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

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At least 343 records · Page 19
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Density Functional Theory Study of the Adsorption and Dissociation of Copper(I) Acetamidinates on Ni(110): The Effect of the Substrate

In order to assess the role of a metal substrates on the thermal chemistry of adsorbed acetamidinate metalorganic compounds, we have studied the surface chemistry of copper(I)–N,N'-dimethylacetamidinate on Ni(110) using density functional theory and contrasted it with similar calculations we previously carried out on Cu(110). At low coverages, it was found that, in its most stable configuration, the molecular adsorption of copper(I)–N,N'-dimethylacetamidinate dimers occurs with the Cu atoms occupying surface hollow sites. In this work, the ligands reorient away from those metal centers, and the N atoms develop new direct bonds with surface Ni atoms. However, this configuration is not stable and decomposes by losing both ligands to the surface. In the final state, the two ligands bind via their N atoms to Ni sites one lattice space away from the sites where the Cu atoms remain, with their molecular planes perpendicular to that of the surface. This is in contrast with what happens in the case of adsorption on Cu(110), where the Cu atoms from the metalorganic complex still occupy hollow sites but where only one of the ligands breaks away and binds directly to the surface; the other remains on top of the two Cu ions. In terms of the energetics of adsorption and decomposition, the reactions on Ni(110) are much more exothermic than on Cu(110). Further analysis of the distribution of charge within the adsorbates shows a minor reduction of the Cu atoms of the dimer upon interaction with the surface; full reduction to metallic copper is complete only when both ligands have fully migrated to their new Ni surface sites.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Mechanistic study of chemical looping reactions between solid carbon fuels and CuO

Copper (Cu) based chemical-looping combustion (CLC) is a promising process that utilizes solid carbon fuel such as coal and biomass. Understanding the reaction kinetics in this process can facilitate the industrial design of CLC units. Here, in this work, molecular dynamics (MD) simulations were performed to investigate the reaction kinetics of n-butane and two simplified solid carbon fuels (lignite and anthracite) with/without copper oxide (CuO) nanoparticle. In addition, experiments were conducted on the thermal characteristics, flammability, and flame speeds of CuO and solid carbon mixtures. For n-butane, oxidation on the CuO surface is the primary reaction since the activation energy of the surface reaction is much lower than that of oxygen (O 2 ) combustion (9.2 vs. 53.3 kcal/mol). On the other hand, for lignite, there is a smaller difference in the activation energy of O 2 combustion and surface reaction (23.04 vs. 6.34 kcal/mol). We hypothesize that some solid carbon fuels can have different reaction kinetics dependent upon temperature. This is proven by the case of a simplified anthracite coal: an Arrhenius plot shows that this solid carbon fuel has two different reaction kinetic regimes and the critical temperature for the change in kinetics is related to the oxygen uncoupling of the CuO nanoparticle. Like the modeling simulations, a change in activation energy is observed in the experimental results, where desorption of molecular oxygen from CuO becomes important.

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

Statistically Driven Metabolite and Lipid Profiling of Patients from the Undiagnosed Diseases Network

Advancements in molecular separations coupled with mass spectrometry have enabled large-scale metabolome analyses for clinical cohorts. A population of interest for metabolome profiling are patients with rare disease for which abnormal metabolic signatures may yield clues into the genetic bases, as well as mechanistic drivers of the disease and possible treatment options. We undertook the metabolome profiling of a large cohort of patients with mysterious conditions characterized through the Un-diagnosed Diseases Network (UDN). Due to the size and enrollment procedures, collection of the metabolomes for UDN pa-tients took place over three years. We describe the study design to adjust for measurements collected over a long time-scale and how this enabled statistical analyses to summarize the metabolome of individual patients. We demonstrate the removal of time-based batch effects, overall statistical characteristics of the UDN population, and two case-studies of interest that demonstrate the utility of metabolome profiling for rare diseases.

