Current status of Dynamical Overlap project

We discuss the adaptation of the Hybrid Monte Carlo algorithm to overlap fermions. We derive a method which can be used to account for the delta function in the fermionic force caused by the differential of the sign function. We discuss the algoritmic difficulties that have been overcome, and mention those that still need to be solved.Comment: Talk given at Workshop on Computational Hadron Physics, Nicosia, September 2005. 8 page

Topology with Dynamical Overlap Fermions

We perform dynamical QCD simulations with $n_f=2$ overlap fermions by hybrid Monte-Carlo method on $6^4$ to $8^3\times 16$ lattices. We study the problem of topological sector changing. A new method is proposed which works without topological sector changes. We use this new method to determine the topological susceptibility at various quark masses.Comment: 15 pages, 3 figure

Sorting signed circular permutations by super short reversals

We consider the problem of sorting a circular permutation by reversals of length at most 2, a problem that finds application in comparative genomics. Polynomial-time solutions for the unsigned version of this problem are known, but the signed version remained open. In this paper, we present the first polynomial-time solution for the signed version of this problem. Moreover, we perform an experiment for inferring distances and phylogenies for published Yersinia genomes and compare the results with the phylogenies presented in previous works.We consider the problem of sorting a circular permutation by reversals of length at most 2, a problem that finds application in comparative genomics. Polynomial-time solutions for the unsigned version of this problem are known, but the signed version rema9096272283FAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULOCAPES - COORDENAÇÃO DE APERFEIÇOAMENTO DE PESSOAL DE NÍVEL SUPERIORCNPQ - CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO2013/08293-72014/04718-6306730/2012-0; 477692/2012-5; 483370/2013-411th International Symposium on Bioinformatics Research and Application

Prevalent Polymorphism in Thyroid Hormone-Activating Enzyme Leaves a Genetic Fingerprint that Underlies Associated Clinical Syndromes

Context: A common polymorphism in the gene encoding the activating deiodinase (Thr92Ala-D2) is known to be associated with quality of life in millions of patients with hypothyroidism and with several organ-specific conditions. This polymorphism results in a single amino acid change within the D2 molecule where its susceptibility to ubiquitination and proteasomal degradation is regulated. Objective: To define the molecular mechanisms underlying associated conditions in carriers of the Thr92Ala-D2 polymorphism. Design, Setting, Patients: Microarray analyses of nineteen postmortem human cerebral cortex samples were performed to establish a foundation for molecular studies via a cell model of HEK-293 cells stably expressing Thr92 or Ala92 D2. Results: The cerebral cortex of Thr92Ala-D2 carriers exhibits a transcriptional fingerprint that includes sets of genes involved in CNS diseases, ubiquitin, mitochondrial dysfunction (chromosomal genes encoding mitochondrial proteins), inflammation, apoptosis, DNA repair and growth factor signaling. Similar findings were made in Ala92-D2-expressing HEK-293 cells and in both cases there was no evidence that thyroid hormone signaling was affected, i.e. the expression level of T3-responsive genes was unchanged, but that several other genes were differentially regulated. The combined microarray analyses (brain/cells) led to the development of an 81-gene classifier that correctly predicts the genotype of homozygous brain samples. In contrast to Thr92-D2, Ala92-D2 exhibits longer half-life and was consistently found in the Golgi. A number of Golgi-related genes were down-regulated in Ala92-D2-expressing cells but were normalized after 24h-treatment with the antioxidant N-acetylecysteine. Conclusions: Ala92-D2 accumulates in the Golgi, where its presence and/or ensuing oxidative stress disrupts basic cellular functions and increases pre-apoptosis. These findings are reminiscent to disease mechanisms observed in other neurodegenerative disorders such as Huntington's disease, and could contribute to the unresolved neurocognitive symptoms of affected carriers

Diagrammatic Quantum Monte Carlo for Two-Body Problem: Exciton

We present a novel method for precise numerical solution of the irreducible two-body problem and apply it to excitons in solids. The approach is based on the Monte Carlo simulation of the two-body Green function specified by Feynman's diagrammatic expansion. Our method does not rely on the specific form of the electron and hole dispersion laws and is valid for any attractive electron-hole potential. We establish limits of validity of the Wannier (large radius) and Frenkel (small radius) approximations, present accurate data for the intermediate radius excitons, and give evidence for the charge transfer nature of the monopolar exciton in mixed valence materials.Comment: 4 pages, 5 figure

