Results for “molecular modelling” — Page 32

DOE OSTI2021

Extreme Molecular Complexity Resulting in a Continuum of Carbonaceous Species in Biomass Burning Tar Balls from Wildfire Smoke

Biomass burning emits a wide range of carbonaceous particles into the atmosphere and has negative impacts on human health and the Earth’s radiative balance. Nonvolatile spherical organic aerosol particles, commonly known as tar balls, represent one of the most abundant particles in aged biomass burning smoke. However, the detailed molecular-level composition of ambient tar balls is largely unknown but critical to access their environmental impacts. Ambient aerosol samples collected during a wildfire event, which were ~90% tar balls by number fraction, were analyzed using ultrahigh resolution Orbitrap Elite mass spectrometry with four complementary ionization modes. Our results show the molecular composition of tar balls to be complex, composed of over 10,000 molecular formulas. Model estimated saturation mass concentrations and relative humidity dependent glass transition temperatures were consistent with low volatility and solid morphology as expected for tar balls. Room-temperature evaporation kinetics showed that these particles were composed of ~90% non-volatile species. The molecular complexity detected here signifies a continuum of carbonaceous species, ranging from C3 to C45 with continuous ranges of oxygenation and hydrogen saturation for each Cn. Approximately 24% of molecular formulas were estimated the be highly aromatic, which could indicate chemical compounds with negative health effects, and which may contribute to visible light absorption. The carbon continuum observed here has significant implications for the molecular characterization of atmospheric organic matter. The level of complexity detected here should not be ignored in future studies and we demonstrate that multiple analytical methods may be required to suitably interpret this complexity on a molecular level.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Computational determination of a primary diffusion mode in γ U-10Mo under irradiation

Low enriched uranium (< 20 % 235 U)-molybdenum (U-Mo) monolithic fuel is the primary candidate for high performance research and test reactors, and is in the process of being qualified to replace highly enriched uranium (≥ 20 % 23 5U) fuel. As part of the qualification process, it is critical to understand and predict the behavior of fission gas bubbles under irradiation, which affects fuel swelling and fuel failure. Mechanistic fuel models are being developed that can both reproduce the existing experimental data for fuel swelling, and be further applied to irradiation conditions beyond the experimental scope. Diffusion of species under irradiation conditions is an important parameter in the mechanistic fuel models; however, no temperature-relevant experimental diffusion data exists. In the present work, radiation-enhanced diffusion coefficients of U, Mo, and Xe in λU-10wt.%Mo were calculated in the temperature range between 300 K and 1400 K via rate-theory models and molecular dynamics simulations with an embedded-atom method interatomic potential for the U-Mo-Xe system. Accordingly, total diffusion coefficients under relevant irradiation conditions are determined using previously obtained intrinsic thermal diffusion and radiation-driven diffusion coefficients, as well as the newly calculated radiation-enhanced diffusion coefficients presented herein. Radiation-enhanced diffusion of U and Mo was dominant in the intermediate temperature range, whereas radiation-enhanced diffusion of Xe did not significantly contribute to total diffusion of Xe at the relevant fission rate densities. Radiation-enhanced diffusion of Xe became faster than both intrinsic thermal diffusion and radiation-driven diffusion at a fission rate density of 5 x 10 22 fissions/m 3 /s, which is higher than the typical fission rate density range in research reactors. The temperature regime that radiation-enhanced diffusion of each element dominated was dependent on the fission rate density. Finally, the total diffusion coefficients of U, Mo, and Xe, updated in this work, will be utilized as parameters in the mechanistic fuel models to help predict the behavior of fission gas bubbles under irradiation more accurately.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2022

Building an extensible cell wall

Abstract This article recounts, from my perspective of four decades in this field, evolving paradigms of primary cell wall structure and the mechanism of surface enlargement of growing cell walls. Updates of the structures, physical interactions, and roles of cellulose, xyloglucan, and pectins are presented. This leads to an example of how a conceptual depiction of wall structure can be translated into an explicit quantitative model based on molecular dynamics methods. Comparison of the model’s mechanical behavior with experimental results provides insights into the molecular basis of complex mechanical behaviors of primary cell wall and uncovers the dominant role of cellulose–cellulose interactions in forming a strong yet extensible network.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Ab Initio Direct Dynamics

