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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 1,387 records · Page 77
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Exploring the capabilities of optical pump X-ray probe NEXAFS spectroscopy to track photo-induced dynamics mediated by conical intersections

X-ray spectroscopy is gaining a growing interest in the scientific community, as it represents a versatile and powerful experimental toolbox for probing the dynamics of both core and valence electronic excitations, nuclear motions and material structure, with element and site specificity. Among the various X-ray based techniques, near-edge X-ray absorption fine structure (NEXAFS) spectroscopy, which investigates the energy and probability of resonant core-to-valence transitions, has started to be applied to organic molecules: a recent UV-pump X-ray probe time-resolved NEXAFS experiment [Wolf et al., Nat. Commun., 2017, 8, 1] has shown the capability of the technique to provide information about the ultrafast internal conversion between the bright ππ* and the dark nπ* electronic states of the nucleobase thymine. In the present contribution we introduce an accurate theoretical approach for the simulation of NEXAFS spectra of organic molecules, employing azobenzene as a test case. The electronic structure calculations, which provide both energy levels and transition probabilities of core-to-valence excitations, were here performed with a high level multiconfigurational method, the restricted active space self consistent field (RASSCF/RASPT2). GS- and nπ*-NEXAFS spectra were obtained on the top of key molecular geometries (as the optimized cis, trans and conical intersection(s) structures) as well as along the fundamental isomerization coordinates (namely, symmetric and asymmetric bendings of the phenyl rings, and torsion around the central dihedral). We eventually characterize and explain the origin of the simulated signals, highlighting the specific signatures that make it possible to follow the excited state evolution from the nπ* Franck–Condon point, towards the conical intersection(s).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Ion implantation of magnesium guests into type II silicon clathrate films: an alternate approach to doping a cage-like silicon allotrope

Type II silicon clathrates, with their unique cage-like structure, offer exciting potential for applications in thermoelectrics, photovoltaics, and quantum materials due to their tunable electronic and thermal properties. This study investigates the use of ion implantation to introduce targeted guest atoms, which act as dopants, into type II Si clathrate films. The focus is on Mg as a test case for implantation, a dopant previously unreported in type II Si clathrates. The effects of ion implantation on the metastable Si clathrate structure were examined through systematic investigation of implant parameters. Time-of-flight secondary ion mass spectrometry depth profiling confirmed the successful implantation of Mg, while X-ray diffraction and confocal Raman spectroscopy demonstrated minimal structural damage at lower fluences, with the clathrate framework retaining its integrity without converting to other phases. At the higher end of the fluence range implantation caused localized transitions from clathrate to amorphous silicon. Implant activation using rapid thermal annealing was examined with the clathrate structure stable up to 500 °C and being converted to diamond silicon above this temperature. Post-implantation and activation structural characterization showed evidence of damage reversal. Electron paramagnetic resonance studies provided indirect evidence of dopant incorporation. These findings establish a foundation for introducing alternative guests/dopants into the Si clathrate cages through ion implantation, advancing their tunability for next-generation quantum and optoelectronic devices.

36 MATERIALS SCIENCE↗
DOE OSTI2021

A two-stage service restoration method for electric power distribution systems

Improving the reliability of power distribution systems is critically important for both utilities and customers. This calls for an efficient service restoration module within a distribution management system to support the implementation of self-healing smart grid networks. Although the emerging smart grid technologies, including distributed generators (DGs) and remote-controlled switches, enhance the self-healing capability and allow faster recovery, they still pose additional complexity to the service restoration problem, especially under cold load pickup (CLPU) conditions. Herein, a novel two-stage restoration framework is proposed to generate a restoration solutions with a sequence of control actions. The first stage generates a restoration plan that supports both the traditional service restoration using feeder reconfiguration and the grid-forming DG-assisted intentional islanding methods. The second stage generates an optimal sequence of switching operations to bring the outaged system quickly to the final restored configuration. The problem is formulated as a mixed-integer linear program that incorporates system connectivity, operating constraints, and the CLPU models. It is demonstrated that on using a multi-feeder test case, the proposed framework is effective in utilizing all available resources to quickly restore the service and generate an optimal sequence of switching actions to be used by the operator to reach the desired optimal configuration.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2018

Towards district scale flood simulations using conventional and anisotropic porosity shallow water models with high-resolution topographic information

