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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 847 records · Page 47
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Adaptive Ensemble Refinement of Protein Structures in High Resolution Electron Microscopy Density Maps with Radical Augmented Molecular Dynamics Flexible Fitting

Recent advances in cryo-electron microscopy (cryo-EM) have enabled modeling macromolecular complexes that are essential components of the cellular machinery. The density maps derived from cryo-EM experiments are often integrated with manual, knowledge or artificial intelligence driven, and physics-guided computational methods to build, fit, and refine molecular structures. Going beyond a single stationary- structure determination scheme, it is becoming more common to interpret the experimental data with an ensemble of models, which contributes to an average observation. Hence, there is a need to decide on the quality of an ensemble of protein structures on-the-fly, while refining them against the density maps. Here, we introduce such an adaptive decision making scheme during the molecular dynamics flexible fitting (MDFF) of biomolecules. Using RADICAL-Cybertools, and the new RADICAL augmented MDFF implementation (R-MDFF) is examined in high-performance computing environments for refinement of two protein systems, Adenylate Kinase and Carbon Monoxide Dehydrogenase. For the test cases, use of multiple replicas in flexible fitting with adaptive decision making in R-MDFF improves the overall correlation to the density by 40% relative to the refinements of the brute-force MDFF. The improvements are particularly significant at high, 2 - 3 Å, map resolutions. More importantly, the ensemble model captures key features of biologically relevant molecular dynamics that is inaccessible to a single-model interpretation. Finally, the pipeline is applicable to systems of growing sizes, which is demonstrated using ensemble refinement of capsid proteins from Chimpanzee adenovirus. The overhead for decision making remaining low and robust to computing environments. The software is publicly available on GitHub and includes a short user guide to install the R-MDFF on different computing environments, from local Linux based workstations to High Performance Computing (HPC) environments.

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

Ligand modulation of the conformational dynamics of the A 2A adenosine receptor revealed by single-molecule fluorescence

G protein-coupled receptors (GPCRs) are the largest class of transmembrane proteins, making them an important target for therapeutics. Activation of these receptors is modulated by orthosteric ligands, which stabilize one or several states within a complex conformational ensemble. The intra- and inter-state dynamics, however, is not well documented. Here, we used single-molecule fluorescence to measure ligand-modulated conformational dynamics of the adenosine A 2A receptor (A 2A R) on nanosecond to millisecond timescales. Experiments were performed on detergent-purified A 2R in either the ligand-free (apo) state, or when bound to an inverse, partial or full agonist ligand. Single-molecule Förster resonance energy transfer (smFRET) was performed on detergent-solubilized A 2A R to resolve active and inactive states via the separation between transmembrane (TM) helices 4 and 6. The ligand-dependent changes of the smFRET distributions are consistent with conformational selection and with inter-state exchange lifetimes ≥ 3 ms. Local conformational dynamics around residue 229 6.31 on TM6 was measured using fluorescence correlation spectroscopy (FCS), which captures dynamic quenching due to photoinduced electron transfer (PET) between a covalently-attached dye and proximal aromatic residues. Global analysis of PET-FCS data revealed fast (150–350 ns), intermediate (50–60 μs) and slow (200–300 μs) conformational dynamics in A 2A R, with lifetimes and amplitudes modulated by ligands and a G-protein mimetic (mini-G s ). Most notably, the agonist binding and the coupling to mini-G s accelerates and increases the relative contribution of the sub-microsecond phase. Molecular dynamics simulations identified three tyrosine residues (Y112, Y288 7.53 , and Y290 7.55 ) as being responsible for the dynamic quenching observed by PET-FCS and revealed associated helical motions around residue 229 6.31 on TM6. As a result, this study provides a quantitative description of conformational dynamics in A 2A R and supports the idea that ligands bias not only GPCR conformations but also the dynamics within and between distinct conformational states of the receptor.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1996

Computational Materials Research

Computational Materials aims to model and predict thermodynamic, mechanical, and transport properties of polymer matrix composites. This workshop, the second coordinated by NASA Langley, reports progress in measurements and modeling at a number of length scales: atomic, molecular, nano, and continuum. Assembled here are presentations on quantum calculations for force field development, molecular mechanics of interfaces, molecular weight effects on mechanical properties, molecular dynamics applied to poling of polymers for electrets, Monte Carlo simulation of aromatic thermoplastics, thermal pressure coefficients of liquids, ultrasonic elastic constants, group additivity predictions, bulk constitutive models, and viscoplasticity characterization.