The reactivity and dynamics of molecular systems can be explored computationally by classical trajectory calculations. The traditional approach involves fitting a functional form of a potential energy surface (PES) to the energies from a large number of electronic structure calculations and then integrating numerous trajectories on this fitted PES to model the molecular dynamics. The ever-decreasing cost of computing and continuing advances in computational chemistry software have made it possible to use electronic structure calculations directly in molecular dynamics simulations without first having to construct a fitted PES. In this “on-the-fly” approach, every time the energy and its derivatives are needed for the integration of the equations of motion, they are obtained directly from quantum chemical calculations. This approach started to become practical in the mid-1990s as a result of increased availability of inexpensive computer resources and improved computational chemistry software. The application of direct dynamics calculations has grown rapidly over the last 25 years and would require a lengthy review article. The present Account is limited to some of our contributions to methods development and various applications. To improve the efficiency of direct dynamics calculations, we developed a Hessian-based predictor-corrector algorithm for integrating classical trajectories. Hessian updating made this even more efficient. Furthermore, this approach was also used to improve algorithms for following the steepest descent reaction paths. For larger molecular systems, we developed an extended Lagrangian approach in which the electronic structure is propagated along with the molecular structure. Strong field chemistry is a rapidly growing area, and to improve the accuracy of molecular dynamics in intense laser fields, we included the time-varying electric field in a novel predictor-corrector trajectory integration algorithm. Since intense laser fields can excite and ionize molecules, we extended our studies to include electron dynamics. Specifically, we developed code for time-dependent configuration interaction electron dynamics to simulate strong field ionization by intense laser pulses. Our initial application of ab initio direct dynamics in 1994 was to CH 2 O → H 2 + CO; the calculated vibrational distributions in the products were in very good agreement with experiment. In the intervening years, we have used direct dynamics to explore energy partitioning in various dissociation reactions, unimolecular dissociations yielding three fragments, reactions with branching after the transition state, nonstatistical dynamics of chemically activated molecules, dynamics of molecular fragmentation by intense infrared laser pulses, selective activation of specific dissociation channels by aligned intense infrared laser fields, angular dependence of strong field ionization, and simulation of sequential double ionization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Coupling of Charge Regulation and Geometry in Soft Ionizable Molecular Assemblies

The size, shape, and charge of structures, such as proteins and amphiphile assemblies, respond in an interconnected manner to solution ionic conditions. Here, we analyze assemblies of an amphiphile (C 16 K 2 ), with two ionizable amino acids [lysine (K)] coupled to a 16-carbon alkyl tail, via small-angle X-ray scattering (SAXS), nonlinear Poisson–Boltzmann theory (nl-PB), and hybrid Monte Carlo-molecular dynamics (MC-MD) simulations. SAXS revealed structural transitions from spherical micelles to cylindrical micelles to bilayers with increasing pH. By combining SAXS-determined structural information and nl-PB, we derived the molecular degree of ionization as a function of pH. The back-calculated titration curves matched the experimental data over an extended pH range, without adjustable parameters. Similarly, the SAXS data on the evolution of spherical micelle structure with ionic strength were combined with nl-PB and MC-MD to derive the bare and effective charges. MC-MD, which considered finite ion sizes, showed that bare and effective charges saturate quickly with increasing salt concentration. Furthermore, the calculated effective charges closely matched results from Zeta-potential measurements. The presented approach has advantages over customary methods for charge regulation, such as the Henderson–Hasselbalch (HH) or Hill models, where molecular ionization/deionization in assemblies is described by effective pKs that are distinct from the pK for isolated molecules. However, these models lack a physical explanation for these pK shifts. By contrast, our approach of combining structural details with an electrostatic model and simulations provides a more intuitive understanding of structure-charge coupling and a framework for understanding charge regulation in many synthetic and biological systems.

ionization↗

NASA NTRS1984

Low-energy proton stopping power of N2, O2 and water vapor and deviations from Bragg's rule

A modified local plasma model, based on the works of Lindhard and Winther; and Bethe, Brown, and Walske, is established. The Gordon-Kim model for molecular electron density is used to calculate stopping power of N2, O2, and water vapor for protons of energy ranging from 40 keV to 2.5 MeV, resulting in good agreement with experimental data. Deviations from Bragg's rule are evaluated and are discussed under the present theoretical model.