Current topographic survey technology provides high-resolution (HR) datasets for urban environments. Incorporating this HR information in models aiming to provide flood risk assessment is desirable because the flood wave propagation is depending on the urban topographic features, i.e. buildings, bridges and street networks. Conceptual, numerical and practical challenges arise from the application of shallow water models to HR urban flood modeling. For example, numerical challenges are occurrence of wet-dry fronts, geometric discontinuities in the urban environment and discontinuous solutions, i.e. shock waves. These challenges can be overcome by using a Godunov-type scheme. However, the computational cost of this type of schemes is high, such that HR two-dimensional shallow water simulations with practical relevance have to be run on supercomputers. The porous shallow water model is an alternative approach that aims to reduce computational cost by using a coarse resolution and accounting for unresolved processes by means of the porosity terms. Usually, a speedup between two and three orders of magnitude in comparison to HR simulations can be obtained. This study presents preliminary results of a practical test case concerning pluvial flooding in a district of the city of Nice, France, caused by the intense rainfall event on October 3rd, 2015. HR topography data set on a 1 m resolution is available for the district, whereby street features of infra-metric dimensions have been included. A reference solution is calculated by a HR shallow water model on a 1 m by 1 m structured computational grid. The porous shallow water model is run on a 10 m by 10 m grid and the influence of the drag source term is studied. The model calculations show a large deviation, which is caused by the poor meshing strategy of the porous shallow water (AP) model. The study also summarizes practical challenges that arise during the application of the AP and HR models to a large urban catchment. The main difficulty is to obtain a good mesh. In smaller scale investigations, the mesh is currently constructed by hand such that the cell edges align with buildings. This approach is not feasible for large scale urban catchments with a large number of buildings. Future steps that have to be taken, such as a strategy for automatic mesh generation, are reported on.

42 ENGINEERING↗
DOE OSTI2017

Establishing a Numerical Modeling Framework for Hydrologic Engineering Analyses of Extreme Storm Events

In this study a numerical modeling framework for simulating extreme storm events was established using the Weather Research and Forecasting (WRF) model. Such a framework is necessary for the derivation of engineering parameters such as probable maximum precipitation that are the cornerstone of large water management infrastructure design. Here this framework was built based on a heavy storm that occurred in Nashville (USA) in 2010, and verified using two other extreme storms. To achieve the optimal setup, several combinations of model resolutions, initial/boundary conditions (IC/BC), cloud microphysics and cumulus parameterization schemes were evaluated using multiple metrics of precipitation characteristics. The evaluation suggests that WRF is most sensitive to IC/BC option. Simulation generally benefits from finer resolutions up to 5 km. At the 15km level, NCEP2 IC/BC produces better results, while NAM IC/BC performs best at the 5km level. Recommended model configuration from this study is: NAM or NCEP2 IC/BC (depending on data availability), 15km or 15km-5km nested grids, Morrison microphysics and Kain-Fritsch cumulus schemes. Validation of the optimal framework suggests that these options are good starting choices for modeling extreme events similar to the test cases. This optimal framework is proposed in response to emerging engineering demands of extreme storm events forecasting and analyses for design, operations and risk assessment of large water infrastructures.

atmospheric model↗
DOE OSTI2017

Development and Implementation of an Optimization Model for Hydropower and Total Dissolved Gas in the Mid-Columbia River System

Managing energy, water, and environmental priorities and constraints within a cascade hydropower system is a challenging multiobjective optimization effort that requires advanced modeling and forecasting tools. Within the mid-Columbia River system, there is currently a lack of specific solutions for predicting how coordinated operational decisions can mitigate the impacts of total dissolved gas (TDG) supersaturation while satisfying multiple additional policy and hydropower generation objectives. In this study, a reduced-order TDG uptake equation is developed that predicts tailrace TDG at seven hydropower facilities on the mid-Columbia River. The equation is incorporated into a general multiobjective river, reservoir, and hydropower optimization tool as a prioritized operating goal within a broader set of system-level objectives and constraints. A test case is presented to assess the response of TDG and hydropower generation when TDG supersaturation is optimized to remain under state water-quality standards. Satisfaction of TDG as an operating goal is highly dependent on whether constraints that limit TDG uptake are implemented at a higher priority than generation requests. According to the model, an opportunity exists to reduce TDG supersaturation and meet hydropower generation requirements by shifting spillway flows to different time periods. In conclusion, a coordinated effort between all project owners is required to implement systemwide optimized solutions that satisfy the operating policies of all stakeholders.

