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At least 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Substrate-Directed Dimensional and Phase Control of Peptide Assemblies on Two-Dimensional van der Waals Materials

Understanding and controlling biomolecular self-assembly on van der Waals (vdW) materials has the potential to advance hybrid bioelectronic devices by enabling precise tuning of the interface and modulation of the resulting electronic properties of the biomolecule-vdW heterostructure. However, how surface properties of vdW materials direct biomolecule assembly remains poorly understood. To fill this knowledge gap, we investigated the assembly of a peptide known to assemble into two-dimensional (2D) crystalline films on MoS 2 on three representative vdW surfaces: WS 2 , MoS 2 , and highly oriented pyrolytic graphite (HOPG). Using in situ atomic force microscopy (AFM), we find that assembly is substrate-dependent, resulting in multilayers on WS 2 , monolayers on MoS 2 , and multiple coexisting phases on HOPG. WS 2 exhibits a higher negative charge, strong long-range electrostatic interactions, and extensive hydration layering that may promote multilayer stacking. In contrast, MoS 2 has stronger short-range interactions with the peptides but much weaker long-range interactions and hydration structure, which may favor monolayer formation. Molecular dynamics simulations predict a corresponding switch from monolayer to multilayer aggregates of the adsorbed monomers, reflected in their relative mobilities. On hydrophobic HOPG, the peptides bind most strongly and remain as monomers with high surface mobility. The peptide dimers comprising the basic unit of the crystals are more compact on HOPG, which has a smaller lattice constant than WS 2 or MoS 2 , suggesting strain contributes to stabilizing multiple phases. Our results provide mechanistic insights into how surface charge and hydration structure, and the lattice structure of the substrates governs peptide assembly on vdW materials, offering a framework to rationally control the 2D peptide-vdW heterostructures.

Molecular dynamics simulations↗
DOE OSTI2025

Binding and Translocation of Substrate Allosterically Promotes Functional Interactions Within the AlkB–AlkG Electron Transfer Complex

The alkane monooxygenase AlkB and rubredoxin AlkG form an electron transfer complex that hydroxylates terminal alkanes to produce alcohols. The recent cryoEM study of Fontimonas thermophila AlkB-AlkG complex revealed its architecture, including a dodecane (D12) substrate at the active site. However, FtAlkBG molecular mechanism of action of remains unknown. Here, in this study, we examined its dynamics and interactions by multiscale computations, including molecular dynamics simulations, elastic network models, and QM/MM of the oxygen activation mechanism at the AlkB catalytic site. D12 maintained stable interactions within the catalytic site during two MD runs, coordinated by hydrophobic residues L263-L264, I267, I133. A third extended run revealed that D12 could translocate to a membrane-exposed site near S49/F46 along a hydrophobic channel gated by I54. During this translocation, D12 was temporarily stabilized at intermediate sites IS1 (lined by I27/L30-G31/G50/L53-I54/P59/S124/A127-V128) and IS2 (I33-G34/L37/L45-F46/S49) before nearly exiting the protein, and diffused back to the active site, assisted by L30. Substrate binding and translocation across those intermediate sites affects the coupling between the iron centers in AlkBG, and interfacial interactions between AlkB-AlkG. The channel was further connected to the cytosol, near two surface-exposed arginines, potentially allowing for O 2 passage. The allosteric effects between D12 putative entry site, catalytic site and AlkB-AlkG interface were analyzed by ENM-based methods which confirmed the cooperative perturbation-responses and strongly correlated movements of residues belonging to those distal regions. Our study provides new mechanistic insights into key sites and their interactions that could be targeted for developing AlkB-variants with desirable alkane conversion functions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Effect of particle shape on stratification in drying films of binary colloidal mixtures

