boundary diffusion of Ag. In this report, the model has been improved by accounting for the enhanced concentration of vacancies in the bulk due to irradiation, which substantially influence bulk diffusivity at low temperatures. To improve the BISON model and make it fission rate dependent, effective diffusivity calculations have been performed that incorporate the radiation modified bulk diffusivity. The microstructure and irradiation-dependent effective diffusivity has also been implemented into BISON, and its predictions for Ag release from tristructural isotropic fuel have been successfully compared to AGR-1 post irradiation measurements. Moreover, a new feature has been developed in the Multiphysics Object-Oriented Simulation Environment (MOOSE) to account for different grain boundary types. The Ag diffusivity in 5 (210)/[001] grain boundaries has been computed and was found to be greater than in random high-angle grain boundaries. The presence of the fission product Pd can also have an important effect on the properties of the silicon carbide layer in tristructural isotropic particles. The penetration of Pd into the silicon carbide layer causes a corrosion reaction that can lead to the failure of the silicon carbide layer; however, this corrosion reaction is not well understood. To enable an improved understanding of the mechanism, ab-initio molecular dynamics simulations of Pd interaction with bulk silicon carbide have been performed. The improved understanding of the reaction will form a basis for future improvements to the BISON’s Pd penetration failure model

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2020

Shock compression of vanadium at extremes: Theory and experiment

Here, the equation of state (EOS) and shock compression of bulk vanadium were investigated using canonical ab initio molecular dynamic simulations, with experimental validation to 865 GPa from shock data collected at Sandia's Z Pulsed Power Facility. In simulations the phase space was sampled along isotherms ranging from 3000 K to 50 000 K, for densities between ρ = 3 and 15 g / cm 3 , with a focus on the liquid regime and the body-centered-cubic phase in the vicinity of the melting limit. The principal Hugoniot predicted from first principles is overall consistent with shock data, while it showed that current multiphase SESAME-type EOS for vanadium needed revision in the liquid regime. A more accurate SESAME EOS was developed using constraints from experiments and simulations. This work emphasizes the need to use a combined theoretical and experimental approach to develop high-fidelity EOS models for extreme conditions.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Molecular Driving Force for Facet Selectivity of Sequence-Defined Amphiphilic Peptoids at Au–Water Interfaces

Shape-controlled colloidal nanocrystal syntheses often require facet-selective solution-phase chemical additives to regulate surface free energy, atom addition/migration fluxes or particle attachment rates. Because of their highly tunable properties and robustness to a wide range of experimental conditions, peptoids represent a very promising class of next generation functional additives for control over nanocrystal growth. However, understanding the origin of facet selectivity at the molecular level is critical to generalizing their design. In this work, we employ molecular dynamics simulations and biased sampling methods and report stronger selectivity to Au(111) than to Au(100) for Nce3Ncp6, a peptoid that has been shown to assist the formation of five-fold twinned Au nanostars. We find that facet-selectivity is achieved through synergistic effects of both peptoid-surface and solvent-surface interactions. Moreover, the amphiphilic nature of Nce3Ncp6 together with the order of peptoid-peptoid and peptoid-surface binding energies, i.e., peptoid-Au(100) < peptoid-peptoid < peptoid-Au(111), further amplifies its distinct collective behavior on different Au surfaces. Our studies provide a fundamental understanding of the molecular origin of facet-selective adsorption and highlight the possibility of future designs and uses of sequence-defined peptoids for predictive syntheses of nanocrystals with designed shapes and properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1997

Low-Density Aerodynamics of the Stardust Sample Return Capsule

The aerodynamics of the Stardust Sample Return Capsule are analyzed in the low- density, transitional flow regime using free-molecular, Direct Simulation Monte Carlo, Navier-Stokes, and Newtonian methods to provide inputs for constructing a transitional flow bridging relation. The accuracy of this bridging relation in reconstructing the aero- dynamic coefficients given by the more exact methods is presented for a range of flight conditions and vehicle attitudes. There is good agreement between the various prediction methods, and a simple sine-squared bridging relation is shown to provide a reasonably good description of the axial force, normal force, and pitching moment over a range of Knudsen numbers from 0.001 to 10. The predictions show a static instability of the Star- dust capsule in the free-molecular regime that persists well into the transitional flow. The addition of a thin disk to the base of the capsule is shown to remove this static instability. However, the extremely high entry velocity of 12.6 km/s for the proposed trajectory introduces difficult design issues for incorporating this disk caused by the high aerothermal loads that occur even under relatively rarefied conditions.

Wilmoth, Richard G.↗
DOE OSTI2022

Energy, angle, and temperature dependencies of the sticking of D atoms on Li surfaces

Detailed experimental and computational information on the response of lithium surfaces to irradiation by slow hydrogenic particles (ions, atoms, molecules) is sparse and mainly speculative. In this work, we present a computational study of the reflection and retention of deuterium (D) atoms at crystalline and amorphous lithium surfaces at 300 and 500 K, where the D atoms have an impact energy in the range of 0.025–5 eV and incident angles of 0° (perpendicular incidence) or 85° (near-grazing incidence). Classical molecular dynamics simulations are performed with the reactive bond-order force field (ReaxFF) potentials. This study provides quantitative information on the deuterium sticking probability and recycling coefficient for lithium surfaces. Further, our results support the ongoing work at the Lithium Tokamak eXperiment-β fusion experiment as well as relevant experiments in the laboratory setting.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2022

Revealing hidden defects through stored energy measurements of radiation damage

With full knowledge of a material’s atomistic structure, it is possible to predict any macroscopic property of interest. In practice, this is hindered by limitations of the chosen characterization techniques. For example, electron microscopy is unable to detect the smallest and most numerous defects in irradiated materials. Instead of spatial characterization, we propose to detect and quantify defects through their excess energy. Differential scanning calorimetry of irradiated Ti measures defect densities five times greater than those determined using transmission electron microscopy. Our experiments also reveal two energetically distinct processes where the established annealing model predicts one. Molecular dynamics simulations discover the defects responsible and inform a new mechanism for the recovery of irradiation-induced defects. The combination of annealing experiments and simulations can reveal defects hidden to other characterization techniques and has the potential to uncover new mechanisms behind the evolution of defects in materials.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2021

The denatured state of HIV ‐1 protease under native conditions

Abstract The denatured state of several proteins has been shown to display transient structures that are relevant for folding, stability, and aggregation. To detect them by nuclear magnetic resonance (NMR) spectroscopy, the denatured state must be stabilized by chemical agents or changes in temperature. This makes the environment different from that experienced in biologically relevant processes. Using high‐resolution heteronuclear NMR spectroscopy, we have characterized several denatured states of a monomeric variant of HIV‐1 protease, which is natively structured in water, induced by different concentrations of urea, guanidinium chloride, and acetic acid. We have extrapolated the chemical shifts and the relaxation parameters to the denaturant‐free denatured state at native conditions, showing that they converge to the same values. Subsequently, we characterized the conformational properties of this biologically relevant denatured state under native conditions by advanced molecular dynamics simulations and validated the results by comparison to experimental data. We show that the denatured state of HIV‐1 protease under native conditions displays rich patterns of transient native and non‐native structures, which could be of relevance to its guidance through a complex folding process.

60 APPLIED LIFE SCIENCES↗