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DOE OSTI2023

Ab initio studies of the impact of the Debye-Waller factor on the structural and dynamical properties of amorphous semiconductors: The case of a-Si

This paper presents a first-principles study of the Debye-Waller factor and the Debye temperature for amorphous silicon (a-Si) from lattice-dynamical calculations and direct molecular-dynamics simulations using density-functional theory (DFT). The effects of temperature and structural disorder on the intensity of the diffraction maxima and the vibrational mean-square displacement (MSD) of Si atoms are studied in the harmonic approximation, with particular emphasis on the bond-length disorder, the presence of coordination defects, and microvoids in a-Si networks. It has been observed that the MSDs associated with tetrahedrally-bonded Si atoms are considerably lower than their dangling-bond counterparts – originating from isolated and vacancy-induced clustered defects – and those on the surface of microvoids, leading to an asymmetric non-gaussian tail in the distribution of atomic displacements. An examination of the effect of anharmonicity on the MSD at high temperatures using direct ab initio molecular-dynamics simulations (without the harmonic approximation) suggests that the vibrational motion in a-Si is practically unaffected by anharmonic effects at temperatures below 400 K, as far as the present DFT calculations are concerned. The Debye temperature of a-Si is found to be in the range of 488–541 K from specific-heat and MSD calculations using first-principles lattice-dynamical calculations in the harmonic approximation, which matches closely with the experimental value of 487–528 K obtained from specific-heat measurements of a-Si at low temperatures.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Simulation-based methodology to assess the lattice defects creation as energy storing process

In nuclear industry, damages caused to in-core structural materials by high-energy neutrons have been studied for years. Recently, the possibility of storing energy through the creation of defects in crystalline materials via heavy particle bombardment was investigated. To evaluate the potential of the Wigner effect as energy-storing process, a graphite-moderated Molten Salt Reactor was adopted as a test case. Neutronics simulations performed with OpenMC Monte Carlo code allowed estimating the amount of energy released during fission events, the fraction that is deposited in graphite, and the fraction that has the potential to cause radiation damages. Additionally, molecular dynamics simulations were then performed to study the evolution of cascades triggered by high-energy neutrons. As a major outcome, a more accurate estimate of the radiation damage with respect to the traditional approaches was obtained, and the fraction of the deposited neutron energy that can be stored through long-lived defects was quantified.

25 ENERGY STORAGE↗

DOE OSTI2024

Fingerprinting Interactions between Proteins and Ligands for Facilitating Machine Learning in Drug Discovery

Molecular recognition is fundamental in biology, underpinning intricate processes through specific protein–ligand interactions. This understanding is pivotal in drug discovery, yet traditional experimental methods face limitations in exploring the vast chemical space. Computational approaches, notably quantitative structure–activity/property relationship analysis, have gained prominence. Molecular fingerprints encode molecular structures and serve as property profiles, which are essential in drug discovery. While two-dimensional (2D) fingerprints are commonly used, three-dimensional (3D) structural interaction fingerprints offer enhanced structural features specific to target proteins. Machine learning models trained on interaction fingerprints enable precise binding prediction. Recent focus has shifted to structure-based predictive modeling, with machine-learning scoring functions excelling due to feature engineering guided by key interactions. Notably, 3D interaction fingerprints are gaining ground due to their robustness. Various structural interaction fingerprints have been developed and used in drug discovery, each with unique capabilities. This review recapitulates the developed structural interaction fingerprints and provides two case studies to illustrate the power of interaction fingerprint-driven machine learning. The first elucidates structure–activity relationships in β2 adrenoceptor ligands, demonstrating the ability to differentiate agonists and antagonists. The second employs a retrosynthesis-based pre-trained molecular representation to predict protein–ligand dissociation rates, offering insights into binding kinetics. Despite remarkable progress, challenges persist in interpreting complex machine learning models built on 3D fingerprints, emphasizing the need for strategies to make predictions interpretable. Binding site plasticity and induced fit effects pose additional complexities. Interaction fingerprints are promising but require continued research to harness their full potential.

