MedWorm.com provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'Computer Physics Communications' source. Thu, 09 Feb 2012 22:12:27 +0100 http://www.medworm.com/index.php?rid=5492477&cid=s_38111_79_f&fid=38111&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22140274%26dopt%3DAbstract Authors: Elking DM, Perera L, Pedersen LG Abstract An implementation of the Hirshfeld (HD) and Hirshfeld-Iterated (HD-I) atomic charge density partitioning schemes is described. Atomic charges and atomic multipoles are calculated from the HD and HD-I atomic charge densities for arbitrary atomic multipole rank l(max) on molecules of arbitrary shape and size. The HD and HD-I atomic charges/multipoles are tested by comparing molecular multipole moments and the electrostatic potential (ESP) surrounding a molecule with their reference ab initio values. In general, the HD-I atomic charges/multipoles are found to better reproduce ab initio electrostatic properties over HD atomic charges/multipoles. A systematic increase in precision for reproducing ab initio electrostatic properties is de... Computer Physics Communications journals http://www.medworm.com/rss/comments.php?id=5492477 Sun, 11 Dec 2011 08:54:11 +0100 5492477 http://www.medworm.com/index.php?rid=5295184&cid=s_38111_79_f&fid=38111&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21969733%26dopt%3DAbstract Authors: Engel GP, Schaefer S Abstract We test a recent proposal to use approximate trivializing maps in a field theory to speed up Hybrid Monte Carlo simulations. Simulating the CPN-1 model, we find a small improvement with the leading order transformation, which is however compensated by the additional computational overhead. The scaling of the algorithm towards the continuum is not changed. In particular, the effect of the topological modes on the autocorrelation times is studied. PMID: 21969733 [PubMed - as supplied by publisher] (Source: Computer Physics Communications) Computer Physics Communications journals http://www.medworm.com/rss/comments.php?id=5295184 Sat, 01 Oct 2011 04:00:00 +0100 5295184 http://www.medworm.com/index.php?rid=5295183&cid=s_38111_79_f&fid=38111&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21969734%26dopt%3DAbstract We present a new numerical technique to solve large-scale eigenvalue problems. It is based on the projection technique, used in strongly correlated quantum many-body systems, where first an effective approximate model of smaller complexity is constructed by projecting out high energy degrees of freedom and in turn solving the resulting model by some standard eigenvalue solver.Here we introduce a generalization of this idea, where both steps are performed numerically and which in contrast to the standard projection technique converges in principle to the exact eigenvalues. This approach is not just applicable to eigenvalue problems encountered in many-body systems but also in other areas of research that result in large-scale eigenvalue problems for matrices which have, roughly speaking, mo... Computer Physics Communications journals http://www.medworm.com/rss/comments.php?id=5295183 Sat, 01 Oct 2011 04:00:00 +0100 5295183 http://www.medworm.com/index.php?rid=5295182&cid=s_38111_79_f&fid=38111&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21969735%26dopt%3DAbstract Authors: Frisch W, Eberl H, Hluchá H Abstract HFOLD (Higgs Full One Loop Decays) is a Fortran program package for calculating all MSSM Higgs two-body decay widths and the corresponding branching ratios at full one-loop level. The package is done in the SUSY Parameter Analysis convention and supports the SUSY Les Houches Accord input and output format. PROGRAM SUMMARY: Program title: HFOLD Catalogue identifier: AEJG_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEJG_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 340 621 No. of bytes in distributed program, including te... Computer Physics Communications journals http://www.medworm.com/rss/comments.php?id=5295182 Sat, 01 Oct 2011 04:00:00 +0100 5295182 http://www.medworm.com/index.php?rid=5095603&cid=s_38111_79_f&fid=38111&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21804642%26dopt%3DAbstract Monte Carlo simulations of the HP model (the "Ising model" of protein folding). Comput Phys Commun. 