13 HYDRO ENERGY↗
DOE OSTI2012

Compression of a spherically symmetric deuterium-tritium plasma liner onto a magnetized deuterium-tritium target

Converging plasma jets may be able to reach the regime of high energy density plasmas (HEDP). The successful application of plasma jets to magneto-inertial fusion (MIF) would heat the plasma by fusion products and should increase the plasma energy density. This paper reports the results of using the University of Wisconsin's 1-D Lagrangian, radiation-hydrodynamics, fusion code BUCKY to investigate two MIF converging plasma jet test cases originally analyzed by Samulyak et al.[Physics of Plasmas 17, 092702 (2010)]. In these cases, 15 cm or 5 cm radially thick deuterium-tritium (DT) plasma jets merge at 60 cm from the origin and converge radially onto a DT target magnetized to 2 T and of radius 5 cm. The BUCKY calculations reported here model these cases, starting from the time of initial contact of the jets and target. Compared to the one-temperature Samulyak et al. calculations, the one-temperature BUCKY results show similar behavior, except that the plasma radius remains about twice as long near maximum compression. One-temperature and two-temperature BUCKY results differ, reflecting the sensitivity of the calculations to timing and plasma parameter details, with the two-temperature case giving a more sustained compression.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2012

Investigation of a polychromatic tomography method for the extraction of the three-dimensional spatial structure of implosion core plasmas

A spectroscopic method has been developed to extract the three-dimentional spatial structure (i.e., spatial distribution of electron temperature and density) of inertial confinement fusion implosion cores based on the analysis of space-resolved spectra from a tracer element recorded along three quasi-orthogonal lines of sight. We discuss a spectral model that computes space-resolved spectra for a given spatial structure. This model is then combined with a multi-objective search and optimization technique driven by a Pareto genetic algorithm to perform the inversion and to extract the spatial structure of the implosion core from a simultaneous and self-consistent analysis of a set of space-resolved spectra. This method is investigated with a series of synthetic data test cases to explore its reliability, requirements, and limitations. We have found a constraint parameter P{sub const} such that the method is robust and the extracted spatial structure is reliable when P{sub const}> 1. The idea of polychromatic tomography is general and has potential to extract the spatial structure of other laboratory high energy-density plasmas.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2012

Reactive sputter deposition of pyrite structure transition metal disulfide thin films: Microstructure, transport, and magnetism

Transition metal disulfides crystallizing in the pyrite structure (e.g., TMS{sub 2}, with TM = Fe, Co, Ni, and Cu) are a class of materials that display a remarkably diverse array of functional properties. These properties include highly spin-polarized ferromagnetism (in Co{sub 1-x}Fe{sub x}S{sub 2}), superconductivity (in CuS{sub 2}), an antiferromagnetic Mott insulating ground state (in NiS{sub 2}), and semiconduction with close to optimal parameters for solar absorber applications (in FeS{sub 2}). Exploitation of these properties in heterostructured devices requires the development of reliable and reproducible methods for the deposition of high quality pyrite structure thin films. In this manuscript, we report on the suitability of reactive sputter deposition from metallic targets in an Ar/H{sub 2}S environment as a method to achieve exactly this. Optimization of deposition temperature, Ar/H{sub 2}S pressure ratio, and total working gas pressure, assisted by plasma optical emission spectroscopy, reveals significant windows over which deposition of single-phase, polycrystalline, low roughness pyrite films can be achieved. This is illustrated for the test cases of the ferromagnetic metal CoS{sub 2} and the diamagnetic semiconductor FeS{sub 2}, for which detailed magnetic and transport characterization are provided. The results indicate significant improvements over alternative deposition techniques such as ex situ sulfidation of metal films, opening up exciting possibilities for all-sulfide heterostructured devices. In particular, in the FeS{sub 2} case it is suggested that fine-tuning of the sputtering conditions provides a potential means to manipulate doping levels and conduction mechanisms, critical issues in solar cell applications. Parenthetically, we note that conditions for synthesis of phase-pure monosulfides and thiospinels are also identified.

