PNNL

Suman Samantray is a research associate working with the Physical Biosciences team in the Catalysis Science group within Pacific Northwest National Laboratory’s Physical and Computational Sciences Directorate. Samantray received his PhD in computational chemical science from Rheinish-Westphalian Technical University (RWTH) Aachen and Juelich Research Center. He received his MS in chemical engineering from SUNY Buffalo, and his BS in chemical engineering from Biju Patnaik University of Technology. Prior to joining Pacific Northwest National Laboratory, he was a postdoctoral fellow at the Institute of Biotechnology, RWTH Aachen.

Samantray's research focuses on the computational modelling of the metalloenzymes that catalyze the reduction of carbon dioxide to organic compounds. His research tools encompass traditional electronic structure methods, including density functional theory, to study the structure, dynamics, and reactivity of the metalloenzymes in its electrochemically coupled state and free energy pertubation methods to study the gas transport and gating mechanism of the metalloenzymes. He also has extensive research experience investigating the thermodynamics and kinetics of protein aggregation occurring in neurodegenerative diseases and elucidating the aggregation pathways of such proteins using molecular dynamics simulations.

• Disordered proteins or bio-materials
• Metalloenzymes
• Carbohydrate polymers
• Soft Interfaces
• Force field development
• Molecular simulation and modeling
• Density functional theory
• Free energy perturbation
• Markov state modeling
• Protein aggregation and dynamics
• Peptidomimetics
• Enzyme bio-catalysis

• Bioengineering
• Computational modeling
• Computational science
• Molecular engineering and simulation
• Protein engineering
• Theoretical and computational chemistry

• PhD in computational chemical science, RWTH Aachen University, Germany
• MS in chemical engineering, The State University of New York at Buffalo
• BS in chemical engineering, Biju Patnaik University of Technology

• American Chemical Society
• European Federation of Biotechnology
• Peer Reviewer, Applied Materials & Interfaces, Molecular Pharmaceutics, International Journal of Molecular Sciences, Biomolecules, Molecules, Frontiers in Molecular Biosciences

• Aachen Institute for Advanced Study in Computational Engineering Science fellowship, RWTH Aachen University, 2018
• College of Science and Engineering Postgraduate Fellowship, University of Galway, 2017

2023

Schäffler M., S. Samantray, and B. Strodel. 2023. "Transition Networks Unveil Disorder-to-Order Transformations in Aβ Caused by Glycosaminoglycans or Lipids" International Journal of Molecular Sciences 24, no. 14: 11238. doi:10.3390/ijms241411238

2022

Samantray, S., Schumann, W., Illig, A-M., Carballo-Pacheco, M., Paul, A., Barz, B. and Strodel, B., 2022. “Molecular dynamics simulations of protein aggregation: protocols for simulation setup and analysis with Markov state models and transition networks.” Methods in Molecular Biology, Pages 235-279, doi:10.1007/978-1-0716-1546-1_12

Olubiyi O.O., S. Samantray, A-M. Illig. 2022. “Chapter 24 - Advances in structure-based virtual screening for drug discovery.” Advances in Protein Molecular and Structural Biology Methods, Pages 387-404, doi:10.1016/B978-0-323-90264-9.00024-6

2021

Fatafta H., S. Samantray, A. Sayyed-Ahmad, O. Coskuner-Weber, and B. Strodel. 2021. “Chapter Five - Molecular simulations of IDPs: From ensemble generation to IDP interactions leading to disorder-to-order transitions.” Progress in Molecular Biology and Translational Science, Volume 183, Pages 135-185. doi:10.1016/bs.pmbts.2021.06.003

Paul A., S. Samantray, M. Anteghini, M. Khaled, and B. Strodel. 2021. “Thermodynamics and kinetics of the amyloid-β peptide revealed by Markov state models based on MD data in agreement with experiment.” Chem. Sci., 12, 6652-6669. doi:10.1039/D0SC04657D

Samantray S., O.O. Olubiyi, and B. Strodel. 2021. "The Influences of Sulphation, Salt Type, and Salt Concentration on the Structural Heterogeneity of Glycosaminoglycans" International Journal of Molecular Sciences 22, no. 21: 11529. doi:10.3390/ijms222111529

Samantray S. and B. Strodel. 2021. “The Effects of Different Glycosaminoglycans on the Structure and Aggregation of the Amyloid-β (16–22) Peptide.” The Journal of Physical Chemistry B 2021 125 (21), 5511-5525. doi:10.1021/acs.jpcb.1c00868

2020

Deike S., S. Rothemund, B. Voigt, S. Samantray, B.  Strodel, and W.H. Binder. 2020. “β-Turn mimetic synthetic peptides as amyloid-β aggregation inhibitors.” Bioorganic Chemistry, Volume 101, 2020, 104012, ISSN 0045-2068. doi:10.1016/j.bioorg.2020.104012.

Samantray S. and D.L. Cheung. 2020. “Effect of the air–water interface on the conformation of amyloid beta.” Biointerphases 1; 15 (6): 061011. doi:10.1116/6.0000620

Samantray S., F. Yin, B. Kav, and B.  Strodel. 2020. “Different Force Fields Give Rise to Different Amyloid Aggregation Pathways in Molecular Dynamics Simulations.” Journal of Chemical Information and Modeling 60 (12), 6462-6475. doi:10.1021/acs.jcim.0c01063

2018

Cheung  D.L. and S. Samantray. 2018. "Molecular Dynamics Simulation of Protein Biosurfactants" Colloids and Interfaces 2, no. 3: 39. doi:10.3390/colloids2030039