A5045651282- Particle physics theoretical and experimental studies
- Quantum Chromodynamics and Particle Interactions
- High-Energy Particle Collisions Research
- HIV Research and Treatment
- Atomic and Subatomic Physics Research
- HIV/AIDS drug development and treatment
- Nuclear physics research studies
- Black Holes and Theoretical Physics
- Physics of Superconductivity and Magnetism
- HIV/AIDS Research and Interventions
- Superconducting Materials and Applications
- Immune Cell Function and Interaction
- Hepatitis C virus research
- vaccines and immunoinformatics approaches
- Quantum, superfluid, helium dynamics
- Quantum Information and Cryptography
- Quantum Mechanics and Applications
- Cold Atom Physics and Bose-Einstein Condensates
- Quantum Computing Algorithms and Architecture
- Nuclear Physics and Applications
- Monoclonal and Polyclonal Antibodies Research
- Quantum many-body systems
- Neutrino Physics Research
- Theoretical and Computational Physics
- Adversarial Robustness in Machine Learning
Los Alamos National Laboratory
2015-2024
Brookhaven National Laboratory
1991-2024
Seoul National University
2017-2024
Thomas Jefferson National Accelerator Facility
2020-2024
University of Bern
2023-2024
Samsung (South Korea)
2023-2024
Lawrence Livermore National Laboratory
2023-2024
Nvidia (United States)
2023-2024
Michigan State University
2019-2023
University of Washington
2007-2023
A SARS-CoV-2 variant carrying the Spike protein amino acid change D614G has become most prevalent form in global pandemic. Dynamic tracking of frequencies revealed a recurrent pattern G614 increase at multiple geographic levels: national, regional, and municipal. The shift occurred even local epidemics where original D614 was well established prior to introduction variant. consistency this highly statistically significant, suggesting that may have fitness advantage. We found grows higher...
The precise identification of the HIV-1 envelope glycoprotein (Env) responsible for productive clinical infection could be instrumental in elucidating molecular basis transmission and designing effective vaccines. Here, we developed a mathematical model 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 acute (clade B) infection. Viral genes evolving individual...
We present results on the chiral and deconfinement properties of QCD transition at finite temperature. Calculations are performed with 2+1 flavors quarks using p4, asqtad HISQ/tree actions. Lattices temporal extent N_tau=6, 8 12 used to understand control discretization errors reliably extrapolate estimates obtained lattice spacings continuum limit. The temperature is defined in terms phase a theory two massless analyzed O(N) scaling fits condensate susceptibility. find consistent from...
We present results for the equation of state in (2+1)-flavor QCD using highly improved staggered quark action and lattices with temporal extent $N_{\tau}=6,~8,~10$, $12$. show that these data can be reliably extrapolated to continuum limit obtain a number thermodynamic quantities speed sound temperature range $(130-400)$ MeV. compare our previous calculations, provide an analytic parameterization pressure, from which other calculated, use phenomenology. energy density crossover region, $145~...
HIV-1 sequences were analyzed to estimate the timing of ancestral sequence main group HIV-1, strains responsible for AIDS pandemic. Using parallel supercomputers and assuming a constant rate evolution, we applied maximum-likelihood phylogenetic methods unprecedented amounts data this calculation. We validated our approach by correctly estimating two historically documented points. comprehensive full-length envelope alignment, estimated date last common ancestor be 1931 (1915–41). Analysis...
Identification of full-length transmitted HIV-1 genomes could be instrumental in pathogenesis, microbicide, and vaccine research by enabling the direct analysis those viruses actually responsible for productive clinical infection. We show 12 acutely infected subjects (9 clade B 3 C) that complete transmitted/founder can inferred single genome amplification sequencing plasma virion RNA. This allowed molecular cloning biological a comprehensive genome-wide assessment genetic imprint left on...
Identification of the transmitted/founder virus makes possible, for first time, a genome-wide analysis host immune responses against infecting HIV-1 proteome. A complete dissection was made primary HIV-1–specific T cell response induced in three acutely infected patients. Cellular assays, together with new algorithms which identify sites positive selection genome, showed that cells rapidly select escape mutations concurrent falling load acute infection. Kinetic and mathematical modeling...
The restricted neutralization breadth of vaccine-elicited antibodies is a major limitation current human immunodeficiency virus-1 (HIV-1) candidate vaccines. In order to permit the efficient identification vaccines with enhanced capacity for eliciting cross-reactive neutralizing (NAbs) and assess overall potency NAb reactivity, we assembled panel 109 molecularly cloned HIV-1 Env pseudoviruses representing broad range genetic geographic diversity. Viral isolates from all circulating subtypes...
We calculate the equation of state in $2+1$ flavor QCD at finite temperature with physical strange quark mass and almost light masses using lattices temporal extent ${N}_{\ensuremath{\tau}}=8$. Calculations have been performed two different improved staggered fermion actions, asqtad p4 actions. Overall, we find good agreement between results obtained these $O({a}^{2})$ discretization schemes. A comparison earlier calculations on coarser is to quantify systematic errors current studies state....
