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At least 991 records · Page 55
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Boson Fermion Nucleus Explanation for Fission Fragment Anisotropy: Monograph #13

Since 1952, anisotropy has been observed in the paths of fission fragments following the assimilation of an incident neutron or photon in the nucleus. Fission fragment flux favors certain angles relative to the path of the incident particle, constituting anisotropy. The amount of anisotropy is dependent on the energy of the incident particle. Fission fragment anisotropy can be explained by the disruption of nuclear structure combined with the requirement of a specific rotational orientation in theta and phi of that structure relative to the incident neutron or photon flux. A specific and limited area in the nucleus can assimilate the incident particle and induce upset within the structure, followed by scission and fission of the nucleus. The orientation and nature of the structure upset dictates fission fragment trajectory and is responsible for fission fragment anisotropy. This concept can be explained and supported by the theory of boson fermion nucleus (BFN) structure.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

A Quantum-Based Approach to Predict Primary Radiation Damage in Polymeric Networks

Initial atomistic-level radiation damage in chemically reactive materials is thought to induce reaction cascades that can result in undesirable degradation of macroscale properties. Ensembles of quantum-based molecular dynamics (QMD) simulations can accurately predict these cascades, but extracting chemical insights from the many underlying trajectories is a labor-intensive process that can require substantial a priori intuition. We develop here a general and automated graph-based approach to extract all chemically distinct structures sampled in QMD simulations and apply our approach to predict primary radiation damage of polydimethylsiloxane (PDMS), the main constituent of silicones. A postprocessing protocol is developed to identify underlying polymer backbone structures as connected components in QMD trajectories. Furthermore, these backbones form a repository of radiation-damaged structures. A scheme for extracting and updating a library of isomorphically distinct structures is proposed to identify the spanning set and aid chemical interpretation of the repository. The analyses are applied to ensembles of cascade QMD simulations in which the four element types in PDMS are selectively excited in primary knock-on atom events. Our approach reveals a much higher degree of combinatorial complexity in this system than was inferred through radiolysis experiments. Probabilities are extracted for radiation-induced network changes including formation of branch points, carbon linkages, cycles, bond scissions, and carbon uptake into the Si–O siloxane backbone network. The general analysis framework presented here is readily extendable to modeling chemical degradation of other polymers and molecular materials and provides a basis for future quantum-informed multiscale modeling of radiation damage.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Materials Data on Fe6P4H23O21 by Materials Project

