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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 1,693 records · Page 94
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

A Fundamentally New Coupled Approach to Contact Mechanics via the Dirichlet‐Neumann Schwarz Alternating Method

Contact phenomena are crucial for understanding the behavior of mechanical systems. However, existing computational approaches for simulating mechanical contact often face numerical challenges, such as inaccurate physical predictions, energy conservation errors, and unwanted oscillations. Here, we introduce an alternative technique for simulating dynamic contact based on the non‐overlapping Schwarz alternating method, originally developed for domain decomposition. In multibody contact scenarios, this method treats each body as a separate, non‐overlapping domain and prevents interpenetration using an alternating Dirichlet–Neumann iterative process. This approach has a strong theoretical foundation, eliminates the need for contact constraints, and offers flexibility, making it ideal for multiscale and multiphysics applications. We conducted a numerical comparison between the Schwarz method and traditional methods, such as the Lagrange multiplier and penalty methods, focusing on a benchmark impact problem. Our results indicate that the Schwarz alternating method outperforms traditional methods in several key areas: it provides more accurate predictions for various measurable quantities and demonstrates exceptional energy conservation capabilities. To address unwanted oscillations in contact velocities and forces, we explored various algorithms and stabilization techniques, ultimately opting for the naïve‐stabilized Newmark scheme for its simplicity and effectiveness. Additionally, we validated the efficiency of the Schwarz method in a three‐dimensional impact problem, highlighting its inherent capacity to accommodate different mesh topologies, time‐integration schemes, and time steps for each interacting body.

Schwarz alternating method↗
DOE OSTI2024

Structure preserving and energy dissipative contact approaches for implicit dynamics

In this work, several structure preserving and energy dissipative contact approaches are proposed and evaluated. The time integration schemes considered are general with regard to the version of constraint type, but here the emphasis was on mortar contact. The proposed mortar contact approach conserves both linear and angular momentum for mortar contact in a novel way. The proposed time integration scheme can conserve energy or provide strict contact dissipation. In addition, the proposed scheme enforces both gap constraints and gap velocity constraints (i.e., persistency). Using a midstep time integrator often causes energy dissipation during initial impact, here this energy can be recovered in a novel way. Enforcing the gap velocity constraint mitigates the contact chatter of the contact pressure and nodes in many problems. Whereas some approaches enforce the persistency condition and gap constraints simultaneously during the solution of the equations of motion (EOM) requiring multipliers for both constraints included in the equation set, here the gap constraint is solved through the equations of motion and the persistency condition is satisfied in the time integration scheme by the velocity update after the equations of motion. It is shown that this approach is strictly dissipative in that a plastic contact condition can be achieved. Analogous to a coefficient of restitution for rigid bodies, any dissipated energy can then be returned upon release if energy conservation is desired. Structure preserving methods are good for long-time dynamics simulations and energy conserving and strictly dissipative methods can overcome stability issues associated with standard time integration algorithms such as the Newmark method.

42 ENGINEERING↗
DOE OSTI2025

Thermal Gradient Effects on Local Hotspot Ignition in 1,3,5,7‐Tetranitro‐1,3,5,7‐tetrazocane (HMX)

Understanding hotspot ignition, growth, and criticality, as well as the timescales of each, is crucial for parameterizing mesoscale and continuum‐level models that rely on a statistical understanding of hotspots. However, these models often consider hotspots to have uniform temperatures or for hotspots of a given temperature and size to always behave the same. Therefore, using molecular dynamics simulations, we assess the influence of thermal distribution effects on hotspot local ignition and time to ignition in 1,3,5,7‐tetranitro‐1,3,5,7‐tetrazocane (HMX) nanoscale hotspots. Finally, by assessing hotspots with a gradient driven from an initial two‐temperature core–shell setup, we show that small increases in the core temperature under a constant average temperature can lead to order‐of‐magnitude effects on reaction and local ignition timescales.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Tumorigenic p53 mutants undergo common structural disruptions including conversion to α‐sheet structure

Abstract The p53 protein is a commonly studied cancer target because of its role in tumor suppression. Unfortunately, it is susceptible to mutation‐associated loss of function; approximately 50% of cancers are associated with mutations to p53, the majority of which are located in the central DNA‐binding domain. Here, we report molecular dynamics simulations of wild‐type (WT) p53 and 20 different mutants, including a stabilized pseudo‐WT mutant. Our findings indicate that p53 mutants tend to exacerbate latent structural‐disruption tendencies, or vulnerabilities, already present in the WT protein, suggesting that it may be possible to develop cancer therapies by targeting a relatively small set of structural‐disruption motifs rather than a multitude of effects specific to each mutant. In addition, α‐sheet secondary structure formed in almost all of the proteins. α‐Sheet has been hypothesized and recently demonstrated to play a role in amyloidogenesis, and its presence in the reported p53 simulations coincides with the recent re‐consideration of cancer as an amyloid disease.

