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At least 1,621 records · Page 90

Mars atmospheric dynamics as simulated by the NASA Ames General Circulation Model. II - Transient baroclinic eddies

A large set of experiments performed with the NASA Ames Mars General Circulation Model is analyzed to determine the properties, structure, and dynamics of the simulated transient baroclinic eddies. There is strong transient baroclinic eddy activity in the extratropics of the Northern Hemisphere during the northern autumn, winter, and spring seasons. The eddy activity remains strong for very large dust loadings, though it shifts northward. The eastward propagating eddies are characterized by zonal wavenumbers of 1-4 and periods of about 2-10 days. The properties of the GCM baroclinic eddies in the northern extratropics are compared in detail with analogous properties inferred from Viking Lander meteorology observations.

Barnes, Jeffrey R.↗

Water around fullerene shape amphiphiles: A molecular dynamics simulation study of hydrophobic hydration

Fullerene C{sub 60} sub-colloidal particle with diameter ∼1 nm represents a boundary case between small and large hydrophobic solutes on the length scale of hydrophobic hydration. In the present paper, a molecular dynamics simulation is performed to investigate this complex phenomenon for bare C{sub 60} fullerene and its amphiphilic/charged derivatives, so called shape amphiphiles. Since most of the unique properties of water originate from the pattern of hydrogen bond network and its dynamics, spatial, and orientational aspects of water in solvation shells around the solute surface having hydrophilic and hydrophobic regions are analyzed. Dynamical properties such as translational-rotational mobility, reorientational correlation and occupation time correlation functions of water molecules, and diffusion coefficients are also calculated. Slower dynamics of solvent molecules—water retardation—in the vicinity of the solutes is observed. Both the topological properties of hydrogen bond pattern and the “dangling” –OH groups that represent surface defects in water network are monitored. The fraction of such defect structures is increased near the hydrophobic cap of fullerenes. Some “dry” regions of C{sub 60} are observed which can be considered as signatures of surface dewetting. In an effort to provide molecular level insight into the thermodynamics of hydration, the free energy of solvation is determined for a family of fullerene particles using thermodynamic integration technique.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Ab initio study of the structure and properties of amorphous silicon hydride from accelerated molecular dynamics simulations

This paper presents a large-scale ab initio simulation study of amorphous silicon hydride (a-Si 1-x H x ) with an emphasis on the structure and properties of the material across a range of hydrogen concentration by combining accelerated molecular dynamics (MD) simulations with first-principles density-functional calculations. The accelerated MD scheme relied on classical metadynamics, which enabled the development of 2500+ high-quality structural models of a-Si 1-x H x , with system sizes ranging from 150 to 6000 atoms and hydrogen concentrations vary from 6 to 20 at. %. The resulting amorphous networks were found to be completely free from any coordination defects and that they all exhibited a pristine band-gap in their electronic spectrum. The microstructural properties of hydrogen distributions were examined with an emphasis on the presence of isolated and clustered environments of hydrogen atoms. The results were compared with experimental data obtained from X-ray diffraction, infrared spectroscopy and nuclear magnetic resonance studies.

36 MATERIALS SCIENCE↗

Ab initio study of the structure and properties of amorphous silicon hydride from accelerated molecular dynamics simulations

This paper presents a large-scale ab initio simulation study of amorphous silicon hydride (a-Si 1-x H x ) with an emphasis on the structure and properties of the material across a range of hydrogen concentration by combining accelerated molecular dynamics (MD) simulations with first-principles density-functional calculations. The accelerated MD scheme relied on classical metadynamics, which enabled the development of 2600+ high-quality structural models of a-Si 1-x H x , with system sizes ranging from 150 to 6,000 atoms and hydrogen concentrations vary from 6 to 20 at. %. The resulting amorphous networks were found to be completely free from any coordination defects and that they all exhibited a pristine band-gap in their electronic spectrum. The microstructural properties of hydrogen distributions were examined with great emphasis on the presence of isolated and clustered environments of hydrogen atoms. The results were compared with a suite of experimental data obtained from x-ray diffraction, infrared spectroscopy, spectroscopic ellipsometry and nuclear magnetic resonance studies.

