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Results for “Molecular dynamics simulation”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 1,243 records · Page 69
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Hybrid interatomic potential for Sn

To design materials for extreme applications, it is important to understand and predict phase transitions and their influence on material properties under high pressures and temperatures. Atomistic modeling can be a useful tool to assess these behaviors. However, this can be difficult due to the lack of fidelity of the interatomic potentials in reproducing this high pressure and temperature extreme behavior. Here, in this work, a hybrid EAM-R—which is the combination of embedded atom method (EAM) and rapid artificial neural network potential—for Tin (Sn) is described which is capable of accurately modeling the complex sequence of phase transitions between different metallic polymorphs as a function of pressure. This hybrid approach ensures that a basic empirical potential like EAM is used as a lower energy bound. By using the final activation function, the neural network contribution to energy must be positive, assuring stability over the whole configuration space. This implementation has the capacity to reproduce density functional theory results at 6 orders of magnitude slower than a pair potential for molecular dynamics simulation, including elastic and plastic characteristics and relative energies of each phase. Using calculations of the Gibbs free energy, it is demonstrated that the potential precisely predicts the experimentally observed phase changes at temperatures and pressures across the whole phase diagram. At 10.2 GPa, the present potential predicts a first-order phase transition between body-centered tetragonal (BCT) β-Sn and another polymorph of BCT-Sn. This structure transforms into body-centered cubic near the experimentally reported value at 33 GPa. Thus, the Sn potential developed in this paper can be used to study complex deformation mechanisms under extreme conditions of high pressure and strain rates unlike existing potentials. Moreover, the framework developed in this paper can be extended for different material systems with complex phase diagrams.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Accurate Calculation of Solvation Properties of Lithium Ions in Nonaqueous Solutions

Here, we perform all-atom molecular dynamics simulations of lithium triflate in 1,2-dimethoxyethane using six different literature force fields. This system is representative of many experimental studies of lithium salts in solvents and polymers. We show that multiple historically common force fields for lithium ions give qualitatively incorrect results when compared with those from experiments and quantum chemistry calculations. We illustrate the importance of correctly selecting force field parameters and give recommendations on the force field choice for lithium electrolyte applications.

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

Mechanistic Insights on Permeation of Water over Iron Cations in Nanoporous Silicon Oxide Films for Selective H 2 and O 2 Evolution

Electrocatalysts encapsulated by an ultrathin and semipermeable oxide layer offer a promising avenue for efficient, selective, and cost-effective production of hydrogen through photoelectrochemical water splitting. This architecture is especially attractive for Z-scheme water splitting, for which a nanoporous oxide film can be leveraged to mitigate undesired, yet kinetically facile, reactions involving redox shuttles, such as aqueous iron cations, by limiting transport of these species to catalytically active sites. In this work, molecular dynamics simulations were combined with electrochemical measurements to provide a mechanistic understanding of permeation of water and Fe(III)/Fe(II) redox shuttles through nanoporous SiO 2 films. It is shown that even for SiO 2 pores with a width as small as 0.8 nm, water does not experience any energy barrier for permeating into the pores due to a favorable interaction with hydrophilic silanol groups on the oxide surface. In contrast, permeation of Fe(III) and Fe(II) into microporous SiO 2 pores is limited due to high energy barriers, which stem from a combination of distortion and dehydration of the second and third ion solvation shells. Furthermore, our simulations and experimental results show that SiO 2 coatings can effectively mitigate undesired Fe(III)/Fe(II) redox reactions at underlying electrodes by attenuating permeation of iron cations, while allowing water to permeate and thus participate in water splitting reactions. In a broader context, our study demonstrates that selectivity of solvated cations can be manipulated by controlling the pore size and surface chemistry of oxide films.

14 SOLAR ENERGY↗
DOE OSTI2022

Cryo-EM, Protein Engineering, and Simulation Enable the Development of Peptide Therapeutics against Acute Myeloid Leukemia

