Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “molecular modelling”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

CASTELO: clustered atom subtypes aided lead optimization—a combined machine learning and molecular modeling method

Background: Drug discovery is a multi-stage process that comprises two costly major steps: pre-clinical research and clinical trials. Among its stages, lead optimization easily consumes more than half of the pre-clinical budget. We propose a combined machine learning and molecular modeling approach that partially automates lead optimization workflow in silico, providing suggestions for modification hot spots. Results: The initial data collection is achieved with physics-based molecular dynamics simulation. Contact matrices are calculated as the preliminary features extracted from the simulations. To take advantage of the temporal information from the simulations, we enhanced contact matrices data with temporal dynamism representation, which are then modeled with unsupervised convolutional variational autoencoder (CVAE). Finally, conventional and CVAE-based clustering methods are compared with metrics to rank the submolecular structures and propose potential candidates for lead optimization. Conclusion: With no need for extensive structure-activity data, our method provides new hints for drug modification hotspots which can be used to improve drug potency and reduce the lead optimization time. It can potentially become a valuable tool for medicinal chemists.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2005

Mechanical Properties of Nanostructured Materials Determined Through Molecular Modeling Techniques

The potential for gains in material properties over conventional materials has motivated an effort to develop novel nanostructured materials for aerospace applications. These novel materials typically consist of a polymer matrix reinforced with particles on the nanometer length scale. In this study, molecular modeling is used to construct fully atomistic models of a carbon nanotube embedded in an epoxy polymer matrix. Functionalization of the nanotube which consists of the introduction of direct chemical bonding between the polymer matrix and the nanotube, hence providing a load transfer mechanism, is systematically varied. The relative effectiveness of functionalization in a nanostructured material may depend on a variety of factors related to the details of the chemical bonding and the polymer structure at the nanotube-polymer interface. The objective of this modeling is to determine what influence the details of functionalization of the carbon nanotube with the polymer matrix has on the resulting mechanical properties. By considering a range of degree of functionalization, the structure-property relationships of these materials is examined and mechanical properties of these models are calculated using standard techniques.

Clancy, Thomas C.↗
NASA NTRS1978

Ames interactive molecular model building system - A 3-D computer modelling system applied to the study of the origin of life

The investigation of specific interactions among biological molecules must take into consideration the stereochemistry of the structures. Thus, models of the molecules are essential for describing the spatial organization of potentially interacting groups, and estimations of conformation are required for a description of spatial organization. Both the function of visualizing molecules, and that of estimating conformation through calculations of energy, are part of the molecular modeling system described in the present paper. The potential uses of the system in investigating some aspects of the origin of life rest on the assumption that translation of conformation from genetic elements to catalytic elements would have been required for the development of the first replicating systems subject to the process of biological evolution.

Coeckelenbergh, Y.↗
DOE OSTI2024

Molecular Models of Atomically Dispersed Uranium at MoS 2 Surfaces Reveal Cooperative Mechanism of Water Reduction

Single atoms of uranium supported on molybdenum sulfide surfaces (U@MoS 2 ) have been recently demonstrated to facilitate the hydrogen evolution reaction (HER) through electrocatalysis. Theoretical calculations have predicted uranium hydroxide moieties bound to edge-sulfur atoms of MoS 2 as a proposed transition state involved in the HER process. However, the isolation of relevant intermediates involved in this process remains a challenge, rendering mechanistic hypotheses unverified. The present work describes the isolation and characterization of a uranium-hydroxide intermediate on molybdenum sulfide surfaces using [(Cp* 3 Mo 3 S 4 )UCp*], a molecular model of a reduced uranium center supported at MoS 2 . Mechanistic investigations highlight the metalloligand cooperativity with uranium involved in the water activation pathway. The corresponding uranium-oxo analogue, [(Cp* 3 Mo 3 S 4 )Cp*U(═O)], was also accessed from the hydroxide cluster via hydrogen atom transfer and from [(Cp* 3 Mo 3 S 4 )UCp*] through an alternative direct oxygen atom transfer. These results provide an atomistic perspective on the reactivity of low-valent uranium at molybdenum sulfide surfaces toward water, modeling key intermediates associated with the HER of U@MoS 2 catalysts.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2023

Molecular Simulation of Lithium Carbonate Reactive Vapor–Liquid Equilibria Using a Deep Potential Model

We developed a first-principles machine learning model for the reactive vapor–liquid phase behavior of molten Li 2 CO 3 . The model was trained on ab initio electronic density functional theory data using the Deep Potential (DP) methodology, and its accuracy was evaluated by comparing model predictions of density and viscosity to experimental measurements. Direct coexistence simulations with the DP model over time scales of tens of nanoseconds were used to observe equilibrium dissociation of Li 2 CO 3 into CO 2 residing primarily in the vapor phase and Li 2 O which remains dissolved in the liquid. The simulations covered a range of temperatures, overall system sizes, and vapor-to-liquid volume ratios. Results were analyzed in terms of the observed chemical composition of the liquid and vapor phases, product structure, and CO 2 partial pressures. In addition, we calculated equilibrium constants for the dissociation reaction by assuming ideal-solution behavior for the liquid. As expected on the basis of thermodynamic arguments and prior experiments for this system, the observed partial pressure of CO 2 in the gas phase depends on both the temperature and the ratio of vapor to liquid volumes, while the calculated equilibrium constants only depend on temperature. DP model predictions for the equilibrium constant of the reaction are generally consistent with the available experimental measurements. Furthermore, the present study establishes the validity of the DP methodology for the description of reactive, multiphase equilibria from first principles, with possible applications to many other systems of scientific and technological interest even in the absence of relevant experimental measurements.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1998

Molecular Modeling of the Compounds with Nonlinear Optical Properties

The molecular polarizability characteristics for a large series of naphthoquinone and quinoline derivatives have been calculated. The dependence of calculated hyperpolarizability on the positions and the number of donor and acceptor substituents is discussed.

