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Results for “molecular simulation”

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At least 1,207 records · Page 67
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Structural basis of agonist specificity of α 1A -adrenergic receptor

α 1 -adrenergic receptors (α 1 -ARs) play critical roles in the cardiovascular and nervous systems where they regulate blood pressure, cognition, and metabolism. However, the lack of specific agonists for all α 1 subtypes has limited our understanding of the physiological roles of different α 1 -AR subtypes, and led to the stagnancy in agonist-based drug development for these receptors. Here we report cryo-EM structures of α 1A -AR in complex with heterotrimeric G-proteins and either the endogenous common agonist epinephrine or the α 1A -AR-specific synthetic agonist A61603. These structures provide molecular insights into the mechanisms underlying the discrimination between α 1A -AR and α 1B -AR by A61603. Guided by the structures and corresponding molecular dynamics simulations, we engineer α 1A -AR mutants that are not responsive to A61603, and α 1B -AR mutants that can be potently activated by A61603. Together, these findings advance our understanding of the agonist specificity for α 1 -ARs at the molecular level, opening the possibility of rational design of subtype-specific agonists.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Thermodynamic driving forces in contact electrification between polymeric materials

Abstract Contact electrification, or contact charging, refers to the process of static charge accumulation after rubbing, or even simple touching, of two materials. Despite its relevance in static electricity, various natural phenomena, and numerous technologies, contact charging remains poorly understood. For insulating materials, even the species of charge carrier may be unknown, and the direction of charge-transfer lacks firm molecular-level explanation. Here, we use all-atom molecular dynamics simulations to investigate whether thermodynamics can explain contact charging between insulating polymers. Based on prior work suggesting that water-ions, such as hydronium and hydroxide ions, are potential charge carriers, we predict preferred directions of charge-transfer between polymer surfaces according to the free energy of water-ions within water droplets on such surfaces. Broad agreement between our predictions and experimental triboelectric series indicate that thermodynamically driven ion-transfer likely influences contact charging of polymers. Furthermore, simulation analyses reveal how specific interactions of water and water-ions proximate to the polymer-water interface explain observed trends. This study establishes relevance of thermodynamic driving forces in contact charging of insulators with new evidence informed by molecular-level interactions. These insights have direct implications for future mechanistic studies and applications of contact charging involving polymeric materials.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Atoms to fibers: Identifying novel processing methods in the synthesis of pitch-based carbon fibers

Understanding and optimizing the key mechanisms used in the synthesis of pitch-based carbon fibers (CFs) are challenging, because unlike polyacrylonitrile-based CFs, the feedstock for pitch-based CFs is chemically hetero- geneous, resulting in complex fabrication leading to inconsistency in the final properties. In this work, we use molecular dynamics simulations to explore the processing and chemical phase space through a framework of CF models to identify their effects on elastic performance. The results are in excellent agreement with experiments. We find that density, followed by alignment, and functionality of the molecular constituents dictate the CF mechanical properties more strongly than their size and shape. Last, we propose a previously unexplored fabrication route for high-modulus CFs. Unlike graphitization, this results in increased sp 3 fraction, achieved via generating high-density CFs. In addition, the high sp 3 fraction leads to the fabrication of CFs with isometric compressive and tensile moduli, enabling their potential applications for compressive loading.

01 COAL, LIGNITE, AND PEAT↗
DOE OSTI2019

Predicting cost-effective carbon fiber precursors: Unraveling the functionalities of oxygen and nitrogen-containing groups during carbonization from ReaxFF simulations

Blends of polyacrylonitrile (PAN) and poly(p-phenylene-2,6-benzobisoxazole) (PBO) as precursors may offer an opportunity to reduce the cost of carbon fiber (CF) production. The all-carbon ring formations and volatile gas production during the heating and carbonization for 9 PAN/PBO blend precursors with varying mixing ratios are studied via the ReaxFF reactive molecular dynamics simulations. Evolutions of oxygen-containing (O-containing) and nitrogen-containing (N-containing) groups are detailed, in order to reveal the reaction mechanisms of the O and N-based CF precursors. Particularly, the O-containing groups are identified to be more efficient for initiating the carbonization, whereas N-containing groups are far longer retained in the graphitic materials and play a key role in capturing and converting carbon radical species into the graphitic networks. Additionally, the PAN/PBO blend precursor with a mole ratio of 1:1 is compared with the pre-oxidized PAN, PAN, and PBO. As a result, it is found that the PAN/PBO blends could be a promising alternative for the cost-effective PAN-based CF precursors, since they can decrease the cost of the CF production by means of: (a) eliminating the pre-oxidation process, (b) having considerable all-carbon ring formations within a short period, and (c) having a relatively fast conversion rate, reaching 95% 6-membered carbon ring formation.