The role of particle shape in evaporation-induced auto-stratification in polydisperse colloidal suspensions is explored with molecular dynamics simulations of mixtures of spheres and aspherical particles. A unified framework based on the competition between diffusion and diffusiophoresis is proposed to understand the effects of shape and size dispersity. In general, particles diffusing more slowly (e.g., larger particles) tend to accumulate more strongly at the evaporation front. However, larger particles have larger surface areas and therefore greater diffusiophoretic mobility. Hence, they are more likely to be driven away from the evaporation front via diffusiophoresis. For a rapidly dried bidisperse suspension containing small and large spheres, the competition leads to “small-on-top” stratification. Here, we employ a computational model in which the diffusion coefficient is inversely proportional to particle mass. For a mixture of spheres and aspherical particles with similar mass, the diffusion contrast is reduced, and the spheres are always enriched at the evaporation front as they have the smallest surface area for a given mass and, therefore, the lowest diffusiophoretic mobility. Furthermore, for a mixture of solid and hollow spheres that have the same outer radius and thus the same surface area, the diffusiophoretic contrast is suppressed, and the system is dominated by diffusion. Consequently, the solid spheres, which have a larger mass and diffuse more slowly, accumulate on top of the hollow spheres. Finally, for a mixture of thin disks and long rods that differ significantly in shape but have similar mass and surface area, both diffusion and diffusiophoresis contrasts are suppressed, and the mixture does not stratify.

Classical molecular dynamic simulations↗
DOE OSTI2025

Control of Permanent Porosity in Type 3 Porous Liquids via Solvent Clustering

Porous liquids (PLs) are an exciting new class of materials for carbon capture due to their high gas adsorption capacity and ease of industrial implementation. They are composed of sorbent particles suspended in a nonadsorbed solvent, forming a liquid with permanent porosity. While PLs have a vast number of potential compositions based on the number of solvents and sorbent materials available, most of the research has been focused on the selection of the sorbent rather than the solvent. Therefore, PL design criteria on the supramolecular structures of the solvent are explored to create a fundamental understanding of how the solvent enables PL formation for rapid discovery of new PL compositions. Atomistic molecular dynamics simulation of eight solvents with a range of molecular sizes, shapes, and intramolecular bonding was performed, identifying that the shape and size of molecular clusters formed in the solvent are the driving predictor of PL formation rather than the size of the individual solvent molecule. The results demonstrate a significant departure from common approaches to PL formation based on the steric exclusion of solvent molecules from the sorbent via the size of the pore aperture. A modeling and experimental validation study further supports these findings. In conclusion, through this computational material design study, a previously unexplored mechanism in PL formation, solvent–solvent clustering, is identified as a critical factor for the accelerated discovery of liquid phase carbon capture materials.

Carbon capture↗
DOE OSTI2024

Source of Processable Vitrimer Viscosities: Swap Frequencies and Steric Factors

Vitrimers exhibit high, processable viscosities, where other polymers do not, and are among the most promising polymers for closed-loop material circularity. We sought to investigate the underlying chemical kinetic factors that result in high viscosities for vitrimers, which are crucial to designing vitrimers with tunable viscosity. To interrogate these factors, we achieved the first simulated predictions of real vitrimer viscosities, using a novel kinetic Monte Carlo molecular dynamics method, overcoming the time and length scale gaps to predict experimental bulk viscosities. The vitrimer architecture investigated is based on poly(dimethylsiloxane) chains and vinylogous urethane bond swaps. We probed the effects of the extent of free swapping groups, %F, the activation energy, E A , and the steric factor, ρ. The steric factor is related to the intrinsic reaction probability for molecules with sufficient energy. All three factors were found to be significant, but the role of ρ was found to be the biggest and also the most underappreciated. The results show that the inclusion of accurate ρ is of critical importance for viscosity predictions, with the evidence suggesting that the typical assumption of ρ = 1 is not valid for vitrimers and that, indeed, very low steric factors are present in bond-swap vitrimers such that values of ρ < 10 –10 may be typical. This greatly influences the bond exchange rates and, ultimately, the viscosities. Recognition of this result is necessary for the prediction of vitrimer viscosities from molecular simulations and to make vitrimers by design from molecular dynamics. We also investigated the effects that E A , ρ, and the number of free swapping groups have upon vitreous range temperatures, TV, with respect to achieving a specific viscosity (η V = 1 × 10 8 Pa·s), as well as for a commonly reported higher viscosity extrapolation (η V = 1 × 10 12 Pa·s). The evidence suggests that vitrimers may follow universal curves for E A vs T V , as a function of ρ. Finally, this study achieves the first of these comparisons of molecular simulations to experiments and reveals critical insights toward creating vitrimers by design, while providing a route for the prediction of T V from kinetic Monte Carlo molecular dynamics simulations.