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

A [CoSiH 2 ] Silylene Synthon Provides Modular Access to Homo- and Heterobimetallic [Co=Si=M] (M = Co, Fe) Silicide Complexes

Base-stabilized [BP 3 iPr ](H) 2 CoSiH 2 (DMAP) (1, [BP 3 iPr ] = PhB(CH 2 P i Pr 2 ) 3 – ; DMAP = 4-dimethylaminopyridine) is a rare instance of a synthon for the simplest “parent” silylene complex (LM=SiH 2 ). Complex 1 was accessed in high yields via double Si–H bond activation in SiH 4 by [BP 3 iPr ]Co(DMAP), and in solution, it undergoes rapid exchange between bound and free DMAP by an associative mechanism (as determined by variable-temperature 1 H NMR dynamic studies). The DMAP ligand of 1 is readily displaced by metal-based fragments that bind silicon and cleave the Si–H bonds of the SiH 2 moiety to produce bimetallic [Co=Si=M] (M = Co, Fe) molecular silicides. Thus, treatment of 1 with 0.5 equiv of (LCo I ) 2 (μ-N 2 ) (L = a tripodal ligand) resulted in the spontaneous formation of [BP 3 iPr ](H) 2 Co=Si=Co(H) 2 L (L = [BP 2 tBu Pz], PhB(CH 2 P t Bu 2 ) 2 (pyrazolyl) - (3); Tp", HB(3,5-diisopropylpyrazolyl) 3 – (4)) with the concomitant release of DMAP. The symmetrical silicide [BP 3 iPr ](H) 2 Co=Si=Co(H) 2 [BP 3 iPr ] (5) was prepared by treatment of a mixture of 1 and [BP 3 iPr ]Co(DMAP) with 2 equiv of Ph 3 B, which in this case is required to sequester DMAP as the elimination product Ph 3 B-DMAP. A heterobimetallic silicide, [BP 3 iPr ](H) 2 Co=Si=Fe(H) 2 [SiP 3 iPr ] (7; [SiP 3 iPr ] = PhSi(CH 2 P i Pr 2 ) 3 ), was obtained via in situ KC 8 reduction of [SiP 3 iPr ]FeCl and subsequent addition of 1 and Ph 3 B. These transformations involving a metal–SiH 2 derivative demonstrate a fundamentally new type of reactivity for silylene complexes and provide a unique synthetic method for construction of molecular silicide complexes.

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

Reinforcement learning in discrete action space applied to inverse defect design

Abstract Reinforcement learning (RL) algorithms that include Monte Carlo Tree Search (MCTS) have found tremendous success in computer games such as Go, Shiga and Chess. Such learning algorithms have demonstrated super-human capabilities in navigating through an exhaustive discrete action search space. Motivated by their success in computer games, we demonstrate that RL can be applied to inverse materials design problems. We deploy RL for a representative case of the optimal atomic scale inverse design of extended defects via rearrangement of chalcogen (e.g. S) vacancies in 2D transition metal dichalcogenides (e.g. MoS 2 ). These defect rearrangements and their dynamics are important from the perspective of tunable phase transition in 2D materials i.e. 2H (semi-conducting) to 1T (metallic) in MoS 2 . We demonstrate the ability of MCTS interfaced with a reactive molecular dynamics simulator to efficiently sample the defect phase space and perform inverse design—starting from randomly distributed S vacancies, the optimal defect rearrangement of defects corresponds a line defect of S vacancies. We compare MCTS performance with evolutionary optimization i.e. genetic algorithms and show that MCTS converges to a better optimal solution (lower objective) and in fewer evaluations compared to GA. We also comprehensively evaluate and discuss the effect of MCTS hyperparameters on the convergence to solution. Overall, our study demonstrates the effectives of using RL approaches that operate in discrete action space for inverse defect design problems.

42 ENGINEERING↗
DOE OSTI2020

Dislocation-graphene interactions in Cu/graphene composites and the effect of boundary conditions: a molecular dynamics study

Here, in this paper, systematic molecular dynamics simulations were employed to study dislocation-graphene interactions in Cu/graphene systems using two carefully selected configurations: (i) edge dislocations in the pileup interacting with graphene during nanoindentation and (ii) complex dislocations interacting with graphene in compression of layered nanopillars. The intrinsic and extrinsic size effects were investigated with respect to varying the Cu lamella thickness and pillar sizes, revealing an anomalous extrinsic size effect: the smaller, the weaker. To understand which boundary conditions are physically consistent, both free and periodic graphene were considered. It was seen that edge dislocations in the pileup continuously transmitted across the free graphene through Cu/graphene interfacial sliding and graphene reorientation, whereas transmission was very difficult for periodic graphene as its in-plane deformation was required. In compression of Cu/graphene nanopillars, the strengthening effect of free graphene was found to be less obvious than that of the periodic case, which could be attributed to free graphene edges acting as dislocation sources after the compressed Cu overflowed the graphene sheet from all directions. We therefore conclude that the strengthening effect of periodic graphene inclusions appears to be overestimated, such that free graphene should be more appropriate.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Structure-Based Design of Dual Bactericidal and Bacteria-Releasing Nanosurfaces

