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At least 739 records · Page 41

Reliable Spectroscopic Constants for CCH-, NH2- and Their Isotopomers from an Accurate Potential Energy Function

Accurate quartic force fields have been determined for the CCH- and NH2- molecular anions using the singles and doubles coupled-cluster method that includes a perturbational estimate of the effects of connected triple excitations, CCSD(T). Very large one-particle basis sets have been used including diffuse functions and up through g-type functions. Correlation of the nitrogen and carbon core electrons has been included, as well as other "small" effects, such as the diagonal Born-Oppenheimer correction, and basis set extrapolation, and corrections for higher-order correlation effects and scalar relativistic effects. Fundamental vibrational frequencies have been computed using standard second-order perturbation theory as well as variational methods. Comparison with the available experimental data is presented and discussed. The implications of our research for the astronomical observation of molecular anions will be discussed.

Lee, Timothy J.↗

Molecular modeling of polymer composite interactions with analytes in electronic nose sensors for environmental monitoring in International Space Station

We report a molecular modeling study to investigate the polymer-carbon black (CB) composite-analyte interactions in resistive sensors. These sensors comprise the JPL Electronic Nose (ENose) sensing array developed for monitoring breathing air in human habitats. The polymer in the composite is modeled based on its stereisomerism and sequence isomerism, while the CB is modeled as uncharged naphthalene rings (with no hydrogens). The Dreiding 2.21 force field is used for the polymer and solvent molecules and graphite parameters are assigned to the carbon black atoms. A combination of molecular mechanics (MM) and molecular dynamics (NPT-MD and NVT-MD) techniques are used to obtain the equilibrium composite structure by inserting naphthalene rings in the polymer matrix. Polymers considered for this work include poly(4- vinylphenol), polyethylene oxide, and ethyl cellulose. Analytes studied are representative of both inorganic (ammonia) and organic (methanol, toluene, hydrazine) compounds. The results are analyzed for the composite microstructure by calculating the radial distribution profiles as well as for the sensor response by predicting the interaction energies of the analytes with the composites.

electronic noise environmental monitoring polymer ↗

Molecular modeling of interactions in electronic nose sensors for environmental monitoring

We report a study aimed at understanding analyte interactions with sensors made from polymer-carbon black composite films. The sensors are used in an Electronic Nose (ENose) which is used for monitoring the breathing air quality in human habitats. The model mimics the experimental conditions of the composite film deposition and formation and was developed using molecular modeling and simulation tools. The Dreiding 2.21 Force Field was used for the polymer and analyte molecules while graphite parameters were assigned to the carbon black atoms. The polymer considered for this work is methyl vinyl ether / maleic acid copolymer. The target analytes include both inorganic (NH3) and organic (methanol) types of compound. Results indicate different composite-analyte interaction behavior.

electronic noise polymer-carbon composite molecula↗

The V1 and V2 Bands of FNO2

There have been few previous spectroscopic studies of FNO2 in excited vibrational states. Bernitt, Miller an dHisatsune obtained low resolution IR spectra of all six fundamentals and determined a harmonic force field.

Spectroscopic Studies↗

Bromine Dioxide, OBrO: The Rotational Spectrum and Molecular Properties

The spectra are well descrie by Hamiltonian which included centrifugal distortion efects for fine and hyperfine terms. The molecular structure and the harmonic force field have been derived, and they as well as fine and hyperfine structure constants, are compared with data of related molecules and ESR data from OBrO isolated in cryogenic salt matrices.

Bromine Dioxide Rotational Spectrum↗

An Ozone Increase in the Antarctic Summer Stratosphere: A Dynamical Response to the Ozone Hole

Profiles of ozone concentration retrieved from the SBUV series of satellites show an increase between 1979 and 1997 in the summertime Antarctic middle stratosphere (approx. 25-10 hPa). Data over the South Pole from ozone sondes confirm the increase. A similar ozone increase is produced in a chemistry climate model that allows feedback between constituent changes and the stratospheric circulation through radiative heating. A simulation that excludes the radiative coupling between predicted ozone and the circulation does not capture this ozone increase. We show that the ozone increase in our model simulations is caused by a dynamical feedback in response to the changes in the stratospheric wind fields forced by the radiative perturbation associated with the Antarctic ozone hole.

