A review of Monte Carlo simulations of polymers with PERM

In this review, we describe applications of the pruned-enriched Rosenbluth method (PERM), a sequential Monte Carlo algorithm with resampling, to various problems in polymer physics. PERM produces samples according to any given prescribed weight distribution, by growing configurations step by step with controlled bias, and correcting "bad" configurations by "population control". The latter is implemented, in contrast to other population based algorithms like e.g. genetic algorithms, by depth-first recursion which avoids storing all members of the population at the same time in computer memory. The problems we discuss all concern single polymers (with one exception), but under various conditions: Homopolymers in good solvents and at the $\Theta$ point, semi-stiff polymers, polymers in confining geometries, stretched polymers undergoing a forced globule-linear transition, star polymers, bottle brushes, lattice animals as a model for randomly branched polymers, DNA melting, and finally -- as the only system at low temperatures, lattice heteropolymers as simple models for protein folding. PERM is for some of these problems the method of choice, but it can also fail. We discuss how to recognize when a result is reliable, and we discuss also some types of bias that can be crucial in guiding the growth into the right directions.Comment: 29 pages, 26 figures, to be published in J. Stat. Phys. (2011

Population dynamics of bovine herpesvirus 1 infection in a dairy herd

An induced outbreak of a bovine herpesvirus 1 (BHV1) infection in a dairy herd is described. The outbreak was induced by injecting three BHV1 seropositive cows with dexamethasone. Within 7 weeks all seronegative cows had seroconverted. Also some seropositive animals showed a significant increase in serum antibody titre. Using these data, parameters of population dynamics such as R0, the basic reproduction ratio, could be estimated. The basic reproduction ratio is a threshold value describing infection dynamics in a population. This parameter is defined as the average number of secondary cases generated by one primary case in a wholly susceptible population of defined density. In this population R0 was estimated to be at least 7. The importance of these findings, and implications for eradication of BHV1 are discussed

Sheep do not have a major role in bovine herpesvirus 1 transmission

With regard to BHV1 eradication programs in cattle it is important to know whether sheep can he a reservoir of BHV1. We therefore performed an experiment that consisted of three phases. In phase 1, 10 sheep were inoculated with high doses of BHV1 and kept in close contact with 5 sheep and 5 calves. All inoculated sheep excreted BHV1 between 8 and 15 days post inoculation and seroconverted. Although BHV1 was isolated from the nasal mucosa of 3 out of 5 sentinel sheep, none of the sentinel sheep produced antibodies against BHV1. One sentinel calf excreted BHV1 through days 12-17; the remaining 4 calves excreted BHV1 between days 18 and 24, suggesting that the first calf was infected by sheep and the remaining 4 sentinel calves were infected by that calf and not by sheep. The bacic reproduction ratio (R0) of BHV1 between sheep and calves was estimated at 0.1, and among calves it was estimated at ≤ 9. In phase 2, all inoculated sheep were treated with dexamethasone and kept in close contact with 5 sheep and 5 calves. All dexamethasone treated sheep re-excreted BHV1 over a 6- to 9-day period. None of the sentinel animals seroconverted. In phase 3, the sentinel sheep and calves of phase 1 were kept in two groups and were treated with dexamethasone. None of the sentinel sheep re-excreted BHV1, whereas 3 out of 5 sentinel calves did. It is concluded that while BHV1 infection in sheep is possible, BHV1 does not spread from sheep easily to cattle