Hinkley, Jeffrey A.↗
NASA NTRS2000

Computer Modeling of the Earliest Cellular Structures and Functions

In the absence of extinct or extant record of protocells (the earliest ancestors of contemporary cells). the most direct way to test our understanding of the origin of cellular life is to construct laboratory models of protocells. Such efforts are currently underway in the NASA Astrobiology Program. They are accompanied by computational studies aimed at explaining self-organization of simple molecules into ordered structures and developing designs for molecules that perform proto-cellular functions. Many of these functions, such as import of nutrients, capture and storage of energy. and response to changes in the environment are carried out by proteins bound to membrane< We will discuss a series of large-scale, molecular-level computer simulations which demonstrate (a) how small proteins (peptides) organize themselves into ordered structures at water-membrane interfaces and insert into membranes, (b) how these peptides aggregate to form membrane-spanning structures (eg. channels), and (c) by what mechanisms such aggregates perform essential proto-cellular functions, such as proton transport of protons across cell walls, a key step in cellular bioenergetics. The simulations were performed using the molecular dynamics method, in which Newton's equations of motion for each item in the system are solved iteratively. The problems of interest required simulations on multi-nanosecond time scales, which corresponded to 10(exp 6)-10(exp 8) time steps.

Pohorille, Andrew↗
DOE OSTI2024

Excited-State and Nonadiabatic Molecular Dynamics Methods with Broad Applicability

Electronically excited states play a pivotal role in the capture, transformation, storage, and emission of radiative energy. Despite much recent progress for small model systems, excited state properties and dynamics in many larger molecular devices and materials have remained elusive for experiment and theory. Nonadiabatic transitions between electronic states turn radiative energy into heat and are particularly difficult to control. This project aims to develop new electronic structure and nonadiabatic molecular dynamics (NAMD) methods to simulate, predict, and ultimately control the flow and transformation of excitation energy in a wide-range of light-driven molecular devices such as dyes, photocatalysts, and fluorescence emitters.

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

High-Performance Semiempirical Excited-State Molecular Dynamics Powered by Graphics Processing Units

Here, this Letter introduces excited-state molecular dynamics in PYSEQM, a GPU-accelerated semiempirical quantum chemistry engine implemented in PyTorch. The new module enables Born–Oppenheimer molecular dynamics (BOMD) using configuration-interaction singles and random phase approximation for excited states, allowing long trajectories and large statistical ensembles to be simulated efficiently on a single GPU. We also implement an extended Lagrangian excited-state BOMD (XL-ESMD) scheme that propagates auxiliary electronic variables, enabling relaxed ground and excited-state convergence thresholds without compromising energy conservation. The excited-state BOMD implementation scales smoothly from small chromophores to a nearly 900-atom dendrimer (taking 6.5 s per MD step). PYSEQM also supports batched execution, allowing many geometries or trajectories to be evaluated in a single GPU launch, substantially increasing throughput and making ensemble-based protocols routine. As a demonstration, we compute absorption, emission, and infrared spectra from trajectories propagated on the ground and first excited states. The XL-ESMD scheme yields identical spectra at significantly lower computational cost, establishing the role of extended Lagrangian based dynamics for efficient excited-state BOMD simulations. Beyond raw performance, PYSEQM’s PyTorch foundation provides automatic differentiation for forces, efficient GPU batching, and seamless interfacing with machine learning models. These capabilities position PYSEQM as a practical platform for machine learning-augmented excited-state dynamics and lay the foundation for future data-driven nonadiabatic excited-state dynamics modeling of ultrafast spectroscopic probes.