Stolarski, R. S.↗

The Influence of the 2006 Indonesian Biomass Burning Aerosols on Tropical Dynamics Studied with the GEOS-5 AGCM

The direct and semi-direct effects of aerosols produced by Indonesian biomass burning (BB) during August November 2006 on tropical dynamics have been examined using NASA's Goddard Earth Observing System, Version 5 (GEOS-5) atmospheric general circulation model (AGCM). The AGCM includes CO, which is transported by resolved and sub-grid processes and subject to a linearized chemical loss rate. Simulations were driven by two sets of aerosol forcing fields calculated offline, one that included Indonesian BB aerosol emissions and one that did not. In order to separate the influence of the aerosols from internal model variability, the means of two ten-member ensembles were compared. Diabatic heating from BB aerosols increased temperatures over Indonesia between 150 and 400 hPa. The higher temperatures resulted in strong increases in upward grid-scale vertical motion, which increased water vapor and CO over Indonesia. In October, the largest increases in water vapor were found in the mid-troposphere (~25%) while the largest increases in CO occurred just below the tropopause (80 ppbv or ~50%). Diabatic heating from the Indonesian BB aerosols caused CO to increase by 9% throughout the tropical tropopause layer in November and 5% in the lower stratosphere in December. The results demonstrate that aerosol heating plays an important role in the transport of BB pollution and troposphere-to-stratosphere transport. Changes in vertical motion and cloudiness induced by aerosol heating can also alter the transport and phase of water vapor in the upper troposphere/lower stratosphere.

Ott, Lesley↗

JavaGenes Molecular Evolution

JavaGenes is a general-purpose, evolutionary software system written in Java. It implements several versions of a genetic algorithm, simulated annealing, stochastic hill climbing, and other search techniques. This software has been used to evolve molecules, atomic force field parameters, digital circuits, Earth Observing Satellite schedules, and antennas. This version differs from version 0.7.28 in that it includes the molecule evolution code and other improvements. Except for the antenna code, JaveGenes is available for NASA Open Source distribution.

Lohn, Jason↗

Inventions Utilizing Microfluidics and Colloidal Particles

Several related inventions pertain to families of devices that utilize microfluidics and/or colloidal particles to obtain useful physical effects. The families of devices can be summarized as follows: (1) Microfluidic pumps and/or valves wherein colloidal-size particles driven by electrical, magnetic, or optical fields serve as the principal moving parts that propel and/or direct the affected flows. (2) Devices that are similar to the aforementioned pumps and/or valves except that they are used to manipulate light instead of fluids. The colloidal particles in these devices are substantially constrained to move in a plane and are driven to spatially order them into arrays that function, variously, as waveguides, filters, or switches for optical signals. (3) Devices wherein the ultra-laminar nature of microfluidic flows is exploited to effect separation, sorting, or filtering of colloidal particles or biological cells in suspension. (4) Devices wherein a combination of confinement and applied electrical and/or optical fields forces the colloidal particles to become arranged into three-dimensional crystal lattices. Control of the colloidal crystalline structures could be exploited to control diffraction of light. (5) Microfluidic devices, incorporating fluid waveguides, wherein switching of flows among different paths would be accompanied by switching of optical signals.

Marr, David W.↗

Theoretical Foundation of Copernicus: A Unified System for Trajectory Design and Optimization

The fundamental methods are described for the general spacecraft trajectory design and optimization software system called Copernicus. The methods rely on a unified framework that is used to model, design, and optimize spacecraft trajectories that may operate in complex gravitational force fields, use multiple propulsion systems, and involve multiple spacecraft. The trajectory model, with its associated equations of motion and maneuver models, are discussed.