36 MATERIALS SCIENCE↗
DOE OSTI2012

Influence of excited state spatial distributions on plasma diagnostics: Atmospheric pressure laser-induced He-H{sub 2} plasma

Atmospheric pressure plasmas in helium-hydrogen mixtures with H{sub 2} molar concentrations ranging from 0.13% to 19.7% were investigated at times from 1 to 25 {mu}s after formation by a Q-switched Nd:YAG laser. Spatially integrated electron density values are obtained using time resolved optical emission spectroscopic techniques. Depending on mixture concentration and delay time, electron densities vary from almost 10{sup 17} cm{sup -3} to about 10{sup 14} cm{sup -3}. Helium based results agree reasonably well with each other, as do values extracted from the H{sub {alpha}} and H{sub {beta}} emission lines. However, in particular for delays up to about 7 {mu}s and in mixtures with less than 1% hydrogen, large discrepancies are observed between results obtained from the two species. Differences decrease with increasing hydrogen partial pressure and/or increasing delay time. In mixtures with molecular hydrogen fraction of 7% or more, all methods yield electron densities that are in good agreement. These findings seemingly contradict the well-established idea that addition of small amounts of hydrogen for diagnostic purposes does not perturb the plasma. Using Abel inversion analysis of the experimental data and a semi-empirical numerical model, we demonstrate that the major part of the detected discrepancies can be traced to differences in the spatial distributions of excited helium and hydrogen neutrals. The model yields spatially resolved emission intensities and electron density profiles that are in qualitative agreement with experiment. For the test case of a 1% H{sub 2} mixture at 5 {mu}s delay, our model suggests that high electron temperatures cause an elevated degree of ionization and thus a reduction of excited hydrogen concentration relative to that of helium near the plasma center. As a result, spatially integrated analysis of hydrogen emission lines leads to oversampling of the plasma perimeter and thus to lower electron density values compared to those obtained from helium lines.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2013

Ions interacting with planar aromatic molecules: Modeling electron transfer reactions

We present theoretical absolute charge exchange cross sections for multiply charged cations interacting with the Polycyclic Aromatic Hydrocarbon (PAH) molecules pyrene C{sub 14}H{sub 10}, coronene C{sub 24}H{sub 12}, or circumcoronene C{sub 54}H{sub 18}. These planar, nearly circular, PAHs are modelled as conducting, infinitely thin, and perfectly circular discs, which are randomly oriented with respect to straight line ion trajectories. We present the analytical solution for the potential energy surface experienced by an electron in the field of such a charged disc and a point-charge at an arbitrary position. The location and height of the corresponding potential energy barrier from this simple model are in close agreement with those from much more computationally demanding Density Functional Theory (DFT) calculations in a number of test cases. The model results compare favourably with available experimental data on single- and multiple electron transfer reactions and we demonstrate that it is important to include the orientation dependent polarizabilities of the molecules (model discs) in particular for the larger PAHs. PAH ionization energy sequences from DFT are tabulated and used as model inputs. Absolute cross sections for the ionization of PAH molecules, and PAH ionization energies such as the ones presented here may be useful when considering the roles of PAHs and their ions in, e.g., interstellar chemistry, stellar atmospheres, and in related photoabsorption and photoemission spectroscopies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2013

Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: An accurate correction scheme for electrostatic finite-size effects