3D structural interaction fingerprints↗

DOE OSTI2024

Ab initio generalized Langevin equation

We introduce a machine learning–based approach called ab initio generalized Langevin equation (AIGLE) to model the dynamics of slow collective variables (CVs) in materials and molecules. In this scheme, the parameters are learned from atomistic simulations based on ab initio quantum mechanical models. Force field, memory kernel, and noise generator are constructed in the context of the Mori–Zwanzig formalism, under the constraint of the fluctuation–dissipation theorem. Combined with deep potential molecular dynamics and electronic density functional theory, this approach opens the way to multiscale modeling in a variety of situations. Here, we demonstrate this capability with a study of two mesoscale processes in crystalline lead titanate, namely the field-driven dynamics of a planar ferroelectric domain wall, and the dynamics of an extensive lattice of coarse-grained electric dipoles. In the first case, AIGLE extends the reach of ab initio simulations to a regime of noise-driven motions not accessible to molecular dynamics. In the second case, AIGLE deals with an extensive set of CVs by adopting a local approximation for the memory kernel and retaining only short-range noise correlations. The scheme is computationally more efficient than molecular dynamics by several orders of magnitude and mimics the microscopic dynamics at low frequencies where it reproduces accurately the dominant far-infrared absorption frequency.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Different Enzyme Conformations Induce Different Mechanistic Traits in HIV‐1 Protease

Abstract The influence of the dynamical flexibility of enzymes on reaction mechanisms is a cornerstone in biological sciences. In this study, we aim to 1) study the convergence of the activation free energy by using the first step of the reaction catalysed by HIV‐1 protease as a case study, and 2) provide further evidence for a mechanistic divergence in this enzyme, as two different reaction pathways were seen to contribute to this step. We used quantum mechanics/molecular mechanics molecular dynamics simulations, on four different initial conformations that led to different barriers in a previous study. Despite the sampling, the four activation free energies still spanned a range of 5.0 kcal ⋅ mol −1 . Furthermore, the new simulations did confirm the occurrence of an unusual mechanistic divergence, with two different mechanistic pathways displaying equivalent barriers. An active‐site water molecule is proposed to influence the mechanistic pathway.

Coimbra, João T. S.↗

DOE OSTI2021

Vibronic Coupling and Exciton Chirality: Electronic and Structural Rearrangement between Helical to Zero Momentum Molecular Exciton States

Helical porphyrin aggregates are attractive macromolecular nanostructures for biomimetic light-harvesting and energy transfer in solar energy technology due to their large light absorbing cross sections and promising energy conservation benefits from chiral-induced spin selectivity. However, with these soft materials, it is imperative that we understand how the nuclear degrees of freedom impact the excitonic energy landscape and dynamics, particularly pertaining to how it influences the chiral angular momentum of the excitons. To this end, we have measured time-resolved depolarization ratios using femtosecond stimulated Raman spectroscopy to uncover the vibronic coupling guided by molecular vibrations between excitons of different angular momentum in helical tetra(sulfonatophenyl)porphyrin aggregates. We find that while transient absorption anisotropy reveals rapid (1 ps lifetime) exciton rotation from helical to achiral states in the Q-band, time-resolved vibrational depolarization ratios evolve on remarkably faster time scales (<500 fs lifetime) for the totally symmetric 1530 cm –1 vibration and the nontotally symmetric 1540 cm –1 vibration. The time-resolved depolarization ratios of the 1540 cm –1 vibration, in particular, show strong evidence of vibronic coupling and nonadiabatic exciton behavior that mediates the nonradiative transition between chiral and achiral excitons. Furthermore, our study shows that for rational design of helical molecular aggregates for exciton transport, the vibronic coupling between excitons of different angular momenta driven by molecular vibrations must be considered especially in the case where chiral-induced spin selectivity is desired.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Challenges in the study of chemistry and photochemistry at air–water interfaces: Toward in situ monitoring of reaction kinetics with spectroscopic techniques

Air–water interfaces, including those on droplet surfaces, have been the subject of many recent experiments due to their propensity for unique chemistry. Here, in this study, an overview of some recent advancements in understanding interfacial reaction kinetics is provided, highlighting non-surface-specific methods—such as mass spectrometry—compared with the advantages of surface-specific techniques—such as reflection–absorption spectroscopy, sum frequency generation, and photoelectron spectroscopy. This Perspective discusses the information depth and time constraints of common surface-specific spectroscopic methods that need to be addressed to monitor interfacial chemistry in situ and uses a few key examples from the literature as case studies. It concludes by advocating for the continued development of advanced spectroscopic methods to further investigate interfacial chemistry, underscoring the need for interdisciplinary collaboration to bridge the gap between molecular-level insights and macroscopic observations in future research.