Here, we report synergistic nanostructured surfaces combining bactericidal and bacteria-releasing properties. A polystyrene-block-poly(methyl methacrylate) (PS-block-PMMA) diblock copolymer is used to fabricate vertically oriented cylindrical PS structures (“PS nanopillars”) on silicon substrates. The results demonstrate that the PS nanopillars (with a height of about 10 nm, size of about 50 nm, and spacing of about 70 nm) exhibit highly effective bactericidal and bacteria-releasing properties (“dual properties”) against Escherichia coli for at least 36 h of immersion in an E. coli solution. Interestingly, the PS nanopillars coated with a thin layer (≈3 nm thick) of titanium oxide (TiO 2 ) (“TiO 2 nanopillars”) show much improved dual properties against E. coli (a Gram-negative bacterium) compared to the PS nanopillars. Moreover, the dual properties emerge against Listeria monocytogenes (a Gram-positive bacterium). To understand the mechanisms underlying the multifaceted property of the nanopillars, coarse-grained molecular dynamics (MD) simulations of a lipid bilayer (as a simplified model for E. coli) in contact with a substrate containing hexagonally packed hydrophilic nanopillars were performed. The MD results demonstrate that when the bacterium–substrate interaction is strong, the lipid heads adsorb onto the nanopillar surfaces, conforming the shape of a lipid bilayer to the structure/curvature of nanopillars and generating high stress concentrations within the membrane (i.e., the driving force for rupture) at the edge of the nanopillars. Membrane rupture begins with the formation of pores between nanopillars (i.e., bactericidal activity) and ultimately leads to the membrane withdrawal from the nanopillar surface (i.e., bacteria-releasing activity). In the case of Gram-positive bacteria, the adhesion area to the pillar surface is limited due to the inherent stiffness of the bacteria, creating higher stress concentrations within a bacterial cell wall. In conclusion, the present study provides insight into the mechanism underlying the “adhesion-mediated” multifaceted property of nanosurfaces, which is crucial for the development of next-generation antibacterial surface coatings for relevant medical applications.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Artificial Photosynthesis with Next Generation Molecular Catalysts

The objective of this project was to develop a new class of molecular photocatalysts for CO 2 reduction that will enable breakthrough advances in artificial photosynthesis. A major limitation of existing photocatalytic assemblies is that only a small fraction of absorbed photons are converted into fuel due to inefficiencies in electron transport between the different system components. In the case of molecular catalysts for reduction of CO 2 , highly reducing electron equivalents are required for catalysis. As a result, the electron flux between the photosensitizer and CO 2 reduction catalyst is heavily biased towards the photosensitizer. One method to direct the electron flux towards productive photocatalysis is to design molecular catalysts for CO 2 reduction that operate at more favorable potentials than existing catalysts. The conventional approach is to tune the potential of the catalyst through selection of the supporting ligands, however, this only leads to incremental improvements due to the existence of an unfavorable scaling relationship between the rate and potential of catalysis. Our hypothesis is that the catalytic rate and potential can be simultaneously enhanced using bimetallic catalysts in which one metal improves the potential of catalysis and the second metal increases the rate of catalysis. During the course of this project, a few studies reported some success in improving photocatalytic CO 2 reduction with heterobimetallic complexes, demonstrating the potential of this approach to catalyst design.

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

Understanding Soil Microbial Sources of Nitrous Acid and their Effect on Carbon-Nitrogen Cycle Interactions

