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2025

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  1. Sangeet S, Sinha A, Nair MB, Mahata A, Sarkar R, Roy S*, "EVOLVE: A Web Platform for AI-Based Protein Mutation Prediction and Evolutionary Phase Exploration", Journal of Chemical Information and Modeling, 2025, May 01, DOI:10.1021/acs.jcim.5c00026

  2. Basu M, Mainan A, Roy, S*,  Mishra PP*. "Emergence of a dynamic G-tetraplex scaffold: uncovering low salt-induced conformational heterogeneity and the folding mechanism of telomeric DNA", Physical Chemistry Chemical Physics, 2025, March 04, DOI:10.1039/D4CP04362FS

  3. Giordano RV, Sinha A, Mainan A; Sanbonmatsu K, Onuchic, J, Roy, S*; Leite V*, â€‹Critical Role of Mg2+ Ions in RNA Folding Transitions: Anchoring the A-Minor Twist in the SAM-II Riboswitch, ASAP

  4.  Jaiswar Akhilesh, Sarkar Raju, Mainan Avijit, Kundu Rimi, Roy Susmita*, Free Energy Landscape of Magnesium Chelation Reveals Dynamic Pre-Chelate Complexes Stabilized by Meta-Sphere RNA-Ion Coordination, ASAP.  

2024

  1. Das N, Samanta T, Gautam S, Khan K. Roy S, Shunmugam R . "Caprolactone-Based Biodegradable Polymer for Selective, Sensitive Detection and Removal of Cu2+ Ions from Water", ACS Polym. Au, 2024 March 6, DOI: 10.1021/acspolymersau.3c00056

  2. Sarkar R, Mainan A, Roy S*. Influence of ion and hydration atmospheres on RNA structure and dynamics:  insights from advanced theoretical and computational methods, Chemical Communications, 2024 March 20, DOI: 10.1039/d3cc06105a

  3. Chakraborty A, Samant D, Sarkar R, Sangeet S, Prusty S, Roy S*. "RNA’s Dynamic Conformational Selection and Entropic Allosteric Mechanism in Controlling Cascade Protein Binding Events" , Journal of Physical Chemistry Letters, 2024, June 3, DOI: 10.1021/acs.jpclett.4c00740

  4. Mainan A, Kundu R, Singh K R, Roy S*. "Magnesium Regulates RNA Ring Dynamics and Folding in Subgenomic Flaviviral RNA" , Journal of Physical Chemistry B, 2024, September 30, DOI:10.1021/acs.jpcb.4c03981

  5. Sinha A, Tony C M A, Roy S*. "How fingers affect folding of a thumb: Inter-subdomain cooperation in the folding of SARS-CoV-2 RdRp protein" , Biophysical Chemistry , 2024, october 18, DOI:10.1016/j.bpc.2024.107342

2023

  1. Sinha A, Sangeet S,  Roy S*. "Evolution of Sequence and Structure of SARS-CoV-2 Spike Protein: A Dynamic Perspective", ACS Omega ,2023 June 21, DOI: 10.1021/acsomega.3c00944

  2. Sarkar R, Singh K R,  Roy S*. "Hierarchical Hydration Dynamics of RNA with Nano-Water-Pool at Its Core", Journal  of Physical Chemistry B, 2023 July 28, DOI: 10.1021/acs.jpcb.3c03553

  3. Sinha A, Roy S*, "Intrinsically Disordered Regions Function as a Cervical Collar to Remotely Regulate the Nodding Dynamics of SARS-CoV-2 Prefusion Spike Heads" , Journal of Physical Chemistry B, 2023 September 22, DOI: 10.1021/acs.jpcb.3c05338

  4. Mohanty A, ..... , Mainan A, Mohanty K S, Roy S*, Orban J*, Kulkarni P* and Salgia R*, "Acquired resistance to KRAS G12C small-molecule inhibitors via genetic/nongenetic mechanisms in lung cancer", Science Advances, 2023 October 13, DOI: 10.1126/sciadv.ade3816

  5. Mainan A, Roy S*, "Dynamic Counterion Condensation Model Decodes Functional Dynamics of RNA Pseudoknot in SARS-CoV-2: Control of Ion-Mediated Pierced Lasso Topology", Journal Of Physical Chemistry Letters, 2023 November 13, DOI:  10.1021/acs.jpclett.3c02755

2022

  1. Jolly M* & Roy S*. Editorial: Emergent Dynamics of Biological Networks, J Biosci 2022, 47, 82. DOI: 10.1007/s12038-022-00324-0

  2. Nayak, S.P., Bagchi, B*. & Roy, S*. Effects of immunosuppressants on T-cell dynamics: Understanding from a generic coarse-grained immune network model. 2022, J Biosci 47, 70. DOI:10.1007/s12038-022-00312-4