Ocampo, Cesar↗

Addition of Electrostatic Forces to EDEM with Applications to Triboelectrically Charged Particles

Tribocharging of particles is common in many processes including fine powder handling and mixing, printer toner transport and dust extraction. In a lunar environment with its high vacuum and lack of water, electrostatic forces are an important factor to consider when designing and operating equipment. Dust mitigation and management is critical to safe and predictable performance of people and equipment. The extreme nature of lunar conditions makes it difficult and costly to carryout experiments on earth which are necessary to better understand how particles gather and transfer charge between each other and with equipment surfaces. DEM (Discrete Element Modeling) provides an excellent virtual laboratory for studying tribocharging of particles as well as for design of devices for dust mitigation and for other purposes related to handling and processing of lunar regolith. Theoretical and experimental work has been performed pursuant to incorporating screened Coulombic electrostatic forces into EDEM Tm, a commercial DEM software package. The DEM software is used to model the trajectories of large numbers of particles for industrial particulate handling and processing applications and can be coupled with other solvers and numerical models to calculate particle interaction with surrounding media and force fields. In this paper we will present overview of the theoretical calculations and experimental data and their comparison to the results of the DEM simulations. We will also discuss current plans to revise the DEM software with advanced electrodynamic and mechanical algorithms.

Hogue, Michael D.↗

Rovibrational Spectroscopic Constants and Fundamental Vibrational Frequencies for Isotopologues of Cyclic and Bent Singlet HC2N isomers

Through established, highly-accurate ab initio quartic force fields (QFFs), a complete set of fundamental vibrational frequencies, rotational constants, and rovibrational coupling and centrifugal distortion constants have been determined for both the cyclic 1(sup 1) 1A' and bent 2(sup 1)A' DCCN, H(C13)CCN, HC(C-13)N, and HCC(N-15) isotopologues of HCCN. Spectroscopic constants are computed for all isotopologues using second-order vibrational perturbation theory (VPT2), and the fundamental vibrational frequencies are computed with VPT2 and vibrational configuration interaction (VCI) theory. Agreement between VPT2 and VCI results is quite good with the fundamental vibrational frequencies of the bent isomer isotopologues in accord to within a 0.1 to 3.2 / cm range. Similar accuracies are present for the cyclic isomer isotopologues. The data generated here serve as a reference for astronomical observations of these closed-shell, highly-dipolar molecules using new, high-resolution telescopes and as reference for laboratory studies where isotopic labeling may lead to elucidation of the formation mechanism for the known interstellar molecule: X 3A0 HCCN.