Descriptions of soil emissions of reactive nitrogen (NO y ) in climate models are underdeveloped or non-existent, due to the fact that details of the mechanisms leading to nitrous acid (HONO) and nitrogen di-oxide (NO 2 ) formation in soil are lacking. This represents a major gap in our understanding of a significant land-atmosphere interaction that prevents us from scaling these processes from the laboratory scale to the ecosystem and global scales. There is a critical need to include these mechanisms into climate models since NO y controls the oxidative capacity of the atmosphere and the lifetime of greenhouse gases and the rate of secondary aerosol formation that directly and indirectly affect climate. The first objective of this proposal is to conduct laboratory and field measurements of NO y fluxes from diverse soil types and determine the mechanism of biogenic NO y formation. The working hypothesis based on preliminary data is that soil HONO and NO 2 is ultimately derived from ammonia-oxidizing archaea (AOA) and bacteria (AOB) that are widespread, but whose abundance varies across ecosystems. In the case of NO 2 , reactive oxygen species derived from iron-containing minerals and heterotrophic bacteria drive NO-to-NO 2 conversion. The approach is to link soil fluxes of HONO and NO 2 to AOA, AOB, and other heterotrophs using a combination of laboratory and field experiments, isotopic analysis, and molecular techniques to address how variability in land surfaces and edaphic properties impact emissions. In addition, we will determine the effect of HONO and NO 2 on nitrogen immobilization and the photo-oxidative capacity of soil. The working hypothesis is that HONO uptake in soil will be a source of nitrosonium and hydroxyl radical that will lead to thermal- and photodegradation of soil organic matter to CO 2 and CO, and the incorporation of N in soil organic matter. We will use surface-sensitive mass spectrometry techniques and gas phase detection to study N-immobilization in soil and subsequent enhancements in reactivity that lead to decomposition of organic matter. The results will be used to reduce the uncertainty in projections from the Community Earth System Model (CESM) stemming from inaccurate representations of soil NO y emissions. The proposed research is significant because, in addition to demonstrating new mechanisms of NO y formation and loss, it will be a crucial first step towards modeling the land-atmosphere exchange of HONO and NO 2 in the CESM. Improved model treatment of land-air exchange of NO y is key for understanding feedbacks between human activity and climate, and addressing societal concerns about the fate of N and C emitted to the atmosphere.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Controlling protein adsorption modes electrostatically

Protein adsorption on surfaces is ubiquitous in biology and in biotechnology. There are various forces required for controlling protein adsorption. Here, we introduce an explicit ion coarse-grained molecular dynamics simulation approach for studying the effects of electrostatics on protein adsorption, and 2D protein assembly on charged surfaces. Our model accounts for the spatial distribution of protein charges. We use catalase as our model protein. We find that the preferential adsorption mode of proteins at low protein concentration on a charged surface is “standing up”. When the protein concentration in a solution increases to reach a critical density on the surface, the adsorption mode switches from “standing up” to a mixed state “flat on” and “standing up”, which increases the lateral correlations among the adsorbed proteins. As such, the changes in the adsorption mode arise from the protein adsorption that cancel the surface charge and the protein–protein repulsion. This correlated surface structure melts as the salt concentration increases because the charged surface is cancelled by the salt ions and the proteins de-adsorb. For the case of strongly charged surfaces the “standing up” conformation remains more favorable even at high protein adsorption at low salt concentrations since in that conformation the surface charge is cancelled more effectively, generating an even more laterally correlated structure. We elucidate the effects of parameters such as surface charge density, salt concentration, and protein charges on the different adsorption modes and the structure and organization of proteins on the charged surfaces. Finally, this study provides a guide for controlling protein assembly on surfaces.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Crystal structure of dihydrofolate reductase from the filarial nematode W. bancrofti in complex with NADPH and folate

Lymphatic filariasis is a debilitating illness with an estimated 50 million cases as of 2018. The majority of cases are caused by the parasitic worm W. bancrofti and additional cases by the worms B. malayi and B. timori. Dihydrofolate reductase (DHFR) is an established target in the treatment of cancer, bacterial, and protozoal infections and may be a potential target for drugs targeting parasitic worm infections, including filariasis. Recent studies have shown that known antifolate compounds, including methotrexate, inhibit the activity of W. bancrofti DHFR (WbDHFR). However, the absence of structural information for filarial DHFRs has limited the study of more in-depth structure-function relationships. We report the structure of WbDHFR complexed with NADPH and folate using X-ray diffraction data measured to 2.47 Å resolution. The structure of WbDHFR reveals the usual DHFR fold and is currently only the second nematode DHFR structure in the Protein Data Bank. The equilibrium dissociation constants for NADPH (90 ± 29 nM) and folate (23 ± 4 nM) were determined by equilibrium titrations. The interactions of known antifolates with WbDHFR were analyzed using molecular docking programs and molecular dynamics simulations. Antifolates with a hydrophobic core and extended linker formed favorable interactions with WbDHFR. These combined data should now facilitate the rational design of filarial DHFR inhibitors, which in turn can be used to determine whether DHFR is a viable drug target for filariasis and whether existing antifolates may be repurposed for its treatment.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Bioelectrochemical reactor to manage anthropogenic sulfate pollution for freshwater ecosystems: Mathematical modeling and experimental validation