Bromley, Dennis↗
DOE OSTI2024

Insight into the autoproteolysis mechanism of the RsgI9 anti‐σ factor from Clostridium thermocellum

Abstract Clostridium thermocellum is a potential microbial platform to convert abundant plant biomass to biofuels and other renewable chemicals. It efficiently degrades lignocellulosic biomass using a surface displayed cellulosome, a megadalton sized multienzyme containing complex. The enzymatic composition and architecture of the cellulosome is controlled by several transmembrane biomass‐sensing RsgI‐type anti‐σ factors. Recent studies suggest that these factors transduce signals from the cell surface via a conserved RsgI extracellular (CRE) domain (also called a periplasmic domain) that undergoes autoproteolysis through an incompletely understood mechanism. Here we report the structure of the autoproteolyzed CRE domain from the C. thermocellum RsgI9 anti‐σ factor, revealing that the cleaved fragments forming this domain associate to form a stable α/β/α sandwich fold. Based on AlphaFold2 modeling, molecular dynamics simulations, and tandem mass spectrometry, we propose that a conserved Asn‐Pro bond in RsgI9 autoproteolyzes via a succinimide intermediate whose formation is promoted by a conserved hydrogen bond network holding the scissile peptide bond in a strained conformation. As other RsgI anti‐σ factors share sequence homology to RsgI9, they likely autoproteolyze through a similar mechanism.

Takayesu, Allen↗
DOE OSTI2023

Long‐Range Electron Transport Rates Depend on Wire Dimensions in Cytochrome Nanowires

Abstract The ability to redirect electron transport to new reactions in living systems opens possibilities to store energy, generate new products, or probe physiological processes. Recent work by Huang et al. showed that 3D crystals of small tetraheme cytochromes (STC) can transport electrons over nanoscopic to mesoscopic distances by an electron hopping mechanism, making them promising materials for nanowires. However, fluctuations at room temperature may distort the nanostructure, hindering efficient electron transport. Classical molecular dynamics simulations of these fluctuations at the nano‐ and mesoscopic scales allowed us to develop a graph network representation to estimate maximum electron flow that can be driven through STC wires. In longer nanowires, transient structural fluctuations at protein‐protein interfaces tended to obstruct efficient electron transfer, but these blockages are ameliorated in thicker crystals where alternative electron transfer pathways become more efficient. The model implies that more flexible proteinprotein interfaces limit the required minimum diameter to carry currents commensurate with conventional electronics.

Chemistry↗
DOE OSTI2024

Counterintuitive Trend of Intrusion Pressure with Temperature in the Hydrophobic Cu 2 (tebpz) MOF

Liquid porosimetry experiments reveal a peculiar trend of the intrusion pressure of water in hydrophobic Cu 2 (3,3',5,5'-tetraethyl-4,4'-bipyrazolate) MOF. At lower temperature (T) range, the intrusion pressure (P i ) increases with T. For higher T values, P i first reaches a maximum and then decreases. This is at odds with the Young–Laplace law, which for systems showing a continuous decrease of contact angle with T predicts a corresponding reduction of the intrusion pressure. Though the Young–Laplace law is not expected to provide quantitative predictions at the subnanoscale of Cu 2 (tebpz) pores, the physical intuition suggests that to a reduction of their hydrophobicity corresponds a reduction of the P i . Molecular dynamics simulations and sychrothron experiments allowed to clarify the mechanism of the peculiar trend of P i with T. At increasing temperatures the vapor density within the MOF’ pores grows significantly, bringing the corresponding partial pressure to ≈5 MPa. This pressure, which is consistent with the shift of P i observed in liquid porosimetry, represents a threshold to be overcame before intrusion takes place. Beyond some value of temperature, the phenomenon of reduction of hydrophobicity (and water surface tension) dominated over the opposite effect of increase of vapor pressure and P i inverts its trend with T.