Xu, Y. J.↗

DOE OSTI2025

Quantitative Measurement of Molecular Permeability to a Synthetic Bacterial Microcompartment Shell System

Not Available

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Boron nitride nanotube precursor formation during high-temperature synthesis: kinetic and thermodynamic modelling

In this work, we performed integrated modelling of the chemical pathways of formation for boron nitride nanotube (BNNT) precursors during high-temperature synthesis in a B/N 2 mixture. Integrated modelling includes quantum chemistry, Quantum–classical molecular dynamics, thermodynamic modelling, and kinetic approaches. We demonstrate that BN compounds are formed via the interaction of molecular nitrogen with small boron clusters, rather than through interactions with less reactive liquid boron. (This process can also be described as N 2 molecule fixation.) Liquid boron evaporates to produce these boron clusters (B m with m ≤ 5), which are subsequently converted into B m N n chains. The production of such chains is crucial to the growth of BNNTs because these chains form the building blocks of bigger and longer BN chains and rings, which are in turn the building blocks of fullborenes and BNNTs. Additionally, kinetic modelling revealed that B 4 N 4 and B 5 N 4 species in particular play a major role in the N 2 molecule fixation process. Furthermore, the formation of these species via reactions with B 4 and B 5 clusters is not adequately described under the assumption of thermodynamic equilibrium, as is demonstrated in our kinetic modelling. Thus, the accumulation of both B 4 N 4 and B 5 N 4 depends on the background gas pressure and the gas cooling rate. Long BN chains and rings, which are precursors of the fullborene and BNNT growth, form via self-assembly of components B 4 N 4 and B 5 N 4 . Our modelling results—particularly the increased densities of B 4 N 4 and B 5 N 4 species at higher gas pressures—explain the experimentally observed effect of gas pressure on the yield of high-quality BNNTs. The catalytic role of hydrogen was also studied; it is shown that HBNH molecules can be the main precursor of BNNT synthesis in the presence of hydrogen.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2021

Mechanism of Rad26-assisted rescue of stalled RNA polymerase II in transcription-coupled repair

Transcription-coupled repair is essential for the removal of DNA lesions from the transcribed genome. The pathway is initiated by CSB protein binding to stalled RNA polymerase II. Mutations impairing CSB function cause severe genetic disease. Yet, the ATP-dependent mechanism by which CSB powers RNA polymerase to bypass certain lesions while triggering excision of others is incompletely understood. Here we build structural models of RNA polymerase II bound to the yeast CSB ortholog Rad26 in nucleotide-free and bound states. This enables simulations and graph-theoretical analyses to define partitioning of this complex into dynamic communities and delineate how its structural elements function together to remodel DNA. We identify an allosteric pathway coupling motions of the Rad26 ATPase modules to changes in RNA polymerase and DNA to unveil a structural mechanism for CSB-assisted progression past less bulky lesions. Our models allow functional interpretation of the effects of Cockayne syndrome disease mutations.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1999

Protein machines and self assembly in muscle organization

The remarkable order of striated muscle is the result of a complex series of protein interactions at different levels of organization. Within muscle, the thick filament and its major protein myosin are classical examples of functioning protein machines. Our understanding of the structure and assembly of thick filaments and their organization into the regular arrays of the A-band has recently been enhanced by the application of biochemical, genetic, and structural approaches. Detailed studies of the thick filament backbone have shown that the myosins are organized into a tubular structure. Additional protein machines and specific myosin rod sequences have been identified that play significant roles in thick filament structure, assembly, and organization. These include intrinsic filament components, cross-linking molecules of the M-band and constituents of the membrane-cytoskeleton system. Muscle organization is directed by the multistep actions of protein machines that take advantage of well-established self-assembly relationships. Copyright 1999 John Wiley & Sons, Inc.

