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A new adaptive grid-size algorithm for the simulation of sedimentation velocity profiles in analytical ultracentrifugation.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 complexe...
Source: Computer Physics Communications - January 15, 2008 Category: Bioinformatics Authors: Brown PH, Schuck P Tags: Comput Phys Commun Source Type: journals

A parallel implementation of the Cellular Potts Model for simulation of cell-based morphogenesis.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 algorit...
Source: Computer Physics Communications - June 1, 2007 Category: Bioinformatics Authors: Chen N, Glazier JA, Izaguirre JA, Alber MS Tags: Comput Phys Commun Source Type: journals

Modeling heart rate variability by stochastic feedback.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 - January 1, 1999 Category: Bioinformatics Authors: Amaral LA, Goldberger AL, Ivanov PCh , Stanley HE Tags: Comput Phys Commun Source Type: journals

An algorithm for a semiempirical nuclear fragmentation model.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
PMID: 11538855 [PubMed - indexed for MEDLINE]
Source: Computer Physics Communications - January 1, 1987 Category: Bioinformatics Authors: Badavi FF, Townsend LW, Wilson JW, Norbury JW Tags: Comput Phys Commun Source Type: journals