The calculation of a protein-ligand binding free energy based on molecular dynamics (MD) simulations generally relies on a thermodynamic cycle in which the ligand is alchemically inserted into the system, both in the solvated protein and free in solution. The corresponding ligand-insertion free energies are typically calculated in nanoscale computational boxes simulated under periodic boundary conditions and considering electrostatic interactions defined by a periodic lattice-sum. This is distinct from the ideal bulk situation of a system of macroscopic size simulated under non-periodic boundary conditions with Coulombic electrostatic interactions. This discrepancy results in finite-size effects, which affect primarily the charging component of the insertion free energy, are dependent on the box size, and can be large when the ligand bears a net charge, especially if the protein is charged as well. This article investigates finite-size effects on calculated charging free energies using as a test case the binding of the ligand 2-amino-5-methylthiazole (net charge +1 e) to a mutant form of yeast cytochrome c peroxidase in water. Considering different charge isoforms of the protein (net charges −5, 0, +3, or +9 e), either in the absence or the presence of neutralizing counter-ions, and sizes of the cubic computational box (edges ranging from 7.42 to 11.02 nm), the potentially large magnitude of finite-size effects on the raw charging free energies (up to 17.1 kJ mol{sup −1}) is demonstrated. Two correction schemes are then proposed to eliminate these effects, a numerical and an analytical one. Both schemes are based on a continuum-electrostatics analysis and require performing Poisson-Boltzmann (PB) calculations on the protein-ligand system. While the numerical scheme requires PB calculations under both non-periodic and periodic boundary conditions, the latter at the box size considered in the MD simulations, the analytical scheme only requires three non-periodic PB calculations for a given system, its dependence on the box size being analytical. The latter scheme also provides insight into the physical origin of the finite-size effects. These two schemes also encompass a correction for discrete solvent effects that persists even in the limit of infinite box sizes. Application of either scheme essentially eliminates the size dependence of the corrected charging free energies (maximal deviation of 1.5 kJ mol{sup −1}). Because it is simple to apply, the analytical correction scheme offers a general solution to the problem of finite-size effects in free-energy calculations involving charged solutes, as encountered in calculations concerning, e.g., protein-ligand binding, biomolecular association, residue mutation, pK{sub a} and redox potential estimation, substrate transformation, solvation, and solvent-solvent partitioning.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2013

Reaction cell for in situ soft x-ray absorption spectroscopy and resonant inelastic x-ray scattering measurements of heterogeneous catalysis up to 1 atm and 250 °C

We present a novel in situ reaction cell for heterogeneous catalysis monitored in situ by x-ray absorption spectroscopy (XAS) and resonant inelastic x-ray scattering (RIXS). The reaction can be carried out at a total pressure up to 1 atm, a regime that has not been accessible to comparable in situ techniques and thus closes the pressure gap to many industrial standard conditions. Two alternate catalyst geometries were tested: (A) a thin film evaporated directly onto an x-ray transparent membrane with a flowing reaction gas mixture behind it or (B) a powder placed behind both the membrane and a gap of flowing reaction gas mixture. To illustrate the working principle and feasibility of our reaction cell setup we have chosen ethylene epoxidation over a silver catalyst as a test case. The evolution of incorporated oxygen species was monitored by total electron/fluorescence yield O K-XAS as well as O K-RIXS, which is a powerful method to separate contributions from inequivalent sites. We find that our method can reliably detect transient species that exist during catalytic reaction conditions that are hardly accessible using other spectroscopic methods.

36 MATERIALS SCIENCE↗
DOE OSTI2014

Refinement of the experimental dynamic structure factor for liquid para-hydrogen and ortho-deuterium using semi-classical quantum simulation

The dynamic structure factor of liquid para-hydrogen and ortho-deuterium in corresponding thermodynamic states (T = 20.0 K, n = 21.24 nm{sup −3}) and (T = 23.0 K, n = 24.61 nm{sup −3}), respectively, has been computed by both the Feynman-Kleinert linearized path-integral (FK-LPI) and Ring-Polymer Molecular Dynamics (RPMD) methods and compared with Inelastic X Ray Scattering spectra. The combined use of computational and experimental methods enabled us to reduce experimental uncertainties in the determination of the true sample spectrum. Furthermore, the refined experimental spectrum of para-hydrogen and ortho-deuterium is consistently reproduced by both FK-LPI and RPMD results at momentum transfers lower than 12.8 nm{sup −1}. At larger momentum transfers the FK-LPI results agree with experiment much better for ortho-deuterium than for para-hydrogen. More specifically we found that for k ∼ 20.0 nm{sup −1} para-hydrogen provides a test case for improved approximations to quantum dynamics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Fitting coupled potential energy surfaces for large systems: Method and construction of a 3-state representation for phenol photodissociation in the full 33 internal degrees of freedom using multireference configuration interaction determined data

