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 307 records · Page 17
All sourcesNASA NTRSDOE OSTI
NASA NTRS1985

Structural basis for stabilization of Z-DNA by cobalt hexaammine and magnesium cations

In the equilibrium between B-DNA and Z-DNA in poly(dC-dG), the [Co(NH3)6]3+ ion stabilizes the Z form 4 orders of magnitude more effectively than the Mg2+ ion. The structural basis of this difference is revealed in Z-DNA crystal structures of d(CpGpCpGpCpG) stabilized by either Na+/Mg2+ or Na+/Mg2+ plus [Co(NH3)6]3+. The crystals diffract X-rays to high resolution, and the structures were refined at 1.25 A. The [Co(NH3)6]3+ ion forms five hydrogen bonds onto the surface of Z-DNA, bonding to a guanine O6 and N7 as well as to a phosphate group in the ZII conformation. The Mg2+ ion binds through its hydration shell with up to three hydrogen bonds to guanine N7 and O6. Higher charge, specific fitting of more hydrogen bonds, and a more stable complex all contribute to the great effectiveness of [Co(NH3)6]3+ in stabilizing Z-DNA.

NASA Discipline Exobiology↗
NASA NTRS2005

Structural and energetic consequences of mutations in a solvated hydrophobic cavity

The structural and energetic consequences of modifications to the hydrophobic cavity of interleukin 1-beta (IL-1beta) are described. Previous reports demonstrated that the entirely hydrophobic cavity of IL-1beta contains positionally disordered water. To gain a better understanding of the nature of this cavity and the water therein, a number of mutant proteins were constructed by site-directed mutagenesis, designed to result in altered hydrophobicity of the cavity. These mutations involve the replacement of specific phenylalanine residues, which circumscribe the cavity, with tyrosine, tryptophan, leucine and isoleucine. Using differential scanning calorimetry to determine the relative stabilities of the wild-type and mutant proteins, we found all of the mutants to be destabilizing. X-ray crystallography was used to identify the structural consequences of the mutations. No clear correlation between the hydrophobicities of the specific side-chains introduced and the resulting stabilities was found.

Solvents/chemistry↗
NASA NTRS2004

The force exerted by the membrane potential during protein import into the mitochondrial matrix

The force exerted on a targeting sequence by the electrical potential across the inner mitochondrial membrane is calculated on the basis of continuum electrostatics. The force is found to vary from 3.0 pN to 2.2 pN (per unit elementary charge) as the radius of the inner membrane pore (assumed aqueous) is varied from 6.5 to 12 A, its measured range. In the present model, the decrease in force with increasing pore width arises from the shielding effect of water. Since the pore is not very much wider than the distance between water molecules, the full shielding effect of water may not be present; the extreme case of a purely membranous pore without water gives a force of 3.2 pN per unit charge, which should represent an upper limit. When applied to mitochondrial import experiments on the protein barnase, these results imply that forces between 11 +/- 2 pN and 13.5 +/- 2.5 pN catalyze the unfolding of barnase in those experiments. A comparison of these results with unfolding forces measured using atomic force microscopy is made.

Models, Molecular↗
NASA NTRS2005

Prediction of Mechanical Properties of Polymers With Various Force Fields

The effect of force field type on the predicted elastic properties of a polyimide is examined using a multiscale modeling technique. Molecular Dynamics simulations are used to predict the atomic structure and elastic properties of the polymer by subjecting a representative volume element of the material to bulk and shear finite deformations. The elastic properties of the polyimide are determined using three force fields: AMBER, OPLS-AA, and MM3. The predicted values of Young s modulus and shear modulus of the polyimide are compared with experimental values. The results indicate that the mechanical properties of the polyimide predicted with the OPLS-AA force field most closely matched those from experiment. The results also indicate that while the complexity of the force field does not have a significant effect on the accuracy of predicted properties, small differences in the force constants and the functional form of individual terms in the force fields determine the accuracy of the force field in predicting the elastic properties of the polyimide.