Air-water interface↗

DOE OSTI2021

Development of Martini 2.2 parameters for N -glycans: a case study of the HIV-1 Env glycoprotein dynamics

N-linked glycans are ubiquitous in nature and play key roles in biology. For example, glycosylation of pathogenic proteins is a common immune evasive mechanism, hampering the development of successful vaccines. Due to their chemical variability and complex dynamics, an accurate molecular understanding of glycans is still limited by the lack of effective resolution of current experimental approaches. Here, we have developed and implemented a reductive model based on the popular Martini 2.2 coarse-grained force field for the computational study of N-glycosylation. We used the HIV-1 Env as a direct applied example of a highly glycosylated protein. Finally, our results indicate that the model not only reproduces many observables in very good agreement with a fully atomistic force field but also can be extended to study large amount of glycosylation variants, a fundamental property that can aid in the development of drugs and vaccines.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Static and dynamic properties of multi-ionic plasma mixtures

Complex plasma mixtures with three or more components are often encountered in astrophysics or in inertial confinement fusion (ICF) experiments. For mixtures containing species with large differences in atomic number Z, the modeling needs to consider at the same time the kinetic theory for low-Z elements combined with the theory of strongly coupled plasma for high-Z elements, as well as all the intermediate situations that can appear in multi-component systems. For such cases, we study the pair distribution functions, self-diffusions, mutual diffusion and viscosity for ternary mixtures at extreme conditions. These quantities can be produced from first principles using orbital free molecular dynamics at the computational expense of very intensive simulations to reach good statistics. Utilizing the first-principles results as reference data, we assess the merit of a global analytic model for transport coefficients, "Pseudo-Ions in Jellium" (PIJ), based on an iso-electronic assumption (iso-n e ). With a multi-component hypernetted-chain integral equation, we verify the quality of the iso-n e prescription for describing the static structure of the mixtures. This semi-analytical modeling compares well with the simulation results and allows one to consider plasma mixtures not accessible to simulations. Further, applications are given for the mix of materials in ICF experiments. A reduction of a multicomponent mixture to an effective binary mixture is also established in the hydrodynamic limit and compared with PIJ estimations for ICF relevant mixtures.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2020

Effect of the orientation of Rydberg atoms on their collisional ionization cross section

Collisional ionization between two Rydberg atoms in relative motion is examined. A classical trajectory Monte Carlo method is used to determine the cross sections associated with Penning ionization. The dependence of the ionization cross section on the magnitude and the direction of orbital angular momentum of the electrons and the direction of the Laplace-Runge-Lenz vector of the electrons is studied. For a given magnitude of angular momentum, there can exist a difference of a factor of up to ~2.5 in the ionization cross section between the orientations with the highest and the lowest ionization cross section. As a result, the case of exchange ionization is examined and its dependence on the magnitude of angular momentum is studied.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2023

Genomic Mysteries of Giant Bacteria: Insights and Implications

Bacteria and Archaea are traditionally regarded as organisms with a simple morphology constrained to a size of 2–3 µm. Nevertheless, the history of microbial research is rich in the description of giant bacteria exceeding tens and even hundreds of micrometers in length or diameter already from its early days, for example, Beggiatoa spp., to the present, for example, Candidatus Thiomargarita magnifica. While some of these giants are still being studied, some were lost to science, with merely drawings and photomicrographs as evidence for their existence. The physiology and biogeochemical role of giant bacteria have been studied, with a large focus on those involved in the sulfur cycle. With the onset of the genomic era, no special emphasis has been given to this group, in an attempt to gain a novel, evolutionary, and molecular understanding of the phenomenon of bacterial gigantism. The few existing genomic studies reveal a mysterious world of hyperpolyploid bacteria with hundreds to hundreds of thousands of chromosomes that are, in some cases, identical and in others, extremely different. These studies on giant bacteria reveal novel organelles, cellular compartmentalization, and novel mechanisms to combat the accumulation of deleterious mutations in polyploid bacteria. In this perspective paper, we provide a brief overview of what is known about the genomics of giant bacteria and build on that to highlight a few burning questions that await to be addressed.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Surface Wettability Analysis from Adsorption Energy and Surface Electrical Charge

Surface wettability is determined by the attraction of a liquid phase to a solid surface. It is typically quantified by using contact angle measurements at mineral surfaces in the case of the flotation of mineral particles. Contact angle research to describe wettability has been investigated at different scales by sessile drop measurements, molecular dynamic simulation, and atomic force microscopy. In this study, the density functional theory (DFT) was employed for predicting the surface free energy and contact angles of a well-known hydrophobic phyllosilicate mineral talc and a well-known hydrophilic phyllosilicate mineral muscovite based on the calculated interfacial energy and surface charge. The results revealed that the predicted contact angle at the atomic scale was larger than the experimental value, and identified two interactions: electrostatic interaction and hydrogen bonding, between the hydrophilic muscovite surface and the water layer, while a water-exclusion zone of 3.346 Å was found between the hydrophobic talc surface and the first water layer. This investigation gives a new perspective for wettability determination at the atomic scale.