Cryogenic electron microscopy (cryo-EM) has emerged as a viable structural tool for molecular therapeutics development against human diseases. However, it remains a challenge to determine structures of proteins that are flexible and smaller than 30 kDa. The 11 kDa KIX domain of CREB-binding protein (CBP), a potential therapeutic target for acute myeloid leukemia and other cancers, is a protein which has defied structure-based inhibitor design. Here, we develop an experimental approach to overcome the size limitation by engineering a protein double-shell to sandwich the KIX domain between apoferritin as the inner shell and maltose-binding protein as the outer shell. To assist homogeneous orientations of the target, disulfide bonds are introduced at the target–apoferritin interface, resulting in a cryo-EM structure at 2.6 Å resolution. We used molecular dynamics simulations to design peptides that block the interaction of the KIX domain of CBP with the intrinsically disordered pKID domain of CREB. The double-shell design allows for fluorescence polarization assays confirming the binding between the KIX domain in the double-shell and these interacting peptides. Further cryo-EM analysis reveals a helix–helix interaction between a single KIX helix and the best peptide, providing a possible strategy for developments of next-generation inhibitors.

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

Amphiphile Organization in Organic Solutions: An Alternative Explanation for Small-Angle X-ray Scattering Features in Malonamide/Alkane Mixtures

In this work, the role of different intermolecular interactions in the aggregation of amphiphiles in an organic solvent is studied for systems of relevance to liquid-liquid extraction (LLE), a chemical process used to selectively recover metals from complex mixtures. Of specific interest is the role, or lack thereof, of hydrogen bonding, which is often assumed to be a main driver of the organic phase structural organization that has been linked to separation efficacy. Toward that end, a series of malonamide extractants in n-dodecane have been studied in the absence of any extracted aqueous solutes, including water. The series of extractants includes N,N'-dimethyl-N,N'-dibutyltetradecylmalonamide (DMDBTDMA), two of its homologs, and N,N'-dimethyl-N,N'-dioctylhexylethoxymalonamide (DMDOHEMA). This simplified model LLE system enables systematic investigation of the role of dipole-dipole and alkyl tail steric interactions in amphiphile aggregation. Small-angle X-ray scattering (SAXS) profiles computed from molecular dynamics trajectories are in good agreement with experimental SAXS data. Molecular dynamics simulations show that malonamide aggregation results from dipole-driven self-association and lacks characteristic aggregate sizes. Mid-q correlation peaks in the SAXS profiles emerge at high concentration for each malonamide. In those densely packed solutions, the correlation peaks are observed to result from alkyl tail-induced spacing between electron-rich polar head groups, with peak positions determined by the different alkyl tail lengths present in the malonamide molecule. This explanation of the SAXS correlation peaks contrasts with the prevailing literature, which attributes mesoscale features observed in small-angle scattering to the formation of microemulsions. Instead, this work finds that these features are present in the absence of water or any reverse micellar organization of the malonamides. As such, molecular-scale malonamide self-association and packing, rather than microemulsion-based colloidal-scale descriptions, is a more appropriate framework for these LLE systems.

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

Low-temperature carbonization of polyacrylonitrile/graphene carbon fibers: A combined ReaxFF molecular dynamics and experimental study

Graphene inclusion in a polymer matrix is a promising route to significantly enhance the mechanical properties of low-grade carbon fibers (CFs). Using ReaxFF molecular dynamics simulation, the atomistic mechanism leading to this enhancement is investigated. We demonstrate that the graphene edges along with the nitrogen and oxygen functional groups play a catalytic role and act as seeds to expedite alignment of the all-carbon rings, which are starting sites for the growth of graphitic structures. To examine the role of this proposed mechanism that enhances the graphitic structure of PAN/graphene CFs, we discuss the experimental results wherein the PAN/graphene CFs carbonized at 1250 C demonstrate 91% (from 632 to 1207 MPa) increase in strength and 101% (from 88 to 177 GPa) enhancement in Young’s modulus compared to PAN-based CFs carbonized at 1500 C. In conclusion, these enhanced mechanical properties of low-grade carbon fibers achieved via graphene inclusion at decreased carbonization temperature provide a means to realize both energy savings and cost reduction.

42 ENGINEERING↗
DOE OSTI2022

1 / ω electric-field noise in surface ion traps from correlated adsorbate dynamics

