Tanmoy Bhattacharya

Bio: Tanmoy Bhattacharya is an academic researcher from Los Alamos National Laboratory. The author has contributed to research in topics: Quantum chromodynamics & Lattice QCD. The author has an hindex of 65, co-authored 286 publications receiving 20521 citations. Previous affiliations of Tanmoy Bhattacharya include Brookhaven National Laboratory & University of Washington.

Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection

Abstract: The precise identification of the HIV-1 envelope glycoprotein (Env) responsible for productive clinical infection could be instrumental in elucidating the molecular basis of HIV-1 transmission and in designing effective vaccines. Here, we developed a mathematical model of random viral evolution and, together with phylogenetic tree construction, used it to analyze 3,449 complete env sequences derived by single genome amplification from 102 subjects with acute HIV-1 (clade B) infection. Viral env genes evolving from individual transmitted or founder viruses generally exhibited a Poisson distribution of mutations and star-like phylogeny, which coalesced to an inferred consensus sequence at or near the estimated time of virus transmission. Overall, 78 of 102 subjects had evidence of productive clinical infection by a single virus, and 24 others had evidence of productive clinical infection by a minimum of two to five viruses. Phenotypic analysis of transmitted or early founder Envs revealed a consistent pattern of CCR5 dependence, masking of coreceptor binding regions, and equivalent or modestly enhanced resistance to the fusion inhibitor T1249 and broadly neutralizing antibodies compared with Envs from chronically infected subjects. Low multiplicity infection and limited viral evolution preceding peak viremia suggest a finite window of potential vulnerability of HIV-1 to vaccine-elicited immune responses, although phenotypic properties of transmitted Envs pose a formidable defense.

Timing the ancestor of the HIV-1 pandemic strains.

Abstract: HIV-1 sequences were analyzed to estimate the timing of the ancestral sequence of the main group of HIV-1, the strains responsible for the AIDS pandemic. Using parallel supercomputers and assuming a constant rate of evolution, we applied maximum-likelihood phylogenetic methods to unprecedented amounts of data for this calculation. We validated our approach by correctly estimating the timing of two historically documented points. Using a comprehensive full-length envelope sequence alignment, we estimated the date of the last common ancestor of the main group of HIV-1 to be 1931 (1915-41). Analysis of a gag gene alignment, subregions of envelope including additional sequences, and a method that relaxed the assumption of a strict molecular clock also supported these results.

Chiral and deconfinement aspects of the QCD transition

Abstract: We present results on the chiral and deconfinement properties of the QCD transition at finite temperature. Calculations are performed with $2+1$ flavors of quarks using the p4, asqtad, and HISQ/tree actions. Lattices with temporal extent ${N}_{\ensuremath{\tau}}=6$, 8, and 12 are used to understand and control discretization errors and to reliably extrapolate estimates obtained at finite lattice spacings to the continuum limit. The chiral transition temperature is defined in terms of the phase transition in a theory with two massless flavors and analyzed using $O(N)$ scaling fits to the chiral condensate and susceptibility. We find consistent estimates from the HISQ/tree and asqtad actions and our main result is ${T}_{c}=154\ifmmode\pm\else\textpm\fi{}9\text{ }\text{ }\mathrm{MeV}$.

Equation of state in ( 2+1 )-flavor QCD

Abstract: We present results for the equation of state in ($2+1$)-flavor QCD using the highly improved staggered quark action and lattices with temporal extent ${N}_{\ensuremath{\tau}}=6$, 8, 10, and 12. We show that these data can be reliably extrapolated to the continuum limit and obtain a number of thermodynamic quantities and the speed of sound in the temperature range 130--400 MeV. We compare our results with previous calculations and provide an analytic parameterization of the pressure, from which other thermodynamic quantities can be calculated, for use in phenomenology. We show that the energy density in the crossover region, $145\text{ }\text{ }\mathrm{MeV}\ensuremath{\le}T\ensuremath{\le}163\text{ }\text{ }\mathrm{MeV}$, defined by the chiral transition, is ${\ensuremath{\epsilon}}_{c}=(0.18--0.5)\text{ }\text{ }\mathrm{GeV}/{\mathrm{fm}}^{3}$, i.e., $(1.2--3.1)\text{ }{\ensuremath{\epsilon}}_{\text{nuclear}}$. At high temperatures, we compare our results with resummed and dimensionally reduced perturbation theory calculations. As a byproduct of our analyses, we obtain the values of the scale parameters ${r}_{0}$ from the static quark potential and ${w}_{0}$ from the gradient flow.

I and i

Abstract: There is, I think, something ethereal about i —the square root of minus one. I remember first hearing about it at school. It seemed an odd beast at that time—an intruder hovering on the edge of reality. Usually familiarity dulls this sense of the bizarre, but in the case of i it was the reverse: over the years the sense of its surreal nature intensified. It seemed that it was impossible to write mathematics that described the real world in …

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

The Theory of Island Biogeography

Abstract: Preface to the Princeton Landmarks in Biology Edition vii Preface xi Symbols Used xiii 1. The Importance of Islands 3 2. Area and Number of Speicies 8 3. Further Explanations of the Area-Diversity Pattern 19 4. The Strategy of Colonization 68 5. Invasibility and the Variable Niche 94 6. Stepping Stones and Biotic Exchange 123 7. Evolutionary Changes Following Colonization 145 8. Prospect 181 Glossary 185 References 193 Index 201