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

CTRAMER: An open-source software package for correlating interfacial charge transfer rate constants with donor/acceptor geometries in organic photovoltaic materials

In this paper, we present CTRAMER (Charge-Transfer RAtes from Molecular dynamics, Electronic structure, and Rate theory)—an opensource software package for calculating interfacial charge-transfer (CT) rate constants in organic photovoltaic (OPV) materials based on ab initio calculations and molecular dynamics simulations. The software is based on identifying representative donor/acceptor geometries within interfacial structures obtained from molecular dynamics simulation of donor/acceptor blends and calculating the corresponding Fermi’s golden rule CT rate constants within the framework of the linearized-semiclassical approximation. While the methods used are well established, the integration of these state-of-the-art tools originating from different disciplines to study photoinduced CT processes with explicit treatment of the environment, in our opinion, makes this package unique and innovative. The software also provides tools for investigating other observables of interest. After outlining the features and implementation details, the usage and performance of the software are demonstrated with results from an example OPV system.

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

Microscopic insights into the solvation of polyethylene glycol chains in water: A machine learning potential approach

Polyethylene glycol (PEG) is a structurally simple, nontoxic, and water-soluble polymer widely utilized in medical and pharmaceutical applications. Notably, when a PEG chain is immersed in water, the surrounding water molecules play a key role in driving conformational changes of this macromolecule. In this study, we explore the solvation behavior of PEG under mechanical strain using molecular dynamics simulations, with an interatomic potential obtained from machine learning. Our focus is on the transition from the favored coil-like conformation to an extended one under external force. Through analyses of radial distribution functions, hydrogen bonding, and solvation dynamics, we uncover how mechanical stretching influences the local hydration environment. Furthermore, we disentangle the enthalpic and entropic contributions to the conformational stability of PEG in water. Surprisingly, our neural network potential model identifies dewetting of PEG C-atoms, and not water H-bonding with PEG O-atoms, as the main enthalpic driving force for the coiling of PEG in water.

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

Scaling Ensembles of Data-Intensive Quantum Chemical Calculations for Millions of Molecules

Deep learning models are efficient computational tools that can accelerate the inverse design of molecules with desired functional properties by generating predictions at a fraction of the time required by traditional quantum chemical approaches. To ensure that a model maintains accuracy and transferability across broad regions of the chemical space explored during the inverse design, it must be trained on massively large volumes of simulation data. This requires running large-scale ensemble quantum chemical calculations on high-performance computing (HPC) systems for data collection. However, the efficient execution of such large ensemble calculations and the management of large volumes of output data require tools that can judiciously utilize computational resources and manage metadata overhead on the file system. Therefore, we present a high-performance, scalable, ensemble management framework for performing data-intensive quantum chemical electronic structure calculations for organic molecules. This framework provides abstractions to plug different ab initio, first principles, and first principles-based semi-empirical methods and executes them efficiently at large scale on HPC systems. It dynamically distributes tasks to resources and uses tiered storage for managing large collections of files. We employed this framework to process over ten million organic molecules and generate open-source datasets that provide UV-vis absorption spectra by running time-dependent density-functional tight-binding calculations. It is the largest database containing molecular optical spectra that were simulated with quantum chemical methods in a consistent manner.