  3. Kulkarni P, Leite VB, Roy S, Bhattacharyya S, Mohanty A, Achuthan S, Singh D, Appadurai R, Rangarajan G, Weninger K, Orban J. Intrinsically disordered proteins: Ensembles at the limits of Anfinsen's dogma. Biophysics Reviews. 2022 Mar 17;3(1):011306.i

  4. Karmi, O., Marjault, HB., Bai, F., Roy, S. et al. A VDAC1-mediated NEET protein chain transfers [2Fe-2S] clusters between the mitochondria and the cytosol and impacts mitochondrial dynamics. Proceedings of the National Academy of Sciences Feb 2022, 119 (7) e2121491119.

  5. Sangeet S, Sarkar R, Mohanty SK, Roy, S*. Quantifying Mutational Response to Track the Evolution of SARS-CoV-2 Spike Variants: Introducing a Statistical-Mechanics-Guided Machine Learning Method. J. Phys. Chem. B. 2022 Sep. DOI: 10.1021/acs.jpcb.2c04574

  6. Vysakh R, Mainan A, Roy S*. Dynamic effects of the spine of hydrated magnesium on viral RNA pseudoknot structure. Phys. Chem. Chem. Phys. 2022 Oct. DOI: 10.1039/d2cp01075e

  7. Nandi S K, Sarkar R, Jaiswar A, Roy S*, Haldar D*. Miniature β-Hairpin Mimetic by Intramolecular Hydrogen Bond and C-H···π Interactions. ACS Omega. 2022 May. DOI: 10.1021/acsomega.2c01168

2021

  1. Kulkarni, P., Achuthan, S., Bhattacharya, S. et al. Protein conformational dynamics and phenotypic switching. Biophys Rev, 2021.

  2. Prusty, Sangram; Sarkar, Raju; Chakraborty, Amrita and Roy, Susmita *. 2021. "Correlation in Domain Fluctuations Navigates Target Search of a Viral Peptide along RNA." Journal of Physical Chemistry B, 2021, November 9, DOI : 10.1021/acs.jpcb/1c07699

  3. Sarkar, Raju; Jaiswar, Akhilesh; Hennelly, Scott; Onuchic, Jose *; Sanbonmatsu, Karissa * and Roy, Susmita *. 2021."Chelated Magnesium Logic Gate Regulates Riboswitch Pseudoknot Formation." Journal of Physical Chemistry B, 2021, June 9, DOI : 10.1021/acs.jpcb.1c02467

  4. Junior, Antonio B. Oliveira; Lin, Xingcheng; Kulkarni, Prakash; Onuchic, José N; Roy, Susmita* and Leite, Vitor B. P.*. 2021."Exploring Energy Landscapes of Intrinsically Disordered Proteins: Insights into Functional Mechanisms." J. Chem. Theory Comput., 17, 3178-3187

  5. Nayak, Sonali Priyadarshini and Roy, Susmita *. 2021."Immune phase transition under steroid treatment." Physical Review E, 103, 062401

2020

  1. Roy, Susmita *; Jaiswar, Akhilesh and Sarkar, Raju. 2020."Dynamic Asymmetry Exposes 2019-nCoV Prefusion Spike." J. Phys. Chem. Lett., 2020, August 3, DOI : 10.1021/acs.jpclett.0c01431

  2. Roy, Susmita * and Bagchi, Biman *. 2020."Fluctuation theory of immune response: A statistical mechanical approach to understand pathogen induced T-cell population dynamics." J. Chem. Phys., 153, 045107

2019

  1. Lipper, Colin H; Stofleth, Jason T; Bai, Fang; Roy, Susmita; Mittler, Ron; Nechushtai, Rachel; Onuchic, Jose N and Jennings, Patricia A. 2019."Redox-dependent gating of VDAC by mitoNEET." Proceedings of the National Academy of Sciences (USA), 116, 19924

  2. Roy, Susmita; Hennelly, Scott P; Lammert, Heiko; Onuchic, Jose N and Sanbonmatsu, Karissa Y. 2019."Magnesium controls aptamer-expression platform switching in the SAM-I riboswitch." Nucleic Acids Research, 47, 3158–3170

  3. Lin, Xingcheng; Kulkarni, Prakash; Bocci, Federico; Schafer, Nicholas P; Roy, Susmita and al., et. 2019."Structural and Dynamical Order of a Disorderd Protein:Molecular Insights into Conformational Switching of PAGE4 at the System Level." Biomolecules, 9, 77