Ion traps are promising architectures for implementing quantum computers, but they suffer from excessive “anomalous” ion motional heating that limit their overall coherence and practicality for scalable quantum computing. The exact microscopic origins of anomalous heating remain an open question, but experiments point to adsorbates on trap electrodes as one likely source. Many different models of anomalous heating have been proposed, but these models have yet to pinpoint the atomistic origin of the experimentally observed 1/ω electric-field noise scaling seen in ion traps at frequencies between 0.1–10 MHz. In this work, we show that a model based on previously proposed surface-induced dipole fluctuations on adsorbates, but which also incorporates interparticle interaction dynamics through molecular dynamics simulations of up to multiple monolayers of adsorbates, gives rise to 1/ω frequency scaling at the MHz frequencies typically employed in ion traps. Overall, these results demonstrate that moderate-to-high densities of adsorbates can give rise to a set of activated motions that produce the 1/ω noise observed in ion traps and that collective adsorbate motions produce the observed noise spectra that a noninteracting model does not capture.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Colloidal Clusters and Networks Formed by Oppositely Charged Nanoparticles with Varying Stiffnesses

Colloidal clusters and gels are ubiquitous in science and technology. Particle softness has a strong effect on interparticle interactions; however, our understanding of the role of this factor in the formation of colloidal clusters and gels is only beginning to evolve. Here, we report the results of experimental and simulation studies of the impact of particle softness on the assembly of clusters and networks from mixtures of oppositely charged polymer nanoparticles (NPs). Experiments were performed below or above the polymer glass transition temperature, at which the interaction potential and adhesive forces between the NPs were significantly varied. Hard NPs assembled in fractal clusters that subsequently organized in a kinetically arrested colloidal gel, while soft NPs formed dense precipitating aggregates, due to the NP deformation and the decreased interparticle distance. Importantly, interactions of hard and soft NPs led to the formation of discrete precipitating NP aggregates at a relatively low volume fraction of soft NPs. A phenomenological model was developed for interactions of oppositely charged NPs with varying softnesses. Furthermore, the experimental results were in agreement with molecular dynamics simulations based on the model. This work provides insight on interparticle interactions before, during, and after the formation of hard–hard, hard–soft, and soft–soft contacts and has impact for numerous applications of reversible colloidal gels, including their use as inks for additive manufacturing.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2021

Anomalous fast atomic dynamics in bulk metallic glasses

It is believed that the strong glass formers tend to be dense packing and have rather slow atomic dynamics. Here, we report that the anomalous fast atomic dynamics exist in an Au 55 Cu 20 Ag 5 Si 20 metallic glass (MG) with good glass forming ability (GFA) by combining X-ray photon correlation spectroscopy measurements with ab initio molecular dynamics simulations. The fast dynamics are mainly originated from the increased mobility of Cu atoms by Ag addition. Ag atoms are inclined to locate at Cu-centered <0, 2, 8, 1> motifs, which slow or accelerate the dynamics of shell Cu atoms, depending on whether Ag atoms appear at the first shells or not, leading to the formation of structural heterogeneity at the atomic level. The results enrich the understanding of atomic dynamics in Cue-Ag-containing MGs and will trigger more studies on the dynamics-GFA relationship in MGs.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2025

Crystal nucleation rates in one-component Yukawa systems

Nucleation in the supercooled Yukawa system is relevant for addressing current challenges in understanding a range of crystallizing systems including white dwarf (WD) stars. We use both brute force and seeded molecular dynamics simulations to study homogeneous nucleation of crystals from supercooled Yukawa liquids. With our improved approach to seeded simulations, we obtain quantitative predictions of the crystal nucleation rate and cluster size distributions as a function of temperature and screening length. These quantitative results show trends towards fast nucleation with short-ranged potentials. They also indicate that for temperatures T > 0.9⁢T m , where T m is the melt temperature, classical homogeneous nucleation is too slow to initiate crystallization but transient clusters of ~100 particles should be common. As a result, we apply these general results to a typical WD model and obtain a delay of ~0.6 Gyr in the onset of crystallization that may be observable.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Exploring structural transitions at grain boundaries in Nb using a generalized embedded atom interatomic potential

The advancement in experimental techniques, like the atom probe tomography and high resolution electron microscopy, is fueling interest in studying structural transformations of grain boundaries in metal and alloys to uncover correlations between mechanical properties and solute or impurity segregation to grain boundaries. Atomistic modeling is an important tool that can pinpoint the intricate dynamics of grain boundary phase transitions, but the lack of accurate interatomic potentials needed to simulate the complex dynamics of grain boundary structural transitions and identify different metastable phases has been the bottleneck. To this end, we use niobium as a model body centered cubic (BCC) metal and develop an interatomic potential to study grain boundary phase transitions. The potential for Nb is based on a generalization of the embedded atomic method potential and has sufficient flexibility to learn complex energy landscapes using a small set of training structures. We systematically test and validate the using data from ab initio density functional theory calculations and experiments. Using this potential, we calculate energies of multiple symmetric-tilt grain boundaries spanning a wide range of misorientation angles. Additionally, we explore different metastable structures of the Σ 27(552) [$1\overline{1}0$] grain boundary and use molecular dynamic simulations to study the coexistence of metastable phases and grain boundary transitions at finite temperature.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Antitoxin control of optimal transcriptional repression in the atypical HigB–HigA toxin–antitoxin system from Proteus vulgaris