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

Two-component dynamics in supercritical $\text {CO}_2$ from inelastic X-ray scattering

Supercritical fluids are characterized by unique thermodynamic properties. One of these properties is the existence of two-component dynamics that is associated with distinct low-frequency and high-frequency vibrational responses of the fluid. However, the origin of this behavior remains unknown. By combining inelastic X-ray scattering and molecular dynamics simulations, we show that this behavior can be connected to density heterogeneities arising from molecular clusters. Analyses of measurements and molecular trajectories suggest that the two-component dynamics emerges due to distinct momentum fluctuations of clustered and unbound molecules. This connection between clusters and two-component dynamics highlights the importance of molecular-structural heterogeneities in supercritical fluids, colloids, and condensed-matter systems.

biophysics↗
DOE OSTI2024

Effect of layer bending on montmorillonite hydration and structure from molecular simulation

Conceptual models of smectite hydration include planar (flat) clay layers that undergo stepwise expansion as successive monolayers of water molecules fill the interlayer regions. However, X-ray diffraction (XRD) studies indicate the presence of interstratified hydration states, suggesting non-uniform interlayer hydration in smectites. Additionally, recent theoretical studies have shown that clay layers can adopt bent configurations over nanometer-scale lateral dimensions with minimal effect on mechanical properties. Therefore, in this study we used molecular simulations to evaluate structural properties and water adsorption isotherms for montmorillonite models composed of bent clay layers in mixed hydration states. Results are compared with models consisting of planar clay layers with interstratified hydration states (e.g. 1W–2W). The small degree of bending in these models (up to 1.5 Å of vertical displacement over a 1.3 nm lateral dimension) had little or no effect on bond lengths and angle distributions within the clay layers. Except for models that included dry states, porosities and simulated water adsorption isotherms were nearly identical for bent or flat clay layers with the same averaged layer spacing. Similar agreement was seen with Na- and Ca-exchanged clays. In conclusion, while the small bent models did not retain their configurations during unconstrained molecular dynamics simulation with flexible clay layers, we show that bent structures are stable at much larger length scales by simulating a 41.6×7.1 nm 2 system that included dehydrated and hydrated regions in the same interlayer.

58 GEOSCIENCES↗
DOE OSTI2024

Axial H-Bonding Solvent Controls Inhomogeneous Spectral Broadening, While Peripheral H-Bonding Solvent Controls Vibronic Broadening: Cresyl Violet in Methanol

The dynamics of the nuclei of both a chromophore and its condensed-phase environment control many spectral features, including the vibronic and inhomogeneous broadening present in spectral line shapes. For the cresyl violet chromophore in methanol, we here analyze and isolate the effect of specific chromophore–solvent interactions on simulated spectral densities, reorganization energies, and linear absorption spectra. Employing both chromophore and its condensed-phase environment control many spectral features, including the vibronic and inhomogeneous broadening present in spectral line shapes. For the cresyl violet chromophore in methanol, we here analyze and isolate the effect of specific chromophore–solvent interactions on simulated spectral densities, reorganization energies, and linear absorption spectra. Employing both force field and ab initio molecular dynamics trajectories along with the inclusion of only certain solvent molecules in the excited-state calculations, we determine that the methanol molecules axial to the chromophore are responsible for the majority of inhomogeneous broadening, with a single methanol molecule that forms an axial hydrogen bond dominating the response. Furthermore, the strong peripheral hydrogen bonds do not contribute to spectral broadening, as they are very stable throughout the dynamics and do not lead to increased energy-gap fluctuations. We also find that treating the strong peripheral hydrogen bonds as molecular mechanical point charges during the molecular dynamics simulation underestimates the vibronic coupling. Including these peripheral hydrogen bonding methanol molecules in the quantum-mechanical region in a geometry optimization increases the vibronic coupling, suggesting that a more advanced treatment of these strongly interacting solvent molecules during the molecular dynamics trajectory may be necessary to capture the full vibronic spectral broadening.