NASA Discipline Musculoskeletal↗

DOE OSTI2022

Role of interfaces on phase formation during severe plastic deformation

The role of interfaces on phase formation during severe plastic deformation (SPD) was investigated using molecular dynamics simulations. It is found that dilute solute additions that segregate to interphase boundaries, and strengthen them, can greatly extend the solubility limits of the bounding phases at steady state, providing a novel approach to processing nanocomposite alloys by SPD. Here, the results are rationalized in terms of a modified effective temperature model, whereby increasing the interface strength leads to higher effective temperatures and correspondingly to higher solubilities. Comparison of the segregation coefficient at the interphase boundary with solubilities in the bounding phases illustrates the effective temperature model is self-consistent and comprehensive. Past experimental studies on severe plastic deformation are found consistent with these observations.

36 MATERIALS SCIENCE↗

NASA NTRS1987

Structure and kinematics of the molecular spiral arms in M51

Mapping of the CO(1-0) emission from the spiral galaxy was made with the Onsala 20 m antenna. The observations show that the emission is considerably enhanced in spiral arms which appear to originate as intense ridges of emission about 1 kpc from the nucleus. One of the main objectives for the 1986 observations was to study the variations of the tangential velocity component of molecular gas across a spiral arm. The radial velocity was found to have a velocity shift similar to that predicted by the density wave theory. The present (1986) observations of the inner southern spiral arm of M51 show that the tangential velocity component also behaves in a way which conforms with the density wave model. The molecular arms were compared with the H alpha ionized gas arms of Tully (1974) and it was found that the ionized gas appears to have its maximum intensity slightly outside the molecular arm.

Rydbeck, G.↗

NASA NTRS2011

Hypersonic Boundary Layer Transition Measurements Using NO2 approaches NO Photo-dissociation Tagging Velocimetry

Measurements of instantaneous and mean streamwise velocity profiles in a hypersonic laminar boundary layer as well as a boundary layer undergoing laminar-to-turbulent transition were obtained over a 10-degree half-angle wedge model. A molecular tagging velocimetry technique consisting of a NO2 approaches?NO photo-dissociation reaction and two subsequent excitations of NO was used. The measurement of the transitional boundary layer velocity profiles was made downstream of a 1-mm tall, 4-mm diameter cylindrical trip along several lines lying within a streamwise measurement plane normal to the model surface and offset 6-mm from the model centerline. For laminar and transitional boundary layer measurements, the magnitudes of streamwise velocity fluctuations are compared. In the transitional boundary layer the fluctuations were, in general, 2-4 times larger than those in the laminar boundary layer. Of particular interest were fluctuations corresponding to a height of approximately 50% of the laminar boundary layer thickness having a magnitude of nearly 30% of the mean measured velocity. For comparison, the measured fluctuations in the laminar boundary layer were approximately 5% of the mean measured velocity at the same location. For the highest 10% signal-to-noise ratio data, average single-shot uncertainties using a 1 ?Es and 50 ?Es interframe delay were ~115 m/s and ~3 m/s, respectively. By averaging single-shot measurements of the transitional boundary layer, uncertainties in mean velocity as low as 39 m/s were obtained in the wind tunnel. The wall-normal and streamwise spatial resolutions were 0.14-mm (2 pixel) and 0.82-mm (~11 pixels), respectively. These measurements were performed in the 31-inch Mach 10 Air Wind Tunnel at the NASA Langley Research Center.

Bathel, Brett F.↗

NASA NTRS1975

Interstellar molecular abundances toward omicron Persei

Extensive scanning of the B1 III star omicron Per has been done with the Copernicus telescope-spectrometer in an effort to determine column densities or meaningful upper limits for several molecules expected to be relatively abundant in H I regions of moderate density. The combination of radio H II, OH, and CO emission-line data with the optical absorption measurements indicates that omicron Per is embedded in the near edge of a dense molecular cloud and that the material seen in front of the star must be close to it. Molecules detected in ultraviolet absorption are H2, HD, CO, and possibly OH. The CO rotational temperature is between 2.2 and 3.8 K. The observed column densities and upper limits from Copernicus and ground-based data are compared with recent models for molecular formation in diffuse clouds.