Summary We have developed an analysis pipeline to facilitate real-time mutation tracking in SARS-CoV-2, focusing initially on the Spike (S) protein because it mediates infection of human cells and is target most vaccine strategies antibody-based therapeutics. To date we identified thirteen mutations that are accumulating. Mutations considered a broader phylogenetic context, geographically, over time, provide early warning system reveal may confer selective advantages transmission or...
BackgroundConcerted evolution is normally used to describe parallel changes at different sites in a genome, but it also observed languages where specific phoneme the same other many words lexicon—a phenomenon known as regular sound change. We develop general statistical model that can detect concerted aligned sequence data and apply study Turkic language family.ResultsLinguistic evolution, unlike genetic substitutional process, dominated by events of evolutionary Our identified more than 70...
ABSTRACT Identifying the specific genetic characteristics of successfully transmitted variants may prove central to development effective vaccine and microbicide interventions. Although human immunodeficiency virus transmission is associated with a population bottleneck, extent which different factors influence diversity viruses unclear. We estimate here number in 69 heterosexual men women primary subtype C infections. From 1,505 env sequences obtained using single genome amplification...
We report on the first lattice calculation of QCD phase transition using chiral fermions with physical quark masses. This uses 2+1 flavors, spatial volumes between (4 fm)(3) and (11 temperatures 139 196 MeV. Each temperature is calculated at a single spacing corresponding to temporal Euclidean extent N(t) = 8. The disconnected susceptibility, χ(disc) shows pronounced peak whose position height depend sensitively mass. find no metastability near which does not change when 5 fm increased 10...
We calculate the quadratic fluctuations of net baryon number, electric charge and strangeness as well correlations among these conserved charges in ($2+1$)-flavor lattice QCD at zero chemical potential. Results are obtained using calculations with tree-level improved gauge highly staggered quark actions almost physical light strange masses three different values cutoff. Our choice parameters corresponds to a value 160 MeV for lightest pseudoscalar Goldstone mass kaon mass. The diagonal...
ABSTRACT Induction of antibodies that neutralize a broad range human immunodeficiency virus type 1 (HIV-1) isolates is major goal vaccine development. To study natural examples neutralization, we analyzed sera from 103 HIV-1-infected subjects. Among progressor patients, 20% neutralized more than 75% panel 20 diverse viral isolates. Little activity was observed in long-term nonprogressors (elite controllers). Breadth neutralization correlated with load, but not CD4 count, history past...
We recently developed a novel strategy to identify transmitted HIV-1 genomes in acutely infected humans using single-genome amplification and model of random virus evolution. Here, we used this approach determine the molecular features simian immunodeficiency (SIV) transmission 18 experimentally Indian rhesus macaques. Animals were inoculated intrarectally (i.r.) or intravenously (i.v.) with stocks SIVmac251 SIVsmE660 that exhibited sequence diversity typical early-chronic infection. 987...
Elucidating virus-host interactions responsible for HIV-1 transmission is important advancing prevention strategies. To this end, single genome amplification (SGA) and sequencing of within the context a model random virus evolution has made possible first time an unambiguous identification transmitted/founder viruses precise estimation their numbers. Here, we applied approach to env analyses in cohort acutely infected men who have sex with (MSM) found that high proportion (10 28; 36%) had...
We used ultra-deep sequencing to obtain tens of thousands HIV-1 sequences from regions targeted by CD8+ T lymphocytes longitudinal samples three acutely infected subjects, and modeled viral evolution during the critical first weeks infection. Previous studies suggested that a single virus established productive infection, but these conclusions were tempered because limited sampling; now, we have greatly increased our confidence in this observation through modeling observed earliest sample...
Scalar and tensor interactions were once competitors to the now well-established $V\ensuremath{-}A$ structure of standard model weak interactions. We revisit these survey constraints from low-energy probes (neutron, nuclear, pion decays) as well collider searches. Currently, most stringent limit on scalar arise ${0}^{+}\ensuremath{\rightarrow}{0}^{+}$ nuclear decays radiative decay $\ensuremath{\pi}\ensuremath{\rightarrow}e\ensuremath{\nu}\ensuremath{\gamma}$, respectively. For future, we...
It is for the first time that quantum simulation high-energy physics (HEP) studied in U.S. decadal particle-physics community planning, and fact until recently, this was not considered a mainstream topic community. This speaks of remarkable rate growth subfield over past few years, stimulated by impressive advancements information sciences (QIS) associated technologies decade, significant investment area government private sectors other countries. High-energy physicists have quickly...
We present results for the isovector axial vector form factors obtained using thirteen <a:math xmlns:a="http://www.w3.org/1998/Math/MathML" display="inline"><a:mrow><a:mn>2</a:mn><a:mo>+</a:mo><a:mn>1</a:mn><a:mo>+</a:mo><a:mn>1</a:mn></a:mrow></a:math>-flavor highly improved staggered quark (HISQ) ensembles generated by MILC collaboration. The calculation of nucleon two- and three-point correlation functions has been done Wilson-clover fermions. In analysis these data, we quantify...