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At least 1,135 records · Page 63
All sourcesNASA NTRSDOE OSTI
NASA NTRS1994

Shock propagation and the generation of magnetohydrodynamic wave fields in inhomogeneous molecular clouds

We develop a simple one-dimensional model for the interaction of a steady, thin, planar shock wave with a nonrigid cloud which may be in motion relative to the surrounding medium, and we apply the model to shocks impinging on, and propagating through, molecular clouds. Both 'adiabatic' (gamma = 5/3) and radiative (gamma = 1) shocks are considered and we allow for the presence of a uniform magnetic field directed either parallel or perpendicular to the shock normal. The former field orientation is equivalent to the hydrodynamic case, and the latter involves only fast MHD shocks. We focus on the manner in which such shocks can generate internal kinetic motions in the cloud on a range of size and density scales through the direct acceleration of cores and clumps by shocks transmitted into them and through the generation of an MHD wavefield via the reflection of the incident shock at clump boundaries. We find that stronger incident Mach numbers and smaller density contrasts lead to more efficient cloud acceleration, as do isothermal intercloud shocks and small intercloud magnetic field strengths. The acceleration efficiency is insensitive to the adiabatic index and the magnetic field strength in the cloud itself. For typical parameter choices, the direct acceleration of clouds and clumps by strong shocks is found to be substantial and could at least in part account for their observed velocity dispersions. If the shocks are moderately weak, the final velocity of the cloud is linearly related to its initial velocity, with higher acceleration giving shallower slopes (i.e., final velocity distributions which are less sensitive to the initial distribution). Compared to the kinetic energy of the postshock cloud, the energy given to the wavefield at each encounter is small, and the heating of the interclump medium by the dissipation of this wavefield is found to be insufficient to balance the cooling rate in the cloud as a whole (although it may be important in particular regions), even if this medium is warm, unless it is also extremely tenuous (n approximately less than 0.1/cu cm). Nevertheless, the correction for the velocity imparted to the cloud leads to a substantial increase in the critical incident Mach numner for wave emission over that reported by Spitzer for the rigid case. The implications of our model for shock-induced star formation are discussed briefly.

Miesch, Mark S.↗
NASA NTRS2020

New Insights into the Chemical Composition of Five Oort Cloud Comets After Re-analysis of their Infrared Spectra

We present revised results for the main molecular species in five Oort Cloud (OC) comets observed with NIRSPEC at the Keck Observatory between 1999 and 2012 (C/1999 S4 (LINEAR), C/2001 A2 (LINEAR), C/2007 W1 (Boattini), C/2012 F6 (Lemmon), and C/2012 S1 (ISON)). The re-evaluation of these data shows the improvement of results in some of the datasets, in particular for comets observed and analyzed before the advent of new and revised fluorescence models and terrestrial retrieval methods introduced since 2011. We observe significant improvements in the resulting rotational temperatures and production rates for all species, and in mixing ratios of minor species (relative to water). The re-analysis also allowed us to quantify species not analyzed previously, mostly due to the lack of molecular models (e.g., ammonia and formaldehyde). We note, however, that the improvement of these revised values is less substantial for comets observed (and/or analyzed) since 2010.

Manuela Lippi↗
DOE OSTI2023

Molecular Rotations, Multiscale Order, Hyperuniformity, and Signatures of Metastability during the Compression/Decompression Cycles of Amorphous Ices

We model, via large-scale molecular dynamics simulations, the isothermal compression of low-density amorphous ice (LDA) to generate high-density amorphous ice (HDA) and the corresponding decompression extending to negative pressures to recover the low-density amorphous phase (LDA HDA ). Both LDA and HDA are nearly hyperuniform and are characterized by a dynamical HBN, showing that amorphous ices are nonstatic materials and implying that nearly hyperuniformity can be accommodated in dynamical networks. In correspondence with both the LDA-to-HDA and the HDA-to-LDA HDA phase transitions, the (partial) activation of rotational degrees of freedom activates a cascade effect that induces a drastic change in the connectivity and a pervasive reorganization of the HBN topology which, ultimately, break the samples’ hyperuniform character. Key to this effect is the rapid rate at which changes occur, and not their magnitude. The inspection of structural properties from the short- to the long-range shows that signatures of metastability are present at all length-scales, hence providing further solid evidence in support of the liquid–liquid critical point scenario. LDA and LDA HDA differ in terms of HBN and structural properties, implying that they are distinct low-density glasses. Our work unveils the role of molecular rotations in the phase transitions between amorphous ices and shows how the unfreezing of rotational degrees of freedom generates a cascade effect that propagates over multiple length-scales. Our findings greatly improve our basic understanding of water and amorphous ices and can potentially impact the field of molecular network-forming materials at large.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Ice Phase Classification Made Easy with Score-Based Denoising