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

Charge regulation effects on colloidal mixture nanoparticles

Changes in pH within a system containing dissociable sites affect the protonation and deprotonation of these groups, thereby influencing their physical properties. In response, the system modifies their surface charge, affecting electrostatic interactions, aggregation, stability, and structural behavior. Although the pH can be tuned in experiments, it is difficult to model this phenomenon using simulations or theoretical approaches. Here, we perform hybrid Monte Carlo-molecular dynamics simulations to model charge regulation effects in an equimolar colloidal charged system. We compare charge regulation effects with those of a system in which the charges of colloidal nanoparticles are not dissociable. The comparison between the two cases modifies the phase diagram, and it changes the volume fraction where a percolation network of nanoparticles is found. Charge regulation is found to destroy network formation, as the charge in the nanoparticles is modified because of the cooperativity dependency of the degree of charge dissociation sites among the nanoparticles favoring cluster formation. Furthermore, our work suggests that the ionic and/or electronic conductivity in functionalized nanoparticles can be modified by changing pH values. It also guides the experimental design of oppositely charged nanoparticles as inks for 3D printing processes.

Classical statistical mechanics↗
DOE OSTI2025

Ultrafast Events in Electrocyclic Ring-Opening Reactions

Electrocyclic reactions are characterized by the concerted formation and cleavage of multiple σ and π bonds in a molecular system and have been extensively studied since they were introduced by Robert Burns Woodward and Roald Hoffmann in 1965. Recent advances and the integration of time-resolved experiments and nonadiabatic quantum molecular dynamics simulations have transformed the traditional understanding of electrocyclic reactions beyond the Woodward–Hoffmann rules. In this review, we focus on recent studies of 1,3-cyclohexadiene and two of its derivatives, α-phellandrene and α-terpinene, to shed light on the underlying mechanisms of electrocyclic photochemical reactions. We highlight recent progress in ultrafast electron diffraction techniques and the simulation approach of ab initio multiple spawning. Together, these approaches can elucidate molecular structure dynamics from femtosecond to picosecond timescales as well as nuclear and electronic responses at conical intersections.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

A model for trapping and re-solution regarding intra-granular bubbles in UO 2 , linked to atomic-scale simulations

In the literature, a clear definition of the irradiation re-solution frequency of gas from bubbles in the UO 2 fuel is absent. Moreover, for intra-granular bubbles, a detailed calculation of the cumulated displaced gas quantities in function of the distance from the radius of the bubble after a re-solution event has never been published. The assessment of these two elements is very useful if we want to increase the adherence of fission gas release codes to our present knowledge of the behavior of fission gases. Hence, we suggest to link the definition of the re-solution frequency to atomic-scale simulations. Furthermore, we present the cumulated displaced gas quantities obtained from Molecular Dynamics calculations, from which we have derived a re-solution profile that can be exploited to better consider the irradiation re-solution phenomenon inside Fission Gas Release codes. On top of that, we have built a new trapping/re-solution model for intra-granular bubbles linked to Molecular Dynamics simulations that can be easily incorporated into Fission Gas Release codes. In conclusion, we also check that the model is properly built through the comparison of the new model against a reference.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2024

Library Screening, In Vivo Confirmation, and Structural and Bioinformatic Analysis of Pentapeptide Sequences as Substrates for Protein Farnesyltransferase