molecular data↗

Free-Energy Calculations. A Mathematical Perspective

Ion channels are pore-forming assemblies of transmembrane proteins that mediate and regulate ion transport through cell walls. They are ubiquitous to all life forms. In humans and other higher organisms they play the central role in conducting nerve impulses. They are also essential to cardiac processes, muscle contraction and epithelial transport. Ion channels from lower organisms can act as toxins or antimicrobial agents, and in a number of cases are involved in infectious diseases. Because of their important and diverse biological functions they are frequent targets of drug action. Also, simple natural or synthetic channels find numerous applications in biotechnology. For these reasons, studies of ion channels are at the forefront of biophysics, structural biology and cellular biology. In the last decade, the increased availability of X-ray structures has greatly advanced our understanding of ion channels. However, their mechanism of action remains elusive. This is because, in order to assist controlled ion transport, ion channels are dynamic by nature, but X-ray crystallography captures the channel in a single, sometimes non-native state. To explain how ion channels work, X-ray structures have to be supplemented with dynamic information. In principle, molecular dynamics (MD) simulations can aid in providing this information, as this is precisely what MD has been designed to do. However, MD simulations suffer from their own problems, such as inability to access sufficiently long time scales or limited accuracy of force fields. To assess the reliability of MD simulations it is only natural to turn to the main function of channels - conducting ions - and compare calculated ionic conductance with electrophysiological data, mainly single channel recordings, obtained under similar conditions. If this comparison is satisfactory it would greatly increase our confidence that both the structures and our computational methodologies are sufficiently accurate. Channel conductance, defined as the ratio of ionic current through the channel to applied voltage, can be calculated in MD simulations by way of applying an external electric field to the system and counting the number of ions that traverse the channel per unit time. If the current is small, a voltage significantly higher than the experimental one needs to be applied to collect sufficient statistics of ion crossing events. Then, the calculated conductance has to be extrapolated to the experimental voltage using procedures of unknown accuracy. Instead, we propose an alternative approach that applies if ion transport through channels can be described with sufficient accuracy by the one-dimensional diffusion equation in the potential given by the free energy profile and applied voltage. Then, it is possible to test the assumptions of the equation, recover the full voltage/current dependence, determine the reliability of the calculated conductance and reconstruct the underlying (equilibrium) free energy profile, all from MD simulations at a single voltage. We will present the underlying theory, model calculations that test this theory and simulations on ion conductance through a channel that has been extensively studied experimentally. To our knowledge this is the first case in which the complete, experimentally measured dependence of the current on applied voltage has been reconstructed from MD simulations.

free energy↗

On Ion Clusters in the Interstellar Gas

In a recent paper V.I. Krassovsky (1958) predicts the occurrence of clusters of large numbers of atoms and molecules around ions in the interstellar gas. He then proposes a number of physicochemical processes that would be considerably enhanced by the high particle density in such clusters. In particular, he suggests that absorption by negative ions formed in the clusters would account for the interstellar extinction without any necessity for the presence of grains. Because of the important consequences that ion clusters could have, it is necessary to examine their occurrence more fully. This note re-examines the formation of ion clusters in space and shows that even ion-molecule pairs are essentially non-existent. Ion clusters have been considered by Bloom and Margenau (1952) from the same point of view as that used by Krassovsky, whose basic reference (Joffe and Semenov 1933) unfortunately is not available. A different approach has been used by Eyring, Hirschfelder, and Taylor (1936) following the methods of chemical equilibrium. Both the references cited here enable one to conclude that clustering is negligible. Therefore, the treatment of Eyring et al. is more appropriate than the method of Bloom and Margenau, which depends on the statistical equilibrium of an atmosphere in a force field.

Donn, Bertram↗

Modeling Modern Methane Emissions from Natural Wetlands: Model Description and Results - 1

Methane is an important greenhouse gas which contributes about 22 percent to the present greenhouse effect. Natural wetlands currently constitute the biggest methane source and were the major source in preindustrial times. Wetland emissions depend highly on the climate, i.e., on soil temperature and water table. To investigate the response of methane emissions from natural wetlands to climate variations, a process-based model that derives methane emissions from natural wetlands as a function of soil temperature, water table, and net primary productivity is used. For its application on the global scale, global data sets for all model parameters are generated. In addition, a simple hydrologic model is developed in order to simulate the position of the water table in wetlands. The hydrologic model is tested against data from different wetland sites, and the sensitivity of the hydrologic model to changes in precipitation is examined. The global methane­ hydrology model constitutes a tool to study temporal and spatial variations in methane emissions from natural wetlands. The model is applied using high-frequency atmospheric forcing fields from European Center for Medium-range Weather Forecasts (ECMWF) re-analyses of the period from 1982 to 1993. We calculate global annual methane emissions from wetlands to be 260 teragrams per year. Twenty-five percent of these methane emissions originate from wetlands north of 30 degrees North Latitude. Only 60 percent of the produced methane is emitted, while the rest is re-oxidized. A comparison of zonal integrals of simulated global wetland emissions and results obtained by an inverse modeling approach shows good agreement. In a test with data from two wetlands the seasonality of simulated and observed methane emissions agrees well.