Abstract Bacterial toxin–antitoxin (TA) pairs transcriptionally autoregulate their expression via a repression/derepression mechanism in response to changing environmental conditions. The structural diversity of TA systems influences the mechanisms of transcriptional regulation. Here, we define the molecular mechanism for the plasmid-encoded HigB–HigA TA pair originally identified in a post-operative infection with antibiotic-resistant Proteus vulgaris. We determine DNA binding and promoter activity by the HigB–HigA complex supported by structural biology and molecular dynamics simulations of an elusive DNA operator–TA repressor complex. To define the optimal oligomeric TA repressor–DNA operator complex required for derepression, we engineered a dedicated trimeric HigB–HigA2 complex that represses transcription more than 26-fold as compared to the tetrameric HigB2–HigA2. These results expand the known diversity of how the HigB–HigA TA family is autoregulated.

Biochemistry & Molecular Biology↗
DOE OSTI2021

Investigation of the effect of local atomic polarization on field-enhanced ion transport in insulating binary oxides: The case of CeO 2

Over the course of more than 70 years, several theoretical models for electric field-enhanced ion diffusion in crystalline insulators have been presented. However, there is no assessment of the validity of these models despite the urge to have a correct description of field-enhanced ion diffusion in several emerging technologies. Herein, an assessment of five models was carried out by computing the field-dependent migration enthalpy ΔH mig (E) for the oxide ion in CeO 2 . The input to these models is the zero-field and zero-temperature migration pathway and/or the activation barrier obtained from an interatomic potential. ΔH mig (E) from these models was compared with reference values obtained from a set of classical molecular-dynamics simulations in the temperature range of 1000 ≤ T ≤ 1600 K and the electric field range of 0 ≤ E ≤ 30 MV/cm. It is revealed that the most successful theoretical models are those that consider local polarization effects induced in the diffusing ion itself and its vicinity. However, all the models did not account for the effect of the electric field and finite temperature on the local polarization, leading to discrepancies between the predicted and the reference ΔH mig (E), particularly at high fields. By comparing results from a rigid-ion potential and a polarizable core-shell potential, it is concluded that an intraionic polarization degree of freedom in the polarizable potential is an important factor in predicting ΔH mig (E), regardless of the field-enhanced diffusion model particularly for low to moderate field. Finally, future more accurate treatments should consider the field- and temperature-dependent interionic and intraionic local polarization effects.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Phonon-mediated lipid raft formation in biological membranes

Short-wavelength collective molecular motions, also known as phonons, have recently attracted much interest in revealing dynamic properties of biological membranes through the use of neutron and x-ray scattering, infrared and Raman spectroscopies, and molecular dynamics simulations. Experimentally detecting unique vibrational patterns such as, shear phonon excitations, viscoelastic crossovers, transverse acoustic phonon gaps, and continuous and truncated optical phonon modes in cellular membranes, to name a few, has proven non-trivial. Here, we review recent advances in liquid thermodynamics that have resulted in the development of the phonon theory of 1 liquids. The theory has important predictions regarding the shear vibrational spectra of fluids, namely the emergence of viscoelastic crossovers and transverse acoustic phonon gaps. Furthermore, we show that these vibrational patterns are common in soft (non-crystalline) materials, including, but not limited to liquids, colloids, liquid crystals (mesogens), block copolymers, and biological membranes. The existence of viscoelastic crossovers and acoustic phonon gaps define the self-diffusion properties of cellular membranes and provide a molecular picture of the transient nature of lipid rafts.1 Importantly, the timescales (picoseconds) for the formation and dissolution of transient lipid rafts match the lifetime of the formation and breakdown of interfacial water hydrogen bonds. Apart from acoustic propagating phonon modes, biological membranes can also support more energetic non-propagating optical phonon excitations, also known as standing waves or breathing modes. Importantly, optical phonons can be truncated due to the existence of finite size nanodomains made up of strongly correlated lipid-cholesterol molecular pairs. These strongly coupled molecular pairs can serve as nucleation centers for the formation of stable rafts at larger length scales, due to correlations of spontaneous fluctuations (Onsager’s regression hypothesis). Finally and importantly, molecular level viscoelastic crossovers, acoustic phonon gaps, and continuous and truncated optical phonon modes may offer insights as to how lipid-lipid and lipid-protein interactions enable biological function.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Bond clusters control rupture force limit in shear loaded histidine-Ni 2+ metal-coordinated proteins