Sorting Signed Circular Permutations by Super Short Reversals

International audienceWe consider the problem of sorting a circular permutation by reversals of length at most 2, a problem that finds application in comparative genomics. Polynomial-time solutions for the unsigned version of this problem are known, but the signed version remained open. In this paper, we present the first polynomial-time solution for the signed version of this problem. Moreover, we perform an experiment for inferring distances and phylogenies for published Yersinia genomes and compare the results with the phylogenies presented in previous works

Numerical Methods for the QCD Overlap Operator IV: Hybrid Monte Carlo

The extreme computational costs of calculating the sign of the Wilson matrix within the overlap operator have so far prevented four dimensional dynamical overlap simulations on realistic lattice sizes, because the computational power required to invert the overlap operator, the time consuming part of the Hybrid Monte Carlo algorithm, is too high. In this series of papers we introduced the optimal approximation of the sign function and have been developing preconditioning and relaxation techniques which reduce the time needed for the inversion of the overlap operator by over a factor of four, bringing the simulation of dynamical overlap fermions on medium-size lattices within the range of Teraflop-computers. In this paper we adapt the HMC algorithm to overlap fermions. We approximate the matrix sign function using the Zolotarev rational approximation, treating the smallest eigenvalues of the Wilson operator exactly within the fermionic force. We then derive the fermionic force for the overlap operator, elaborating on the problem of Dirac delta-function terms from zero crossings of eigenvalues of the Wilson operator. The crossing scheme proposed shows energy violations which are better than O($\Delta\tau^2$) and thus are comparable with the violations of the standard leapfrog algorithm over the course of a trajectory. We explicitly prove that our algorithm satisfies reversibility and area conservation. Finally, we test our algorithm on small $4^4$, $6^4$, and $8^4$ lattices at large masses.Comment: v2 60 pages; substantial changes to all parts of the article; v3 minor revsion

CoVITEST: A Fast and Reliable Method to Monitor Anti-SARS-CoV-2 Specific T Cells From Whole Blood

Cellular and humoral immune responses are essential for COVID-19 recovery and protection against SARS-CoV-2 reinfection. To date, the evaluation of SARS-CoV-2 immune protection has mainly focused on antibody detection, generally disregarding the cellular response, or placing it in a secondary position. This phenomenon may be explained by the complex nature of the assays needed to analyze cellular immunity compared with the technically simple and automated detection of antibodies. Nevertheless, a large body of evidence supports the relevance of the T cell's role in protection against SARS-CoV-2, especially in vulnerable individuals with a weakened immune system (such as the population over 65 and patients with immunodeficiencies). Here we propose to use CoVITEST (Covid19 anti-Viral Immunity based on T cells for Evaluation in a Simple Test), a fast, affordable and accessible in-house assay that, together with a diagnostic matrix, allows us to determine those patients who might be protected with SARS-CoV-2-reactive T cells. The method was established using healthy SARS-CoV-2-naïve donors pre- and post-vaccination (n=30), and further validated with convalescent COVID-19 donors (n=51) in a side-by-side comparison with the gold standard IFN-? ELISpot. We demonstrated that our CoVITEST presented reliable and comparable results to those obtained with the ELISpot technique in a considerably shorter time (less than 8 hours). In conclusion, we present a simple but reliable assay to determine cellular immunity against SARS-CoV-2 that can be used routinely during this pandemic to monitor the immune status in vulnerable patients and thereby adjust their therapeutic approaches. This method might indeed help to optimize and improve decision-making protocols for re-vaccination against SARS-CoV-2, at least for some population subsets.Copyright © 2022 Egri, Olivé, Hernández-Rodríguez, Castro, De Guzman, Heredia, Segura, Fernandez, de Moner, Torradeflot, Ballús, Martinez, Vazquez, Costa, Dobaño, Mazza, Mazzotti, Pascal, Juan, González-Navarro and Calderón

Computational Physics on Graphics Processing Units

The use of graphics processing units for scientific computations is an emerging strategy that can significantly speed up various different algorithms. In this review, we discuss advances made in the field of computational physics, focusing on classical molecular dynamics, and on quantum simulations for electronic structure calculations using the density functional theory, wave function techniques, and quantum field theory.Comment: Proceedings of the 11th International Conference, PARA 2012, Helsinki, Finland, June 10-13, 201

Light Hadron Masses from Lattice QCD

This article reviews lattice QCD results for the light hadron spectrum. We give an overview of different formulations of lattice QCD, with discussions on the fermion doubling problem and improvement programs. We summarize recent developments in algorithms and analysis techniques, that render calculations with light, dynamical quarks feasible on present day computer resources. Finally, we summarize spectrum results for ground state hadrons and resonances using various actions.Comment: 53 pages, 24 figures, one table; Rev.Mod.Phys. (published version); v2: corrected typ