42 ENGINEERING↗
DOE OSTI2025

Advancing Multiscale Simulation of Plasma-Surface Interfaces

We report the development of an atomistic-informed, surface-state-dependent predictive model for particle exchange in a carbon-tungsten plasma-surface interface. The predictive model uses machine learning (ML) techniques to learn the energy and angular distributions for particle exchange and rate functions for surface state evolution from molecular dynamics simulations of cumulative bombardment of tungsten by energetic carbon ions. Each predictive component is sensitive to the energy and trajectory of incident plasma species and the surface state. The surface state is represented by a set of surface state descriptors, which were derived from the atomistic surface state for each independent carbon bombardment event. These descriptors are representative of the composition and degree of amorphization of the outermost angstrom of surface material and were chosen to optimize predictive performance for particle exchange at the interface. The distributions for particle exchange (reflection/sputtering) are demonstrated to vary with each surface state descriptor, motivating the development of surface-state-dependent particle exchange models for plasma simulations. The performance of various ML methods was compared, including polynomial quantile regression, artificial neural networks, k-nearest neighbors, and random forest algorithms, with polynomial regression performing the best for interpolation and extrapolation of learned relationships. In addition to the particle exchange model, a neutral network was developed and used to identify data sufficiency throughout surface descriptor space, which will enable real-time feedback during future data production to ensure data is produced where it is most needed, and we provide commentary on improvements to the data production workflow for future endeavors.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Experimental and Computational Insights into the Structural Dynamics of the Fc Fragment of IgG1 Subtype from Biosimilar VEGF‐Trap

The constant fragment (Fc) of the immunoglobulin G1 (IgG1) subtype is increasingly recognized as a crucial scaffold in the development of advanced therapeutics due to its enhanced specificity, efficacy, and extended half‐life. A prime example is VEGF‐Trap (Aflibercept), a recombinant fusion protein that merges the Fc region of the IgG1 subtype with the binding domains of vascular endothelial growth factor receptors (VEGFR)‐1 and VEGFR‐2. The Fc region's role in N‐glycosylation is particularly important, as it significantly influences protein stability. Herein, the first near‐physiological temperature structures of the N‐glycan‐bound Fc fragment of IgG1 subtype from a biosimilar VEGF‐Trap are presented, determined using the SPring‐8 Angstrom Compact free electron LAser (SACLA) and the Turkish Light Source (Turkish DeLight). Comparative analysis with cryogenic structures, including existing data, reveals alternate conformations within the glycan‐binding pocket. Furthermore, molecular dynamics simulations indicate the presence of a high degree of structural plasticity, explaining how the protein adapts its structure through conformational changes. The observed structural fluctuations/conformational changes demonstrate the effect of N‐glycans on protein stability. These findings offer new insights into the molecular basis of Fc‐mediated functions and provide valuable information for the design of next‐generation therapeutics.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Mechanistic Insights into Molecular Copper Hydride Catalysis: the Kinetic Stability of CuH Monomers toward Aggregation is a Critical Parameter for Catalyst Performance

The activity of molecular copper hydride (CuH) complexes towards the selective insertion of unsaturated hydrocarbons under mild conditions has contributed significantly to versatile methodologies for upgrading these feedstocks. However, these catalysts are particularly susceptible to deleterious aggregation, leading to the depletion of active CuH species. Little is known about the mechanisms of CuH aggregation, how it influences overall catalyst performance, and how it can be controlled. We address these challenges with mechanistic studies on a model reaction of unactivated alkene hydroboration catalyzed by (IPr*CPh 3 )CuH (LCuH). Here, we report a comprehensive mechanistic investigation of this system, identifying an aggregation pathway that continuously depletes catalytically active LCuH to form inactive CuH clusters during turnover. Deactivation of LCuH is controlled primarily by the competition between the kinetics of the initial LCuH dimerization step and that of alkene insertion. We therefore propose that a more comprehensive understanding of CuH catalyst performance must account for the kinetics of the initial LCuH dimerization step, revising a previously explored thermodynamic understanding of CuH aggregation, where the concentration of active species is controlled by equilibria established between CuH dimers and monomers. With a series of (NHC)CuH congeners (NHC = N-heterocyclic carbene), we demonstrate that ostensibly minor structural modifications to the ligand peripheries can drastically affect the LCuH dimerization kinetics, while maintaining reactivity towards on–cycle alkene insertion. We employed a computational approach based on molecular dynamics simulations to provide an in-depth understanding of how specific structural ligand modifications can substantially increase the kinetic stability of monomeric CuH catalysts. Our combined experimental and computational studies suggest strategies for rational ligand design that can be broadly applied to molecular catalyst systems that are susceptible to deactivation via aggregation pathways.

