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

(An)Isotropic models in scalar and scalar-tensor cosmologies

We study how the constants $G$ and $\Lambda$ may vary in different theoretical models (general relativity with a perfect fluid, scalar cosmological models (\textquotedblleft quintessence\textquotedblright) with and without interacting scalar and matter fields and a scalar-tensor model with a dynamical $\Lambda$) in order to explain some observational results. We apply the program outlined in section II to study three different geometries which generalize the FRW ones, which are Bianchi \textrm{V}, \textrm{VII}$_{0}$ and \textrm{IX}, under the self-similarity hypothesis. We put special emphasis on calculating exact power-law solutions which allow us to compare the different models. In all the studied cases we arrive to the conclusion that the solutions are isotropic and noninflationary while the cosmological constant behaves as a positive decreasing time function (in agreement with the current observations) and the gravitational constant behaves as a growing time function

About Bianchi I with VSL

In this paper we study how to attack, through different techniques, a perfect fluid Bianchi I model with variable G,c and Lambda, but taking into account the effects of a $c$-variable into the curvature tensor. We study the model under the assumption,div(T)=0. These tactics are: Lie groups method (LM), imposing a particular symmetry, self-similarity (SS), matter collineations (MC) and kinematical self-similarity (KSS). We compare both tactics since they are quite similar (symmetry principles). We arrive to the conclusion that the LM is too restrictive and brings us to get only the flat FRW solution. The SS, MC and KSS approaches bring us to obtain all the quantities depending on \int c(t)dt. Therefore, in order to study their behavior we impose some physical restrictions like for example the condition q<0 (accelerating universe). In this way we find that $c$ is a growing time function and Lambda is a decreasing time function whose sing depends on the equation of state, w, while the exponents of the scale factor must satisfy the conditions $\sum_{i=1}^{3}\alpha_{i}=1$ and $\sum_{i=1}^{3}\alpha_{i}^{2}<1,$ $\forall\omega$, i.e. for all equation of state$,$ relaxing in this way the Kasner conditions. The behavior of $G$ depends on two parameters, the equation of state $\omega$ and $\epsilon,$ a parameter that controls the behavior of $c(t),$ therefore $G$ may be growing or decreasing.We also show that through the Lie method, there is no difference between to study the field equations under the assumption of a $c-$var affecting to the curvature tensor which the other one where it is not considered such effects.Nevertheless, it is essential to consider such effects in the cases studied under the SS, MC, and KSS hypotheses.Comment: 29 pages, Revtex4, Accepted for publication in Astrophysics & Space Scienc

Risk-Stratified Screening for Colorectal Cancer Using Genetic and Environmental Risk Factors:A Cost-Effectiveness Analysis Based on Real-World Data

Background &amp; Aims: Previous studies on the cost-effectiveness of personalized colorectal cancer (CRC) screening were based on hypothetical performance of CRC risk prediction and did not consider the association with competing causes of death. In this study, we estimated the cost-effectiveness of risk-stratified screening using real-world data for CRC risk and competing causes of death. Methods: Risk predictions for CRC and competing causes of death from a large community-based cohort were used to stratify individuals into risk groups. A microsimulation model was used to optimize colonoscopy screening for each risk group by varying the start age (40–60 years), end age (70–85 years), and screening interval (5–15 years). The outcomes included personalized screening ages and intervals and cost-effectiveness compared with uniform colonoscopy screening (ages 45–75, every 10 years). Key assumptions were varied in sensitivity analyses. Results: Risk-stratified screening resulted in substantially different screening recommendations, ranging from a one-time colonoscopy at age 60 for low-risk individuals to a colonoscopy every 5 years from ages 40 to 85 for high-risk individuals. Nevertheless, on a population level, risk-stratified screening would increase net quality-adjusted life years gained (QALYG) by only 0.7% at equal costs to uniform screening or reduce average costs by 1.2% for equal QALYG. The benefit of risk-stratified screening improved when it was assumed to increase participation or costs less per genetic test. Conclusions: Personalized screening for CRC, accounting for competing causes of death risk, could result in highly tailored individual screening programs. However, average improvements across the population in QALYG and cost-effectiveness compared with uniform screening are small.</p

Flux Phase as a Dynamic Jahn-Teller Phase: Berryonic Matter in the Cuprates?

There is considerable evidence for some form of charge ordering on the hole-doped stripes in the cuprates, mainly associated with the low-temperature tetragonal phase, but with some evidence for either charge density waves or a flux phase, which is a form of dynamic charge-density wave. These three states form a pseudospin triplet, demonstrating a close connection with the E X e dynamic Jahn-Teller effect, suggesting that the cuprates constitute a form of Berryonic matter. This in turn suggests a new model for the dynamic Jahn-Teller effect as a form of flux phase. A simple model of the Cu-O bond stretching phonons allows an estimate of electron-phonon coupling for these modes, explaining why the half breathing mode softens so much more than the full oxygen breathing mode. The anomalous properties of $O^{2-}$ provide a coupling (correlated hopping) which acts to stabilize density wave phases.Comment: Major Revisions: includes comparisons with specific cuprate phonon modes, 16 eps figures, revte

Study of the temperature distribution in Si nanowires under microscopic laser beam excitation

The use of laser beams as excitation sources for the characterization of semiconductor nanowires (NWs) is largely extended. Raman spectroscopy and photoluminescence (PL) are currently applied to the study of NWs. However, NWs are systems with poor thermal conductivity and poor heat dissipation, which result in unintentional heating under the excitation with a focused laser beam with microscopic size, as those usually used in microRaman and microPL experiments. On the other hand, the NWs have subwavelength diameter, which changes the optical absorption with respect to the absorption in bulk materials. Furthermore, the NW diameter is smaller than the laser beam spot, which means that the optical power absorbed by the NW depends on its position inside the laser beam spot. A detailed analysis of the interaction between a microscopic focused laser beam and semiconductor NWs is necessary for the understanding of the experiments involving laser beam excitation of NWs. We present in this work a numerical analysis of the thermal transport in Si NWs, where the heat source is the laser energy locally absorbed by the NW. This analysis takes account of the optical absorption, the thermal conductivity, the dimensions, diameter and length of the NWs, and the immersion medium. Both free standing and heat-sunk NWs are considered. Also, the temperature distribution in ensembles of NWs is discussed. This analysis intends to constitute a tool for the understanding of the thermal phenomena induced by laser beams in semiconductor NWs