36 MATERIALS SCIENCE↗

Persistent topological features of dynamical systems

Inspired by an early work of Muldoon et al., Physica D 65, 1–16 (1993), we present a general method for constructing simplicial complex from observed time series of dynamical systems based on the delay coordinate reconstruction procedure. The obtained simplicial complex preserves all pertinent topological features of the reconstructed phase space, and it may be analyzed from topological, combinatorial, and algebraic aspects. In focus of this study is the computation of homology of the invariant set of some well known dynamical systems that display chaotic behavior. Persistent homology of simplicial complex and its relationship with the embedding dimensions are examined by studying the lifetime of topological features and topological noise. The consistency of topological properties for different dynamic regimes and embedding dimensions is examined. The obtained results shed new light on the topological properties of the reconstructed phase space and open up new possibilities for application of advanced topological methods. The method presented here may be used as a generic method for constructing simplicial complex from a scalar time series that has a number of advantages compared to the mapping of the same time series to a complex network.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

New Nonreactive Force Field for Accurate Molecular Dynamics Simulations of TATB at Extreme Conditions

Insensitive high explosives based on TATB (1,3,5-triamino-2,4,6-trinitrobenzene) are needed in applications when safety is of paramount importance, but the basic material properties that give rise to its insensitivity are not fully understood. Molecular dynamics modeling using empirical force fields (FFs) has been the main route to characterize many complicated dynamical properties of TATB single crystal, but these FFs have not been comprehensively tested at extreme conditions typical of detonation. We collect a benchmark data set of (quasi)static TATB physical properties as determined by experiments and electronic structure calculations and apply this data set to validate four existing TATB FFs along with a new TATB FF that we develop here and denote as the CEA-LLNL-Missouri (CLM) FF. Benchmark data include vibrational spectra, the TATB crystal temperature–pressure–volume equation of state and lattice parameters, properties of TATB crystal polymorphs and transitions to the gaseous and liquid states, dimer energy landscapes, the pressure-dependent elastic tensor, and the energy landscape for inelastic deformation via sliding of TATB crystal layers. As a general assessment, we find that the two existing nonreactive FFs are more accurate in describing TATB’s physical properties compared to the two variants of the ReaxFF reactive FF considered. The new CLM FF is found to consistently yield similar or better agreement with experiments and electronic structure theory than any of the existing FF models, and it presents a distinct improvement in accurately modeling TATB elasticity and equation of state. So this work is expected to help improve the accuracy of FF-based modeling of complicated dynamic responses that ultimately govern the safety and performance characteristics of this material.

36 MATERIALS SCIENCE↗

Vibrations and Phase Stability in Mixed Valence Antimony Oxide

α-Sb 2 O 4 (cervantite) and β-Sb 2 O 4 (clinocervantite) are mixed valence compounds with equal proportions of Sb III and Sb V as represented in the formula Sb III Sb V O 4 . Their structure and properties can be difficult to calculate owing to the Sb III lone-pair electrons. Here, we present a study of the lattice dynamics and vibrational properties using a combination of inelastic neutron scattering, Mössbauer spectroscopy, nuclear inelastic scattering, and density functional theory (DFT) calculations. DFT calculations that account for lone-pair electrons match the experimental densities of phonon states. Mössbauer spectroscopy reveals the β phase to be significantly harder than the α phase. Calculations with O vacancies reveal the possibility for nonstoichiometric proportions of Sb III and Sb V in both phases. An open question is what drives the stability of the α phase over the β phase, as the latter shows pronounced kinetic stability and lower symmetry despite being in the high-temperature phase. Since the vibrational entropy difference is small, it is unlikely to stabilize the α phase. In conclusion, our results suggest that the α phase is more stable only because the material is not fully stoichiometric.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Ultrafast nano-imaging and nano-spectroscopy

Ultrafast pump–probe nano-imaging combines scanning probe-based optical near-field microscopy with ultrafast spectroscopy to enable imaging with deep sub-wavelength spatial resolution, femtosecond temporal resolution and simultaneous spectral resolution. Ultrafast nano-imaging has gained increased attention for its ability to provide far-from-equilibrium excitation and excited-state contrast. With coherent and nonlinear probing, coupled electron, spin and lattice dynamics on elementary timescale and length scale can be resolved. Through nano-movies, ultrafast nano-imaging visualizes correlated quantum dynamics underlying the properties of solid-state materials, semiconductors, molecular electronic, photonic, photovoltaic and other functional materials. With nanometre spatial resolution, this method probes elementary dynamic processes across multiple length scales that are otherwise obscured in conventional ultrafast spectroscopy in which heterogeneities are spatially averaged. Furthermore, this Primer describes the theoretical background and experimental implementation of ultrafast nano-imaging; signal interpretation and modelling; representative examples and a perspective for the future development of the field.

