Biomedical subjects

Y Bar-Yam

Publications and source records attributed to Y Bar-Yam.

4 recordsLinked to original sources

PubMed1995

Motion of polymer ends in homopolymer and heteropolymer collapse.

To investigate the polymer coil-to-globule transition we performed simulations for the kinetics of homopolymer and heteropolymer collapse. Our stimulations made use of abstract models of long flexible polymers to obtain extensive statistical sampling. For a variety of these models, the simulations suggest that collapse of long polymers is dominated by diffusion of the polymer ends, which accrete monomers and small aggregates. The growth of the end aggregate was found to be nearly linear in time for homopolymers and largely unaffected by variations in microstructure. In contrast, for heteropolymers the presence of non-aggregating (hydrophilic) monomers dramatically slows and alters the growth of the end mass. In models simulated, the end mass grows roughly as the cube root of time, but still dominates aggregation along the contour. In a model where only pairwise bonding is allowed, the collapse is uniform since more flexible end motion does not result in continued end accretion. The possible significance of our results for biopolymer kinetics is discussed.

Algorithms↗

PubMed1995

Applications of parallel computing to biological problems.

Parallel computers should provide the greatest processing power and memory for scientific simulations in the coming decades. This review discusses general strategies and specific algorithms for the use of various parallel architectures in simulations of biological and artificial polymers. General strategies include space partitioning (domain decomposition cell methods) and distributed independent simulations. Specific algorithms include cellular automata for efficient abstract polymer simulation. One algorithm, the two-space algorithm, is particularly efficient both for parallel and serial computation. Three applications, 2D melts, gel electrophoresis, and polymer collapse, are described. Simulations of high-density melts in 2D show that contrary to expectations, polymers do not completely segregate at the highest densities; instead, polymer interpenetration is significant. Preliminary simulations of gel electrophoresis show its behavior in the diffusive regimen and demonstrate the use of Cellular Automaton Machines (CAMs). Polymer collapse is studied in the regime of large departures from good solvent conditions. In this regime, kinetics plays a significant role. Collapse is dominated (nucleated) by migration of the chain ends.

Algorithms↗

PubMed1993

Cellular automaton simulation of pulsed field gel electrophoresis.

We describe simulation techniques well suited to detailed investigation of the microscopic behavior of DNA during electrophoretic separation in the diffusive regime. Long polymers moving diffusively in a medium are simulated using microscopic Monte-Carlo steps. Simulations rely upon a recently introduced two-space abstract polymer that enables fine-grained massively parallel simulation. Tests of the two-space polymer dynamics are reviewed. The scaling with polymer length of the size and relaxation time of isolated polymers are shown to agree with universal scaling relations. The relaxation time is found to be significantly faster than the alternative bond-fluctuation method. Simplicity of implementation enables simulation on cellular automaton machines (CAM) including CAM-6, and a prototype of the new CAM-8, as well as other massively parallel architectures. Preliminary simulations of polymers migrating under an external field through a random medium of obstacles in two dimensions are described. Two sequences of simulations are performed, with different obstacle densities corresponding to pore sizes larger and smaller than the polymer radius of gyration. In the dilute medium polymers are characteristically draped on single obstacles. In the denser medium draping across multiple obstacles results in reduced orientation in the field direction. A demonstration of rapid 90 degrees field direction switching results in polymer motion toward the expected intermediate direction.

Algorithms↗

PubMed1988

The technique of transvaginal sonography with the use of a 6.5 MHz probe.

Ultrasonography has become an important tool in infertility and obstetric practice. Its use in gynecology, while effective, has been less. This article describes the use of a high-frequency 6.5 MHz probe specially designed for intravaginal use. The technique is presented, along with a description of its uses and findings by organ. Patient acceptance has been universal. Its high resolution makes this technique more useful in general gynecologic practice.

Fallopian Tubes↗