Geochemistry & Geophysics↗

DOE OSTI2020

Exploring the Role of Inorganic and Organic Interfaces on CO 2 and CH 4 Partitioning: Case Study of Silica, Illite, Calcite, and Kerogen Nanopores on Gas Adsorption and Nanoscale Transport Behaviors

The adsorption, partitioning, and diffusion of CO 2 and CH 4 in organic–inorganic pores composed of kerogen with silica, illite, or calcite are studied using density functional theory and classical molecular dynamics simulations. The adsorption and partitioning behavior of CO 2 and CH 4 molecules is found to be a function of chemistry of the solid interface, pore size, and surface area. CO 2 molecules are preferentially adsorbed compared to CH 4 molecules on silica, illite, calcite, and kerogen surfaces due to significant contributions of electrostatic interactions with the atoms of the associated surfaces. CO 2 and CH 4 molecules display higher adsorption energy on calcite and silica compared to those on illite and kerogen because of enhanced interactions with the positively charged calcium ions on the calcite surface and the hydroxyl group (-OH) on the silica surface. Enhanced internal nanopores and the availability of adsorption active sites in illite and kerogen matrices aid in higher partitioning of the gas molecules into these pores. CO 2 has a significant influence on the clustering and swelling of kerogen fragments compared to CH 4 . Higher CO 2 adsorption on inorganic and kerogen surfaces results in lower overall self-diffusivities compared to CH 4 . This study illustrates surface and pore size controls on the adsorption, partitioning, and self-diffusivities of CO 2 and CH 4 at conditions relevant for subsurface energy applications. The chemistry of the surfaces along with the availability of internal pores and active adsorption sites influences the adsorption behavior of gases. Our results suggest that CO 2 stored in depleted gas reservoirs may preferentially inhabit nanoconfined pores.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Beryllium-driven structural evolution at the divertor surface

Erosion of the beryllium first wall material in tokamak reactors has been shown to result in transport and deposition on the tungsten divertor. Experimental studies of beryllium implantation in tungsten indicate that mixed W–Be intermetallic deposits can form, which have lower melting temperatures than tungsten and can trap tritium at higher rates. To better understand the formation and growth rate of these intermetallics, we performed cumulative molecular dynamics (MD) simulations of both high and low energy beryllium deposition in tungsten. In both cases, a W–Be mixed material layer (MML) emerged at the surface within several nanoseconds, either through energetic implantation or a thermally-activated exchange mechanism, respectively. While some ordering of the material into intermetallics occurred, fully ordered structures did not emerge from the deposition simulations. Targeted MD simulations of the MML to further study the rate of Be diffusion and intermetallic growth rates indicate that for both cases, the gradual re-structuring of the material into an ordered intermetallic layer is beyond accessible MD time scales(≤1 μs). However, the rapid formation of the MML within nanoseconds indicates that beryllium deposition can influence other plasma species interactions at the surface and begin to alter the tungsten material properties. Therefore, beryllium deposition on the divertor surface, even in small amounts, is likely to cause significant changes in plasma-surface interactions and will need to be considered in future studies.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2021

Evaluation of overtime phenotypic variation of yeasts in chronic vulvovaginal candidosis cases

