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Graph transformation method for calculating waiting times in Markov chains

Semen A. Trygubenko, David J. Wales
2006 Journal of Chemical Physics  
We present a number of examples to demonstrate the efficiency and robustness of this approach.  ...  All the states and the rules for transitions between them must be known in advance.  ...  The computational requirements of the exact summation method are independent of E. Note the log 10 scale on the vertical axis.  ... 
doi:10.1063/1.2198806 pmid:16821910 fatcat:wk3zfriftbayhefkcndjfsehuy

Reviews and Descriptions of Tables and Books

1964 Mathematics of Computation  
(There is an error in the first graph for p, k = 6, 7; the leftmost vertical line should be deleted). Appendix 4 lists n(p, k, d) for p = 2(1)7, k = p -1 (l)\p(p -1) and all pertinent values of d.  ...  For p = 4(1)7 and k = 0(1)%p(p -1), Appendix 2 lists the number of graphs with p points and k lines of the following six types: NPik = labeled graphs; Cp,k = labeled connected graphs; Sp,k = labeled stars  ...  This book does not purport to cover all the fine details of programming for a 1401 system; for this the reader is referred to the 1401 reference manual (A24-1403) published by IBM.  ... 
doi:10.1090/s0025-5718-64-99166-5 fatcat:m7qw3r6wvbedzhvmw7djxjfnr4

Theory and applications of fluctuating-charge models [article]

Jiahao Chen
2010 arXiv   pre-print
Analyzing the spatial symmetries of these properties allows us to shed light on the role of charge conservation in the electronegativity equalization process.  ...  A graph-theoretic analysis of the topology of charge transfer allows us to relate the fundamental quantities of charge transfer back to the more familiar variables that represent atomic partial charges  ...  We now prove this. as the each pair of vertices is connected by at most one edge e k for a simple graph.  ... 
arXiv:1004.0186v1 fatcat:myvl3kal6zg5tchdrzcjo3qhgi

14th International Symposium on Mathematical Programming

1990 Mathematical programming  
to the well known serious steps und null steps of bundle methods a third type of steps is used to generate the model of dom .  ...  It is shown that for the success of the variant dom must ful ll a regularity property and that the choice of the normal vectors must meet some demands.Both requirements are ful lled if dom is polyhedral  ...  nature by constructing a one-to-one mapping between the graph vertices and points in a geometric space, generally R p .  ... 
doi:10.1007/bf01580875 fatcat:3jtclwmntzgjxkqs5uecombdaa

The Quadratic Assignment Problem [chapter]

Rainer E. Burkard, Eranda Çela, Panos M. Pardalos, Leonidas S. Pitsoulis
1998 Handbook of Combinatorial Optimization  
This paper aims at describing the state of the art on quadratic assignment problems (QAPs).  ...  The paper will appear in the Handbook of Combinatorial Optimization to be published by Kluwer Academic Publishers, P. Pardalos and D.-Z. Du, eds.  ...  A number of codes to compute lower bounds are available. A FORTRAN code which computes the GLB is due to Burkard and Derigs [29] , and is able to compute the bound for instances of size up to 256.  ... 
doi:10.1007/978-1-4613-0303-9_27 fatcat:mm3iphjj4bhv5htk2rtljohu2i

Execution of compute-intensive applications into parallel machines

Catherine Houstis, Sarantos Kapidakis, Evangelos P. Markatos, Erol Gelenbe
1997 Information Sciences  
The approach to scheduling and load balancing ranges from very specialized and directly dependent on the application, in the application layer, to a more general approach taken by the operating system  ...  Scheduling and load balancing of applications on distributed or shared memory machine architectures can be executed by optimizing algorithms in various levels of the architecture.  ...  In most approaches the compiler either tries to gure out a good distribution from the control and data ow graphs of a program or explores a small number of canonical distributions for suitable ones 78]  ... 
doi:10.1016/s0020-0255(96)00174-0 fatcat:pszidonmirajdpcon4lsmucxxu

SuperLU_DIST

Xiaoye S. Li, James W. Demmel
2003 ACM Transactions on Mathematical Software  
We present the main algorithmic features in the software package SuperLU DIST, a distributedmemory sparse direct solver for large sets of linear equations.  ...  The solver is based on sparse Gaussian elimination, with an innovative static pivoting strategy proposed earlier by the authors.  ...  ACKNOWLEDGMENTS We thank the anonymous referees for the detailed comments which very much improved the presentation.  ... 
doi:10.1145/779359.779361 fatcat:o4isnd7es5afjiqrium5zy5bta

Mean field theory of spin glasses [article]

Francesco Zamponi
2014 arXiv   pre-print
These lecture notes focus on the mean field theory of spin glasses, with particular emphasis on the presence of a very large number of metastable states in these systems.  ...  These notes have been prepared for a course of the PhD program in Statistical Mechanics at SISSA, Trieste and at the University of Rome "Sapienza".  ...  T = 0.63 > T d , T d > T = 0.6 > T K , T = 0.5 < T K (it can be done by Mathematica 15 or writing a program in C/Fortran/...).  ... 
arXiv:1008.4844v5 fatcat:qpu7x7r6fjbmjkactz63gu3ypa