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

Self‐Lubricating Tribo‐Catalytic Activity of 2D High Entropy Alloy Nanoflakes

High Entropy Alloys (HEAs) have garnered attention due to their remarkable tribological attributes. Predominantly, failure mechanisms in HEAs emanate from stress‐induced dislocations, culminating in crack propagation and film delamination. In this study, we report on the synthesis of 2D HEA of (MoWNbTaV) 0.2 S 2 which facilitates shear‐induced energy dissipation at sliding interfaces. The ball‐on‐disk tribological investigations demonstrate unprecedentedly low average coefficients of friction (0.076) and wear rates (10 −9 mm 3 (N∙m) −1 ) under high contact pressures (0.936 GPa) within ambient conditions. Employing multi‐scale characterizations alongside molecular dynamic simulations, we elucidate that the presence of the HEA triggers tribocatalytic activity under high contact pressures emerging as a pivotal factor in extending lubricant lifespan during tribological tests. The resilient lubriciousness coupled with the facile spray coating methodology of (MoWNbTaV) 0.2 S 2 in ambient environments paves the way for the development of a new class of solid lubricants based on 2D HEA.

2D solid lubricant↗
DOE OSTI2025

Delineating the Impact of Diluent on High-Concentration Electrolytes for Developing High-Voltage LiNi 0.5 Mn 1.5 O 4 Spinel Cathode

LiNi 0.5 Mn 1.5 O 4 (LNMO) is a high-voltage spinel cathode with low nickel content, making it an attractive candidate for next-generation lithium-ion batteries (LIBs). However, its application is limited by interfacial instability with conventional carbonate-based electrolytes at high voltages. In this work, a localized saturated electrolyte (LSE) capable of stably operating up to 4.85 V is investigated. Molecular dynamics simulations and Fourier transform infrared spectroscopy reveal that adding “non-solvating” 1,1,2,2-tetrafluoroethyl-2,2,3,3-tetrafluoropropyl ether diluent in the saturated electrolyte, more PF 6 − anions are present in the first solvation shell of Li + , at the expense of solvent molecules. This tailored solvation environment promotes the formation of a robust, LiF-rich cathode-electrolyte interphase that mitigates transition metal dissolution and parasitic side reactions. The optimized LSE enables excellent cycling performance, with 95% capacity retention in Li|LNMO half-cells after 100 cycles and 94% retention in Li 4 Ti 5 O 12 |LNMO full cells after 250 cycles, even at a practically relevant LNMO cathode loading of ≈15 mg cm −2 . In conclusion, these results highlight the benefits of electrolyte engineering and solvation structure control in advancing high-voltage LIB technologies.

LNMO cathode↗
DOE OSTI2025

Supercooling of Alaskan Beetle Larvae as a Winter Survival Strategy

Insects are able to survive subfreezing temperatures by either limiting ice crystal formation in their bodies or through freeze avoidance. Beetle larvae are able to avoid freezing in winter by dehydrating in the fall months and replacing their body water content with high concentrations of glycerol. This enables the body fluid of the insect to supercool, and even vitrify, recovering unharmed when the temperature warms in the spring. Using nondestructive, high‐energy X‐ray synchrotron diffraction experiments, direct insight into how cryopreservation occurs at the atomic level within the beetle larvae has been obtained. The results shed light on the molecular‐level interactions associated with the mechanism responsible for surviving freezing temperatures. The molecular models of severely dehydrated Alaskan beetle larvae, based on glycerol‐water mixtures, yield a total of 4.2 ± 1.2 intermolecular hydrogen bonds per glycerol molecule at 275 K, in good agreement with existing molecular dynamics simulations. Most importantly, they show that if just over half the body fluid content is water, the water clusters are too small to form ice crystals that cause cellular damage.

Benmore, Chris J. [X‐Ray Science Division Advanced↗
DOE OSTI2021

The FMO-DFTB Method

Although the fragment molecular orbital (FMO) method enables electronic structure calculations with near-linear scaling behavior with respect to system size, the computational cost of ab initio methods typically employed in conjunction with FMO is still prohibitive for routine calculations of very large systems or long timescale molecular dynamics simulations. We, therefore, combined the FMO and density-functional tight-binding (DFTB) method, which is one of the emerging semi-empirical quantum chemical methods, and have demonstrated that FMO-DFTB is capable of performing geometry optimizations for systems containing up to one million atoms using limited computational resources. In this chapter, we will review the basics of the DFTB method first before introducing FMO-DFTB, focusing on the relationship with density functional theory and other FMO methodologies. We also demonstrate the latest scalings of FMO-DFTB2 and DFTB3 using three-dimensional water clusters, showing that the most favorable scaling is O(N1.16). Applications of FMO-DFTB to various systems are briefly summarized, and an outlook to future applications is provided.

