Study of microscopic dynamics of complex fluids containing charged hydrophobic species by neutron scattering coupled with molecular dynamics simulations . (Etude de la dynamique d'ions hydrophobes en solutions aqueuses par diffusion de neutrons et par simulation nume'rique). - Debsindhu Bhowmik (2011)

An automated analysis workflow for optimization of force-field parameters using neutron scattering data. - Vickie E. Lynch; Jose M. Borreguero; Debsindhu Bhowmik; Panchapakesan Ganesh; Bobby G. Sumpter; Thomas Proffen; Monojoy Goswami (J. Comput. Phys., 2017)

Deep clustering of protein folding simulations. - Debsindhu Bhowmik; Shang Gao 008; Michael T. Young; Arvind Ramanathan (BMC Bioinform., 2018)

Visual Analytics for Deep Embeddings of Large Scale Molecular Dynamics Simulations. - Junghoon Chae; Debsindhu Bhowmik; Heng Ma; Arvind Ramanathan; Chad A. Steed (IEEE BigData, 2019)

Towards Native Execution of Deep Learning on a Leadership-Class HPC System. - Srikanth B. Yoginath; Md. Maksudul Alam; Arvind Ramanathan; Debsindhu Bhowmik; Nouamane Laanait; Kalyan S. Perumalla (IPDPS Workshops, 2019)

Deep Generative Model Driven Protein Folding Simulations. - Heng Ma; Debsindhu Bhowmik; Hyungro Lee; Matteo Turilli; Michael T. Young; Shantenu Jha; Arvind Ramanathan (PARCO, 2019)

DeepDriveMD: Deep-Learning Driven Adaptive Molecular Simulations for Protein Folding. - Hyungro Lee; Matteo Turilli; Shantenu Jha; Debsindhu Bhowmik; Heng Ma; Arvind Ramanathan (DLS@SC, 2019)

ProtTrans: Towards Cracking the Language of Life's Code Through Self-Supervised Deep Learning and High Performance Computing. - Ahmed Elnaggar; Michael Heinzinger; Christian Dallago; Ghalia Rehawi; Yu Wang; Llion Jones; Tom Gibbs; Tamas Feher; Christoph Angerer; Martin Steinegger; Debsindhu Bhowmik; Burkhard Rost (CoRR, 2020)

Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19. - Atanu Acharya; Rupesh Agarwal; Matthew B. Baker; Jérôme Baudry; Debsindhu Bhowmik; Swen Böhm; Kendall G. Byler; Sam Yen-Chi Chen; Leighton Coates; Connor J. Cooper; Omar Demerdash; Isabella Daidone; et al. (J. Chem. Inf. Model., 2020)

How Distinct Structural Flexibility within SARS-CoV-2 Spike Protein Reveals Potential Therapeutic Targets. - Serena H. Chen; M. Todd Young; John Gounley; Christopher B. Stanley; Debsindhu Bhowmik (IEEE BigData, 2021)

Secure Collaborative Environment for Seamless Sharing of Scientific Knowledge. - Srikanth B. Yoginath; Mathieu Doucet; Debsindhu Bhowmik; David Heise; Folami Alamudun; Hong-Jun Yoon; Christopher B. Stanley (SMC, 2021)

Using GANs with adaptive training data to search for new molecules. - Andrew E. Blanchard; Christopher B. Stanley; Debsindhu Bhowmik (J. Cheminformatics, 2021)

Dynamic Profiling of β-Coronavirus 3CL Mpro Protease Ligand-Binding Sites. - Eunice Cho; Margarida Rosa; Ruhi Anjum; Saman Mehmood; Mariya Soban; Moniza Mujtaba; Khair Bux; Syed Tarique Moin; Mohammad Tanweer; Sarath Dantu; Alessandro Pandini; Junqi Yin; et al. (J. Chem. Inf. Model., 2021)

Computational Workflow for Accelerated Molecular Design Using Quantum Chemical Simulations and Deep Learning Models. - Andrew E. Blanchard; Pei Zhang; Debsindhu Bhowmik; Kshitij Mehta; John Gounley; Samuel Temple Reeve; Stephan Irle; Massimiliano Lupo Pasini (SMC, 2022)

Language models for the prediction of SARS-CoV-2 inhibitors. - Andrew E. Blanchard; John Gounley; Debsindhu Bhowmik; Mayanka Chandra Shekar; Isaac Lyngaas; Shang Gao 008; Junqi Yin; Aristeidis Tsaris; Feiyi Wang; Jens Glaser (Int. J. High Perform. Comput. Appl., 2022)

ProtTrans: Toward Understanding the Language of Life Through Self-Supervised Learning. - Ahmed Elnaggar; Michael Heinzinger; Christian Dallago; Ghalia Rehawi; Yu Wang; Llion Jones; Tom Gibbs; Tamas Feher; Christoph Angerer; Martin Steinegger; Debsindhu Bhowmik; Burkhard Rost (IEEE Trans. Pattern Anal. Mach. Intell., 2022)

Automating Genetic Algorithm Mutations for Molecules Using a Masked Language Model. - Andrew E. Blanchard; Mayanka Chandra Shekar; Shang Gao 008; John Gounley; Isaac Lyngaas; Jens Glaser; Debsindhu Bhowmik (IEEE Trans. Evol. Comput., 2022)

Adaptive language model training for molecular design. - Andrew E. Blanchard; Debsindhu Bhowmik; Zachary R. Fox; John Gounley; Jens Glaser; Belinda S. Akpa; Stephan Irle (J. Cheminformatics, 2023)

Transferring a Molecular Foundation Model for Polymer Property Predictions. - Pei Zhang; Logan T. Kearney; Debsindhu Bhowmik; Zachary R. Fox; Amit K. Naskar; John Gounley (J. Chem. Inf. Model., 2023)

Enhancing molecular design efficiency: Uniting language models and generative networks with genetic algorithms. - Debsindhu Bhowmik; Pei Zhang; Zachary R. Fox; Stephan Irle; John Gounley (Patterns, 2024)