Fe6P4(H3O7)3(H2)7 crystallizes in the monoclinic C2/c space group. The structure is three-dimensional and consists of sixteen hydrogen molecules, eight molecular hydrogen molecules, and one Fe6P4(H3O7)3 framework. In the Fe6P4(H3O7)3 framework, there are four inequivalent Fe+2.50+ sites. In the first Fe+2.50+ site, Fe+2.50+ is bonded to four O2- atoms to form distorted FeO4 tetrahedra that share corners with two FeO6 octahedra, a cornercorner with one FeO4 tetrahedra, a cornercorner with one PO4 tetrahedra, and a cornercorner with one PO4 trigonal pyramid. The corner-sharing octahedra tilt angles range from 54–63°. There are a spread of Fe–O bond distances ranging from 1.97–2.09 Å. In the second Fe+2.50+ site, Fe+2.50+ is bonded to six O2- atoms to form distorted FeO6 octahedra that share a cornercorner with one FeO4 tetrahedra, corners with two equivalent PO4 tetrahedra, corners with two equivalent PO4 trigonal pyramids, and a faceface with one FeO6 octahedra. There are a spread of Fe–O bond distances ranging from 2.00–2.29 Å. In the third Fe+2.50+ site, Fe+2.50+ is bonded to six O2- atoms to form FeO6 octahedra that share corners with two equivalent FeO4 tetrahedra, corners with four equivalent PO4 tetrahedra, and faces with two equivalent FeO6 octahedra. There are a spread of Fe–O bond distances ranging from 2.02–2.11 Å. In the fourth Fe+2.50+ site, Fe+2.50+ is bonded in a square co-planar geometry to four O2- atoms. There are two shorter (1.98 Å) and two longer (2.14 Å) Fe–O bond lengths. There are two inequivalent P1+ sites. In the first P1+ site, P1+ is bonded to four O2- atoms to form PO4 tetrahedra that share corners with four FeO6 octahedra and a cornercorner with one FeO4 tetrahedra. The corner-sharing octahedra tilt angles range from 28–57°. There are a spread of P–O bond distances ranging from 1.54–1.57 Å. In the second P1+ site, P1+ is bonded to four O2- atoms to form PO4 trigonal pyramids that share corners with two equivalent FeO6 octahedra and a cornercorner with one FeO4 tetrahedra. The corner-sharing octahedra tilt angles range from 32–61°. There are a spread of P–O bond distances ranging from 1.49–1.91 Å. There are five inequivalent H1+ sites. In the first H1+ site, H1+ is bonded in a single-bond geometry to one O2- atom. The H–O bond length is 0.98 Å. In the second H1+ site, H1+ is bonded in a single-bond geometry to one O2- atom. The H–O bond length is 0.99 Å. In the third H1+ site, H1+ is bonded in a single-bond geometry to one O2- atom. The H–O bond length is 0.97 Å. In the fourth H1+ site, H1+ is bonded in a single-bond geometry to one O2- atom. The H–O bond length is 0.98 Å. In the fifth H1+ site, H1+ is bonded in a single-bond geometry to one O2- atom. The H–O bond length is 0.99 Å. There are eleven inequivalent O2- sites. In the first O2- site, O2- is bonded in a distorted single-bond geometry to two Fe+2.50+ and one H1+ atom. In the second O2- site, O2- is bonded in a bent 120 degrees geometry to one Fe+2.50+ and one P1+ atom. In the third O2- site, O2- is bonded in a distorted single-bond geometry to three Fe+2.50+ and one H1+ atom. In the fourth O2- site, O2- is bonded in a bent 150 degrees geometry to one Fe+2.50+ and one P1+ atom. In the fifth O2- site, O2- is bonded in a distorted trigonal non-coplanar geometry to one P1+ and two H1+ atoms. In the sixth O2- site, O2- is bonded in a 3-coordinate geometry to two Fe+2.50+ and one P1+ atom. In the seventh O2- site, O2- is bonded in a distorted trigonal planar geometry to two equivalent Fe+2.50+ and one H1+ atom. In the eighth O2- site, O2- is bonded in a 3-coordinate geometry to two Fe+2.50+ and one P1+ atom. In the ninth O2- site, O2- is bonded in a bent 120 degrees geometry to one Fe+2.50+ and one P1+ atom. In the tenth O2- site, O2- is bonded in a distorted bent 150 degrees geometry to one Fe+2.50+ and one P1+ atom. In the eleventh O2- site, O2- is bonded in a bent 150 degrees geometry to one Fe+2.50+ and one P1+ atom.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Role of Capping Agents in the Synthesis of Salicylate-Capped Zinc Oxide Nanoparticles

Capping agents are often used for controlling the size, aggregation, and properties of nanoparticles. To guide the design of improved nanomaterials for targeted performance, one can use mechanistic insights into the interactions between capping agents and nanoparticles. Here, we employ density functional theory (DFT), reactive force-field molecular dynamics (ReaxFF MD) simulations, and optical spectroscopy to study the interactions between salicylate, as a model capping agent, and zinc oxide (ZnO) nanoparticles. In this work, we find that salicylate strongly interacts with the nanoparticle via the formation of O–Zn bonds in a distorted six-membered coordination ring structure. We describe the mechanisms of capping of ZnO nanoparticles by salicylate via three different binding modes. Simulations indicate that salicylate undergoes dissociative adsorption at the highly active surface Zn sites via a hydrogen-transfer process, thereby forming a tridentate configuration. The water-mediated interaction also facilitates the dissociative adsorption, leading to two salicylate O atoms coordinating with a surface Zn atom, while the other salicylate O atom bonds with another surface Zn atom. For molecular adsorption, binding free energies indicate that salicylate binds more strongly to ZnO, often in a bidentate configuration, than water does. The formation of the salicylate–ZnO complex is substantiated by UV–visible and Fourier transform infrared spectra. We find that the C=O stretching mode of salicylate becomes softened when it interacts with the nanoparticle, suggesting chemisorption of salicylate on ZnO. Although DFT predicts strong interaction between salicylate and ZnO, ReaxFF MD simulation indicates the moderate interaction between these two components in aqueous solution. Water molecules in close contact with the nanoparticle surface undergo dissociation, thus resulting in a surface hydroxyl, a reactive oxygen species that may influence the nanoparticle’s catalytic properties. Overall, the atomic-level information provided here can guide the selection process of salicylate as an appropriate agent for ZnO nanoparticle synthesis when strong interactions of particles with capping agents are required.