Protein farnesylation is a post-translational modification where a 15-carbon farnesyl isoprenoid is appended to the C-terminal end of a protein by farnesyltransferase (FTase). This process often causes proteins to associate with the membrane and participate in signal transduction pathways. The most common substrates of FTase are proteins that have C-terminal tetrapeptide CaaX box sequences where the cysteine is the site of modification. However, recent work has shown that five amino acid sequences can also be recognized, including the pentapeptides CMIIM and CSLMQ. In this work, peptide libraries were initially used to systematically vary the residues in those two parental sequences using an assay based on Matrix Assisted Laser Desorption Ionization–Mass Spectrometry (MALDI-MS). In addition, 192 pentapeptide sequences from the human proteome were screened using that assay to discover additional extended CaaaX-box motifs. Selected hits from that screening effort were rescreened using an in vivo yeast reporter protein assay. The X-ray crystal structure of CMIIM bound to FTase was also solved, showing that the C-terminal tripeptide of that sequence interacted with the enzyme in a similar manner as the C-terminal tripeptide of CVVM, suggesting that the tripeptide comprises a common structural element for substrate recognition in both tetrapeptide and pentapeptide sequences. Molecular dynamics simulation of CMIIM bound to FTase further shed light on the molecular interactions involved, showing that a putative catalytically competent Zn(II)-thiolate species was able to form. Bioinformatic predictions of tetrapeptide (CaaX-box) reactivity correlated well with the reactivity of pentapeptides obtained from in vivo analysis, reinforcing the importance of the C-terminal tripeptide motif. This analysis provides a structural framework for understanding the reactivity of extended CaaaX-box motifs and a method that may be useful for predicting the reactivity of additional FTase substrates bearing CaaaX-box sequences.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Quantum Ornstein-Zernike theory for two-temperature two-component plasmas

Laboratory plasma production almost always preferentially heats either the ions or electrons, leading to a two-temperature state. In this state, density functional theory molecular dynamic simulation is the state of the art for modeling bulk material properties. We construct a statistical mechanics model for the two temperature limit that is theoretically consistent with the molecular dynamics method. We proceed to derive the electron-ion multi-temperature quantum Ornstein-Zernike equations for the first time. This allows the construction of a two-temperature two-component plasma model using the average atom from which we can compute bulk material properties at a fraction of the computation time of the two-temperature density functional theory simulation. The accuracy of the model is benchmarked against ion pair correlation and self-diffusion results from ab initio simulation. Here, we proceed to compute the viscosity and ion thermal conductivity as a function of both ion and electron temperature.

Ab initio molecular dynamics↗
DOE OSTI2025

200-fold increase in dynamic strength of platinum at 430 GPa without a phase transformation

Here, the high-pressure strength of solid platinum is studied at the National Ignition Facility via Rayleigh-Taylor ripple growth under ramp compression. Laser-driven experiments reached pressures up to 430 GPa, collecting velocimetry and radiography data. Despite no phase transformation, the observed ripple growth aligns with hydrodynamic simulations using an amplified Steinberg-Guinan model, resulting in a 200-fold increase in strength. Molecular dynamics simulations of platinum ramp compression yield similar von Mises stress at comparable high pressure and high strain rate conditions. These findings represent the highest-pressure strength measurements ever achieved for platinum and offer critical insight into its significant strengthening behavior under high pressure and strain rate conditions.

Righi, Gaia [Lawrence Livermore National Laborator↗
DOE OSTI2024

Mean force emission theory for classical bremsstrahlung in strongly coupled plasmas

This work presents mean force emission theory, which extends the classical theory of bremsstrahlung emission to strongly coupled plasmas. In the high-frequency limit, the theory reduces to solving for the electron trajectory during a binary collision, but where the electron–ion interactions occur through the potential of mean force. In the low-frequency limit, it uses an autocorrelation formalism that captures effects of multiple collisions and strongly correlated motion. The predictions are benchmarked by comparison with first-principles classical molecular dynamics simulations of a fully ionized hydrogen plasma in which all interactions are repulsive. The comparison shows good agreement up to Coulomb coupling strengths of Γ∼30. The theory improves upon traditional models by including strong coupling effects and systematically including the effect of multiple collisions. Furthermore, mean force emission theory provides evidence that the Drude correction factor commonly used in quantum calculations of optical quantities may not be adequate at strong coupling.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Self-Assembled Oligomers Facilitate Amino Acid-Driven CO 2 Capture at the Air–Aqueous Interface