Accurate identification of ice phases is essential for understanding various physicochemical phenomena. However, such classification for structures simulated with molecular dynamics is complicated by the complex symmetries of ice polymorphs and thermal fluctuations. For this purpose, both traditional order parameters and data-driven machine learning approaches have been employed, but they often rely on expert intuition, specific geometric information, or large training data sets. In this work, we present an unsupervised phase classification framework that combines a score-based denoiser model with a subsequent model-free classification method to accurately identify ice phases. Further, the denoiser model is trained on perturbed synthetic data of ideal reference structures, eliminating the need for large data sets and labeling efforts. The classification step utilizes the smooth overlap of atomic position (SOAP) descriptors as the atomic fingerprint, ensuring Euclidean symmetries and transferability to various structural systems. Our approach achieves a remarkable 100% accuracy in distinguishing ice phases of test trajectories using only seven ideal reference structures of ice phases as model inputs. This demonstrates the generalizability of the score-based denoiser model in facilitating phase identification for complex molecular systems. The proposed classification strategy can be broadly applied to investigate structural evolution and phase identification for a wide range of materials, offering new insights into the fundamental understanding of water and other complex systems.

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

Design and evaluation of novel analogs of 2-amino-4-boronobutanoic acid (ABBA) as inhibitors of human gamma-glutamyl transpeptidase

Inhibitors of gamma-glutamyl transpeptidase (GGT1, aka gamma-glutamyl transferase) are needed for the treatment of cancer, cardiovascular illness and other diseases. Compounds that inhibit GGT1 have been evaluated in the clinic, but no inhibitor has successfully demonstrated specific and systemic GGT1 inhibition. All have severe side effects. L-2-amino-4-boronobutanoic acid (l-ABBA), a glutamate analog, is the most potent GGT1 inhibitor in vitro. In this study, we have solved the crystal structure of human GGT1 (hGGT1) with ABBA bound in the active site. The structure was interrogated to identify interactions between the enzyme and the inhibitor. Based on these data, a series of novel ABBA analogs were designed and synthesized. Their inhibitory activity against the hydrolysis and transpeptidation activities of hGGT1 were determined. The lead compounds were crystalized with hGGT1 and the structures solved. The kinetic data and structures of the complexes provide new insights into the critical role of protein structure dynamics in developing compounds for inhibition of hGGT1.

60 APPLIED LIFE SCIENCES↗
NASA NTRS1997

A 2000 Solar Mass Rotating Molecular Disk Around NGC 6334A

We present millimeter and centimeter wave spectroscopic observations of the H II region NGC 6334A. We have mapped the source in several transitions of CO, CS, and NH3. The molecular emission shows a distinct flattened structure in the east-west direction. This structure is probably a thick molecular disk or torus (2.2 x 0.9 pc) responsible for the bipolarity of the near-infrared (NIR) and radio continuum emission which extends in two "lobes" to the north and south of the shell-like H II region. The molecular disk is rotating from west to east (omega approximately equals 2.4 km/s.pc) about an axis approximately parallel to the radio and NIR emission lobes. By assuming virial equilibrium, we find that the molecular disk contains approximately 2000 solar mass. Single-component gas excitation model calculations show that the molecular gas in the disk is warmer and denser (T(sub k) approximately equals 60 K, n approximately equals 3000/cc) than the gas to the north and south (T(sub k) approximately equals 50 K, n approximately equals 400/cc). High resolution (approximately 5 sec) NH3 (3, 3) images of NGC 6334A reveal several small (approximately 0.1 pc) clumps, one of which lies southwest of the radio continuum shell, and is spatially coincident with a near-infrared source, IRS 20. A second NH3 clump is coincident with an H2O maser and the center of a molecular outflow. The dense gas tracers, CS J = 5 approaches 4 and 7 approaches 6, peak near IRS 20 and the H2O maser, not at NGC 6334A. IRS 20 has a substantial far-infrared (FIR) luminosity L(sub FIR) approximately 10(exp 5) solar luminosity, which indicates the presence of an O 7.5 star but has no detected radio continuum (F(sub 6 cm) < 0.02 Jy). The combination of dense gas, a large FIR luminosity and a lack of radio continuum can best be explained if IRS 20 is a protostar. A third clump of NH3 emission lies to the west of IRS 20 but is not associated with any other molecular or continuum features. The star formation activity in the region has moved west of NGC 6334A to IRS 20 and the H2O maser position. We suggest that NGC 6334A, IRS 20, and the H2O maser spot are part of a "protocluster" of stars which is condensing from the massive molecular disk. The similarity between the structure around NGC 6334A and other large (r approximately 1 pc), massive (M approximately 10(exp 3) solar mass), rotating disks (K3-50A and G10.6-0.4) suggests that this may be a common mechanism by which open clusters form.