Mehta, Kshitij↗
DOE OSTI2024

Photoinduced Electron–Nuclear Dynamics of Fullerene and Its Monolayer Networks in Solvated Environments

The recently synthesized monolayer fullerene network in a quasi-hexagonal phase (qHP-C 60 ) exhibits superior electron mobility and optoelectronic properties compared to molecular fullerene (C 60 ), making it highly promising for a variety of applications. However, the microscopic carrier dynamics of qHP-C 60 remain unclear, particularly in realistic environments, which are of significant importance for applications in optoelectronic devices. Unfortunately, traditional ab initio methods are prohibitive for capturing the real-time carrier dynamics of such large systems due to their high computational cost. In this work, we present the first real-time electron–nuclear dynamics study of qHP-C 60 using velocity-gauge density functional tight binding, which enables us to perform several picoseconds of excited-state electron–nuclear dynamics simulations for nanoscale systems with periodic boundary conditions. When applied to C 60 , qHP-C 60 , and their solvated counterparts, we demonstrate that water/moisture significantly increases the electron–hole recombination time in C 60 but has little impact on qHP-C 60 . Our excited-state electron–nuclear dynamics calculations show that qHP-C 60 is extremely unique and enable exploration of time-resolved dynamics for understanding excited-state processes of large systems in complex, solvated environments.

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

Neural network representation of electronic structure from ab initio molecular dynamics

Despite their rich information content, electronic structure data amassed at high volumes in ab initio molecular dynamics simulations are generally under-utilized. Here we introduce a transferable high-fidelity neural network representation of such data in the form of tight-binding Hamiltonians for crystalline materials. This predictive representation of ab initio electronic structure, combined with machine-learning boosted molecular dynamics, enables efficient and accurate electronic evolution and sampling. When it is applied to a one-dimension charge-density wave material, carbyne, we are able to compute the spectral function and optical conductivity in the canonical ensemble. The spectral functions evaluated during soliton-antisoliton pair annihilation process reveal significant renormalization of low-energy edge modes due to retarded electron-lattice coupling beyond the Born–Oppenheimer limit. The availability of an efficient and reusable surrogate model for the electronic structure dynamical system will enable calculating many interesting physical properties, paving the way to previously inaccessible or challenging avenues in materials modeling.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2024

Efficient Mixed-Precision Matrix Factorization of the Inverse Overlap Matrix in Electronic Structure Calculations with AI-Hardware and GPUs

In recent years, a new kind of accelerated hardware has gained popularity in the artificial intelligence (AI) community which enables extremely high-performance tensor contractions in reduced precision for deep neural network calculations. In this article, we exploit Nvidia Tensor cores, a prototypical example of such AI-hardware, to develop a mixed precision approach for computing a dense matrix factorization of the inverse overlap matrix in electronic structure theory, S –1 . This factorization of S –1 , written as ZZT = S –1 , is used to transform the general matrix eigenvalue problem into a standard matrix eigenvalue problem. Here we present a mixed precision iterative refinement algorithm where Z is given recursively using matrix–matrix multiplications and can be computed with high performance on Tensor cores. To understand the performance and accuracy of Tensor cores, comparisons are made to GPU-only implementations in single and double precision. Additionally, we propose a nonparametric stopping criteria which is robust in the face of lower precision floating point operations. The algorithm is particularly useful when we have a good initial guess to Z, for example, from previous time steps in quantum-mechanical molecular dynamics simulations or from a previous iteration in a geometry optimization.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Evaluating diffusion and the thermodynamic factor for binary ionic mixtures

Molecular dynamics (MD) simulations are a powerful tool for the calculation of transport properties in mixtures. Not only are MD simulations capable of treating multicomponent systems, they are also applicable over a wide range of temperatures and densities. In plasma physics, this is particularly important for applications such as inertial confinement fusion. While many studies have focused on the effect of plasma coupling on transport properties, here we focus on the effects of mixing. We compute the thermodynamic factor, a measure of ideal/non-ideal mixing, for three binary ionic mixtures. Here, we consider mixtures of hydrogen and carbon, hydrogen and argon, and argon and carbon, each at 500 randomly generated state points in the warm dense matter and plasma regimes. The calculated thermodynamic factors indicate different mixing behavior across phase space, which can significantly affect the corresponding mutual diffusion coefficients. As MD simulations are still computationally expensive, we apply modern data science tools to predict the thermodynamic factor over a large phase space. Further, we propose a more accurate approximation to the mutual diffusion coefficient than the commonly applied Darken relation.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Improved Precision Scaling for Simulating Coupled Quantum-Classical Dynamics