Dynamic noncovalent interactions are pivotal to the structure and function of biological proteins and have been used in bioinspired materials for similar roles. Metal-coordination bonds, in particular, are especially tunable and enable control over static and dynamic properties when incorporated into synthetic materials. Despite growing efforts to engineer metal-coordination bonds to produce strong, tough, and self-healing materials, the systematic characterization of the exact contribution of these bonds towards mechanical strength and the effect of geometric arrangements is missing, limiting the full design potential of these bonds. In this work, we engineer the cooperative rupture of metal-coordination bonds to increase the rupture strength of metal-coordinated peptide dimers. Utilizing all-atom steered molecular dynamics simulations on idealized bidentate histidine-Ni 2+ coordinated peptides, we show that histidine-Ni 2+ bonds can rupture cooperatively in groups of two to three bonds. We find that there is a strength limit, where adding additional coordination bonds does not contribute to the additional increase in the protein rupture strength, likely due to the highly heterogeneous rupture behavior exhibited by the coordination bonds. Further, we show that this coordination bond limit is also found natural metal-coordinated biological proteins. Using these insights, we quantitatively suggest how other proteins can be rationally designed with dynamic noncovalent interactions to exhibit cooperative bond breaking behavior. Altogether, this work provides a quantitative analysis of the cooperativity and intrinsic strength limit for metal-coordination bonds with the aim of advancing clear guiding molecular principles for the mechanical design of metal-coordinated materials.

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

Machine learning interatomic potential for predicting the thermal properties of uranium nitride

We present a combined computational and experimental investigation of the thermal properties of uranium nitride (UN), focusing on the development of a machine learning interatomic potential (MLIP) using the moment tensor potential framework. The MLIP was trained on density functional theory (DFT) data and validated against various quantities including energies, forces, elastic constants, phonon dispersion, and defect formation energies, achieving excellent agreement with DFT calculations, prior experimental results, and our thermal conductivity measurement. The potential was then employed in molecular dynamics simulations to predict key thermal properties such as melting point, thermal expansion, specific heat, and lattice thermal conductivity. To further assess model accuracy, we fabricated a UN sample and performed new thermal conductivity measurements representative of single-crystal properties, which showed strong agreement with the MLIP predictions. This work confirms the reliability and predictive capability of the developed potential for determining the thermal properties of UN.

36 - MATERIALS SCIENCE↗
DOE OSTI2024

Heterogeneous flexibility can contribute to chromatin segregation in the cell nucleus

The highly and slightly condensed forms of chromatin, heterochromatin and euchromatin, respectively, segregate in the cell nucleus. Heterochromatin is more abundant in the nucleus periphery. Here, in this work, we study the mechanism of heterochromatin segregation by modeling interphase chromosomes as diblock ring copolymers confined in a rigid spherical shell using molecular dynamics simulations. In our model, heterochromatin and euchromatin are distinguished by their bending stiffnesses only, while an interaction potential between the spherical shell and chromatin is used to model lamin-associated proteins. Our simulations indicate that in the absence of attractive interactions between the nuclear shell and the chromatin, most heterochromatin segregates towards the nuclear interior due to the depletion of less flexible heterochromatin segments from the nuclear periphery. This inverted chromatin distribution, which is opposite to the conventional case with heterochromatin dominating at the periphery, is in accord with experimental observations in rod cells. This “inversion” is also found to be independent of the heterochromatin concentration and chromosome number. The chromatin distribution at the periphery found in vivo can be recovered by further increasing the bending stiffness of heterochromatin segments or by turning on attractive interactions between the nuclear shell and heterochromatin. Our results indicate that the bending stiffness of chromatin could be a contributor to chromosome organization along with differential effects of HP ⁢1⁢𝛼-driven phase segregation and of loop extruders and interactions with the nuclear envelope and topological constraints.

biomolecular & subcellular processes↗