Kraemer, Kathleen E.↗
DOE OSTI2022

Thermal neutron scattering cross sections for amorphous carbon

Carbon materials are commonly found in both nuclear reactors and experimental systems. Various carbon structures occur in nuclear applications ranging from crystalline and nuclear graphite to the amorphous carbon seen in next-generation advanced reactor designs. Amorphous carbon is based on a randomized graphite-like structure and offers the unique ability to disperse impurities throughout the bulk composition. A graphite-like amorphous carbon system was modeled using the classical molecular dynamics (MD) code LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator). An improved version of the temperature-dependent Adaptive Intermolecular Reactive Empirical Bond Order (AIREBO) potential was used to model the carbon-carbon atomic interactions for the temperature at 300 K along with densities 1.60, 1.70, 1.85, and 2.23 g/cm{sup 3}. From the normalized velocity autocorrelation function (VACF), the phonon density of state (DOS) was then calculated as the Fourier transform of the normalized VACF. This DOS was then used as the primary input for the evaluation of the thermal scattering law (TSL, i.e. S(α,β)) and associated neutron thermal scattering cross sections. The TSL was analyzed using the Full Law Analysis Scattering System Hub (FLASSH). The amorphous structure results in shifts of the phonon DOS to lower energy modes than typically displayed for ideal crystalline graphite. This impact on the DOS is directly reflected in the TSL. Furthermore, the typical optical peak at 0.25 eV for the ideal graphite disappears for amorphous carbon, in good agreement with the expected structure. (authors)

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
NASA NTRS1975

Effect of molecular anisotropy on the intensity and degree of polarization of light scattered from model atmospheres

Computations of the intensity, flux, degree of polarization, and the positions of neutral points are presented for models of the terrestrial gaseous and hazy atmospheres by incorporating the molecular anisotropy due to air in the Rayleigh scattering optical thickness and phase matrix. Molecular anisotropy causes significant changes in the intensity, flux and the degree of polarization of the scattered light. The positions of neutral points do not change significantly. When the Rayleigh scattering optical thickness is kept constant and the molecular anisotropy factor is included only in the Rayleigh phase matrix, the flux does not change and the intensity and positions of neutron points change by a small amount. The changes in the degree of polarization are still significant.

Bahethi, O. P.↗
DOE OSTI2023

Dimensionally reduced machine learning model for predicting single component octanol–water partition coefficients

Abstract MF-LOGP, a new method for determining a single component octanol–water partition coefficients ( $$LogP$$ LogP ) is presented which uses molecular formula as the only input. Octanol–water partition coefficients are useful in many applications, ranging from environmental fate and drug delivery. Currently, partition coefficients are either experimentally measured or predicted as a function of structural fragments, topological descriptors, or thermodynamic properties known or calculated from precise molecular structures. The MF-LOGP method presented here differs from classical methods as it does not require any structural information and uses molecular formula as the sole model input. MF-LOGP is therefore useful for situations in which the structure is unknown or where the use of a low dimensional, easily automatable, and computationally inexpensive calculations is required. MF-LOGP is a random forest algorithm that is trained and tested on 15,377 data points, using 10 features derived from the molecular formula to make $$LogP$$ LogP predictions. Using an independent validation set of 2713 data points, MF-LOGP was found to have an average $$RMSE$$ RMSE = 0.77 ± 0.007, $$MAE$$ MAE = 0.52 ± 0.003, and $${R}^{2}$$ R 2 = 0.83 ± 0.003. This performance fell within the spectrum of performances reported in the published literature for conventional higher dimensional models ( $$RMSE$$ RMSE = 0.42–1.54, $$MAE$$ MAE = 0.09–1.07, and $${R}^{2}$$ R 2 = 0.32–0.95). Compared with existing models, MF-LOGP requires a maximum of ten features and no structural information, thereby providing a practical and yet predictive tool. The development of MF-LOGP provides the groundwork for development of more physical prediction models leveraging big data analytical methods or complex multicomponent mixtures. Graphical Abstract

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

New Insights into the Chemical Composition of Five Oort Cloud Comets after Re-analysis of Their Infrared Spectra