Water in protein cavities: A procedure to identify internal water and exchange pathways and application to fatty acid-binding protein

Dirk Bakowies, Wilfred F. van Gunsteren
2002 Proteins: Structure, Function, and Bioinformatics  
A computational approach based on Delaunay triangulation is presented to identify internal water molecules in proteins and to capture pathways of exchange with the bulk.  ...  Differences between the two forms of the protein are observed and discussed. Proteins 2002;47:534 -545.  ...  Later, we show that specific properties of spherical triangulations may be used for significant improvements that render the computer program being executed in trivial amounts of computer time.  ... 
doi:10.1002/prot.10079 pmid:12001232 fatcat:uwztyhhknfedlc6ppsiqkjlpwu

Scaling Properties, Fractals, and the Renormalisation Group Approach to Percolation [article]

D. Stauffer
2007 arXiv   pre-print
For Encyclopedia of Complexity and Systems Science (Springer Verlag). No abstract. I. Definition and Introduction II. Methods III. Quantities and Exponents IV.  ...  Methods This section summarises some of the methods employed to find percolation properties, first by pencil and paper, and then with the help of computers for which Fortran programs are published e.g.  ...  Similar, only more difficult, is the evaluation of n s with a maximum s usually 10 to 20; the general formula is n s = t g st p s (1 − p) t (2) where the perimeter t is the number of empty neighbours and  ... 
arXiv:0704.3848v1 fatcat:kr62tpnyjbcbbdvlqzpq6bbdbi

Operational, regional-scale, chemical weather forecasting models in Europe

J. Kukkonen, T. Balk, D. M. Schultz, A. Baklanov, T. Klein, A. I. Miranda, A. Monteiro, M. Hirtl, V. Tarvainen, M. Boy, V.-H. Peuch, A. Poupkou (+13 others)
2011 Atmospheric Chemistry and Physics Discussions  
Consequently, this present article aims to bring the field up to date with the most comprehensive summary and assessment of the state of CWF. 5 European-wide projects on chemical weather modeling This  ...  (CWFIS) to represent the integrated system responsible for the prediction and dissemination of chemical weather forecasts.  ...  Comparison studies of the various chemical sub-models.  ... 
doi:10.5194/acpd-11-5985-2011 fatcat:ea5r4uylxbcxje6jeak7cnq2hy

dfnWorks: A discrete fracture network framework for modeling subsurface flow and transport

Jeffrey D. Hyman, Satish Karra, Nataliia Makedonska, Carl W. Gable, Scott L. Painter, Hari S. Viswanathan
2015 Computers & Geosciences  
Given a set 110 of PSLGs X with arbitrary orientation in R 3 , one can define a local feature size at a point p as the radius of 111 the smallest sphere centered at p that intersects two non-incident vertices  ...  The generation portion of dfnGEN, fram , is 90 written in C++ and LaGriT is written in Fortran.  ...  relies on domain decomposition for parallelism, and was originally developed as part 186 of the Department of Energy SciDAC-2 groundwater program.  ... 
doi:10.1016/j.cageo.2015.08.001 fatcat:azjqid23jrcbzbq5ahpcv5ljau

Computational Methods for Multidimensional Neutron Diffusion Problems

Song Han, Sandra Dulla, Piero Ravetto
2009 Science and Technology of Nuclear Installations  
The validation of the methods proposed is carried out by comparisons of results for reference structures.  ...  The flexibility and the possibility to obtain neutron importances allow the use of the module for parametric studies, design assessments, and integral parameter evaluations as well as for future sensitivity  ...  of the conclusion from Generation IV 1.3.  ... 
doi:10.1155/2009/973605 fatcat:ki4dkh5tbzf33igyrhhuob2jcq

CP2K: An electronic structure and molecular dynamics software package - Quickstep: Efficient and accurate electronic structure calculations

Thomas D. Kühne, Marcella Iannuzzi, Mauro Del Ben, Vladimir V. Rybkin, Patrick Seewald, Frederick Stein, Teodoro Laino, Rustam Z. Khaliullin, Ole Schütt, Florian Schiffmann, Dorothea Golze, Jan Wilhelm (+27 others)
2020 Journal of Chemical Physics  
Excellent performance for electronic structure calculations is achieved using novel algorithms implemented for modern high-performance computing systems.  ...  The emphasis is put on density functional theory and multiple post-Hartree-Fock methods using the Gaussian and plane wave approach and its augmented all-electron extension.  ...  The action of the response operator on the trial vector X for a number of excited states may also be computed simultaneously.  ... 
doi:10.1063/5.0007045 pmid:33687235 fatcat:a5o4bngmcrcslmfj3dcsr5blxi

CP2K: An electronic structure and molecular dynamics software package

Gloria Tabacchi
2020 Figshare  
article on CP2K  ...  Mundy, Christian Plessl, Matt Watkins, Joost VandeVondele, Matthias Krack, Jürg HutterThe Journal of Chemical Physics, May 2020, American Institute of PhysicsDOI: 10.1063/5.0007045An open-access review  ...  The action of the response operator on the trial vector X for a number of excited states may also be computed simultaneously.  ... 
doi:10.6084/m9.figshare.12520709 fatcat:geqacrvi5jbwndgg33wu6nl3hq
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