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year-2013

Publications during 2013

Article Reference A brief summary of the progress on the EFDA tungsten materials program
The long-term objective of the European Fusion Development Agreement (EFDA) fusion materials programme is to develop structural and armor materials in combination with the necessary production and fabrication technologies for reactor concepts beyond the International Thermonuclear Experimental Reactor. The programmatic roadmap is structured into four engineering research lines which comprise fabrication process development, structural material development, armor material optimization, and irradiation performance testing, which are complemented by a fundamental research programme on “Materials Science and Modeling.” This paper presents the current research status of the EFDA experimental and testing investigations, and gives a detailed overview of the latest results on materials research, fabrication, joining, high heat flux testing, plasticity studies, modeling, and validation experiments.
Article Reference A First-Principles Study of the Role of Quaternary-N Doping on the Oxygen Reduction Reaction Activity and Selectivity of Graphene Edge Sites
 
Article Reference A first-principles study of the structural, electronic and elastic properties of solid nitromethane under pressure
 
Article Reference A prototypical ionic liquid explored by ab initio molecular dynamics and Raman spectroscopy
We present an analysis of the liquid and of a small isolated cluster of n-ethyl ammonium nitrate based on “first principles” molecular dynamics. We discover that the peculiar properties of ionic liquids make such compounds ideal candidates for such an analysis. We have been able to characterize some important features of the liquid structure and we have validated our simulations by comparing our findings with experimental vibrational spectra of the liquid phase. Theoretical spectra, which present a remarkable agreement with the measurements, besides the assignment of the main spectra features, allow an interpretation of the spectra at high frequencies where the vibrational motions involve the hydrogen-bonded atoms, thus providing a picture of the hydrogen bonding network that exists in such compounds.
Article Reference A first-principles theoretical study of hydrogen‑bond dynamics and vibrational spectral diffusion in aqueous ionic solution: Water in the hydration shell of a fluoride ion
 
Article Reference Ab initio and classical molecular dynamics studies of the structural and dynamical behavior of water near a hydrophobic graphene sheet
The behavior of water near a graphene sheet is investigated by means of ab initio and classical molecular dynamics simulations. The wetting of the graphene sheet by ab initio water and the relation of such behavior to the strength of classical dispersion interaction between surface atoms and water are explored. The first principles simulations reveal a layered solvation structure around the graphene sheet with a significant water density in the interfacial region implying no drying or cavitation effect. It is found that the ab initio results of water density at interfaces can be reproduced reasonably well by classical simulations with a tuned dispersion potential between the surface and water molecules. Calculations of vibrational power spectrum from ab initio simulations reveal a shift of the intramolecular stretch modes to higher frequencies for interfacial water molecules when compared with those of the second solvation later or bulk-like water due to the presence of free OH modes near the graphene sheet. Also, a weakening of the water-water hydrogen bonds in the vicinity of the graphene surface is found in our ab initio simulations as reflected in the shift of intermolecular vibrational modes to lower frequencies for interfacial water molecules. The first principles calculations also reveal that the residence and orientational dynamics of interfacial water are somewhat slower than those of the second layer or bulk-like molecules. However, the lateral diffusion and hydrogen bond relaxation of interfacial water molecules are found to occur at a somewhat faster rate than that of the bulk-like water molecules. The classical molecular dynamics simulations with tuned Lennard-Jones surface-water interaction are found to produce dynamical results that are qualitatively similar to those of ab initio molecular dynamics simulations.
Incollection Reference Ab Initio Molecular Dynamics
 
Phdthesis Reference Ab initio molecular dynamics study of nanoscale heat transfer and energy conversion
In this thesis, ab initio molecular dynamics simulation based on a plane wave/pseudopotential implementation of density functional theory was adopted to investigate nanoscale heat transfer and energy conversions for semiconductors. The first one investigates the heat conduction process occurring in Si/Ge superlattices at selected stages from the initial point of nonzero temperature gradient to the final state of thermal equilibrium. The second one studies the thermal energy transportation phenomena spanning from heat conduction of thermal radiation with the modeling of variable gap distances in different thin layer systems. The third one presents an ab initio molecular dynamics study of femtosecond laser processing of germanium. As the first work of studying the nanoscale energy transport spanning from heat conduction to thermal radiation and the femtosecond laser material interaction in mechanical engineering, the simulation results highlight the promising application of the first-principles molecular dynamics in thermal engineering. We believe our results and the conclusion drawn will be quite useful in helping to resolving the heat transfer and energy conversion problem during the miniaturization of integrated circuits and molecular electronics.
Article Reference Ab initio–driven trajectory-based nuclear quantum dynamics in phase space
We derive a Bohmian trajectory-based quantum dynamics approach for the calculation of adiabatic and nonadiabatic quantum effects in ab initio on-the-fly molecular dynamics simulations. The method is designed for calculations in the full, unconstrained, phase space of molecular systems described within density functional theory and time-dependent density functional theory. The problem of solving quantum hydrodynamic equations using trajectories in high dimensions is addressed using an expansion of the nuclear amplitude in atom centered Gaussians that are propagated along the quantum trajectories. In this work, we investigate the adiabatic limit of this theory, even though the full nonadiabatic case is derived. The method is first tested on the H2mathmsubmrow/mrowmn2/mn/msub/math molecule and then applied to the study of the proton transfer dynamics in the phase space of the molecular complex (H3mathmsubmrow/mrowmn3/mn/msub/mathN-H-NH3mathmsubmrow/mrowmn3/mn/msub/math)+mathmsupmrow/mrowmo+/mo/msup/math.
Incollection Reference Ab-Initio Calculations of the Vibrational Properties of Nanostructures
 
