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Results for “conformational ensembles”

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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117 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

On the Rapid Calculation of Binding Affinities for Antigen and Antibody Design and Affinity Maturation Simulations

The accurate and efficient calculation of protein-protein binding affinities is an essential component in antibody and antigen design and optimization, and in computer modeling of antibody affinity maturation. Such calculations remain challenging despite advances in computer hardware and algorithms, primarily because proteins are flexible molecules, and thus, require explicit or implicit incorporation of multiple conformational states into the computational procedure. The astronomical size of the amino acid sequence space further compounds the challenge by requiring predictions to be computed within a short time so that many sequence variants can be tested. In this study, we compare three classes of methods for antibody/antigen (Ab/Ag) binding affinity calculations: (i) a method that relies on the physical separation of the Ab/Ag complex in equilibrium molecular dynamics (MD) simulations, (ii) a collection of 18 scoring functions that act on an ensemble of structures created using homology modeling software, and (iii) methods based on the molecular mechanics-generalized Born surface area (MM-GBSA) energy decomposition, in which the individual contributions of the energy terms are scaled to optimize agreement with the experiment. When applied to a set of 49 antibody mutations in two Ab/HIV gp120 complexes, all of the methods are found to have modest accuracy, with the highest Pearson correlations reaching about 0.6. In particular, the most computationally intensive method, i.e., MD simulation, did not outperform several scoring functions. The optimized energy decomposition methods provided marginally higher accuracy, but at the expense of requiring experimental data for parametrization. Within each method class, we examined the effect of the number of independent computational replicates, i.e., modeled structures or reinitialized MD simulations, on the prediction accuracy. We suggest using about ten modeled structures for scoring methods, and about five simulation replicates for MD simulations as a rule of thumb for obtaining reasonable convergence. We anticipate that our study will be a useful resource for practitioners working to incorporate binding affinity calculations within their protein design and optimization process.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

SARS-CoV2 Docking Dataset

Description: Small-molecule conformations and docking scores for 1.4 billion molecules docked against 6 protein targets from SARS-CoV2: MPro 5R84, MPro 6WQF, NSP15 6WLC, PLPro 7JIR, Spike 6M0J, and a hand-optimized model of the RNA-dependent RNA polymerase. Docking was carried out using the Autodock-GPU program performing 20 independent structure minimizations per dock - saving 3 results per molecule. Scores reported include the Autodock free energy estimate as well as RF3 and VS-DUD-E v2 machine-learned rescoring models. Protein structure files and maps in the format input to Autodock-GPU are included. Literature Ref: Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19, J. Chem. Inf. Model. 2020, 60(12): 5832–5852.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Microscopic entropy of AdS3 black holes revisited

A bstract We revisit the microscopic description of AdS 3 black holes in light of recent progress on their higher dimensional analogues. The grand canonical partition function that follows from the AdS 3 /CFT 2 correspondence describes BPS and nearBPS black hole thermodynamics. We formulate an entropy extremization principle that accounts for both the black hole entropy and a constraint on its charges, in close analogy with asymptotically AdS black holes in higher dimensions. We are led to interpret supersymmetric black holes as ensembles of BPS microstates satisfying a charge constraint that is not respected by individual states. This interpretation provides a microscopic understanding of the hitherto mysterious charge constraints satisfied by all BPS black holes in AdS. We also develop thermodynamics and a nAttractor mechanism of AdS 3 black holes in the nearBPS regime.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

A principle of maximum ignorance for semiclassical gravity

The principle of maximum ignorance posits that the coarse-grained description of a system is maximally agnostic about its underlying microscopic structure. We briefly review this principle for random matrix theory and for the eigenstate thermalization hypothesis. We then apply this principle in holography to construct ensembles of random mixed states. This leads to an ensemble of microstates which models our microscopic ignorance, and which on average reproduces the effective semiclassical physics of a given bulk state. We call this ensemble the state-averaging ansatz. The output of our model is a prediction for semiclassical contributions to variances and higher statistical moments over the ensemble of microstates. The statistical moments provide coarse-grained — yet gravitationally non-perturbative — information about the microstructure of the individual states of the ensemble. We show that these contributions exactly match the on-shell action of known wormhole configurations of the gravitational path integral. These results strengthen the view that wormholes simply parametrize the ignorance of the microstructure of a fundamental state, given a fixed semiclassical bulk description.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Lattice quantum chromodynamics at large isospin density

We present an algorithm to compute correlation functions for systems with the quantum numbers of many identical mesons from lattice quantum chromodynamics (QCD). The algorithm is numerically stable and allows for the computation of n-pion correlation functions for n ϵ {1, … , N} using a single N × N matrix decomposition, improving on previous algorithms. We apply the algorithm to calculations of correlation functions with up to 6144 charged pions using two ensembles of gauge field configurations generated with quark masses corresponding to a pion mass m π = 170 MeV and spacetime volumes of (4.4 3 × 8.8) fm 4 and (5.8 3 × 11.6) fm 4 . We also discuss statistical techniques for the analysis of such systems, in which the correlation functions vary over many orders of magnitude. In particular, we observe that the many-pion correlation functions are well-approximated by log-normal distributions, allowing the extraction of the energies of these systems. Using these energies, the large-isospin-density, zero-baryon-density region of the QCD phase diagram is explored. A peak is observed in the energy density at an isospin chemical potential μ I ~ 1.5m π , signaling the transition into a Bose-Einstein condensed phase. The isentropic speed of sound, c s , in the medium is seen to exceed the ideal-gas (conformal) limit ($c^{2}_{s} ≤ 1/3)$ over a wide range of chemical potential before falling towards the asymptotic expectation at μ I ~ 15m π . These, and other thermodynamic observables, indicate that the isospin chemical potential must be large for the system to be well described by an ideal gas or perturbative QCD.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