Abstract Chronic vulvovaginal candidosis results either from reinfection or from the ability of Candida spp. to persist in the vulva and/or vagina. Persistence is usually associated with increased antifungal (mainly azoles) resistance rates, which can explain treatment failure, and/or increased expression of virulence factors by Candida spp. The aim of this study was to assess the mechanisms leading to Candida spp persistence, by studying sequential isolates from women with chronic vulvovaginal candidosis, focusing on strains genotypes, azole resistance, and ability to form biofilms along the period of clinical evaluation. The strains were identified at species level by automated analysis of biochemical profiles and molecular typing evaluated by polymorphic DNA analysis. The capacity to form biofilm was assessed with a microtiter plate assay. Fluconazole susceptibility was determined by the microdilution broth assay at both pH 7 (following the recommended guideline) and pH 4.5 (as representative of vaginal pH). We studied samples from 17 clinically recurrent cases. In 53% of the chronic cases there were two or more isolates that had a phylogenetic relationship while the remaining (47%) were caused by different species. In those cases where related strains were involved in recurrence, we verified an increase in MIC at pH 7 and also an increased capacity to form biofilms over time. Significant correlation between these two parameters was observed only in cases caused by C. glabrata, evidencing the importance of these two factors to enhance persistence in the vaginal mucosa for this particular species.

Faria-Gonçalves, Paula↗

DOE OSTI2022

Structural evolution in Au- and Pd-based metallic glass forming liquids and the case for improved molecular dynamics force fields

The results of a combined experimental and computational investigation of the structural evolution of Au 81 Si 19 , Pd 82 Si 18 , and Pd 77 Cu 6 Si 17 metallic glass forming liquids are presented. Electrostatically levitated metallic liquids are prepared, and synchrotron x-ray scattering studies are combined with embedded atom method molecular dynamics simulations to probe the distribution of relevant structural units. Metal–metalloid based metallic glass forming systems are an extremely important class of materials with varied glass forming ability and mechanical processibility. High quality experimental x-ray scattering data are in poor agreement with the data from the molecular dynamics simulations, demonstrating the need for improved interatomic potentials. The first peak in the x-ray static structure factor in Pd 77 Cu 6 Si 17 displays evidence for a Curie–Weiss type behavior but also a peak in the effective Curie temperature. In conclusion, a proposed order parameter distinguishing glass forming ability, 1/(S(T,q 1 )−1, shows a peak in the effective Curie temperature near a crossover temperature established by the behavior of the viscosity, T A .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

Direct Ab Initio Simulation of the Synthesis of BaZrO 3 and the Microstructure Impacts on Proton Transport

Controlling and predicting the processing-structure-performance relationship in functional materials is a grand challenge in materials science, with important implications for a wide range of emerging applications; a high fidelity understanding of the performance impact of microstructures formed under synthesis conditions is required to develop advanced materials, such as solid-state fuel cells and electrolyzers. Using the ceramic BaZrO 3 as a case study, we directly simulate the synthesis and investigate how proton transport is dictated by microstructures. We develop a framework that couples density functional theory (DFT), machine-learning interatomic potential (MLIP) driven molecular dynamics, and grand canonical Monte Carlo to perform large-scale, microstructure-resolved, atomistic simulations of proton transport in experimentally representative polycrystalline structures. Our fully ab initio approach, using a MLIP as a proxy for DFT, allows us to quantify the competition between two distinct diffusion mechanisms: one associated with grain-boundary regions and another within grains. When the impacts of grain boundaries are taken into account, proton transport exhibits substantial deviation from the bulk oxide limit. This addresses long-standing discrepancies between theory and experiments. Our integrated approach provides atomistic insight into microstructure-dependent proton pathways in BaZrO 3 and establishes a general protocol for predicting processing-structure-performance relationships.

organic↗

DOE OSTI2022

Analysis of vibronic coupling in a 4f molecular magnet with FIRMS

Vibronic coupling, the interaction between molecular vibrations and electronic states, is a fundamental effect that profoundly affects chemical processes. In the case of molecular magnetic materials, vibronic, or spin-phonon, coupling leads to magnetic relaxation, which equates to loss of magnetic memory and loss of phase coherence in molecular magnets and qubits, respectively. The study of vibronic coupling is challenging, and most experimental evidence is indirect. Here we employ far-infrared magnetospectroscopy to directly probe vibronic transitions in [Yb(trensal)] (where H 3 trensal = 2,2,2-tris(salicylideneimino)trimethylamine). We find intense signals near electronic states, which we show arise due to an “envelope effect” in the vibronic coupling Hamiltonian, which we calculate fully ab initio to simulate the spectra. We subsequently show that vibronic coupling is strongest for vibrational modes that simultaneously distort the first coordination sphere and break the C 3 symmetry of the molecule. With this knowledge, vibrational modes could be identified and engineered to shift their energy towards or away from particular electronic states to alter their impact. Hence, these findings provide new insights towards developing general guidelines for the control of vibronic coupling in molecules.

36 MATERIALS SCIENCE↗