Nishimoto, Yoshio↗
DOE OSTI2025

Speciation and diffusive dynamics in hydrated grain boundaries of complex oxide Gd2Ti2O7

Abstract Grain boundaries in polycrystalline materials significantly affect their properties, such as ionic transport, corrosion, and chemical durability. The pyrochlore compound (Gd 2 Ti 2 O 7 ) is employed as a model for complex oxides and is known for its diverse applications, including nuclear waste immobilization. Density functional theory-based first-principles molecular dynamics simulations were performed at different temperatures on the hydrated grain boundary system. The results show extensive transformations within the grain boundaries among hydrous water species (OH − , H 2 O, and H 3 O + ). The temperature dependence of self-diffusion coefficients follows Arrhenius behavior, with an activation energy of 35.9 kJ/mol for hydrogen and 46.3 kJ/mol for oxygen. The lifetime of OH − is about three to four times longer than that of H 2 O at temperatures from 800 to 2100 K, suggesting the greater stability of OH − over H 2 O, a unique characteristic of the grain boundaries. The estimated lifetime of the hydrous species decreases as the temperature increases, with an activation energy of 9.9 kJ/mol for OH − and 13.4 kJ/mol for H 2 O. While Gd 3 + is more mobile than Ti 4+ , both the Gd 3 + and Ti 4+ cations are orders of magnitude less mobile than the water species. The results suggest that water species are much more mobile within grain boundaries than in the bulk crystal and have the potential to penetrate deep into polycrystalline materials through grain boundaries, leading to grain boundary degradation and dissolution. The different mobilities of cations in complex oxides can lead to leaching of certain cations and incongruent dissolution during the chemical weathering of Earth and industrial materials.

B. Ghosh, Dipta↗
DOE OSTI2024

Negative thermal expansion coefficient and amorphization in defective 4H-SiC

This paper presents thermal expansion coefficient (TEC) and amorphization in 4H-SiC containing point defects at different concentrations. We considered vacancy defects, interstitial defects, and Frenkel pair defects and investigated the thermomechanical response of the lattice over a wide range of temperatures using classical molecular dynamics simulations. The results show that 4H-SiC with vacancy defects exhibits a negative TEC above a critical defect density of around 9% (irrespective of the temperature). With interstitial defects, it exhibits a positive TEC (regardless of the defect density), and with Frenkel pair defects it shows a transition from positive TEC to negative TEC for a defect density greater than 8%. The coupling between temperature-induced expansion and defect-introduced stress in the lattice forms the mechanistic basis for the observed variation in TEC. Furthermore, the specific heat decreases rapidly with an increase in defect density at room temperature, with the highest sensitivity of the lattice observed for the Frenkel pair defects followed by interstitial defects and then by vacancy defects. Finally, these findings highlight the critical implications of defects on thermal expansion behavior of 4H-SiC with applications in radiation environments.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Spontaneous rearrangement of acetylated xylan on hydrophilic cellulose surfaces

The interaction of xylan, an abundant plant polysaccharide, with cellulose microfibrils is essential for secondary cell wall strength. A deeper understanding of these interactions is crucial both to improve our understanding of plant cell wall architecture and to design alternate strategies to overcome cellulose recalcitrance for the production of biofuels and sustainable biomaterials. Naturally occurring acetate or glucuronic acid substitutions on xylan have been shown to influence xylan-cellulose interactions. In this work, we use unrestrained molecular dynamics simulations to determine the interactions with the (110) hydrophilic face of cellulose fibers of four different xylans. In the absence of cellulose, all xylans, independent of the substitution pattern, adopt a highly flexible threefold helical screw conformation. However, when xylan is spatially close to a cellulose surface 1,2 linked acetyl xylans (2AcX) adopt rigid twofold helical screw conformations. The 2AcX conformations are primarily stabilized by interactions between the acetylated oxygen and the glycosidic linkage with C-O6 of cellulose. In contrast, the glycosidic oxygens and acetyl decorations for 1,3 linked acetyl groups (3AcX) are oriented away from the cellulose surface and the 3AcX xylans maintain threefold helical screw conformations on the cellulose surface. Our results show that evenly spaced chemical functionalization (with acetyl groups) and the position of substitution (1,2) on xylan backbone play key roles in tuning the xylan-cellulose interactions to stabilize the twofold helical screw conformations of xylan on the cellulose surface. A comparison with previous experimental findings further suggests that 1,2 substitutions induce twofold helical screw conformations of xylan on the cellulose surface irrespective of the chemical nature of the substituent, while 1,3 substitutions primarily bind lignin in threefold helical screw conformations rather than cellulose in plant cell walls.