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

Understanding and Manipulating Counterion Condensation within Charged Polymer Electrolytes for Selective and Low Resistant Membrane Separations

Polymeric ion-exchange membranes are found at the heart of numerous electrochemical systems spanning separations (electrodialysis and membrane capacitive deionization) and energy conversion and storage (flow batteries, fuel cells, and electrolyzers). The ion-exchange membrane separators need to be ion conducting but electron insulating, and in many scenarios selective for a particular ion to conduct. Because of their polymeric nature, the molecular architectures of ion-exchange membranes lack the molecular precision found in many inorganic materials. Plus, they contain numerous structural defects that impede ionic transport. As a result of their poor structure, it has been difficult to carefully probe the underlying physics that governs ion transport in ion-exchange membranes. We investigated counterion condensation phenomena in ion-exchange membranes and correlated it to bulk ionic charge transport and selectivity in precisely defined and long-range ordered materials afforded through the principles of directed self-assembly. A multi-faceted approach spanning i.) advanced metrology, two-dimensional atomic force microscopy, x-ray scattering, and ion-exchange equilibria, and ii.) molecular simulations (classical molecular dynamics and ab-inito molecular dynamics) that bridge multiple time and length scales, were employed to correlate the extent of counterion condensation to ionic conductivity and selectivity. After uncovering the extent of the condensation phenomena in this project, new macromolecular chemistries were employed to manipulate the ion pairing interactions of the condensed counterions to tethered ions on the polymer backbone so more facile and selective conduction rates can be attained. The research has aided in the rational design of polymeric ion-exchange membrane separators with high current density for electrochemical systems and subsequently better energy efficiency.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Development of interatomic potential and effect of ordering on defect properties in CrMnV

Developing materials that can withstand extreme environments, such as high radiation doses and elevated temperatures, is crucial for next-generation particle accelerators, including the 2.4 MW Long-Baseline Neutrino Facility. High-Entropy Alloys have emerged as promising candidates for beam window materials due to their superior mechanical strength, corrosion resistance, and radiation tolerance. In this study, we focus on the Cr–Mn–V alloy system, developing and employing machine-learning interatomic potentials (MLIPs) to investigate the formation of an ordered phase and its influence on defect properties. Using hybrid Monte Carlo-Molecular Dynamics simulations, we observe the formation of a B2-ordered phase at lower temperatures, consistent with Density Functional Theory (DFT) predictions. Ordered structures display a bimodal distribution of migration energies and reduced mean square displacement values, indicating suppressed vacancy diffusion. Our results also show that the migration energy barrier varies based on the atomic species, with Mn and V exhibiting the highest and lowest average barriers, respectively. These findings suggest that atomic ordering inhibits defect mobility, potentially enhancing the radiation resistance of CrMnV alloys. The validated MLIP provides a reliable framework for simulations that are faster than traditional DFT while maintaining the accuracy required to study defect and ordering properties.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Properties of Gaseous Deprotonated L-Cysteine S-Sulfate Anion [cysS-SO3]−: Intramolecular H-Bond Network, Electron Affinity, Chemically Active Site, and Vibrational Fingerprints