Microscopy↗

Dynamical effects on the core-mantle boundary from depth-dependent thermodynamical properties of the lower mantle

A common assumption in modeling dynamical processes in the lower mantle is that both the thermal expansivity and thermal conductivity are reasonably constant. Recent work from seismic equation of state leads to substantially higher values for the thermal conductivity and much lower thermal expansivity values in the deep mantle. The dynamical consequences of incorporating depth-dependent thermodynamic properties on the thermal-mechanical state of the lower mantle are examined with the spherical-shell mean-field equations. It is found that the thermal structure of the seismically resolved anomalous zone at the base of the mantle is strongly influenced by these variable properties and, in particular, that the convective distortion of the core-mantle boundary (CMB) is reduced with the decreasing thermal expansivity. Such a reduction of the dynamically induced topography from pure thermal convection would suggest that some other dynamical mechanism must be operating at the CMB.

Zhang, Shuxia↗

Variations of light emission and carrier dynamics around V-defects in InGaN quantum wells

Time- and spectrally-resolved scanning near-field optical microscopy was applied to study spatial variations of photoluminescence (PL) spectra and carrier dynamics in polar InGaN/GaN single quantum wells (QWs) emitting from 410 nm to 570 nm. The main attention was devoted to variations of PL properties and carrier dynamics around V-defects. The PL intensity, peak wavelength, and linewidth, as well as the radiative and nonradiative recombination times, were found to be different in V-defect-rich and defect-free regions. The radiative lifetime close to the defects was longer up to several times, which is attributed to an increased electron and hole wave function separation in the QW plane. PL decay times, measured using excitation and collection through the near-field probe, were one to two orders of magnitude shorter than PL decay times measured in the far field. This shows that the near-field PL decay and the integrated PL intensity are primarily determined by the carrier out-diffusion from under the probe. Only in the immediate vicinity of the V-defects, the near-field PL decays due to the nonradiative recombination at dislocations. The area of such enhanced nonradiative recombination is limited to just a few percent of the total QW area. This shows that recombination via dislocations and V-defects does not play a decisive role in the overall nonradiative recombination and internal quantum efficiency of polar InGaN/GaN QWs.

36 MATERIALS SCIENCE↗

The dynamical evolution of poor clusters of galaxies: Growth and properties of the first-ranked galaxy

We report N-body simulations of the dynamical evolution of isolated clusters of 50 galaxies containing a dark matter component that comprises 90% of the cluster mass. For our adopted physical scaling, the line-of-sight velocity dispersion of the cluster is 310 km/s and the initial core radius is 250 kpc. Our results are applicable to (1) present-day poor clusters, (2) the small systems that may have merged to produce present-day rich clusters, and (3) virialized subclumps within larger systems, in between major substructure merger events. We have evolved a total of 10 cluster models, using N = 40,000 particles per model. The models are fully self-consistent in that each galaxy is represented as an extended structure containing many particles and the gravitational potential arises from the particles alone. Dark matter is apportioned between the galaxy halos and a smoothly distributed common group halo, the intracluster background (ICB). The percentage of cluster mass initially in the ICB, Beta, is chosen to be 50, 75, or 90. Increasing Beta has the effect of removing mass from dark halos around galaxies and distributing it throughout the cluster. The initial conditions were constructed by randomly sampling a King distribution with W(sub 0) = 6. The galaxies are also King models; the masses of the galaxies follow a Schechter distribution function.

Bode, Paul W.↗

Ab initio simulations of liquid electrolytes for energy conversion and storage

Understanding physicochemical properties of liquid electrolytes is essential for predicting and optimizing device performance for a wide variety of emerging energy technologies, including photoelectrochemical water splitting, supercapacitors, and batteries. We review recent progress and open challenges in predicting structural, dynamical, and electronic properties of the liquids using first-principles approaches. We briefly summarize the basic concepts of first-principles molecular dynamics (FPMD), and we discuss how FPMD methods have enriched our understanding of a number of liquids, including aqueous solutions, organic electrolytes and ionic liquids. We also discuss technical challenges in extending FPMD simulations to the study of liquid electrolytes in more complex environments, including the interface between electrolytes and electrodes, which is a key component in many energy storage and conversion systems.