Odegard, Gregory M.↗
NASA NTRS2012

A DNA-Inspired Encryption Methodology for Secure, Mobile Ad Hoc Networks

Users are pushing for greater physical mobility with their network and Internet access. Mobile ad hoc networks (MANET) can provide an efficient mobile network architecture, but security is a key concern. A figure summarizes differences in the state of network security for MANET and fixed networks. MANETs require the ability to distinguish trusted peers, and tolerate the ingress/egress of nodes on an unscheduled basis. Because the networks by their very nature are mobile and self-organizing, use of a Public Key Infra structure (PKI), X.509 certificates, RSA, and nonce ex changes becomes problematic if the ideal of MANET is to be achieved. Molecular biology models such as DNA evolution can provide a basis for a proprietary security architecture that achieves high degrees of diffusion and confusion, and resistance to cryptanalysis. A proprietary encryption mechanism was developed that uses the principles of DNA replication and steganography (hidden word cryptography) for confidentiality and authentication. The foundation of the approach includes organization of coded words and messages using base pairs organized into genes, an expandable genome consisting of DNA-based chromosome keys, and a DNA-based message encoding, replication, and evolution and fitness. In evolutionary computing, a fitness algorithm determines whether candidate solutions, in this case encrypted messages, are sufficiently encrypted to be transmitted. The technology provides a mechanism for confidential electronic traffic over a MANET without a PKI for authenticating users.

Shaw, Harry↗
NASA NTRS2012

Observing Planets and Small Bodies in Sputtered High Energy Atom (SHEA) Fluxes

The evolution of the surfaces of bodies unprotected by either strong magnetic fields or thick atmospheres in the Solar System is caused by various processes, induced by photons, energetic ions and micrometeoroids. Among these processes, the continuous bombardment of the solar wind or energetic magnetospheric ions onto the bodies may significantly affect their surfaces, with implications for their evolution. Ion precipitation produces neutral atom releases into the exosphere through ion sputtering, with velocity distribution extending well above the particle escape limits. We refer to this component of the surface ejecta as sputtered high-energy atoms (SHEA). The use of ion sputtering emission for studying the interaction of exposed bodies (EB) with ion environments is described here. Remote sensing in SHEA in the vicinity of EB can provide mapping of the bodies exposed to ion sputtering action with temporal and mass resolution. This paper speculates on the possibility of performing remote sensing of exposed bodies using SHEA The evolution of the surfaces of bodies unprotected by either strong magnetic fields or thick atmospheres in the Solar System is caused by various processes, induced by photons, energetic ions and micrometeoroids. Among these processes, the continuous bombardment of the solar wind or energetic magnetospheric ions onto the bodies may significantly affect their surfaces, with implications for their evolution. Ion precipitation produces neutral atom releases into the exosphere through ion sputtering, with velocity distribution extending well above the particle escape limits. We refer to this component of the surface ejecta as sputtered high-energy atoms (SHEA). The use of ion sputtering emission for studying the interaction of exposed bodies (EB) with ion environments is described here. Remote sensing in SHEA in the vicinity of EB can provide mapping of the bodies exposed to ion sputtering action with temporal and mass resolution. This paper speculates on the possibility of performing remote sensing of exposed bodies using SHEA and suggests the need for quantitative results from laboratory simulations and molecular physic modeling in order to understand SHEA data from planetary missions. In the Appendix, referenced computer simulations using existing sputtering data are reviewed.

Milillo, A.↗
NASA NTRS2014

A Classification Scheme for Young Stellar Objects Using the WIDE-FIELD INFRARED SURVEY EXPLORER ALLWISE Catalog: Revealing Low-Density Star Formation in the Outer Galaxy

We present an assessment of the performance of WISE and the AllWISE data release in a section of the Galactic Plane. We lay out an approach to increasing the reliability of point source photometry extracted from the AllWISE catalog in Galactic Plane regions using parameters provided in the catalog. We use the resulting catalog to construct a new, revised young star detection and classification scheme combining WISE and 2MASS near and mid-infrared colors and magnitudes and test it in a section of the Outer Milky Way. The clustering properties of the candidate Class I and II stars using a nearest neighbor density calculation and the two-point correlation function suggest that the majority of stars do form in massive star forming regions, and any isolated mode of star formation is at most a small fraction of the total star forming output of the Galaxy. We also show that the isolated component may be very small and could represent the tail end of a single mechanism of star formation in line with models of molecular cloud collapse with supersonic turbulence and not a separate mode all to itself.