Article Reference Additive Effect on Reductive Decomposition and Binding of Carbonate-Based Solvent toward Solid Electrolyte Interphase Formation in Lithium-Ion Battery
The solid?electrolyte interphase (SEI) formed through the reductive decomposition of solvent molecules plays a crucial role in the stability and capability of a lithium-ion battery (LIB). Here we investigated the effects of adding vinylene carbonate (VC) to ethylene carbonate (EC) solvent, a typical electrolyte in LIBs, on the reductive decomposition. We focused on both thermodynamics and kinetics of the possible processes and used density functional theory-based molecular dynamics with explicit solvent and Blue-moon ensemble technique for the free energy change. We considered Li+ in only EC solvent (EC system) and in EC solvent with a VC additive (EC/VC system) to elucidate the additive effects. In addition to clarifying the equilibrium properties, we evaluated the free energy changes along several EC or VC decomposition pathways under one-electron (1e) reduction condition. Two-electron (2e) reduction and attacks of anion radicals to intact molecules were also examined. The present results completely reproduce the gaseous products observed in the experiments. We also found a new mechanism involving the VC additive: the VC additive preferentially reacts with the EC anion radical to suppress the 2e reduction of EC and enhance the initial SEI formation, contrary to the conventional scenario in which VC additive is sacrificially reduced and its radical oligomerization becomes the source of SEI. Because our mechanism needs only 1e reduction, the irreversible capacity at the SEI formation will decrease, which is also consistent with the experimental observations. These results reveal the primary role of VC additive in the EC solvent.
Article Reference Aggregation and Cooperative Effects in the Aldol Reactions of Lithium Enolates
Density functional theory and Car–Parrinello molecular dynamics simulations have been carried out for model aldol reactions involving aggregates of lithium enolates derived from acetaldehyde and acetone. Formaldehyde and acetone have been used as electrophiles. It is found that the geometries of the enolate aggregates are in general determined by the most favorable arrangements of the point charges within the respective LinOn clusters. The reactivity of the enolates follows the sequence monomer≫dimertetramer. In lithium aggregates, the initially formed aldol adducts must rearrange to form more stable structures in which the enolate and alkoxide oxygen atoms are within the respective LinOn clusters. Positive cooperative effects, similar to allosteric effects found in several proteins, are found for the successive aldol reactions in aggregates. The corresponding transition structures show in general sofa geometries.
Article Reference Amplification of Conformational Effects via tert-Butyl Groups: Hexa-tert-butyl Decacyclene on Cu(100) at Room Temperature
The design of molecular systems as functional elements for use in next-generation electronic sensors and devices often relies on the addition of functional groups acting as spacers to modify adsorbate?substrate interactions. Although advantageous in many regards, these spacer groups have the secondary effect of amplifying internal conformational effects of the parent molecule. Here we investigate one such molecule?2,5,8,11,14,17-hexa-tert-butyl-decacyclene (HBDC, C60H66)?deposited on Cu(100) at monolayer and submonolayer coverages using an ultra-high vacuum (UHV) scanning tunneling microscope (STM). By combining submolecular resolution imaging with computational methods, we describe a variety of properties related to the effects of adding tert-butyl spacers to a decacyclene core, including the molecular conformation, structure, and chiral separation of the molecular adlayer, strong intermolecular interactions, and a metastable pinned conformation of the molecule brought on by deformation under high-bias conditions that enable an examination of its diffusive 2D molecular gas at room temperature. Collectively, these observations provide direct insight into the effect of adding spacers to a flexible molecular core such as decacyclene as relates to both intermolecular and adsorbate?substrate interfaces.
Article Reference An ab initio study of the peak tensile strength of tungsten with an account of helium point defects
Analyses in the present work focus on understanding the effect of helium (He) point defects on the peak tensile strength of tungsten (W) using an ab initio simulation framework. Nine W nanostructure samples that include three different grain boundary (GB) configurations for each of the following case: first without any He point defects, second with He point defects solely in substitutional sites, and third with He point defects solely in interstitial sites, are analyzed. Peak tensile strength of the examined nanostructures is analyzed as a function of temperature, the type of He point defect site, and the type of GB configuration. The tensile strength decreases by up to 21\% in the presence of GBs when compared with the single crystalline case. Presence of interstitial He point defects leads to highest increase in the tensile strength. A linear relationship between structural fractal dimension and tensile strength is observed in all examined structures. Therefore, a fractal dimension based empirical relationship is developed to characterize the strength of the examined nanostructures as a function of temperature, type of He point defect site, and type of GB configuration. The developed relation is found to predict strength data for structures that were not included in the empirical relation development, establishing a notion that fractal dimension could be a possible way to interpret infinitesimal material volume quantum mechanical strength data for higher scale continuum plasticity modeling.
Article Reference An NMR crystallography DFT-D approach to analyse the role of intermolecular hydrogen bonding and π–π interactions in driving cocrystallisation of indomethacin and nicotinamide
 