Timofeeva, Tatiana V.↗
DOE OSTI2022

Molecular Modeling Predicts Novel Antibody Escape Mutations in the Respiratory Syncytial Virus Fusion Glycoprotein

Respiratory syncytial virus (RSV) causes severe disease in young infants, particularly those with heart or lung diseases or born prematurely. Because no vaccine is currently available, monoclonal antibodies are used to prevent severe RSV disease in high-risk infants. While it is known that RSV evolves to avoid recognition by antibodies, screening tools that can predict which changes to the virus may lead to antibody resistance are greatly needed.

molecular modeling↗
DOE OSTI2026

Molecular Modeling of Surfactant Interaction on Phospholipid Bilayers Mimicking Corneal Epithelium

Surfactants found in consumer products can compromise eye corneal membrane integrity upon accidental exposure. Traditional in vitro and in vivo approaches to evaluate membrane–surfactant interaction pose experimental limitations such as species variability, reproducibility, and most often do not provide the overall picture. These limitations motivate the use of in silico models to study phenomena like cellular disruption assays caused by surfactants at the molecular scale. In this work, coarse-grained molecular dynamics simulations have been employed to investigate how nonionic alcohol ethoxylate (AE) and anionic surfactant alcohol ethoxy sulfate (AES) interact with lipid bilayer liposomes that mimic corneal epithelial cell membranes. The spherical liposome is composed of 1,2-dihexadecanoyl-sn-glycero-3-phosphocholine (DPPC), 1,2-di(9Z-octadecenoyl)-sn-glycero-3-phosphoethanolamine (DOPE), 1,2-di(9Z-octadecenoyl)-sn-glycero-3-phospho-l-serine (DOPS), and cholesterol, resembling the composition of the corneal epithelial cells’ membrane bilayer. The simulation consisted of varying degrees of representative surfactant compositions and two initial types of surfactant configurations within or outside the liposome. Our results reveal that both surfactants induce outer leaflet bulging, agreeing with membrane solubilization models. The more highly ethoxylated surfactant, AE, caused more consistent inner leaflet disruption than AES, resulting in significantly more water permeation and membrane thinning. In addition, both surfactants increase the lateral diffusion of lipids within the membrane layers, with higher ethoxylated AE showing a stronger effect than AES. This study demonstrates how surfactant structure and localization influence bilayer membrane integrity, offering mechanistic insights into the irritation potential, thus guiding the rational design of effective surfactant-based formulations.

Lipids↗
NASA NTRS2015

Fracture of Carbon Nanotube - Amorphous Carbon Composites: Molecular Modeling

Carbon nanotubes (CNTs) are promising candidates for use as reinforcements in next generation structural composite materials because of their extremely high specific stiffness and strength. They cannot, however, be viewed as simple replacements for carbon fibers because there are key differences between these materials in areas such as handling, processing, and matrix design. It is impossible to know for certain that CNT composites will represent a significant advance over carbon fiber composites before these various factors have been optimized, which is an extremely costly and time intensive process. This work attempts to place an upper bound on CNT composite mechanical properties by performing molecular dynamics simulations on idealized model systems with a reactive forcefield that permits modeling of both elastic deformations and fracture. Amorphous carbon (AC) was chosen for the matrix material in this work because of its structural simplicity and physical compatibility with the CNT fillers. It is also much stiffer and stronger than typical engineering polymer matrices. Three different arrangements of CNTs in the simulation cell have been investigated: a single-wall nanotube (SWNT) array, a multi-wall nanotube (MWNT) array, and a SWNT bundle system. The SWNT and MWNT array systems are clearly idealizations, but the SWNT bundle system is a step closer to real systems in which individual tubes aggregate into large assemblies. The effect of chemical crosslinking on composite properties is modeled by adding bonds between the CNTs and AC. The balance between weakening the CNTs and improving fiber-matrix load transfer is explored by systematically varying the extent of crosslinking. It is, of course, impossible to capture the full range of deformation and fracture processes that occur in real materials with even the largest atomistic molecular dynamics simulations. With this limitation in mind, the simulation results reported here provide a plausible upper limit on achievable CNT composite properties and yield some insight on the influence of processing conditions on the mechanical properties of CNT composites.

Jensen, Benjamin D.↗
DOE OSTI2023

Exploring the Structural, Dynamic, and Functional Properties of Metal–Organic Frameworks through Molecular Modeling

This review spotlights the role of atomic-level modeling in research on metal-organic frameworks (MOFs), especially the key methodologies of density functional theory (DFT), Monte Carlo (MC) simulations, and molecular dynamics (MD) simulations. The discussion focuses on how periodic and cluster-based DFT calculations can provide novel insights into MOF properties, with a focus on predicting structural transformations, understanding thermodynamic properties and catalysis, and providing information or properties that are fed into classical simulations such as force field parameters or partial charges. Classical simulation methods, highlighting force field selection, databases of MOFs for high-throughput screening, and the synergistic nature of MC and MD simulations, are described. By predicting equilibrium thermodynamic and dynamic properties, these methods offer a wide perspective on MOF behavior and mechanisms. Additionally, the incorporation of machine learning (ML) techniques into quantum and classical simulations is discussed. These methods can enhance accuracy, expedite simulation setup, reduce computational costs, as well as predict key parameters, optimize geometries, and estimate MOF stability. By charting the growth and promise of computational research in the MOF field, the aim is to provide insights and recommendations to facilitate the incorporation of computational modeling more broadly into MOF research.

36 MATERIALS SCIENCE↗