Snow, T. P., Jr.↗

NASA NTRS2003

Salt modulates the stability and lipid binding affinity of the adipocyte lipid-binding proteins

Adipocyte lipid-binding protein (ALBP or aP2) is an intracellular fatty acid-binding protein that is found in adipocytes and macrophages and binds a large variety of intracellular lipids with high affinity. Although intracellular lipids are frequently charged, biochemical studies of lipid-binding proteins and their interactions often focus most heavily on the hydrophobic aspects of these proteins and their interactions. In this study, we have characterized the effects of KCl on the stability and lipid binding properties of ALBP. We find that added salt dramatically stabilizes ALBP, increasing its Delta G of unfolding by 3-5 kcal/mol. At 37 degrees C salt can more than double the stability of the protein. At the same time, salt inhibits the binding of the fluorescent lipid 1-anilinonaphthalene-8-sulfonate (ANS) to the protein and induces direct displacement of the lipid from the protein. Thermodynamic linkage analysis of the salt inhibition of ANS binding shows a nearly 1:1 reciprocal linkage: i.e. one ion is released from ALBP when ANS binds, and vice versa. Kinetic experiments show that salt reduces the rate of association between ANS and ALBP while simultaneously increasing the dissociation rate of ANS from the protein. We depict and discuss the thermodynamic linkages among stability, lipid binding, and salt effects for ALBP, including the use of these linkages to calculate the affinity of ANS for the denatured state of ALBP and its dependence on salt concentration. We also discuss the potential molecular origins and potential intracellular consequences of the demonstrated salt linkages to stability and lipid binding in ALBP.

NASA Discipline Cell Biology↗

NASA NTRSDate not supplied

INCREASING THE TRANSPARENCY AND REPRODUCIBILITY OF SPACE RADIATION SCIENCE: THE RADIATION BIOLOGY ONTOLOGY

Among the primary objectives of the Open/Open-Source Science paradigm are making scientific investigation data transparent and results reproducible [1], objectives shared by the FAIR principles [2]. To accomplish this, the conceptual framework that includes all the investigation objects needs to be accurately captured and communicated to all data consumers. A large part of this requires using metadata standards to annotate data collected. These standards should be readily accessible, informed by scientific community consensus and sufficiently specific to encompass all of the important aspects of the investigation. Starting in 2020 we have been co-leading an open consortium to develop a new metadata standard, the Radiation Biology Ontology (RBO), through the Open Biological and Biomedical Ontologies (OBO) Foundry [3]. We began by transforming many of the terms from the National Council on Radiation Protection and Measurement into concepts that can be formally related to existing OBO Foundry classes or attributes. We then identified and imported into the RBO existing OBO Foundry classes that have obvious relevance for radiation biomedicine (for example, concepts from the Environment Ontology that describe radiative processes, and concepts from the Gene Ontology dealing with molecular and cellular responses to radiation). Finally, we scrutinized datasets from investigations of radiation effects held in NASA GeneLab and LSDA repositories and added additional classes, instances, and attributes into the RBO that should be used to annotate these data. We developed the RBO using the open-source tools of GitHub and publish the RBO periodically through the NIH/NCBI BioPortal website, so systems worldwide can leverage the knowledge it contains [4]. This initial phase of concept modeling has yielded an RBO that at present has more than 300 declared concepts, with more than 3500 additional concepts imported from other OBO Foundry ontologies. While this first phase has focused on concepts for annotating samples, environments, exposures, and measurements, the next phase will center on supporting annotation of results and findings, such as concept models of molecular, cellular and tissue effects. The value of the RBO will be determined in part by our ability to engage the community in its development, and we have established a Radiobiology Informatics Consortium with unrestricted membership as the owner of the RBO in order to encourage investigators, system owners and other to join in this effort. Anyone can report issues or request new concept modeling or other features directly on GitHub. By using the BioPortal application programming interface, systems can pose dynamic queries to the latest version of the RBO for information on individual classes or entire hierarchies; this design eliminates the need for systems to be updated in order to use newer versions of the RBO. We hope to contribute to the advancement of open radiobiological science through the continued, open development of the RBO, that will provide more precise, machine-interpretable descriptions of investigations, as well as support data meta-analysis through machine learning or other artificial intelligence methods. REFERENCES [1] Open science in space. Nature Medicine, 2021. 27(9): p. 1485-1485. [2] Wilkinson, M.D., et al., The FAIR Guiding Principles for scientific data management and stewardship. Sci Data, 2016. 3: p. 160018. [3] Smith, B., et al., The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol, 2007. 25(11): p. 1251-5. [4] Whetzel, P.L., et al., BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res, 2011. 39(Web Server issue): p. W541-5.

