Flat histogram simulation of lattice polymer systems

We demonstrate the use of a new algorithm called the Flat Histogram sampling algorithm for the simulation of lattice polymer systems. Thermodynamics properties, such as average energy or entropy and other physical quantities such as end-to-end distance or radius of gyration can be easily calculated using this method. Ground-state energy can also be determined. We also explore the accuracy and limitations of this method. Key words: Monte Carlo algorithms, flat histogram sampling, HP model, lattice polymer systemsComment: 7 RevTeX two-column page

Determining the density of states for classical statistical models: A random walk algorithm to produce a flat histogram

We describe an efficient Monte Carlo algorithm using a random walk in energy space to obtain a very accurate estimate of the density of states for classical statistical models. The density of states is modified at each step when the energy level is visited to produce a flat histogram. By carefully controlling the modification factor, we allow the density of states to converge to the true value very quickly, even for large systems. This algorithm is especially useful for complex systems with a rough landscape since all possible energy levels are visited with the same probability. In this paper, we apply our algorithm to both 1st and 2nd order phase transitions to demonstrate its efficiency and accuracy. We obtained direct simulational estimates for the density of states for two-dimensional ten-state Potts models on lattices up to $200 \times 200$ and Ising models on lattices up to $256 \times 256$. Applying this approach to a 3D $\pm J$ spin glass model we estimate the internal energy and entropy at zero temperature; and, using a two-dimensional random walk in energy and order-parameter space, we obtain the (rough) canonical distribution and energy landscape in order-parameter space. Preliminary data suggest that the glass transition temperature is about 1.2 and that better estimates can be obtained with more extensive application of the method.Comment: 22 pages (figures included

Broad histogram relation for the bond number and its applications

We discuss Monte Carlo methods based on the cluster (graph) representation for spin models. We derive a rigorous broad histogram relation (BHR) for the bond number; a counterpart for the energy was derived by Oliveira previously. A Monte Carlo dynamics based on the number of potential moves for the bond number is proposed. We show the efficiency of the BHR for the bond number in calculating the density of states and other physical quantities.Comment: 7 pages, 7 figure

DNA methylation screening after roux-en Y gastric bypass reveals the epigenetic signature stems from genes related to the surgery per se

[Abstract] Background/objectives: Obesity has been associated with gene methylation regulation. Recent studies have shown that epigenetic signature plays a role in metabolic homeostasis after Roux-en Y gastric bypass (RYGB). To conduct a genome-wide epigenetic analysis in peripheral blood to investigate whether epigenetic changes following RYGB stem from weight loss or the surgical procedure per se. Subjects/methods: By means of the Infinium Human Methylation 450 BeadChip array, global methylation was analyzed in blood of 24 severely obese women before and 6 months after RYGB and in 24 normal-weight women (controls). Results: In blood cells, nine DMCpG sites showed low methylation levels before surgery, methylation levels increased after RYGB and neared the levels measured in the controls. Additionally, 44 CpG sites associated with the Wnt and p53 signaling pathways were always differently methylated in the severely obese patients as compared to the controls and were not influenced by RYGB. Finally, 1638 CpG sites related to inflammation, angiogenesis, and apoptosis presented distinct methylation in the post-surgery patients as compared to the controls. Conclusion: Bariatric surgery per se acts on CpGs related to inflammation, angiogenesis, and endothelin-signaling. However, the gene cluster associated with obesity remains unchanged, suggesting that weight loss 6 months after RYGB surgery cannot promote this effect.This study’s data collection, DNA and statistical analysis was supported by São Paulo Research Foundation (FAPESP) (grants #2017/07220–7, #2016/05638–1 and #2015/18669–0). Also, statistical and bioinformatics analysis was supported by “Centro de Investigacion Biomedica En Red” (CIBERobn) and grants (PI17/01287) from the “Instituto de Salud Carlos III” (ISCIII), Spain, co-financed by the European Regional Development Fund (FEDER), MINECO grants MTM2014–52876-R and MTM2017–82724-R, and by the Xunta de Galicia (Grupos de Referencia Competitiva ED431C-2016-015 and Centro Singular de Investigación de Galicia ED431G/01), all of them through the ERDF. A Diaz-Lagares is funded by a research contract “Juan Rodés” (JR17/00016) and Ana B Crujeiras is funded by a research contract “Miguel Servet” (CP17/00088) from the ISCIII, co-financed by the European Regional Development Fund (FEDER)Brasil. Fundação de Amparo à Pesquisa do Estado de São Paulo; #2017/07220–7Brasil. Fundação de Amparo à Pesquisa do Estado de São Paulo; #2016/05638–1Brasil. Fundação de Amparo à Pesquisa do Estado de São Paulo; #2015/18669–0Xunta de Galicia; ED431C-2016-015Xunta de Galicia; ED431G/0

Altered pathways in methylome and transcriptome longitudinal analysis of normal weight and bariatric surgery women