We present revised results for the main molecular species in five Oort Cloud comets observed with near-infrared echelle grating spectrometer (NIRSPEC) at the Keck Observatory between 1999 and 2012 (C/1999 S4 (LINEAR), C/2001 A2 (LINEAR), C/2007 W1 (Boattini), C/2012 F6 (Lemmon), and C/2012 S1 (ISON)). The re-evaluation of these data shows the improvement of results in some of the data sets, in particular for comets observed and analyzed before the advent of new and revised fluorescence models and terrestrial retrieval methods introduced since 2011. We observe significant improvements in the resulting rotational temperatures and the production rates for all species, and in mixing ratios of minor species (relative to water). The re-analysis also allowed us to quantify species not analyzed previously, mostly due to the lack of molecular models (e.g., ammonia and formaldehyde). We note, however, that the improvement of these revised values is less substantial for comets observed (and/or analyzed) since 2010.

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

Thermal Neutron Scattering Cross Sections for Graphitic Amorphous Carbon

Carbon materials are commonly found in both nuclear reactors and experimental systems. Various carbon structures occur in nuclear applications ranging from crystalline and nuclear graphite to the amorphous carbon seen in next-generation advanced reactor designs. Amorphous carbon is based on a randomized graphite-like structure and offers the unique ability to disperse impurities throughout the bulk composition. A graphite-like amorphous carbon system was modeled using the classical molecular dynamics (MD) code LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator). An improved version of the temperature-dependent Adaptive Intermolecular Reactive Empirical Bond Order (AIREBO) potential was used to model the carbon-carbon atomic interactions for the temperature at 300 K along with densities 1.60, 1.70, 1.85, and 2.23 g/cm 3 . From the normalized velocity autocorrelation function (VACF), the phonon density of state (DOS) was then calculated as the Fourier transform of the normalized VACF. This DOS was then used as the primary input for the evaluation of the thermal scattering law (TSL, i.e. S(α,β)) and associated neutron thermal scattering cross sections. The TSL was analyzed using the Full Law Analysis Scattering System Hub (FLASSH). The amorphous structure results in shifts of the phonon DOS to lower energy modes than typically displayed for ideal crystalline graphite. This impact on the DOS is directly reflected in the TSL. Furthermore, the typical features and the optical graphitic peak at 0.25 eV for the ideal graphite DOS disappear for graphite-like amorphous carbon, which shows good agreement with the expected structure.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2025

Advancing material modeling in hydrocodes using a concurrent finite-element and molecular dynamics multiscale framework

We present a multiscale simulation framework that couples the finite-element method with molecular dynamics. Bypassing traditional equations of state (EOS) by using in-line atomistic simulations, the method offers the advantage of incorporating detailed microscale physics not easily represented with coarse-grained models. Coupling consistency with the continuum code is ensured through the use of lifting and restriction operators, in line with heterogeneous multiscale methods. The concurrent continuum-atomistic framework is validated through comparison with experimental results and conventional EOS models, and demonstrated in a shock-driven hydrodynamic flow simulation under extreme conditions. We further evaluate the framework's usability by comparing it to state-of-the-art EOS models of deuterium. A computational performance study reveals that the atomistic EOS evaluation is a feasible alternative to conventional approaches, and demonstrates a weak scaling of 99% efficiency. These results highlight the framework's potential for large-scale multiscale modeling across a broad range of materials and conditions.

Computer science↗
DOE OSTI2026

Free Energy and Flexibility Analysis of Autoinhibited Human BRAF

The RAF serine/threonine protein kinases function as direct effectors of RAS in the intracellular transmission of extracellular growth signals, and they are key targets for drug discovery, given the high incidence of oncogenic mutations in RAF and other components of this signaling pathway. In its inactive state, RAF is held in an autoinhibited conformation in the cytosol through a combination of intramolecular interactions and binding to a regulatory 14−3−3 protein dimer. Activation of RAF is initiated by its interaction with membrane-localized GTP-bound RAS, which induces conformational changes that release RAF from its autoinhibited state. However, the molecular mechanisms governing RAF activation remain incomplete, largely due to the challenges in experimentally capturing the intermediate conformational states in this process. To address this gap, we developed a comprehensive all-atom model of BRAF based on existing cryo-EM structures. Using this model, we performed extensive molecular dynamics simulations to evaluate the stability and free energy landscape of autoinhibited BRAF in solution. Our analysis reveals conformational flexibility within the autoinhibited complex, suggesting that this dynamic behavior may play a role in facilitating BRAF activation upon engagement with the membrane-bound RAS.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