1,2 Ac↗
DOE OSTI2023

Patterns in interactions of variably acetylated xylans with hydrophobic cellulose surfaces

The recalcitrance of plant cell wall lignocellulosic biomass to deconstruction is a major hurdle to sustainable biofuel/bioproduct economy. A multitude of interactions stabilize lignocellulosic biomass structure. Among these, tight packing of hemicellulose-cellulose is partly responsible for biomass recalcitrance. Here, unrestrained molecular dynamics simulations are employed to understand the influence of the nature and pattern of naturally-occuring acetyl decorations of the xylan backbone on interactions with the (100) hydrophobic cellulose surface. Periodically O2-acetylated xylan (2AcX) assume twofold helical screw conformations that are stabilized by a combination of multiple hydrophobic contacts and hydrogen bonds with the hydrophobic cellulose surface. In contrast, acetylation at the O3 position in xylan obstructs interactions, thereby adopting threefold helical screw conformations that potentially preferably interact with lignin rather than cellulose. Fully acetylated xylan desorbs from the surface implying a minimum number of unsubstituted residues on the xylan backbone is required for interaction with the surface. Here, the substituted residues must form ~ 20% fewer contacts than the unsubstituted residues to sustain stable twofold helical screw xylan conformations on the cellulose surface. Thus, specific roles of macromolecular conformations of cellulose and hemicellulose in influencing the supramolecular interactions and function of plant cell walls have been determined.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Integrated data-driven and experimental approaches to accelerate lead optimization targeting SARS-CoV- 2 main protease

Identification of potential therapeutic candidates can be expedited by integrating computational modeling with domain aware machine learning (ML) approaches followed by experimental validation. Generative deep learning models have been recently developed that can generate thousands of new candidates, but their physiochemical properties are typically not optimized. Using our deep learning models and a scaffold as a starting point, we generated tens of thousands of compounds for SARS-CoV-2 M pro that preserve the core scaffold. Here we utilized and implemented several computational tools such as structural alert and toxicity analysis, high throughput virtual screening, ML-based 3D quantitative structure–activity relationships, multi-parameter optimization, and graph neural networks on libraries of generated candidates to predict biological activity and binding affinity a priori. From these collective computational results, eight promising candidates were identified and tested experimentally using Native Mass Spectrometry (MS) and FRET-based functional assays. Two compounds, with quinazoline-2-thiol and acetylpiperidine core moiety showed IC 50 values in the low micromolar range: 2.95±0.0017 µM and 3.41±0.0015 µM, respectively. The molecular dynamics simulations further highlight that binding of these compounds results in allosteric modulations in the chain B and the interface domains of the M pro . The key fragments from these top hits can be used as input for closed loop lead optimization in the integrated pipeline.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

The heterogeneous nature of mechanically accelerated grain growth

Abstract While grain growth is traditionally viewed as a purely thermally driven process, nanocrystalline metals can undergo grain growth under mechanical loads, even at room temperature. We performed a detailed atomistic study of the heterogeneous nature of mechanically accelerated grain growth in a polycrystalline Pt nanowire. Using molecular dynamics simulations, we compared the grain-growth behavior of individual grains during tensile and shear cyclic loading, for three different equivalent strain levels, and at two temperatures. Pure thermal grain growth with no mechanical loading provided a baseline reference case. On average, grains that were already susceptible to thermal grain growth were stimulated to grow faster with mechanical loading, as expected. However, when analyzed on a grain-by-grain basis, the results were far more complex: grains that grew fastest under one stimuli were less accelerated under other stimuli. Even when the magnitude of loading changed, the relative growth of individual grains was distorted. We interpret this complexity from the perspective of superimposed growth mechanisms.

Chen, Elton Y.↗