Ryan, David E. [Pacific Northwest National Laborat↗
DOE OSTI2020

Data-guided Multi-Map variables for ensemble refinement of molecular movies

Driving molecular dynamics simulations with data-guided collective variables offer a promising strategy to recover thermodynamic information from structure-centric experiments. In this study, the three-dimensional electron density of a protein, as it would be determined by cryo-EM or x-ray crystallography, is used to achieve simultaneously free-energy costs of conformational transitions and refined atomic structures. Unlike previous density-driven molecular dynamics methodologies that determine only the best map-model fits, our work employs the recently developed Multi-Map methodology to monitor concerted movements within equilibrium, non-equilibrium, and enhanced sampling simulations. Construction of all-atom ensembles along the chosen values of the Multi-Map variable enables simultaneous estimation of average properties, as well as real-space refinement of the structures contributing to such averages. Using three proteins of increasing size, we demonstrate that biased simulation along the reaction coordinates derived from electron densities can capture conformational transitions between known intermediates. The simulated pathways appear reversible with minimal hysteresis and require only low-resolution density information to guide the transition. The induced transitions also produce estimates for free energy differences that can be directly compared to experimental observables and population distributions. The refined model quality is superior compared to those found in the Protein Data Bank. We find that the best quantitative agreement with experimental free-energy differences is obtained using medium resolution density information coupled to comparatively large structural transitions. Practical considerations for probing the transitions between multiple intermediate density states are also discussed.

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

Ab-initio molecular dynamics study of eutectic chloride salt: MgCl2–NaCl–KCl

Ionic liquid materials are viable candidates as a heat transfer fluid (HTF) in a wide range of applications, notably within concentrated solar power (CSP) technology and molten salt reactors (MSRs). For next-generation CSP and MSR technologies that strive for higher power generation efficiency, a HTF with wide liquid phase range and energy storage capabilities is crucial. Studies have shown that eutectic chloride salts exhibit thermal stability at high temperatures, high heat storage capacity, and are less expensive than nitrate and carbonate salts. However, the experimental data needed to fully evaluate the potential of eutectic chloride salts as a HTF contender are scarce and entail large uncertainties. Considering the high cost and potential hazards associated with the experimental methods used to determine the properties of ionic liquids, molecular modeling can be used as a viable alternative resource. In this study, the eutectic ternary chloride salt MgCl 2 –NaCl–KCl is modeled using ab-initio molecular dynamics simulations (AIMDs) in the liquid phase. Using the simulated data, the thermophysical and transport properties of eutectic chloride salt can be calculated: density, viscosity, heat capacity, diffusion coefficient, and ionic conductivity. For an initial model validation, experimental pair-distribution function data were obtained from X-ray total scattering techniques and compared to the theoretical pair-distribution function. Additionally, theoretical viscosity values are compared to experimental viscosity values for a similar system. The results provide a starting foundation for a MgCl 2 –NaCl–KCl model that can be extended to predict other fundamental properties.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2021

Using a Coarse-Grained Modeling Framework to Identify Oligomeric Motifs with Tunable Secondary Structure

Coarse-grained modeling can be used to explore general theories that are independent of specific chemical detail. In this paper, we present cg_openmm, a Python-based simulation framework for modeling coarse-grained hetero-oligomers and screening them for structural and thermodynamic characteristics of cooperative secondary structures. cg_openmm facilitates the building of coarse-grained topology and random starting configurations, setup of GPU-accelerated replica exchange molecular dynamics simulations with the OpenMM software package, and features a suite of postprocessing thermodynamic and structural analysis tools. In particular, native contact analysis, heat capacity calculations, and free energy of folding calculations are used to identify and characterize cooperative folding transitions and stable secondary structures. In this work, we demonstrate the capabilities of cg_openmm on a simple 1–1 Lennard-Jones coarse-grained model, in which each residue contains 1 backbone and 1 side-chain bead. By scanning both nonbonded and bonded force-field parameter spaces at the coarse-grained level, we identify and characterize sets of parameters which result in the formation of stable helices through cooperative folding transitions. Furthermore, we show that the geometries and stabilities of these helices can be tuned by manipulating the force-field parameters.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Conformational restriction shapes the inhibition of a multidrug efflux adaptor protein