2011 Sep 1;182(9):1896-1899 Authors: Li YW, Wüst T, Landau DP Using Wang-Landau sampling with suitable Monte Carlo trial moves (pull moves and bond-rebridging moves combined) we have determined the density of states and thermodynamic properties for a short sequence of the HP protein model. For free chains these proteins are known to first undergo a collapse "transition" to a globule state followed by a second "transition" into a native state. When placed in the proximity of an attractive surface, there is a competition between surface adsorption and folding that leads to an intriguing sequence of "transitions". These transitions depend upon the relative interaction strengths and... Computer Physics Communications journals http://www.medworm.com/rss/comments.php?id=5095603 Fri, 05 Aug 2011 14:33:19 +0100 5095603 http://www.medworm.com/index.php?rid=5049795&cid=s_38111_79_f&fid=38111&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21760640%26dopt%3DAbstract Authors: Blank M, Krassnigg A In the functional approach to quantum chromodynamics, the properties of hadronic bound states are accessible via covariant integral equations, e.g. the Bethe-Salpeter equation for mesons. In particular, one has to deal with linear, homogeneous integral equations which, in sophisticated model setups, use numerical representations of the solutions of other integral equations as part of their input. Analogously, inhomogeneous equations can be constructed to obtain off-shell information in addition to bound-state masses and other properties obtained from the covariant analogue to a wave function of the bound state. These can be solved very efficiently using well-known matrix algorithms for eigenvalues (in the homogeneous case) and the solution of linear system... Computer Physics Communications journals http://www.medworm.com/rss/comments.php?id=5049795 Thu, 30 Jun 2011 23:00:00 +0100 5049795 http://www.medworm.com/index.php?rid=4855181&cid=s_38111_79_f&fid=38111&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21572587%26dopt%3DAbstract Authors: Gramada A, Bourne PE Multipole expansions offer a natural path to coarse-graining the electrostatic potential. However, the validity of the expansion is restricted to regions outside a spherical enclosure of the distribution of charge and, therefore, not suitable for most applications that demand accurate representation at arbitrary positions around the molecule. We propose and demonstrate a distributed multipole expansion approach that resolves this limitation. We also provide a practical algorithm for the computational implementation of this approach. The method allows the partitioning of the charge distribution into subsystems so that the multipole expansion of each component of the partition, and therefore of their superposition, is valid outside an enclosing surface of th... Computer Physics Communications journals http://www.medworm.com/rss/comments.php?id=4855181 Tue, 24 May 2011 18:00:06 +0100 4855181 http://www.medworm.com/index.php?rid=4088116&cid=s_38111_79_f&fid=38111&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20957064%26dopt%3DAbstract Authors: Ambia-Garrido J, Vainrub A, Pettitt BM New methods based on surfaces or beads have allowed measurement of properties of single DNA molecules in very accurate ways. Theoretical coarse grained models have been developed to understand the behavior of single stranded and double stranded DNA. These models have been shown to be accurate and relatively simple for very short systems of 6-8 base pairs near surfaces. Comparatively less is known about the influence of a surface on the secondary structures of longer molecules important to many technologies. Surface fields due to either applied potentials and/or dielectric boundaries are not in current surface mounted coarse grained models. To gain insight into longer and surface mounted sequences we parameterized a discretized worm-like c... Computer Physics Communications journals http://www.medworm.com/rss/comments.php?id=4088116 Sat, 23 Oct 2010 03:25:07 +0100 4088116 http://www.medworm.com/index.php?rid=3655688&cid=s_38111_79_f&fid=38111&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20532187%26dopt%3DAbstract Authors: Lu B, Cheng X, Huang J, McCammon JA A Fortran program package is introduced for rapid evaluation of the electrostatic potentials and forces in biomolecular systems modeled by the linearized Poisson-Boltzmann equation. The numerical solver utilizes a well-conditioned boundary integral equation (BIE) formulation, a node-patch discretization scheme, a Krylov subspace iterative solver package with reverse communication protocols, and an adaptive new version of fast multipole method in which the exponential expansions are used to diagonalize the multipole to local translations. The program and its full description, as well as several closely related libraries and utility tools are available at http://lsec.cc.ac.cn/lubz/afmpb.html and a mirror site at http://mccammon.ucsd.edu/. This... Computer Physics Communications journals