informatics↗

NASA NTRSDate not supplied

INCREASING THE TRANSPARENCY AND REPRODUCIBILITY OF SPACE RADIATION SCIENCE: THE RADIATION BIOLOGY ONTOLOGY

Among the primary objectives of the Open/Open-Source Science paradigm are making scientific investigation data transparent and results reproducible [1], objectives shared by the FAIR principles [2]. To accomplish this, the conceptual framework that includes all the investigation objects needs to be accurately captured and communicated to all data consumers. A large part of this requires using metadata standards to annotate data collected. These standards should be readily accessible, informed by scientific community consensus and sufficiently specific to encompass all of the important aspects of the investigation. Starting in 2020 we have been co-leading an open consortium to develop a new metadata standard, the Radiation Biology Ontology (RBO), through the Open Biological and Biomedical Ontologies (OBO) Foundry [3]. We began by transforming many of the terms from the National Council on Radiation Protection and Measurement into concepts that can be formally related to existing OBO Foundry classes or attributes. We then identified and imported into the RBO existing OBO Foundry classes that have obvious relevance for radiation biomedicine (for example, concepts from the Environment Ontology that describe radiative processes, and concepts from the Gene Ontology dealing with molecular and cellular responses to radiation). Finally, we scrutinized datasets from investigations of radiation effects held in NASA GeneLab and LSDA repositories and added additional classes, instances, and attributes into the RBO that should be used to annotate these data. We developed the RBO using the open-source tools of GitHub and publish the RBO periodically through the NIH/NCBI BioPortal website, so systems worldwide can leverage the knowledge it contains [4]. This initial phase of concept modeling has yielded an RBO that at present has more than 300 declared concepts, with more than 3500 additional concepts imported from other OBO Foundry ontologies. While this first phase has focused on concepts for annotating samples, environments, exposures, and measurements, the next phase will center on supporting annotation of results and findings, such as concept models of molecular, cellular and tissue effects. The value of the RBO will be determined in part by our ability to engage the community in its development, and we have established a Radiobiology Informatics Consortium with unrestricted membership as the owner of the RBO in order to encourage investigators, system owners and other to join in this effort. Anyone can report issues or request new concept modeling or other features directly on GitHub. By using the BioPortal application programming interface, systems can pose dynamic queries to the latest version of the RBO for information on individual classes or entire hierarchies; this design eliminates the need for systems to be updated in order to use newer versions of the RBO. We hope to contribute to the advancement of open radiobiological science through the continued, open development of the RBO, that will provide more precise, machine-interpretable descriptions of investigations, as well as support data meta-analysis through machine learning or other artificial intelligence methods.

knowledge↗

NASA NTRS1997

Cure Chemistry of Phenylethynyl Terminated Oligomers

The ability to process high performance polymers into quality, void-free composites has been significantly advanced using oligomers terminated with reactive groups which cure or crosslink at elevated temperature without the evolution of volatile byproducts. Several matrix resin systems of considerable interest to the aerospace community utilize phenylethynyl-terminated imide (PETI) technology to achieve this advantage. The present paper addresses the cure chemistry of PETI oligomers. The thermal cure of a low molecular weight model compound was studied using a variety of analytical techniques including differential scanning calorimetry, Fourier transform infrared spectroscopy, and liquid chromatography-mass spectroscopy. The studies indicate an extremely complex cure process. Many stable products were isolated and this paper reports current work on identification of those products. The intent of this research is to provide fundamental insight into the molecular structure of the cured PETI engineering materials so that performance and durability can be more fully assessed.

Wood, Karen H.↗