L-cysteine S-sulfate, Cys-SSO3H, and their derivatives play essential roles in biological chemistry and pharmaceutical synthesis, yet their intrinsic molecular properties have not been studied to date. In this contribution, the deprotonated anion [cysS-SO3]− was introduced in the gas phase by electrospray and characterized by size-selected, cryogenic, negative ion photoelectron spectroscopy. The electron affinity of the [cysS-SO3]• radical was determined to be 4.95 ± 0.10 eV. In combination with theoretical calculations, it was found that the most stable structure of [cysS-SO3]− (S1) is stabilized via three intramolecular hydrogen bonds (HBs); i.e., one O-H……N between the -COOH and -NH2 groups, and two N-H……O HBs between -NH2 and -SO3, in which the amino group serves as both HB acceptor and donor. In addition, a nearly iso-energetic conformer (S2) with the formation of an O-H……N-H……O-S chain-type binding motif competes with S1 in the source. The most reactive site of the molecule susceptible for electrophilic attacks is the linkage S atom. Theoretically predicted infrared spectra indicate that O-H and N-H stretching modes are the fingerprint region (2800 to 3600 cm−1) to distinguish different isomers. The obtained information lays out a foundation to better understand the transformation and structure–reactivity correlation of Cys-SSO3H in biologic settings.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2020

Reversible Oxidation Quantified by Optical Properties in Epitaxial Fe2CrO4+d Films on (001) MgAl2O4

We report on the structural and optical properties of Fe2CrO4+d epitaxial films grown by molecular beam epitaxy on MgAl2O4 (001) as a function of ?. The average Fe valence can be correlated with the out-of-plane lattice parameter and the extent of light absorption in the infrared spectral region. Over-oxidized films (0 < d < 0.5) exhibit reduced lattice parameters and suppressed infrared absorption. We discuss the behavior of a novel infrared transition at ~0.6 eV in stoichiometric Fe2CrO4 films deposited on MgAl2O4 (MAO) at or above 400 °C. This research provides new insight into the atomic structure, optical processes, oxidation states, electronic structure, and application potentials of Fe2CrO4+d.

ellipsometry, Epitaxy, thin film, oxidation, reduc↗
DOE OSTI2022

Explicitly antisymmetrized neural network layers for variational Monte Carlo simulation

The combination of neural networks and quantum Monte Carlo methods has arisen as a promising path forward for highly accurate electronic structure calculations. Previous proposals have combined equivariant neural network layers with a final antisymmetric layer in order to satisfy the antisymmetry requirements of the electronic wavefunction. However, to date it is unclear if one can represent antisymmetric functions of physical interest, and it is difficult to precisely measure the expressiveness of the antisymmetric layer. Here, this work attempts to address this problem by introducing explicitly antisymmetrized universal neural network layers. This approach has a computational cost which increases factorially with respect to the system size, but we are nonetheless able to apply it to small systems to better understand how the structure of the antisymmetric layer affects its performance. We first introduce a generic antisymmetric (GA) neural network layer, which we use to replace the entire antisymmetric layer of the highly accurate ansatz known as the FermiNet. We demonstrate that the resulting FermiNet-GA architecture can yield effectively the exact ground state energy for small atoms and molecules. We then consider a factorized antisymmetric (FA) layer which more directly generalizes the FermiNet by replacing the products of determinants with products of antisymmetrized neural networks. We find, interestingly, that the resulting FermiNet-FA architecture does not significantly outperform the FermiNet. This strongly suggests that the sum of products of antisymmetries is a key limiting aspect of the FermiNet architecture. To explore this further, we investigate a slight modification of the FermiNet, called the full determinant mode, which replaces each product of determinants with a single combined determinant. We find that the full single-determinant FermiNet closes a large part of the gap between the standard single-determinant FermiNet and FermiNet-GA on small atomic and molecular problems. Surprisingly, on the nitrogen molecule at a dissociating bond length of 4.0 Bohr, the full single-determinant FermiNet can outperform the largest standard FermiNet calculation with 64 determinants.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Self-consistent implementation of locally scaled self-interaction-correction method