Anthropogenic sulfate loading into otherwise low-sulfate freshwater systems can cause significant ecological consequences as a biogeochemical stressor. To address this challenge, in situ bioremediation technologies have been developed to leverage naturally occurring microorganisms that transform sulfate into sulfide rather than implementing resource-intensive physio-chemical processes. However, bioremediation technologies often require the supply of electron donors to facilitate biological sulfate reduction. Bioelectrochemical systems (BES) can be an alternative approach for supplying molecular hydrogen as an electron donor for sulfate-reducing bacteria through water electrolysis. Although the fundamental mechanisms behind BESs have been studied, limited research has evaluated the design and operational parameters of treatment systems when developing BESs on a scale relevant to environmental systems. Further, this study aimed to develop an application-based mathematical model to evaluate the performance of BESs across a range of reactor configurations and operational modes. The model was based on sulfate transformation by hydrogenotrophic sulfate-reducing bacteria coupled with the recovery of solid iron sulfide species formed by the oxidative dissolution of dissolved ferrous iron from a stainless steel anode. Sulfate removal closely corresponded to the rate of electrolytic hydrogen production and hydraulic residence time but was less sensitive to specific microbial rate constants. The mathematical model results were compared to experimental data from a pilot-scale BES tested with nonacidic mine drainage as a case study. The close agreement between the mathematical model and the pilot-scale BES experiment highlights the efficacy of using a mathematical model as a tool to develop a conceptual design of a scaled-up treatment system.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Chemical significance of x-ray photoelectron spectroscopy binding energy shifts: A Perspective

The principal intent of this Perspective is to review the mechanisms that are responsible for the shifts of binding energies, ΔBE, observed in x-ray photoelectron spectroscopy (XPS) measurements and so to relate the shifts to the electronic structure and the chemical bonding in the systems studied. To achieve this goal, several theoretical considerations are necessary beyond just the calculation of XPS BEs. Though briefly discussed here, we are not primarily interested in absolute values of BE or quantitation using relative intensities. Within the molecular orbital (MO) theory framework, it is shown that the analysis of orbital properties is critical for the correct interpretation of XPS. In particular, rigorous definitions are given for the initial state and final state contributions to BEs and to BE shifts, ΔBE. It is first shown how the BEs of core levels are related to the electronic structure by consideration of the BEs for a model atomic system to establish the origins and magnitudes of BE shifts. The mechanisms established for the model system are then applied to a review of XPS measurements and MO theory on a set of real examples. An important focus of the paper is to demonstrate that, in many cases, initial state mechanisms allow for a definitive interpretation of the XPS BE shifts and that an important role of theory is to provide qualitative explanations rather than quantitative agreement with XPS measurements. The mechanisms established are a guide to the interpretation of XPS measurements and consideration of these mechanisms may suggest additional calculations that would be useful. It is concluded that there is still a bright future for the coupling of ab initio MO theory with XPS measurements.

Materials Science↗
DOE OSTI2021

Bridging the gap between simulated and experimental ionic conductivities in lithium superionic conductors

Lithium superionic conductors (LSCs) are of major importance as solid electrolytes for next-generation all-solid-state lithium-ion batteries. While ab initio molecular dynamics have been extensively applied to study these materials, there are often large discrepancies between predicted and experimentally measured ionic conductivities and activation energies due to the high temperatures and short time scales of such simulations. Here, we present a strategy to bridge this gap using moment tensor potentials (MTPs). We show that MTPs trained on energies and forces computed using the van der Waals optB88 functional yield much more accurate lattice parameters, which in turn leads to accurate prediction of ionic conductivities and activation energies for the Li 0·33 La 0·56 TiO 3 , Li 3 YCl 6 and Li 7 P 3 S 11 LSCs. NPT MD simulations using the optB88 MTPs also reveal that all three LSCs undergo a transition between two quasi-linear Arrhenius regimes at relatively low temperatures. This transition can be traced to an increase in the number and diversity of diffusion pathways, in some cases with a change in the dimensionality of diffusion. Furthermore, this work presents not only an approach to develop high accuracy MTPs, but also outlines the diffusion characteristics for LSCs which is otherwise inaccessible through ab initio computation.

