Biomedical subjects

Vishal Mehra

Publications and source records attributed to Vishal Mehra.

3 recordsLinked to original sources

PubMed2003

Structure optimization in an off-lattice protein model.

We study an off-lattice protein toy model with two species of monomers interacting through modified Lennard-Jones interactions. Low energy configurations are optimized using the pruned-enriched-Rosenbluth method (PERM), hitherto employed to native state searches only for off-lattice models. For two dimensions we found states with lower energy than previously proposed putative ground states for all chain lengths >/=13. This indicates that PERM has the potential to produce native states also for more realistic protein models. For d=3, where no published ground states exist, we present some putative lowest energy states for future comparison with other methods.

Journal Article↗

PubMed2003

Growth-based optimization algorithm for lattice heteropolymers.

An improved version of the pruned-enriched-Rosenbluth method (PERM) is proposed and tested on finding lowest energy states in simple models of lattice heteropolymers. It is found to outperform not only the previous version of PERM, but also all other fully blind general purpose stochastic algorithms which have been employed on this problem. In many cases, it found new lowest energy states missed in previous papers. Limitations are discussed.

Journal Article↗

PubMed2002

Trapping reaction with mobile traps.

We present the Monte Carlo results for the two-species trapping reaction A+B-->B with diffusing A and B on lattices in one, two, and three dimensions. We use an algorithm that permits one to simulate the survival probabilities of A particles down to <10(-30) with high accuracy. The results for the survival probability agree much better with the exact asymptotic predictions of Bramson and Lebowitz [Phys. Rev. Lett. 61, 2397 (1988)] than with the heuristics of Kang and Redner [J. Phys. A 17, L451 (1984)]. But there are very large deviations from either, which show that even these simulations are far from asymptotia. This is supported by the rms displacement of A particles, which clearly shows that the asymptotic regime has not been reached, at least for d=2 and d=3.

Journal Article↗