[Abstract] DNA methylation could provide a link between environmental, genetic factors and weight control and can modify gene expression pattern. This study aimed to identify genes, which are differentially expressed and methylated depending on adiposity state by evaluating normal weight women and obese women before and after bariatric surgery (BS). We enrolled 24 normal weight (BMI: 22.5 ± 1.6 kg/m2) and 24 obese women (BMI: 43.3 ± 5.7 kg/m2) submitted to BS. Genome-wide methylation analysis was conducted using Infinium Human Methylation 450 BeadChip (threshold for significant CpG sites based on delta methylation level with a minimum value of 5%, a false discovery rate correction (FDR) of q < 0.05 was applied). Expression levels were measured using HumanHT-12v4 Expression BeadChip (cutoff of p ≤ 0.05 and fold change ≥2.0 was used to detect differentially expressed probes). The integrative analysis of both array data identified four genes (i.e. TPP2, PSMG6, ARL6IP1 and FAM49B) with higher methylation and lower expression level in pre-surgery women compared to normal weight women: and two genes (i.e. ZFP36L1 and USP32) that were differentially methylated after BS. These methylation changes were in promoter region and gene body. All genes are related to MAPK cascade, NIK/NF-kappaB signaling, cellular response to insulin stimulus, proteolysis and others. Integrating analysis of DNA methylation and gene expression evidenced that there is a set of genes relevant to obesity that changed after BS. A gene ontology analysis showed that these genes were enriched in biological functions related to adipogenesis, orexigenic, oxidative stress and insulin metabolism pathways. Also, our results suggest that although methylation plays a role in gene silencing, the majority of effects were not correlated.São Paulo Research Foundation; 2017/07220-7São Paulo Research Foundation; #2016/05638-1São Paulo Research Foundation; #2013/12819-4São Paulo Research Foundation; #2015/18669-0Instituto de Salud Carlos III; PI17/01287Ministerio de Economía y Empresa; MTM2014-52876-RMinisterio de Economía y Empresa; MTM2017-82724-RXunta de Galicia; ED431C-2016-015Xunta de Galicia; ED431G/0

Experimental study of negative photoconductivity in n-PbTe(Ga) epitaxial films

We report on low-temperature photoconductivity (PC) in n-PbTe(Ga) epitaxial films prepared by the hot-wall technique on -BaF_2 substrates. Variation of the substrate temperature allowed us to change the resistivity of the films from 10^8 down to 10_{-2} Ohm x cm at 4.2 K. The resistivity reduction is associated with a slight excess of Ga concentration, disturbing the Fermi level pinning within the energy gap of n-PbTe(Ga). PC has been measured under continuous and pulse illumination in the temperature range 4.2-300 K. For films of low resistivity, the photoresponse is composed of negative and positive parts. Recombination processes for both effects are characterized by nonexponential kinetics depending on the illumination pulse duration and intensity. Analysis of the PC transient proves that the negative photoconductivity cannot be explained in terms of nonequilibrium charge carriers spatial separation of due to band modulation. Experimental results are interpreted assuming the mixed valence of Ga in lead telluride and the formation of centers with a negative correlation energy. Specifics of the PC process is determined by the energy levels attributed to donor Ga III, acceptor Ga I, and neutral Ga II states with respect to the crystal surrounding. The energy level corresponding to the metastable state Ga II is supposed to occur above the conduction band bottom, providing fast recombination rates for the negative PC. The superposition of negative and positive PC is considered to be dependent on the ratio of the densities of states corresponding to the donor and acceptor impurity centers.Comment: 7 pages, 4 figure

Non-Minimal Warm Inflation and Perturbations on the Warped DGP Brane with Modified Induced Gravity

We construct a warm inflation model with inflaton field non-minimally coupled to induced gravity on a warped DGP brane. We incorporate possible modification of the induced gravity on the brane in the spirit of $f(R)$-gravity. We study cosmological perturbations in this setup. In the case of two field inflation such as warm inflation, usually entropy perturbations are generated. While it is expected that in the case of one field inflation these perturbations to be removed, we show that even in the absence of the radiation field, entropy perturbations are generated in our setup due to non-minimal coupling and modification of the induced gravity.Comment: 29 pages, 7 figures, Accepted by Gen. Rel Gravi

Use of homeopathic products in pigs feed improves the percentage, quality and marbling of meat

Abstract Studies and innovations on alternative feed additives, especially on homeopathic remedies have been highlighted in order to replace or reduce the use of antibiotics in pig production. This paper aimed to assess the addition of homeopathic products in pig diet and their effects on the growth performance, serum metabolites, nutrient and energy digestibility, carcass traits and meat quality. A total of 60 immunocastrated male pigs, weighing on average 30.91 ± 0.95 kg, were distributed in two treatments, 10 replicates and three animals/experimental unit. There was no effect (P≥0.05) of treatment on the growth performance and serum metabolites. The percentage of acid-insoluble ash recovered in the diet was greater (P≤0.01) in diets containing homeopathic products. The apparent digestible energy of diets containing homeopathic products was reduced (P≤0.01) in the growing phase and reduced (P≤0.01) the apparent digestibility coefficients of dry matter, crude protein, soluble neutral and acid detergent fibers, and gross energy in the growing and finishing phases. Pig that received diets with homeopathic products had higher (P≤0.05) amount of meat, percentage of meat and marbling. The use of homeopathic products in diets improves the percentage and quality of meat, as well as the marbling of the pig carcass, maintaining the performance