60,609 research outputs found
Efficient electronic structure calculation for molecular ionization dynamics at high x-ray intensity
We present the implementation of an electronic-structure approach dedicated
to ionization dynamics of molecules interacting with x-ray free-electron laser
(XFEL) pulses. In our scheme, molecular orbitals for molecular core-hole states
are represented by linear combination of numerical atomic orbitals that are
solutions of corresponding atomic core-hole states. We demonstrate that our
scheme efficiently calculates all possible multiple-hole configurations of
molecules formed during XFEL pulses. The present method is suitable to
investigate x-ray multiphoton multiple ionization dynamics and accompanying
nuclear dynamics, providing essential information on the chemical dynamics
relevant for high-intensity x-ray imaging.Comment: 28 pages, 6 figure
MGOS: A library for molecular geometry and its operating system
The geometry of atomic arrangement underpins the structural understanding of molecules in many fields. However, no general framework of mathematical/computational theory for the geometry of atomic arrangement exists. Here we present "Molecular Geometry (MG)'' as a theoretical framework accompanied by "MG Operating System (MGOS)'' which consists of callable functions implementing the MG theory. MG allows researchers to model complicated molecular structure problems in terms of elementary yet standard notions of volume, area, etc. and MGOS frees them from the hard and tedious task of developing/implementing geometric algorithms so that they can focus more on their primary research issues. MG facilitates simpler modeling of molecular structure problems; MGOS functions can be conveniently embedded in application programs for the efficient and accurate solution of geometric queries involving atomic arrangements. The use of MGOS in problems involving spherical entities is akin to the use of math libraries in general purpose programming languages in science and engineering. (C) 2019 The Author(s). Published by Elsevier B.V
Wavelet-Based Linear-Response Time-Dependent Density-Functional Theory
Linear-response time-dependent (TD) density-functional theory (DFT) has been
implemented in the pseudopotential wavelet-based electronic structure program
BigDFT and results are compared against those obtained with the all-electron
Gaussian-type orbital program deMon2k for the calculation of electronic
absorption spectra of N2 using the TD local density approximation (LDA). The
two programs give comparable excitation energies and absorption spectra once
suitably extensive basis sets are used. Convergence of LDA density orbitals and
orbital energies to the basis-set limit is significantly faster for BigDFT than
for deMon2k. However the number of virtual orbitals used in TD-DFT calculations
is a parameter in BigDFT, while all virtual orbitals are included in TD-DFT
calculations in deMon2k. As a reality check, we report the x-ray crystal
structure and the measured and calculated absorption spectrum (excitation
energies and oscillator strengths) of the small organic molecule
N-cyclohexyl-2-(4-methoxyphenyl)imidazo[1,2-a]pyridin-3-amine
Analysis of Three-Dimensional Protein Images
A fundamental goal of research in molecular biology is to understand protein
structure. Protein crystallography is currently the most successful method for
determining the three-dimensional (3D) conformation of a protein, yet it
remains labor intensive and relies on an expert's ability to derive and
evaluate a protein scene model. In this paper, the problem of protein structure
determination is formulated as an exercise in scene analysis. A computational
methodology is presented in which a 3D image of a protein is segmented into a
graph of critical points. Bayesian and certainty factor approaches are
described and used to analyze critical point graphs and identify meaningful
substructures, such as alpha-helices and beta-sheets. Results of applying the
methodologies to protein images at low and medium resolution are reported. The
research is related to approaches to representation, segmentation and
classification in vision, as well as to top-down approaches to protein
structure prediction.Comment: See http://www.jair.org/ for any accompanying file
Hierarchical bounding structures for efficient virial computations: Towards a realistic molecular description of cholesterics
We detail the application of bounding volume hierarchies to accelerate
second-virial evaluations for arbitrary complex particles interacting through
hard and soft finite-range potentials. This procedure, based on the
construction of neighbour lists through the combined use of recursive
atom-decomposition techniques and binary overlap search schemes, is shown to
scale sub-logarithmically with particle resolution in the case of molecular
systems with high aspect ratios. Its implementation within an efficient
numerical and theoretical framework based on classical density functional
theory enables us to investigate the cholesteric self-assembly of a wide range
of experimentally-relevant particle models. We illustrate the method through
the determination of the cholesteric behaviour of hard, structurally-resolved
twisted cuboids, and report quantitative evidence of the long-predicted phase
handedness inversion with increasing particle thread angles near the
phenomenological threshold value of . Our results further highlight
the complex relationship between microscopic structure and helical twisting
power in such model systems, which may be attributed to subtle geometric
variations of their chiral excluded-volume manifold
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The hybrid grid implemented DSMC method used in 2D triangular micro cavity flows
This paper was presented at the 3rd Micro and Nano Flows Conference (MNF2011), which was held at the Makedonia Palace Hotel, Thessaloniki in Greece. The conference was organised by Brunel University and supported by the Italian Union of Thermofluiddynamics, Aristotle University of Thessaloniki, University of Thessaly, IPEM, the Process Intensification Network, the Institution of Mechanical Engineers, the Heat Transfer Society, HEXAG - the Heat Exchange Action Group, and the Energy Institute.In this study a new hybrid grid is implemented in a 2D DSMC solver to be used in 2D triangular micro cavity flows. Currently DSMC is the prominent method to analyze micro scale gas flows which are rarefied. Because of the computational cost, DSMC solvers are generally used in rarefied gas conditions in which continuum based solvers are useless. If the efficiency of DSMC solvers is improved, the application range of these solvers can be increased further where the continuum based solvers dominate. Indexing the particles according to their cells is one of the main steps in the DSMC method. Either the particles are traced cell-by-cell along their trajectories or coordinate transformation techniques are used in this step. The first option requires complex trigonometric operations and search algorithms which are computationally expensive. But it can be used in both structured and unstructured grids. Although the second option is computationally more efficient, it demands specially tailored structured grids which are more geometry dependent compared to the unstructured grids. Here it is shown that a novel hybrid grid structure can be used successfully in 2D DSMC solver to analyze triangular shaped lid-driven micro cavity flows. Hybrid grids used in this study are much less dependent of the geometry like unstructured grids. Additionally, hybrid grids like structured grids facilitate coordinate transformation techniques in order to increase the efficiency of the particle indexing step in the DSMC method
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