Scaling functions for eigenstate entanglement crossovers in harmonic lattices

For quantum matter, eigenstate entanglement entropies obey an area law or log-area law at low energies and small subsystem sizes and cross over to volume laws for high energies and large subsystems. This transition is captured by crossover functions, which assume a universal scaling form in quantum critical regimes. We demonstrate this for the harmonic lattice model, which describes quantized lattice vibrations and is a regularization for free scalar field theories, modeling, e.g., spin-0 bosonic particles. In one dimension, the ground-state entanglement obeys a log-area law. For dimensions d ≥ 2, it displays area laws, even at criticality. The distribution of excited-state entanglement entropies is found to be sharply peaked around subsystem entropies of corresponding thermodynamic ensembles in accordance with the eigenstate thermalization hypothesis. Numerically, we determine crossover scaling functions for the quantum critical regime of the model and do a large-deviation analysis. We show how infrared singularities of the system can be handled and how to access the thermodynamic limit using a perturbative trick for the covariance matrix. Eigenstates for quasi-free bosonic systems are not Gaussian. Here, we resolve this problem by considering appropriate squeezed states instead. For these, entanglement entropies can be evaluated efficiently.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

Residue Specific Characterization of Electrostatics, Conformational Heterogeneity, and Dynamics of Electron Transfer Proteins with Linear and Nonlinear Infrared Spectroscopy. Final Report

The goal of this research project was to further our understanding of biological electron transfer through the development and application of new methods for studying proteins and their complexes with high spatial and temporal detail. The approach was based on incorporation of reporter bonds with distinct vibrational frequencies at specific locations in proteins and their characterization through the interaction of the bonds with pulses of infrared light. The project focused on the proteins plastocyanin (Pc) and cytochrome (cyt) f, two electron transfer partners in photosynthesis. The first thrust of the project was the incorporation of carbon deuterium bonds as non-perturbative probes at a ligand to the copper ion of Pc and their use to detect changes in the bonding due to the number of electrons at the metal and how the bonding changes upon association with cyt f. Toward developing more advanced approaches to characterize proteins, we incorporated a stronger reporter, the cyano group of cyanophenylalanine, at several locations in Pc and measured the frequency dynamics in the absence and presence of cyt f. The acquired data improved the current model for the protein complex. Notably, the data indicated that the majority of the population is involved in a loosely bound complex, providing insight into the nature of the ensembles formed by electron transfer protein complexes that is not available via other approaches. In addition to learning about the protein complex, we made strides toward developing and improving the new experimental approach to study highly dynamic behaviors of proteins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics

We develop a generalizable AI-driven workflow that leverages heterogeneous HPC resources to explore the time-dependent dynamics of molecular systems. We use this workflow to investigate the mechanisms of infectivity of the SARS-CoV-2 spike protein, the main viral infection machinery. Our workflow enables more efficient investigation of spike dynamics in a variety of complex environments, including within a complete SARS-CoV-2 viral envelope simulation, which contains 305 million atoms and shows strong scaling on ORNL Summit using NAMD. We present several novel scientific discoveries, including the elucidation of the spike’s full glycan shield, the role of spike glycans in modulating the infectivity of the virus, and the characterization of the flexible interactions between the spike and the human ACE2 receptor. We also demonstrate how AI can accelerate conformational sampling across different systems and pave the way for the future application of such methods to additional studies in SARS-CoV-2 and other molecular systems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Accurate determination of solvation free energies of neutral organic compounds from first principles

The main goal of molecular simulation is to accurately predict experimental observables of molecular systems. Another long-standing goal is to devise models for arbitrary neutral organic molecules with little or no reliance on experimental data. While separately these goals have been met to various degrees, for an arbitrary system of molecules they have not been achieved simultaneously. For biophysical ensembles that exist at room temperature and pressure, and where the entropic contributions are on par with interaction strengths, it is the free energies that are both most important and most difficult to predict. We compute the free energies of solvation for a diverse set of neutral organic compounds using a polarizable force field fitted entirely to ab initio calculations. The mean absolute errors (MAE) of hydration, cyclohexane solvation, and corresponding partition coefficients are 0.2 kcal/mol, 0.3 kcal/mol and 0.22 log units, i.e. within chemical accuracy. The model (ARROW FF) is multipolar, polarizable, and its accompanying simulation stack includes nuclear quantum effects (NQE). The simulation tools’ computational efficiency is on a par with current state-of-the-art packages. The construction of a wide-coverage molecular modelling toolset from first principles, together with its excellent predictive ability in the liquid phase is a major advance in biomolecular simulation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