Article Reference Argonne applications for the IBM Blue Gene/Q, Mira
A varied collection of scientific and engineering codes has been adapted and enhanced to take advantage of the IBM Blue Gene®/Q architecture and thus enable research that was previously out of reach. Computational research teams from a number of disciplines collaborated with the staff of the Argonne Leadership Computing Facility to assess which of Blue Gene/Q's many novel features could be exploited for each application to equip it to tackle existing problem classes with greater fidelity and in some cases to address new phenomena. The quad floating-point units and the five-dimensional torus interconnect are among the features that were demonstrated to be effective for a number of important applications. Furthermore, data obtained from the hardware counters provided insights that were valuable in guiding the code modifications. Hardware features and programming techniques that were effective across multiple codes are documented as well. First, we have confirmed that there is no significant code rewrite needed to run today's production codes with good performance on Mira, an IBM Blue Gene/Q supercomputer. Performance improvements are already demonstrated, even though our measurements are all on pre-production software and hardware. The application domains included biology, materials science, combustion, chemistry, nuclear physics, and industrial-scale design of nuclear reactors, jet engines, and the efficiency of transportation systems.
Article Reference Atom-Scale Reaction Pathways and Free-Energy Landscapes in Oxygen Plasma Etching of Graphene
We report first-principles molecular dynamics calculations combined with rare events sampling techniques that clarify atom-scale mechanisms of oxygen plasma etching of graphene. The obtained reaction pathways and associated free-energy landscapes show that the etching proceeds near vacancies via a two-step mechanism, formation of precursor lactone structures and the subsequent exclusive CO2 desorption. We find that atomic oxygen among the plasma components is most efficient for etching, providing a guidline in tuning the plasma conditions.
Article Reference Atomic Oxygen Chemisorption on Carbon Nanotubes Revisited with Theory and Experiment
Density-functional-theory based calculations of two single-walled carbon nanotubes of different chirality settle open issues on the sidewall chemisorption of atomic oxygen at low concentrations. Ether groups are the thermodynamically favored configurations. If kinetically trapped in epoxide groups, oxygen introduces characteristic new levels in the gap of the nanotube that are detected with scanning tunneling spectroscopy experiments. Discrepancies with previous predictions are shown to originate from the inadequacy of previous models to describe low-concentration oxygen adsorbated on nanotubes.
Article Reference Biomolecular Adsorption at Aqueous Silver Interfaces: First-Principles Calculations, Polarizable Force-Field Simulations, and Comparisons with Gold
The molecular simulation of biomolecules adsorbed at noble metal interfaces can assist in the development of bionanotechnology applications. In line with advances in polarizable force fields for adsorption at aqueous gold interfaces, there is scope for developing a similar force field for silver. One way to accomplish this is via the generation of in vacuo adsorption energies calculated using first-principles approaches for a wide range of different but biologically relevant small molecules, including water. Here, we present such first-principles data for a comprehensive range of bio-organic molecules obtained from plane-wave density functional theory calculations using the vdW-DF functional. As reported previously for the gold force field, GolP-CHARMM (Wright, L. B.; Rodger, P. M.; Corni, S.; Walsh, T. R. GolP-CHARMM: first-principles based force-fields for the interaction of proteins with Au(111) and Au(100). J. Chem. Theory Comput. 2013, 9, 1616?1630), we have used these data to construct a a new force field, AgP-CHARMM, suitable for the simulation of biomolecules at the aqueous Ag(111) and Ag(100) interfaces. This force field is derived to be consistent with GolP-CHARMM such that adsorption on Ag and Au can be compared on an equal footing. Our force fields are used to evaluate the water overlayer stability on both silver and gold, finding good agreement with known behaviors. We also calculate and compare the structuring (spatial and orientational) of liquid water adsorbed at both silver and gold. Finally, we report the adsorption free energy of a range of amino acids at both the Au(111) and Ag(111) aqueous interfaces, calculated using metadynamics. Stronger adsorption on gold was noted in most cases, with the exception being the carboxylate group present in aspartic acid. Our findings also indicate differences in the binding free energy profile between silver and gold for some amino acids, notably for His and Arg. Our analysis suggests that the relatively stronger structuring of the first water layer on silver, relative to gold, could give rise to these differences.
Article Reference Biophysical Characterization of Genistein in Its Natural Carrier Human Hemoglobin Using Spectroscopic and Computational Approaches
 
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