Recently proposed local self-interaction correction (LSIC) method is a one-electron self-interaction-correction (SIC) method that uses an iso-orbital indicator to apply the SIC at each point in space by scaling the exchange–correlation and Coulomb energy densities. The LSIC method is exact for the one-electron densities, also recovers the uniform electron gas limit of the uncorrected density functional approximation, and reduces to the well-known Perdew–Zunger SIC (PZSIC) method as a special case. This article presents the self-consistent implementation of the LSIC method using the ratio of Weizsäcker and Kohn–Sham kinetic energy densities as an iso-orbital indicator. The atomic forces as well as the forces on the Fermi-Löwdin orbitals are also implemented for the LSIC energy functional. Results show that LSIC with the simplest local spin density functional predicts atomization energies of the AE6 dataset better than some of the most widely used generalized-gradient-approximation (GGA) functional and barrier heights of the BH6 database better than some of the most widely used hybrid functionals. The LSIC method [a mean absolute error (MAE) of 0.008 Å] predicts bond lengths of a small set of molecules better than the PZSIC-LSDA (MAE 0.042 Å) and LSDA (0.011 Å). Furthermore, this work shows that accurate results can be obtained from the simplest density functional by removing the self-interaction-errors using an appropriately designed SIC method.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1986

Microwave spectrum and structure of bicyclo /1.1.1/ pentanone and comparison with several theoretical structures

The microwave spectra of five isotopic species of bicyclo (1.1.1) pentanone have been investigated. The rotational constants along with various centrifugal distortion constants for each species have been determined. From the rotational constants, a complete r(s) structure has been determined for the heavy atoms. Analysis of Stark effect measurements has shown the dipole moment to be along the a principal inertial axis with a magnitude of 3.164 (5) D. These results are compared with those obtained by four current theoretical methods: molecular mechanics (MM2), MNDO, and Hartree-Fock ab initio theory with STO-3G and 3-21G basis sets.

Mcrae, Glenn A.↗
NASA NTRS1988

Large molecules in diffuse interstellar clouds

The effects of the presence of a substantial component of large molecules on the chemistry of diffuse molecular clouds are explored, and detailed models of the zeta Persei and zeta Ophiuchi clouds are constructed. The major consequence is a reduction in the abundances of singly charged atomic species. The long-standing discrepancy between cloud densities inferred from rotational and fine-structure level populations and from the ionization balance can be resolved by postulating a fractional abundance of large molecules of 1 x 10 to the -7th for zeta Persei and 6 x 10 to the -7th for zeta Ophiuchi. If the large molecules are polycyclic aromatic hydrocarbons (PAH) containing about 50 carbon atoms, they contain 1 percent of the carbon in zeta Persei and 7 percent in zeta Ophiuchi. Other consequences of the possible presence of PAH molecules are discussed.

Lepp, S.↗
NASA NTRS2002

Assembly of Colloidal Materials Using Bioadhesive Interactions

We have pursued the use of biological crosslinking molecules of several types to make colloidal materials at relatively low volume fraction of colloidal particles. The objective is to make binary alloys of colloidal particles, made of two different colloidal particles coated with complementary biological lock-and-key binding molecules, which assemble due to the biological specificity. The long-term goal is to use low affinity lock-and-key biological interactions, so that the can anneal to form crystalline states. We have used a variety of different surface chemistries in order to make colloidal materials. Our first system involved using selectin-carbohydrate (sialyl-Lewis) interactions; this chemistry is derived from immune system. This chemical interaction is of relatively low affinity, with timescales for dissociation of several seconds. Furthermore, the adhesion mediated by these molecules can be reversed by the chelation of calcium atoms; thus assembled structures can be disassembled reversibly. Our second system employed avidin-biotin chemistry. This well-studied system is of high affinity, and is generally irreversible on a laboratory time-scale. Thus, we would expect selectin-carbohydrate interactions at high molecular density and avidin-biotin interactions to give kinetically-trapped structures; however, at low densities, we would expect significant differences in the structure and dynamics of the two materials, owing to their very different release rates. We have also begun to use a third chemistry - DNA hybridization. By attaching single stranded DNA oligonucleotide chains to beads, we can drive the assembly of colloidal materials by hybridization of complementary DNA chains. It is well known that DNA adenosine-thymine (A-T) and guanine-cytosine (G-C) bases hybridize pairwise with a Gibbs free energy change of 1.7 kcal/mol per base; thus, the energy of the assembly can be modulated by altering the number of complementary bases in the DNA chains. Using these different crosslinking molecules, we have assembled colloidal materials from different-sized colloidal particles, A and B. In the first sets of experiment, we used high densities of adhesion molecules, and 0.96 micron (A) and 5.5 micron (B) diameter particles. The high density of adhesion molecules means that the structures are kinetically trapped in nonequilibrium configurations. The structure of the suspension can be varied by changing the number ratio of the two types of colloidal particles, NA and NB, where A is the smaller particle. With carbohydrate-selectin or avidin-biotin interactions, large NA/NB leads to the formation of colloidal micelles, with the large center B particle surrounded by many smaller A particles. As the ratio NA/NB decreases, the structures become more extended, approaching the formation of macro-Rouse polymers - extended linear chains where A beads are connected with intervening small B linkers.