Direct air capture of CO 2 using amino acid absorbents, such as glycine or sarcosine, is constrained by the relatively slow mass transfer of CO 2 through the air–aqueous interface. Our recent study showed a marked improvement in CO 2 capture by introducing CO 2 -permeable oligo-dimethylsiloxane (ODMS-MIM + ) oligomers with cationic (imidazolium, MIM + ) headgroups. Here, in this work, we have employed all-atom molecular dynamics simulations in combination with subensemble analysis using network theory to provide a detailed molecular picture of the behavior of CO 2 and the glycinate anions (Gly – ) at the ODMS-MIM + decorated air–aqueous interfaces. We show that the cationic head groups of the surfactants enhance the concentration and lifetime of Gly – in the interfacial region, while ODMS tails promote the physisorption of CO 2 in the interfacial region. Together, these two factors increase the effective region of contact and the probability of interactions between CO 2 and Gly – compared to that of the pure air–aqueous interface. The fundamental insights gained in this work establish essential foundations for developing hybrid systems with oligomer-decorated interfaces to maximize the overall CO 2 capture rates.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Quantum Molecular Charge-Transfer Model for Multistep Auger–Meitner Decay Cascade Dynamics

The fragmentation of molecular cations following inner-shell decay processes in molecules containing heavy elements underpins the X-ray damage effects observed in X-ray scattering measurements of biological and chemical materials, as well as in medical applications involving Auger electron-emitting radionuclides. Traditionally, these processes are modeled using simulations that describe the electronic structure at an atomic level, thereby omitting molecular bonding effects. This work addresses the gap by introducing a novel approach that couples Auger–Meitner decay to nuclear dynamics across multiple decay steps, by developing a decay spawning dynamics algorithm and applying it to potential energy surfaces characterized with ab initio molecular dynamics simulations. We showcase the approach on a model decay cascade following K-shell ionization of IBr and subsequent Kβ fluorescence decay. We examine two competing channels that undergo two decay steps, resulting in ion pairs with a total 3+ charge state. This approach provides a continuous description of the electron transfer dynamics occurring during the multistep decay cascade and molecular fragmentation, revealing the combined inner-shell decay and charge transfer time scale to be approximately 75 fs. In conclusion, our computed kinetic energies of ion fragments show good agreement with experimental data.

Ab initio molecular dynamics↗
DOE OSTI2025

Data-driven equation-free dynamics applied to many-protein complexes: The microtubule tip relaxation

Microtubules (MTs) constitute the largest components of the eukaryotic cytoskeleton and play crucial roles in various cellular processes, including mitosis and intracellular transport. The property allowing MTs to cater to such diverse roles is attributed to dynamic instability, which is coupled to the hydrolysis of GTP (guanosine-5'-triphosphate) to GDP (guanosine-5'-diphosphate) within the β-tubulin monomers. Understanding the equilibrium dynamics and the structural features of both GDP- and GTP-complexed MT tips, especially at an all-atom level, remains challenging for both experimental and computational methods because of their dynamic nature and the prohibitive computational demands of simulating large, many-protein systems. This study employs the “equation-free” multiscale computational method to accelerate the relaxation of all-atom simulations of MT tips toward their putative equilibrium conformation. Using large MT lattice systems (14 protofilaments × 8 heterodimers) comprising ~21-38 million atoms, we applied this multiscale approach to leapfrog through time and nearly double the computational efficiency in realizing relaxed all-atom conformations of GDP- and GTP-complexed MT tips. Commencing from an initial 4 μs unbiased all-atom simulation, we interleave coarse projective “equation-free” jumps with short bursts of all-atom molecular dynamics simulation to realize an additional effective simulation time of 1.875 μs. Our 5.875 μs of effective simulation trajectories for each system expose the subtle yet essential differences in the structures of MT tips as a function of whether β-tubulin monomer is complexed with GDP or GTP, as well as the lateral interactions within the MT tip, offering a refined understanding of features underlying MT dynamic instability. Furthermore, the approach presents a robust and generalizable framework for future explorations of large biomolecular systems at atomic resolution.

Wu, Jiangbo [University of Chicago, IL (United Sta↗