In this paper, we present a superpolynomial improvement in the precision scaling of quantum simulations for coupled quantum-classical systems. Such systems are found in, e.g., molecular-dynamics simulations within the Born-Oppenheimer approximation. By employing a framework based on the Koopman–von Neumann formulation of classical mechanics, we express the Liouville equation of motion as unitary dynamics and utilize phase kickback from a dynamical quantum simulation to calculate the quantum forces acting on classical particles. This approach allows us to simulate the dynamics of these classical particles without the overheads associated with measuring gradients and solving the equations of motion on a classical computer, resulting in a superpolynomial advantage at the price of increased space complexity. We demonstrate that these simulations can be performed in both microcanonical and canonical ensembles, enabling the estimation of thermodynamic properties from the prepared probability density. Published by the American Physical Society 2024

Simon, Sophia (ORCID:0000000332612338)↗
DOE OSTI2021

Nonadiabatic Molecular Dynamics Study of the Relaxation Pathways of Photoexcited Cyclooctatetraene

In the current study, we present nonadiabatic (NAMD) and adiabatic molecular dynamics simulations of the transition-state dynamics of photoexcited cyclooctatetraene (COT). The equilibrium-state structure and absorption spectra are analyzed using the semiempirical Austin Model 1 potential. The NAMD simulations are obtained by a surface-hopping algorithm. We analyzed in detail an active excited to ground state relaxation pathway accompanied by an S 2 /S 3 (D 2d ) → S 1 (D 8h ) → S o (D 4h ) → S o (D 2d ) double-bond shifting mechanism. The simulated excitation lifetime is in good agreement with experiment. The first excited singlet state S1 plays a crucial role in the photochemistry. Here, the obtained critical molecular conformations, energy barrier, and transition-state lifetime results will provide a basis for further investigations of the bond-order inversion and photoswitching process of COT.

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

Ab initio Molecular Dynamics Beyond Density Functional Theory

The funding from this award supported the development of new theoretical methods that both increase the accuracy of quantum simulations beyond that of density functional theory, as well as reduce the cost of such simulations, for example, through machine learning and algorithmic improvements. The improvements lead to, in some cases, orders of magnitude increases in simulation speed as well as orders of magnitude increase in accuracy, compared to before this work was started. This translates to both greater certainty in making predictions about chemical phenomena that are currently studied computationally, as well as laying the ground-work for the study of new areas of chemistry that have not traditionally been simulated, because of the new time-scales and accuracies that can be reached.

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

Structural Color Production in Melanin-Based Disordered Colloidal Nanoparticle Assemblies in Spherical Confinement

Melanin is a ubiquitous natural pigment that exhibits broadband absorption and high refractive index. Despite its widespread use in structural color production, how the absorbing material, melanin, affects the generated color is unknown. Using a combined molecular dynamics and finite-difference time-domain computational approach, here we investigates structural color generation in one-component melanin nanoparticle-based supraparticles (called supraballs) as well as binary mixtures of melanin and silica (nonabsorbing) nanoparticle-based supraballs. Experimentally produced one-component melanin and one-component silica supraballs, with thoroughly characterized primary particle characteristics using neutron scattering, produce reflectance profiles similar to the computational analogs, confirming that the computational approach correctly simulates both absorption and multiple scattering from the self-assembled nanoparticles. These combined approaches demonstrate that melanin's broadband absorption increases the primary reflectance peak wavelength, increases saturation, and decreases lightness factor. Additionally, the dispersity of nanoparticle size more strongly influences the optical properties of supraballs than packing fraction, as evidenced by the production of a larger range of colors when size dispersity is varied versus packing fraction. For binary melanin and silica supraballs, the chemistry-based stratification allows for more diverse color generation and finer saturation tuning than does the degree of mixing/demixing between the two chemistries.

broadband absorption↗