A recently reported algorithm for representing adiabatic states coupled by conical intersections using a quasi-diabatic state Hamiltonian in four and five atom systems is extended to treat nonadiabatic processes in considerably larger molecules. The method treats all internal degrees of freedom and uses electronic structure data from ab initio multireference configuration interaction wave functions with nuclear configuration selection based on quasi-classical surface hopping trajectories. The method is shown here to be able to treat ∼30 internal degrees of freedom including dissociative and large amplitude internal motion. Two procedures are introduced which are essential to the algorithm, a null space projector which removes basis functions from the fitting process until they are needed and a partial diagonalization technique which allows for automated, but accurate, treatment of the vicinity of extended seams of conical intersections of two or more states. These procedures are described in detail. The method is illustrated using the photodissociaton of phenol, C{sub 6}H{sub 5}OH(X{sup ~1}A{sup ′}) + hv → C{sub 6}H{sub 5}OH(A{sup ~1}A{sup ′}, B{sup ~1}A{sup ′′}) → C{sub 6}H{sub 5}O(X{sup ~2}B{sub 1}, A{sup ~2}B{sub 2}) + H as a test case. Ab initio electronic structure data for the 1,2,3{sup 1}A states of phenol, which are coupled by conical intersections, are obtained from multireference first order configuration interaction wave functions. The design of bases to simultaneously treat large amplitude motion and dissociation is described, as is the ability of the fitting procedure to smooth the irregularities in the electronic energies attributable to the orbital changes that are inherent to nonadiabatic processes.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2014

Analysis, testing, and operation of the MAGI thermal control system

The Aerospace Corporation has completed the development of the Mineral and Gas Identifier (MAGI) sensor - an airborne multi-spectral infrared instrument that is designed to discriminate surface composition and to detect gas emissions from the environment. Sensor performance was demonstrated in a series of flights aboard a Twin Otter aircraft in December 2011 as a stepping stone to a future satellite sensor design. To meet sensor performance requirements the thermal control system was designed to operate the HgCdTe focal plane array (FPA) at 50 K with a 1.79 W heat rejection load to a 44.7 K sink and the optical assembly at 100 K with a 7.5 W heat load to a 82.3 K sink. Two commercial off-theshelf (COTS) Sunpower Stirling cryocoolers were used to meet the instrument’s cooling requirements. A thermal model constructed in Thermal Desktop was used to run parametric studies that guided the mechanical design and sized the two cryocoolers. This paper discusses the development, validation, and operation of the MAGI thermal control system. Detailed energy balances and temperature predictions are presented for various test cases to demonstrate the utility and accuracy of the thermal model. Model inputs included measured values of heat lift as a function of input power and cold tip temperature for the two cryocoolers. These measurements were also used to make predictions of the cool-down behavior from ambient conditions. Advanced heater software was developed to meet unique requirements for both sensor cool-down rate and stability at the set point temperatures.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2014

Recovering position-dependent diffusion from biased molecular dynamics simulations

All atom molecular dynamics (MD) models provide valuable insight into the dynamics of biophysical systems, but are limited in size or length by the high computational demands. The latter can be reduced by simulating long term diffusive dynamics (also known as Langevin dynamics or Brownian motion) of the most interesting and important user-defined parts of the studied system, termed collective variables (colvars). A few hundred nanosecond-long biased MD trajectory can therefore be extended to millisecond lengths in the colvars subspace at a very small additional computational cost. In this work, we develop a method for determining multidimensional anisotropic position- and timescale-dependent diffusion coefficients (D) by analysing the changes of colvars in an existing MD trajectory. As a test case, we obtained D for dihedral angles of the alanine dipeptide. An open source Mathematica{sup ®} package, capable of determining and visualizing D in one or two dimensions, is available at https://github.com/lbf-ijs/DiffusiveDynamics . Given known free energy and D, the package can also generate diffusive trajectories.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Defect-mediated relaxation in the random tiling phase of a binary mixture: Birth, death and mobility of an atomic zipper

This paper describes the mechanism of defect-mediated relaxation in a dodecagonal square-triangle random tiling phase exhibited by a simulated binary mixture of soft discs in 2D. We examine the internal transitions within the elementary mobile defect (christened the “zipper”) that allow it to move, as well as the mechanisms by which the zipper is created and annihilated. The structural relaxation of the random tiling phase is quantified and we show that this relaxation is well described by a model based on the distribution of waiting times for each atom to be visited by the diffusing zipper. This system, representing one of the few instances where a well defined mobile defect is capable of structural relaxation, can provide a valuable test case for general theories of relaxation in complex and disordered materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