BioSim Lab @ UB

Computational Modeling + Theory + Data Science

Welcome to the BioSim lab at the Department of Chemistry - University at Buffalo! Our team of researchers, led by Hung Nguyen, Ph.D., specializes in developing and applying computational methods & tools to study biological systems at the molecular level. By combining expertise in chemistry, biophysics, polymer physics & molecular biology, we aim to uncover the fundamental principles underlying the behavior of biomolecules, their interactions and functions. Our ultimate goal is to advance our understanding of biological processes and contribute to the development of new therapeutic approaches.

To learn more, check out our research and publications. We’re expanding our lab!!

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contact us

nguyenh [at] buffalo.edu
+1 716 645 4166
471 Natural Sciences Complex, Buffalo NY, 14260

news

Aug, 2024 Hung gave a talk at ACS ‘24 Fall, Denver CO. It was nice to catch up with old friends & colleagues, and meet many new potential collaborators.
Aug, 2024 Dibya joins us as the second postdoc in the lab :tada: Welcome! Looking forward to working with you!
Jun, 2024 Check out our new preprint on BioRxiv, which is a collaborative effort with the Trcek’s and other labs. We showed that mRNA retains most of its structure inside germ granule, and that RNA-RNA homotypic interactions are limited, and are mostly formed by scattered intermolecular base pairing.
Apr, 2024 The first undergrad joins the lab, woohoo. :tada: Welcome, Neth!
Apr, 2024 Two manuscripts have been accepted to J. Phys. Chem. Lett. and J. Chem. Theory Comput.. Congratulations!
Dec, 2023 Delighted to welcome TWO new members joining the lab :tada: Hiranmay (who will join us as the first ever postdoc) and Samia (as a new grad student)! Cannot wait for all the science coming out of them!
Dec, 2023 Check out our new preprint on BioRxiv about salt dependence of the self-association propensity of CAG repeats!
Oct, 2023 Super excited to welcome Peter, the very first grad student, joining the lab! :tada: Looking forward to working with you!
Oct, 2023 Check out the preprint from Thirumalai’s lab (with our small contributions) about DNA modeling in the presence of ions bioRxiv!
Aug, 2023 Hung got invited to give a talk at the Genome, Environment and Microbiome (GEM) Community of Excellence Work-in-Progress in the Jacobs School of Medicine and Biomedical Sciences, UB.
Aug, 2023 The BioSim lab officially starts at UB! :smile: :tada: We have multiple open positions! Prospective students and postdocs please contact Hung.
Jun, 2023 Our recent work has been accepted and now appears on PNAS! We establish a link between structures & thermodynamics of monomeric RNAs and their propensity to undergo phase separation & aggregation.
May, 2023 Hung gives talk at multiple universities in Vietnam :vietnam:! Excited to discuss science with colleagues and students there!
Apr, 2023 Check out our work of IDP on bioRxiv! Also, try out the code to run simulations using OpenMM with GPU acceleration.
Mar, 2023 Hung has been offered a tenure-track Assistant Professor position in the Department of Chemistry - UB! Excited to start the new lab Fall ‘23! :blue_heart: :bison:

selected publications

  1. 2024_mRNA.jpg
    The Folding of Germ Granule mRNAs Controls Intermolecular Base Pairing in Germ Granules and Maintains Normal Fly Development
    Siran Tian, Hung T. Nguyen, Ziqing Ye, Silvi Rouskin, D. Thirumalai, and Tatjana Trcek
    bioRxiv, 2024
  2. 2023_DNA.png
    Competition between Stacking and Divalent Cation-Mediated Electrostatic Interactions Determines the Conformations of Short DNA Sequences
    Balaka Mondal, Debayan Chakraborty, Naoto Hori, Hung T. Nguyen, and D. Thirumalai
    J. Chem. Theory Comput., 2024
  3. 2023_CAG.jpg
    Salt-Dependent Self-Association of Trinucleotide Repeat RNA Sequences
    Hiranmay Maity, Hung T. Nguyen, Naoto Hori, and D. Thirumalai
    J. Phys. Chem. Lett., 2024
  4. 2023_PNAS.png
    Odd-even disparity in the population of slipped hairpins in RNA repeat sequences with implications for phase separation
    Hiranmay Maity, Hung T. Nguyen, Naoto Hori, and D. Thirumalai
    Proc. Nat. Acad. Sci., 2023
  5. 2022_NatChem.png
    Condensates in RNA repeat sequences are heterogeneously organized and exhibit reptation dynamics
    Hung T. Nguyen, Naoto Hori, and D. Thirumalai
    Nat. Chem., 2022