Biogeochemical processes↗

Li-Doped Ionic Liquid Electrolytes: From Bulk Phase to Interfacial Behavior

Ionic liquids have been proposed as candidate electrolytes for high-energy density, rechargeable batteries. We present an extensive computational analysis supported by experimental comparisons of the bulk and interfacial properties of a representative set of these electrolytes as a function of Li-salt doping. We begin by investigating the bulk electrolyte using quantum chemistry and ab initio molecular dynamics to elucidate the solvation structure of Li(+). MD simulations using the polarizable force field of Borodin and coworkers were then performed, from which we obtain an array of thermodynamic and transport properties. Excellent agreement is found with experiments for diffusion, ionic conductivity, and viscosity. Combining MD simulations with electronic structure computations, we computed the electrochemical window of the electrolytes across a range of Li(+)-doping levels and comment on the role of the liquid environment. Finally, we performed a suite of simulations of these Li-doped electrolytes at ideal electrified interfaces to evaluate the differential capacitance and the equilibrium Li(+) distribution in the double layer. The magnitude of differential capacitance is in good agreement with our experiments and exhibits the characteristic camel-shaped profile. In addition, the simulations reveal Li(+) to be highly localized to the second molecular layer of the double layer, which is supported by additional computations that find this layer to be a free energy minimum with respect to Li(+) translation.

molecular dynamics↗

Molecular Dynamics Modeling of Carbon Nanotube Composite Fracture Using ReaxFF

Carbon nanotube (CNT) fiber reinforced composites with specific tensile strengths and moduli approaching those of aerospace grade carbon fiber composites have recently been reported. This achievement was enabled by the emerging availability of high N/tex yarns in kilometer-scale quantities. While the production of this yarn is an impressive advance, its strength is still much lower than that of the individual CNTs comprising the yarn. Closing this gap requires understanding load transfer between CNTs at the nanometer dimensional scale. This work uses reactive molecular dynamics simulations to gain an understanding at the nanometer scale of the key factors that determine CNT nanocomposite mechanical performance, and to place more realistic upper bounds on the target properties. While molecular dynamics simulations using conventional force fields can predict elastic properties, the ReaxFF reactive forcefield can also model fracture behavior because of its ability to accurately describe bond breaking and formation during a simulation. The upper and lower bounds of CNT composite properties are investigated by comparing systems composed of CNTs continuously connected across the periodic boundary with systems composed of finite length CNTs. These lengths, effectively infinite for the continuous tubes and an aspect ratio of 13 for the finite length case, result from practical limitations on the number of atoms that can be included in a simulation. Experimentally measured aspect ratios are typically on the order of 100,000, so the calculated results should represent upper and lower limits on experimental mechanical properties. Finally, the effect of various degrees of covalent crosslinking between the CNTs and amorphous carbon matrix is considered to identify the amount of CNT-matrix covalent bonding that maximizes overall composite properties.

Jensen, Benjamin D.↗

The dependence of the oceans MOC on mesoscale eddy diffusivities: A model study

The dependence of the depth and strength of the ocean's global meridional overturning cells (MOC) on the specification of mesoscale eddy diffusivity (K) is explored in two ocean models. The GISS and MIT ocean models are driven by the same prescribed forcing fields, configured in similar ways, spun up to equilibrium for a range of K 's and the resulting MOCs mapped and documented. Scaling laws implicit in modern theories of the MOC are used to rationalize the results. In all calculations the K used in the computation of eddy-induced circulation and that used in the representation of eddy stirring along neutral surfaces, is set to the same value but is changed across experiments. We are able to connect changes in the strength and depth of the Atlantic MOC, the southern ocean upwelling MOC, and the deep cell emanating from Antarctica, to changes in K.

Global ocean↗