Abstract Membrane efflux pumps play a major role in bacterial multidrug resistance. The tripartite multidrug efflux pump system from Escherichia coli , AcrAB-TolC, is a target for inhibition to lessen resistance development and restore antibiotic efficacy, with homologs in other ESKAPE pathogens. Here, we rationalize a mechanism of inhibition against the periplasmic adaptor protein, AcrA, using a combination of hydrogen/deuterium exchange mass spectrometry, cellular efflux assays, and molecular dynamics simulations. We define the structural dynamics of AcrA and find that an inhibitor can inflict long-range stabilisation across all four of its domains, whereas an interacting efflux substrate has minimal effect. Our results support a model where an inhibitor forms a molecular wedge within a cleft between the lipoyl and αβ barrel domains of AcrA, diminishing its conformational transmission of drug-evoked signals from AcrB to TolC. This work provides molecular insights into multidrug adaptor protein function which could be valuable for developing antimicrobial therapeutics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Exploring the formation of gold/silver nanoalloys with gas-phase synthesis and machine-learning assisted simulations

While nanoalloys are of paramount scientific and practical interest, the main processes leading to their formation are still poorly understood. Key structural features in the alloy systems, including the crystal phase, chemical ordering, and morphology, are challenging to control at the nanoscale, making it difficult to extend their use to industrial applications. Here, in this contribution, we focus on the gold/silver system that has two of the most prevalent noble metals and combine experiments with simulations to uncover the formation mechanisms at the atomic level. Nanoparticles were produced using a state-of-the-art inert-gas aggregation source and analyzed using transmission electron microscopy and energy-dispersive X-ray spectroscopy. Machine-learning-assisted molecular dynamics simulations were employed to model the crystallization process from liquid droplets to nanocrystals. Our study finds a preponderance of nanoparticles with five-fold symmetric morphology, including icosahedra and decahedra which is consistent with previous results on mono-metallic nanoparticles. However, we observed that gold atoms, rather than silver atoms, segregate at the surface of the obtained nanoparticles for all the considered alloy compositions. These segregation tendencies are in contrast to previous studies and have consequences on the crystallization dynamics and the subsequent crystal ordering. We finally showed that the underpinning of this surprising segregation dynamics is due to charge transfer and electrostatic interactions rather than surface energy considerations.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Peridynamic Model for Single-Layer Graphene Obtained from Coarse Grained Bond Forces

An ordinary state-based peridynamic material model is proposed for single sheet graphene. The model is calibrated using coarse grained molecular dynamics simulations. The coarse graining method allows the dependence of bond force on bond length to be determined, including the horizon. The peridynamic model allows the horizon to be rescaled, providing a multiscale capability and allowing for substantial reductions in computational cost compared with molecular dynamics. The calibrated peridynamic model is compared to experimental data on the deflection and perforation of a graphene monolayer by an atomic force microscope probe.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Assessment of software methods for estimating protein-protein relative binding affinities

A growing number of computational tools have been developed to accurately and rapidly predict the impact of amino acid mutations on protein-protein relative binding affinities. Such tools have many applications, for example, designing new drugs and studying evolutionary mechanisms. In the search for accuracy, many of these methods employ expensive yet rigorous molecular dynamics simulations. By contrast, non-rigorous methods use less exhaustive statistical mechanics, allowing for more efficient calculations. However, it is unclear if such methods retain enough accuracy to replace rigorous methods in binding affinity calculations. This trade-off between accuracy and computational expense makes it difficult to determine the best method for a particular system or study. Here, eight non-rigorous computational methods were assessed using eight antibody-antigen and eight non-antibody-antigen complexes for their ability to accurately predict relative binding affinities (ΔΔG) for 654 single mutations. In addition to assessing accuracy, we analyzed the CPU cost and performance for each method using a variety of physico-chemical structural features. This allowed us to posit scenarios in which each method may be best utilized. Most methods performed worse when applied to antibody-antigen complexes compared to non-antibody-antigen complexes. Rosetta-based JayZ and EasyE methods classified mutations as destabilizing (ΔΔG < -0.5 kcal/mol) with high (83–98%) accuracy and a relatively low computational cost for non-antibody-antigen complexes. Some of the most accurate results for antibody-antigen systems came from combining molecular dynamics with FoldX with a correlation coefficient (r) of 0.46, but this was also the most computationally expensive method. Overall, our results suggest these methods can be used to quickly and accurately predict stabilizing versus destabilizing mutations but are less accurate at predicting actual binding affinities. This study highlights the need for continued development of reliable, accessible, and reproducible methods for predicting binding affinities in antibody-antigen proteins and provides a recipe for using current methods.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Experimental determination of the temperature-dependent Van Hove function in a Zr 80 Pt 20 liquid