A multiscale cohesive law for carbon fiber networks

Better predictive models of mechanical failure in low-weight heat shield composites would aid material certification for missions with aggressive atmospheric entry conditions. In this study, we develop such a model for the rapid engineering analysis of the failure limits of phenolic impregnated carbon ablator (PICA) - a leading heat shield material whose structural component is a carbon fiber network. We hypothesize inelastic deformation failure mechanisms and model their behavior using molecular dynamics simulations to calculate the binding energy. We then upscale this binding energy to the macroscale using a renormalization argument. The approach delivers insightful and reasonably accurate macroscale predictions that compare favorably to experiments. In application, the model is validated for a particular variety of PICA by comparison to experiment and would then be used to study design scenarios in different entry conditions.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Phase diagram of the TIP4P/Ice water model by enhanced sampling simulations

In this work, we studied the phase diagram for the TIP4P/Ice water model using enhanced sampling molecular dynamics simulations. Our approach is based on the calculation of ice–liquid free energy differences from biased coexistence simulations that reversibly sample the melting and growth of layers of ice. We computed a total of 19 melting points for five different ice polymorphs, which are in excellent agreement with the melting lines obtained from the integration of the Clausius–Clapeyron equation. For proton-ordered and fully proton-disordered ice phases, the results are in very good agreement with previous calculations based on thermodynamic integration. For the partially proton-disordered ice III, we find a large increase in stability that is in line with previous observations using direct coexistence simulations for the TIP4P/2005 model. This issue highlights the robustness of the approach employed here for ice polymorphs with diverse degrees of proton disorder. Our approach is general and can be applied to the calculation of other complex phase diagrams.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
NASA NTRSDate not supplied

Scalable Variable Charge Molecular Dynamics Simulations of Metal-Oxide Systems

Interfaces between metals and oxides are an important feature in many technologically relevant materials, e.g., oxidation of metal surfaces, oxide-dispersion strengthened (ODS) alloys, dielectric components, and thermal barrier coatings among others. Experimental studies of such interfaces are challenging since the majority are buried within the bulk, making computational modeling an attractive alternative. Molecular dynamics (MD) simulations operate at the length scales relevant to many interface-mediated mechanisms, but the requisite interatomic potentials for metal-oxide systems require computationally expensive variable charge schemes to account for the disparate bonding types, thus often limiting their effectiveness. Here we introduce several improvements to the charge transfer interatomic potential (CTIP) model which enable greater computational efficiency for large scale MD simulations. Then, using a new CTIP parametrization for the Ni-O system, we demonstrate its capabilities to capture critical atomic scale mechanisms associated with metal-oxide interfaces. Long time scale simulations (>10 ns) are used to investigate high temperature oxidation and oxide precipitation from the melt, and large length scale simulations (> 1 million atoms) are used to study the interaction of dislocations with oxide particles. We have implemented the new CTIP model in the widely used, open-source MD code LAMMPS.

Gabriel Plummer↗
DOE OSTI2023

PTM‐Psi : A python package to facilitate the computational investigation of p ost‐ t ranslational m odification on p rotein s tructures and their i mpacts on dynamics and functions

Abstract Post‐translational modification (PTM) of a protein occurs after it has been synthesized from its genetic template, and involves chemical modifications of the protein's specific amino acid residues. Despite of the central role played by PTM in regulating molecular interactions, particularly those driven by reversible redox reactions, it remains challenging to interpret PTMs in terms of protein dynamics and function because there are numerous combinatorially enormous means for modifying amino acids in response to changes in the protein environment. In this study, we provide a workflow that allows users to interpret how perturbations caused by PTMs affect a protein's properties, dynamics, and interactions with its binding partners based on inferred or experimentally determined protein structure. This Python‐based workflow, called PTM‐Psi , integrates several established open‐source software packages, thereby enabling the user to infer protein structure from sequence, develop force fields for non‐standard amino acids using quantum mechanics, calculate free energy perturbations through molecular dynamics simulations, and score the bound complexes via docking algorithms. Using the S ‐nitrosylation of several cysteines on the GAP2 protein as an example, we demonstrated the utility of PTM‐Psi for interpreting sequence–structure–function relationships derived from thiol redox proteomics data. We demonstrate that the S ‐nitrosylated cysteine that is exposed to the solvent indirectly affects the catalytic reaction of another buried cysteine over a distance in GAP2 protein through the movement of the two ligands. Our workflow tracks the PTMs on residues that are responsive to changes in the redox environment and lays the foundation for the automation of molecular and systems biology modeling.

59 BASIC BIOLOGICAL SCIENCES↗