WIDE-FIELD↗
NASA NTRS2016

Evaluation of Methods for Molecular Dynamics Simulation of Ionic Liquid Electric Double Layers

We investigate how systematically increasing the accuracy of various molecular dynamics modeling techniques influences the structure and capacitance of ionic liquid electric double layers (EDLs). The techniques probed concern long-range electrostatic interactions, electrode charging (constant charge versus constant potential conditions), and electrolyte polarizability. Our simulations are performed on a quasi-two-dimensional, or slab-like, model capacitor, which is composed of a polarizable ionic liquid electrolyte, [EMIM][BF4], interfaced between two graphite electrodes. To ensure an accurate representation of EDL differential capacitance, we derive new fluctuation formulas that resolve the differential capacitance as a function of electrode charge or electrode potential. The magnitude of differential capacitance shows sensitivity to different long-range electrostatic summation techniques, while the shape of differential capacitance is affected by charging technique and the polarizability of the electrolyte. For long-range summation techniques, errors in magnitude can be mitigated by employing two-dimensional or corrected three dimensional electrostatic summations, which lead to electric fields that conform to those of a classical electrostatic parallel plate capacitor. With respect to charging, the changes in shape are a result of ions in the Stern layer (i.e. ions at the electrode surface) having a higher electrostatic affinity to constant potential electrodes than to constant charge electrodes. For electrolyte polarizability, shape changes originate from induced dipoles that soften the interaction of Stern layer ions with the electrode. The softening is traced to ion correlations vertical to the electrode surface that induce dipoles that oppose double layer formation. In general, our analysis indicates an accuracy dependent differential capacitance profile that transitions from the characteristic camel shape with coarser representations to a more diffuse profile with finer representations.

Haskins, Justin B.↗
NASA NTRS2018

Molecular Dynamics of ULTEM 9085 for 3D Manufacturing: Spectra, Thermodynamic Properties, and Shear Viscosity.

We present results of a molecular dynamic analysis of welding at the polymer-polymer interface. The analysis is performed for polyetherimide/ polycarbonate polymer blends. The work is motivated by the applications to 3D manufacturing in space. In the first part of the report, we discuss bulk and spectral characteristics of the amorphous polymer blends. The vibrational and infra-red spectra obtained using auto-correlation functions calculations in molecular dynamics are compared with the experimental spectra. The mechanical and thermal properties of the samples including heat capacity, bulk modulus, and thermal expansion coefficients are estimated and compared with experimental values. In the second part of the report, we discuss the result of molecular dynamical modeling of shear viscosity in a fully atomistic model of amorphous polymer blends with flat interface. The key result of the research is the demonstration of shear thinning behavior of the shear viscosity as a function of shear rate which is in good agreement with experimental data.

Luchinsky, Dmitry G.↗
NASA NTRS2017

Modeling Chemical Reactions in Classical Molecular Dynamics Simulations

An algorithm capable of incorporating multi-step reaction mechanisms into atomistic molecular dynamics (MD) simulations using traditional fixed valence force fields is proposed and implemented within the framework of LAMMPS (Large-scale Atomic Molecular Massively Parallel Simulator). This extension, referred to as fix bond/react, enables bonding topology modifications during a running MD simulation using pre- and post-reaction bonding templates to carry out a pre-specified reaction. Candidate reactants are first identified by interatomic separation, followed by the application of a generalized topology matching algorithm to confirm they match the pre-reaction template. This is followed by a topology conversion to match the post-reaction template and a dynamic relaxation to minimize high energy configurations. Two case studies, the condensation polymerization of nylon 6,6 and the formation of a highly-crosslinked epoxy, are simulated to demonstrate the robustness, stability, and speed of the algorithm. Improvements which could increase its utility are discussed.

Jacob R Gissinger↗
NASA NTRS2004

Stress Distribution During Deformation of Polycrystalline Aluminum by Molecular-Dynamics and Finite-Element Modeling

In this paper, a multiscale modelling strategy is used to study the effect of grain-boundary sliding on stress localization in a polycrystalline microstructure with an uneven distribution of grain size. The development of the molecular dynamics (MD) analysis used to interrogate idealized grain microstructures with various types of grain boundaries and the multiscale modelling strategies for modelling large systems of grains is discussed. Both molecular-dynamics and finite-element (FE) simulations for idealized polycrystalline models of identical geometry are presented with the purpose of demonstrating the effectiveness of the adapted finite-element method using cohesive zone models to reproduce grain-boundary sliding and its effect on the stress distribution in a polycrystalline metal. The yield properties of the grain-boundary interface, used in the FE simulations, are extracted from a MD simulation on a bicrystal. The models allow for the study of the load transfer between adjacent grains of very different size through grain-boundary sliding during deformation. A large-scale FE simulation of 100 grains of a typical microstructure is then presented to reveal that the stress distribution due to grain-boundary sliding during uniform tensile strain can lead to stress localization of two to three times the background stress, thus suggesting a significant effect on the failure properties of the metal.

Yamakov, V.↗