25 ENERGY STORAGE↗
DOE OSTI2022

Temperature Effects in Flexible Adsorption Processes for Amorphous Microporous Polymers

A collection of atomistic molecular simulations is reported that illustrate the impact of adsorption temperature on species uptake and adsorbate-induced structural rearrangement for amorphous polymers of intrinsic microporosity. Temperature-sensitive structural rearrangement is evaluated by contrasting two methods: standard grand canonical Monte Carlo simulations using a rigid framework approximation and a combined Monte Carlo/molecular dynamics approach that fully incorporates framework flexibility. We report single-component gas phase adsorption isotherms for CH 4 , C 2 H 4 , C 2 H 6 , C 3 H 6 , C 3 H 8 , and CO 2 across a temperature range of 250–400 K for models of an archetypal polymer of intrinsic microporosity, PIM-1. A quadratic model is presented that captures two main mechanisms of temperature-dependent adsorption-induced deformation of PIM-1 up to a relative swelling of 1.15: thermal expansion and an increased propensity to swell as a function of species uptake. Two case studies are reported that highlight the critical role of operating temperature in industrial storage and separation applications. The first study focuses on methane storage and delivery applications using a pressure–temperature swing adsorption application (PTSA). We demonstrate that larger working capacities are accompanied by increased volumetric strain between adsorption–desorption steps. The second case study considers PIM-1 as an adsorbent to separate an exemplar ternary syngas mixture at operating temperatures ranging 300–550 K. Here, a temperature threshold of ~400 K is identified, beyond which adsorption-induced PIM-1 swelling is negligible and the solubility selectivity-loading curve transitions to exhibiting a nearly linear relationship.

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

Photon-recoil and laser-focusing limits to Rydberg gate fidelity

Limits to Rydberg gate fidelity that arise from the entanglement of internal states of neutral atoms with the motional degrees of freedom due to the momentum kick from photon absorption and re-emission is quantified. This occurs when the atom is in a superposition of internal states but only one of these states is manipulated by visible or UV photons. The Schrödinger equation that describes this situation is presented and two cases are explored. In the first case, the entanglement arises because the spatial wave function shifts due to the separation in time between excitation and stimulated emission. For neutral atoms in a harmonic trap, the decoherence can be expressed within a sudden approximation when the duration of the laser pulses are shorter than the harmonic oscillator period. In this limit, the decoherence is given by simple analytic formulas that account for the momentum of the photon, the temperature of the atoms, the harmonic oscillator frequency, and atomic mass. In the second case, there is a reduction in gate fidelity because the photons causing absorption and stimulated emission are in focused beam modes. This leads to a dependence of the optically induced changes in the internal states on the center of mass atomic position. In the limit where the time between pulses is short, the decoherence can be expressed as a simple analytic formula involving the laser waist, temperature of the atoms, the trap frequency, and the atomic mass. These limits on gate fidelity are studied for the standard π-2π-π Rydberg gate and a protocol based on a single adiabatic pulse with a Gaussian envelope.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2024

Foldy: An open-source web application for interactive protein structure analysis

Foldy is a cloud-based application that allows non-computational biologists to easily utilize advanced AI-based structural biology tools, including AlphaFold and DiffDock. With many deployment options, it can be employed by individuals, labs, universities, and companies in the cloud without requiring hardware resources, but it can also be configured to utilize locally available computers. Foldy enables scientists to predict the structure of proteins and complexes up to 6000 amino acids with AlphaFold, visualize Pfam annotations, and dock ligands with AutoDock Vina and DiffDock. In our manuscript, we detail Foldy’s interface design, deployment strategies, and optimization for various user scenarios. We demonstrate its application through case studies including rational enzyme design and analyzing proteins with domains of unknown function. Furthermore, we compare Foldy’s interface and management capabilities with other open and closed source tools in the field, illustrating its practicality in managing complex data and computation tasks. Our manuscript underlines the benefits of Foldy as a day-to-day tool for life science researchers, and shows how Foldy can make modern tools more accessible and efficient.

59 BASIC BIOLOGICAL SCIENCES↗