Atanu Acharya
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Towards understanding and enhancing electrical conductivity of bacterial pili protein
Open Date: 2017-05-01
Close Date: 2019-02-01
Positions (1)
Atanu Acharya
Syracuse University
Syracuse University’s ACompChemLab is recruiting a Postdoctoral Researcher in Computational Chemistry focused on multiscale modeling , QM/MM , molecular dynamics , and machine learning for biosystems . The position is based in the Acharya group at Syracuse University and involves studying complex biological systems such as bacteria, viruses, and light-sensitive proteins, with emphasis on native protein, lipid, and sugar environments. The successful candidate will work on preparing biochemical systems in native environments, running equilibrium and non-equilibrium MD simulations, performing free-energy calculations, setting up electronic structure and multiscale QM/MM calculations, building databases for ML models, developing models for electronic properties, and carrying out network analysis related to allosteric processes. The role also includes helping other students, preparing presentations, publishing peer-reviewed papers, and presenting at conferences. Eligibility highlights: Ph.D. in Chemistry, Biochemistry, Biophysics, Biomedical Engineering, Chemical Engineering, or a related field; experience in electronic structure theory, QM/MM and/or MD simulations; machine learning in a biochemical context; coding/scripting (Python, Tcl); familiarity with at least one MD package (NAMD, AMBER, CHARMM, GROMACS, etc.); experience with biochemical/biophysical systems; Python ML/data science libraries; and molecular visualization tools such as VMD, PyMOL, or UCSF Chimera. Funding: Full-time postdoc with a salary range of $62,400-$67,400. The initial appointment is for one year and may be renewed depending on performance and funding availability. Dr. Acharya also indicates support for career development and efforts to secure independent research funding. How to apply: Submit the online application through Syracuse University’s employment site. Attach a CV, cover letter, and three references. The posting is open until filled, so early application is advisable. Research keywords: computational chemistry, multiscale modeling, QM/MM, molecular dynamics, machine learning, biophysical chemistry, allostery, free-energy calculations, electronic structure, biosystems.
Articles (15)
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2024
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2024
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2023
Lymphocyte-specific protein tyrosine kinase (LCK) is essential for T cell antigen receptor (TCR)–mediated signal transduction. Here, we report two siblings homozygous for a novel LCK variant (c.1318C>T; P440S) characterized by T cell lymphopenia with skewed memory phenotype, infant-onset recurrent infections, failure to thrive, and protracted diarrhea. The patients’ T cells show residual TCR signal transduction and proliferation following anti-CD3/CD28 and phytohemagglutinin (PHA) stimulation. We demonstrate in mouse models that complete (Lck−/−) versus partial (LckP440S/P440S) loss-of-function LCK causes disease with differing phenotypes. While both Lck−/− and LckP440S/P440S mice exhibit arrested thymic T cell development and profound T cell lymphopenia, only LckP440S/P440S mice show residual T cell proliferation, cytokine production, and intestinal inflammation. Furthermore, the intestinal disease in the LckP440S/P440S mice is prevented by CD4+ T cell depletion or regulatory T cell transfer. These findings demonstrate that P440S LCK spares sufficient T cell function to allow the maturation of some conventional T cells but not regulatory T cells—leading to intestinal inflammation.
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2023
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2023
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2023
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2022
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2022
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2022
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2022
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2022
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2021
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2021
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2021
Collaborators (12)
Xiaoxiao Yang
University of Georgia
Jose Duca
Novartis Institutes for BioMedical Research Inc
Jitender Mehla
Research Assistant Professor
University of Oklahoma
Kyo Han Ahn
Professor
Pohang University of Science and Technology
E. Jeffrey North
Creighton University
Jens Neu
Assistant Professor
University of North Texas
Elena W.Y. Hsieh
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Chayan Dutta
Assistant Professor
University of Georgia
Nikhil S. Malvankar
Yale University
Bingchen Yu
Assistant Professor
University of Georgia
Sourav Sarkar
Research Assistant Professor
Pohang University of Science and Technology
Laura Zanetti-Polzi
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