Even though the viscosity is one of the most fundamental properties of liquids, the connection with the atomic structure of the liquid has proven elusive. By combining inelastic neutron scattering with the electrostatic levitation technique, the time-dependent pair-distribution function (i.e., the Van Hove function) has been determined for liquid Zr 80 Pt 20 . We show that the decay time of the first peak of the Van Hove function is directly related to the Maxwell relaxation time of the liquid, which is proportional to the shear viscosity. This result demonstrates that the local dynamics for increasing or decreasing the coordination number of local clusters by one determines the viscosity at high temperature, supporting earlier predictions from molecular dynamics simulations.

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

Melatonin-Induced Modulation of Cholesterol-Enriched Model Neuronal Membranes

Melatonin, a hormone primarily produced by the brain’s pineal gland, not only regulates circadian rhythms, but also influences the structural and biophysical properties of neuronal membranes. Its amphiphilic nature enables direct incorporation into lipid bilayers and preferential interactions with cholesterol-rich lipid rafts, critical hubs for cellular signaling and membrane organization. Despite increasing recognition of its membrane activity, the molecular basis of melatonin’s interactions with coexisting liquid-ordered (L o ) and liquid-disordered (L d ) phases remains unclear. Here, in this study, we combine small-angle neutron scattering (SANS) and all-atom molecular dynamics simulations to examine model neuronal membranes composed of DSPC, DOPC, POPC, and cholesterol. Our results show that melatonin preserves domain morphology while adopting distinct orientations within the bilayer and at the membrane interface, allowing both lateral and transmembrane bridging across lipid phases. These findings establish the molecular underpinnings of melatonin’s modulation of membrane heterogeneity and provide strong support for its receptor-independent actions.

atomistic simulations↗
DOE OSTI2026

Assessing the Limitations of Self-Interaction-Corrected Functionals for Describing the Hydrated Electron

Simulating the hydrated electron using density functional theory is challenging due to the prevalence of self-interaction error in standard functionals. Hybrid functionals like PBEh(40) can reasonably describe the chemistry of an excess electron in water and partially mitigate self-interaction error by incorporating exact Hartree–Fock exchange, but they are computationally expensive making them impractical for large-scale and long-time ab initio molecular dynamics simulations. Explicit self-interaction correction schemes that are applied on an orbital-by-orbital basis offer a potential alternative when the correction is limited to the singly occupied molecular orbital obtained with a generalized gradient approximation functional. Here, we examine whether the Perdew–Zunger self-interaction correction scheme applied to the revPBE functional can provide a computationally efficient and physically sensible alternative to PBEh(40) for the hydrated electron. We find that functionals incorporating a self-interaction correction scheme should be viewed with caution when applied to the hydrated electron and its reactivity. Furthermore, we show that it is critical to consider extensive sampling and diverse chemical environments when validating their performance.

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

Static and Dynamic Correlations in Water: Comparison of Classical Ab Initio Molecular Dynamics at Elevated Temperature with Path Integral Simulations at Ambient Temperature

It is a common practice in ab initio molecular dynamics (AIMD) simulations of water to use an elevated temperature to overcome the overstructuring and slow diffusion predicted by most current density functional theory (DFT) models. The simulation results obtained in this distinct thermodynamic state are then compared with experimental data at ambient temperature based on the rationale that a higher temperature effectively recovers nuclear quantum effects (NQEs) that are missing in the classical AIMD simulations. In this work, we systematically examine the foundation of this assumption for several DFT models as well as for the many-body MB-pol model. Here, we find for the cases studied that a higher temperature does not correctly mimic NQEs at room temperature, which is especially manifest in significantly different three-molecule correlations as well as hydrogen bond dynamics. In many of these cases, the effects of NQEs are the opposite of the effects of carrying out the simulations at an elevated temperature.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