25 ENERGY STORAGE↗

Structural and dynamic changes associated with beneficial engineered single-amino-acid deletion mutations in enhanced green fluorescent protein

The beneficial engineered single-amino-acid deletion variants EGFP{sup D190Δ} and EGFP{sup A227Δ} have been studied. Single-amino-acid deletions are a common part of the natural evolutionary landscape but are rarely sampled during protein engineering owing to limited and prejudiced molecular understanding of mutations that shorten the protein backbone. Single-amino-acid deletion variants of enhanced green fluorescent protein (EGFP) have been identified by directed evolution with the beneficial effect of imparting increased cellular fluorescence. Biophysical characterization revealed that increased functional protein production and not changes to the fluorescence parameters was the mechanism that was likely to be responsible. The structure EGFP{sup D190Δ} containing a deletion within a loop revealed propagated changes only after the deleted residue. The structure of EGFP{sup A227Δ} revealed that a ‘flipping’ mechanism was used to adjust for residue deletion at the end of a β-strand, with amino acids C-terminal to the deletion site repositioning to take the place of the deleted amino acid. In both variants new networks of short-range and long-range interactions are generated while maintaining the integrity of the hydrophobic core. Both deletion variants also displayed significant local and long-range changes in dynamics, as evident by changes in B factors compared with EGFP. Rather than being detrimental, deletion mutations can introduce beneficial structural effects through altering core protein properties, folding and dynamics, as well as function.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

WE-FG-BRA-08: Potential Role of the Glycolytic Oscillator in Acute Hypoxia in Tumors

Purpose: Oscillatory dynamics in acute hypoxia have been observed, but poorly understood. They have mostly been attributed to vascular perturbations, but no link has yet been made to metabolic causes. We set out to determine the fundamental frequencies and test for coherence in tumor oxygen dynamics and spatial properties. Methods: Severe combined immunodeficient (SCID) mice were inoculated onto bilateral flanks with human derived head and neck carcinoma (UW-SCC22) cell line xenografts. Oxygen dynamics were monitored in the tumor every minute for an hour using three modalities: blood oxygen level dependent - magnetic resonance imaging (BOLD-MRI), hemoglobin oxygen saturation photoacoustic, and locally manufactured optical probes for spectral fitting. A statistical test was used to separate fluctuating from non-fluctuating voxels and pixels in BOLD-MRI and photoacoustic data respectively. The power spectrum density (PSD) and the autocorrelation functions were calculated for the time series of each voxel, pixel and region, of the BOLD-MRI, photoacoustic or fiber optic data respectively. Results: Using all three techniques, intermittent oxygen dynamics with both coherent and incoherent signatures was observed in the tumors. Upon averaging the PSDs of fluctuating voxels and pixels, it was found that these oscillations occurred with periods of minutes to tens of minutes from all three approaches. Observations from the BOLD-MRI and photoacoustic data showed that clusters of voxels oscillated in a synchronized manner. Conclusion: We were able to use three different modalities to show that fluctuation in tumor oxygen is both coherent and incoherent, with periods of minutes to tens of minutes. These periods are very similar to those from the well-established metabolic, non-linear biomechanical phenomenon called the glycolytic oscillator. This may provide an additional explanation to the cause of cyclic hypoxia. Such dynamics could have profound implications in hypofractionated radiotherapy regiments and could help guide treatment and make it more patient specific. The authors would like to thank the University of Wisconsin Carbone Cancer Center (UWCCC) for the funds to complete this project. This work is also supported in part by NIH/NCI P30 CA014520- UW Comprehensive Cancer Center Support”.