Hammer, Daniel A.↗
NASA NTRS1981

Quantum chemical calculation of the equilibrium structures of small metal atom clusters

The application of ab initio quantum mechanical approaches in the study of metal atom clusters requires simplifying techniques that do not compromise the reliability of the calculations. Various aspects of the implementation of the effective core potential (ECP) technique for the removal of the metal atom core electrons from the calculation were examined. The ECP molecular integral formulae were modified to bring out the shell characteristics as a first step towards fulfilling the increasing need to speed up the computation of the ECP integrals. Work on the relationships among the derivatives of the molecular integrals that extends some of the techniques pioneered by Komornicki for the calculation of the gradients of the electronic energy was completed and a formulation of the ECP approach that quite naturally unifies the various state-of-the-art "shape- and Hamiltonian-consistent" techniques was discovered.

Kahn, L. R.↗
DOE OSTI2023

Metallization and spin fluctuations in Cu-doped lead apatite

An electronic structure and magnetic properties analysis of the recently proposed Cu-doped lead apatite is performed. Here, we show that electronic structures of differently Cu-substituted structures are characterized by localized molecular Cu-O bands at or near the Fermi level. The Cu substitutions can happen at both Pb1 and Pb2 sites, leading to metallic and semiconducting systems differently. The electronic systems in these bands are highly unstable magnetically and form clusters of rigidly ferromagnetically coupled magnetic moments on Cu and neighboring oxygen atoms with a total moment of about 1µ B . The ground state of uniformly Cu-doped lead apatite appears to be magnetic and semiconducting. The nonuniform distribution of two Cu atoms at the nearest Pb2 sites leads to an antiferromagnetic semiconducting state with formation energy close to uniformly distributed Cu configurations. The inclusion of quantum spin fluctuations confirms the stability of magnetic Cu-O clusters. Our calculations revealed the absence of the long-range magnetic order between uniformly distributed Cu-O clusters, creating the spin glass type of system.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Coarse-grained simulation of colloidal self-assembly, cation exchange, and rheology in Na/Ca smectite clay gels

Knowledge Gap: The aggregation of clay minerals—layered silicate nanoparticles—strongly impacts fluid flow, solute migration, and solid mechanics in soils, sediments, and sedimentary rocks. Experimental and computational characterization of clay aggregation is inhibited by the delicate water-mediated nature of clay colloidal interactions and by the range of spatial scales involved, from 1 nm thick platelets to flocs with dimensions up to micrometers or more. Simulations: Using a new coarse-grained molecular dynamics (CGMD) approach, we predicted the microstructure, dynamics, and rheology of hydrated smectite (more precisely, montmorillonite) clay gels containing up to 2,000 clay platelets on length scales up to 0.1 μm. Further, simulations investigated the impact of simulation time, platelet diameters (6 to 25nm), and the ratio of Na to Ca exchangeable cations on the assembly of tactoids (i.e., stacks of parallel clay platelets) and larger aggregates (i.e., assemblages of tactoids). We analyzed structural features including tactoid size and size distribution, basal spacing, counterion distribution in the electrical double layer, clay association modes, and the rheological properties of smectite gels. Findings: Our results demonstrate new potential to characterize and understand clay aggregation in dilute suspensions and gels on a scale of thousands of particles with explicit representation of counterion clouds and with accuracy approaching that of all-atom molecular dynamics (MD) simulations. For example, our simulations predict the strong impact of Na/Ca ratio on clay tactoid formation and the shear-thinning rheology of clay gels.