http://www.medworm.com/rss/comments.php?id=3655688 Mon, 31 May 2010 23:00:00 +0100 3655688 http://www.medworm.com/index.php?rid=3284746&cid=s_38111_79_f&fid=38111&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20161693%26dopt%3DAbstract Authors: Deng S By utilizing a novel three-layer dielectric model for the interface between a spherical quantum dot and the surrounding matrix, a robust numerical method for calculating the self-polarization energy of a spherical quantum dot with a finite confinement barrier is presented in this paper. The proposed numerical method can not only overcome the inherent mathematical divergence in the self-polarization energy which arises for the simplest and most widely used step-like model of the dielectric interface, but also completely eliminate the potential numerical divergence which may occur in the Bolcatto-Proetto's formula [J. Phys.: Condens. Matter 13, 319-334 (2001)], an approximation method commonly employed for more realistic three-layer dielectric models such as the linear an... Computer Physics Communications journals http://www.medworm.com/rss/comments.php?id=3284746 Fri, 19 Feb 2010 09:40:06 +0100 3284746 http://www.medworm.com/index.php?rid=1819520&cid=s_38111_79_f&fid=38111&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18196178%26dopt%3DAbstract Authors: Brown PH, Schuck P Analytical ultracentrifugation allows one to measure in real-time the concentration gradients arising from the application of a centrifugal force to macromolecular mixtures in solution. In the last decade, the ability to efficiently solve the partial differential equation governing the ultracentrifugal sedimentation and diffusion process, the Lamm equation, has spawned significant progress in the application of sedimentation velocity analytical ultracentrifugation for the study of biological macromolecules, for example, the characterization of protein oligomeric states and the study of reversible multi-protein complexes in solution. The present work describes a numerical algorithm that can provide an improvement in accuracy or efficiency over existing algori... Computer Physics Communications journals http://www.medworm.com/rss/comments.php?id=1819520 Tue, 15 Jan 2008 05:00:00 +0100 1819520 http://www.medworm.com/index.php?rid=1819521&cid=s_38111_79_f&fid=38111&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18084624%26dopt%3DAbstract Authors: Chen N, Glazier JA, Izaguirre JA, Alber MS The Cellular Potts Model (CPM) has been used in a wide variety of biological simulations. However, most current CPM implementations use a sequential modified Metropolis algorithm which restricts the size of simulations. In this paper we present a parallel CPM algorithm for simulations of morphogenesis, which includes cell-cell adhesion, a cell volume constraint, and cell haptotaxis. The algorithm uses appropriate data structures and checkerboard subgrids for parallelization. Communication and updating algorithms synchronize properties of cells simulated on different processor nodes. Tests show that the parallel algorithm has good scalability, permitting large-scale simulations of cell morphogenesis (10(7) or more cells) and broadening... Computer Physics Communications journals http://www.medworm.com/rss/comments.php?id=1819521 Fri, 01 Jun 2007 04:00:00 +0100 1819521 http://www.medworm.com/index.php?rid=1819522&cid=s_38111_79_f&fid=38111&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D11542688%26dopt%3DAbstract Authors: Amaral LA, Goldberger AL, Ivanov PCh , Stanley HE We consider the question of how the cardiac rhythm spontaneously self-regulates and propose a new mechanism as a possible answer. We model the neuroautonomic regulation of the heart rate as a stochastic feedback system and find that the model successfully accounts for key characteristics of cardiac variability, including the 1/f power spectrum, the functional form and scaling of the distribution of variations of the interbeat intervals, and the correlations in the Fourier phases which indicate nonlinear dynamics. PMID: 11542688 [PubMed - indexed for MEDLINE] (Source: Computer Physics Communications) Computer Physics Communications journals http://www.medworm.com/rss/comments.php?id=1819522 Fri, 01 Jan 1999 05:00:00 +0100 1819522 http://www.medworm.com/index.php?rid=1819523&cid=s_38111_79_f&fid=38111&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D11538855%26dopt%3DAbstract Authors: Badavi FF, Townsend LW, Wilson JW, Norbury JW PMID: 11538855 [PubMed - indexed for MEDLINE] (Source: Computer Physics Communications) Computer Physics Communications journals http://www.medworm.com/rss/comments.php?id=1819523 Thu, 01 Jan 1987 05:00:00 +0100 1819523