60 APPLIED LIFE SCIENCES↗

Bespoke Liquid/Liquid Interfaces (Final Technical Report)

The goal of DE-SC0001815 was to advance the basic science of liquid:liquid interface formation, to develop a deeper understanding of the mechanisms of phase separation and the essential relationships between solution composition, organization and dynamics that underlie the kinetic regime of solvent extraction. This included learning how interfacial organization and dynamics alters the properties of the primary coordination sphere of ions and the free energy of transport of ions complexes across a phase boundary. We relied primarily upon classical molecular dynamics studies to determine the equilibrium ensembles of these complex systems, but also utilized ab-initio MD and cluster-based density functional theory (DFT) calculations when more detailed investigation of the electronic structure was needed. We continued development of graph-theory based analyses to elucidate hierarchical correlations and expanded into geometric topology methods to quantify the collectively organized structures that can organize at a liquid/liquid interface during solute transport. One of the main conclusions was from the observation of two distinct mechanisms for solute transport - those that derive from amplifications of interfacial heterogeneity and surface roughness, and those wherein surface roughness has been dampened and instead collectively organized macrostructures work to bring solutes into the organic phase. It was our aim to create a concrete chemical model of the underlying driving forces behind interfacial primary and secondary structure formation and to map out the energetic features of solute transport so that tailored liquid/liquid can be developed that have characteristic kinetic features associated with mass transport.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Modeling and measuring limb fine-motor unsteadiness

Fine-motor unsteadiness its properties, conceptual and analytical models, and experimental measurements is examined. Based on a data review, the tentative model derived includes: neuromuscular system, grip interface, and control system dynamic elements. The properties of this model change with muscle tension and match a wide group of extant data. A simple experiment was performed to investigate the amplitude/force relationships of the tremor mode. As the finger-pull force increased from 5 to 20 Newtons, the tremor mode frequency for a given individual stayed within roughly + or - 1 Hz over a range from 9-12 Hz, while the average magnitude of the rms tremor acceleration increased tenfold. A standardized test for making such measurements is given and applications in the fields of psychophysiological stress and strain measurements are mentioned.

Magdaleno, R. E.↗

Ce–O Covalence in Silicate Oxyapatites and Its Influence on Luminescence Dynamics

Cerium substituting gadolinium in Ca2Gd8(SiO4)6O2 occupies two intrinsic sites of distinct coordination. The coexistence of an ionic bonding at a 4F site and an ionic–covalent mixed bonding at a 6H site in the same crystalline compound provides an ideal system for comparative studies of ion–ligand interactions. Experimentally, the spectroscopic properties and photoluminescence dynamics of this white-phosphor are investigated. An anomalous thermal quenching of the photoluminescence of Ce3+ at the 6H site is analyzed. Theoretically, ab initio calculations are conducted to reveal the distinctive properties of the Ce–O coordination at the two Ce3+ sites. The calculated eigenstates of Ce3+ at the 6H site suggest a weak Ce–O covalent bond formed between Ce3+ and one of the coordinated oxygen ions not bonded with Si4+. The electronic energy levels and frequencies of local vibrational modes are correlated with specific Ce–O pairs to provide a comparative understanding of the site-resolved experimental results. On the basis of the calculated results, we propose a model of charge transfer and vibronic coupling for interpretation of the anomalous thermal quenching of the Ce3+ luminescence. The combination of experimental and theoretical studies in the present work provides a comprehensive understanding of the spectroscopy and luminescence dynamics of Ce3+ in crystals of ionic–covalent coordination.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Enhancement of Raman scattering signal of a few molecules using photonic nanojet mediated SERS technique

Now a days, single molecule surface enhanced Raman spectroscopy (SMSERS) has become a fascinating tool for studying the structural properties, static and dynamic events of single molecules (instead of ensemble average), with the help of efficient plasmonic nanostructures. This is extremely useful in the field of proteomics because the structural properties of protein molecules are heterogeneous. Even though, SMSERS provides wealthy information about single molecules, it demands high quality surface enhanced Raman scattering (SERS) substrates. So far, a very few researchers succeeded in demonstrating the single molecule Raman scattering using conventional SERS technique. However, the experimental S/N of the Raman signal has been found to be very poor. Recently, with the help of photonic nanojet of an optical microsphere, we were able to enhance the SERS signal of a few molecules adsorbed on the SERS substrates (gold symmetric and asymmetric nanodimers and trimers dispersed on a glass slide). Herein, we report a few details about photonic nanojet mediated SERS technique, a few experimental results and a detailed theoretical study on symmetric and asymmetric nanosphere dimers to understand the dependence of localised surface plasmon resonance (LSPR) wavelength of a nanodimer on the nanogap size and polarization of the excitation light.

77 NANOSCIENCE AND NANOTECHNOLOGY↗