42 ENGINEERING↗
DOE OSTI2021

CHARMM-GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field

Explicit treatment of electronic polarizability in empirical force fields (FFs) represents an extension over a traditional additive or pairwise FF and provides a more realistic model of the variations in electronic structure in condensed phase, macromolecular simulations. To facilitate utilization of the polarizable FF based on the classical Drude oscillator model, Drude Prepper has been developed in CHARMM-GUI. Drude Prepper ingests additive CHARMM protein structures file (PSF) and pre-equilibrated coordinates in CHARMM, PDB, or NAMD format, from which the molecular components of the system are identified. These include all residues and patches connecting those residues along with water, ions, and other solute molecules. This information is then used to construct the Drude FF-based PSF using molecular generation capabilities in CHARMM, followed by minimization and equilibration. In addition, inputs are generated for molecular dynamics (MD) simulations using CHARMM, GROMACS, NAMD, and OpenMM. Validation of the Drude Prepper protocol and inputs is performed through conversion and MD simulations of various heterogeneous systems that include proteins, nucleic acids, lipids, polysaccharides, and atomic ions using the aforementioned simulation packages. Stable simulations are obtained in all studied systems, including 5 μs simulation of ubiquitin, verifying the integrity of the generated Drude PSFs. Additionally, the ability of the Drude FF to model variations in electronic structure is shown through dipole moment analysis in selected systems. Finally, the capabilities and availability of Drude Prepper in CHARMM-GUI is anticipated to greatly facilitate the application of the Drude FF to a range of condensed phase, macromolecular systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Effect of interfacial structures on phonon transport across atomically precise Si/Al heterojunctions

Phonons are important carriers of energy and information in many cryogenic devices used for quantum information science and in fundamental physics experiments such as dark matter detectors. In these systems phonon behavior can be dominated by interfaces, hence there is increasing demand for a more detailed understanding of interfacial phonon transport in relevant material systems. Previous studies have focused on understanding thermal transport over the entire phonon spectrum at and above room temperature. At ultra-low temperatures, however, knowledge is missing regarding athermal phonon behavior due to the challenge in modeling the extreme conditions in micro-scale, heterogeneous cryogenic systems, as well as extracting single-phonon information from a large ensemble. In this work, we delineate interfacial phonon transport using a combination of classical molecular dynamics (MD) and phonon wave packet simulations, to illustrate the consistency and differences between the ensemble- and single-phonon dynamics. We consider three single-crystal Si surface reconstructions --- (1×1), (v3×v3) and (7×7) --- and model both experimentally observed Si(1×1)/Al interfaces and hypothesized Si(v3×v3)/Al and Si(7×7)/Al interfaces. The overall interfacial thermal conductance calculated from non-equilibrium MD shows that for the Si(1×1)/Al system, the presence of Al twin grain boundaries can hinder phonon transport and reduce thermal conductance by 2--12% relative to single-crystal Al; whereas the Si (v3×v3) and (7×7) reconstructions can enhance it by 6--19%. Normal mode decomposition reveals that both the increase and decrease in conductance are related to inelastic phonon scattering. Single-phonon wave packet simulations show results consistent with NEMD, while further suggesting that phonon polarization conversion is significant even when elastic transmission dominates, and that the interfacial structures have anisotropic impacts on atomic vibrations along different lattice directions. Our findings suggest alternative perspectives in achieving selective phonon transport through controlling interfacial structures of materials with atomically-precise fabrication techniques, and that the phonon wave packet formalism is a potentially powerful method for developing a detailed understanding of non-equilibrium phenomena in the low-temperature limit.

Lu, Zexi↗