2018

  1. Lin, Xingcheng; Roy, Susmita; Jolly, Mohit Kumar; Bocci, Federico; Schafer, Nicholas; Tsai, Min Yeh; Kulkarni, Prakash; Orban, John; Grishaev, Alexander; Weninger, Keith; Rangarajan, Govindan; Levine, Herbert and Onuchic, José N. 2018."PAGE4 and Conformational Switching: Insights from Molecular Dynamics Simulations and Implications for Prostate Cancer." Journal of Molecular Biology, 430, 2422-2438

2017

  1. Roy, Susmita; Onuchic, José N and Sanbonmatsu, Karissa Y. 2017."Cooperation between magnesium pre-organization and metabolite binding controls collapse of the SAM-I riboswitch. (Feature and Cover Article) ." Biophysical Journal, 113, 348-359

  2. Roy, Susmita; Lammert, Heiko; Hayes, Ryan L; Chen, Bin; LeBlanc, Regan; Dayie, Theodore Kwaku; Onuchic, José N and Sanbonmatsu, Karissa Y. 2017."A magnesium-induced triplex pre-organizes the SAM-II riboswitch.." PLOS Computational Biology, 13, e1005406

2015

  1. Roy, Susmita; Yashonath, Subramanian and Bagchi, Biman. 2015."Mode coupling theory analysis of electrolyte dynamics : Time dependent diffusion and dynamic structure factor." J. Chem. Phys. , 142, 124502

  2. Sarkar, Sarmistha; Banerjee, Saikat; Roy, Susmita; Ghosh, Rikhia; Ray, Partha Pratim and Bagchi, Biman. 2015."Composition dependent non-ideality in aqueous binary mixtures as a signature of avoided spinodal decomposition." J. Chem. Sci., 127, 49–59

2014

  1. Bagchi, Kushal and Roy, Susmita*. 2014."Sensitivity of water dynamics to biologically significant surfaces of monomeric Insulin: Role of topology and electrostatic Interactions." J. Phys. Chem. B , 118, 3805

  2. Roy, Susmita; Shrinivas, Krishna and Bagchi, Biman. 2014."A stochastic chemical dynamic approach to correlate autoimmunity and optimal vitamin-D range.." PLoS ONE , 9, e100635

  3. Roy, Susmita and Bagchi, Biman. 2014."A comparative study of protein unfolding in aqueous urea and DMSO solutions: Surface polarity,solvent specificity and sequence of secondary structure melting.." J.Chem.Phys., B118, 5691

  4. Hazra, Milan Kumar; Roy, Susmita and Bagchi, Biman. 2014."Hydrophobic hydration driven self-assemblyof Curcumin in water: Similarities to nucleation and growth under large metastability ,and an analysis of water dynamics at heterogeneous surface.." J.Chem.Phys., 141, 18C501

  5. Ghosh, Rikhia; Banerjee, Saikat; Hazra, Milan; Roy, Susmita and Bagchi, Biman. 2014."Sensitivity of polarization to the nature of protein-water interactions: Study of biological water in four different protein-water system.." J.Chem.Phys., 141, 22D531

  6. Ghosh, Rikhia; Roy, Susmita and Bagchi, Biman. 2014."Multidimensional free energy surface of unfolding of HP-36: Microscopic origin of ruggedness .." J.Chem.Phys., 141, 135101

2013

  1. Roy, Susmita and Bagchi, Biman. 2013." Solvation dynamics of Tryptophan in water-dimethyl sulfoxide binary mixture: In search of molecular origin of composition dependent multiple anomalies.." J. Chem. Phys, 139, 034308

  2. Ghosh, Rikhia; Roy, Susmita and Bagchi, Biman. 2013."Solvent sensitivity of protein unfolding: Dynamical study of Chicken Villin Head-piece Subdomain in water-ethanol binary mixture.." J. Phys. Chem., B117, 15625

2012

  1. Roy, Susmita and Bagchi, Biman. 2012." Free energy barriers for escape of water molecules from protein hydration layer.." J. Phys. Chem., B116, 2958

  2. Roy, Susmita; Jana, Biman and Bagchi, Biman. 2012." Dimethyl sulfoxide induced structural transformations and non-monotonic concentration dependence of conformational fluctuation around active site of Lysozyme.." J. Phys. Chem., 136, 115103

  3. Roy, Susmita and Bagchi, Biman. 2012."Chemical unfolding of Chicken Villin Headpiece in aqueous dimethyl sulfoxide solution: cosolvent concentration dependence, pathway, and microscopic mechanism.." J. Phys. Chem., B117, 4488

2011

3. Ghosh, Rikhia; Roy, Susmita and Bagchi, Biman. 2011." Fluctuation quench and hydrophobic collapse of polymers and biopolymers in water-DMSO binary mixture at low DMSO concentrations.." J.Indian Chem.Soc, 88, 1223

2010

2. Banerjee, Saikat; Roy, Susmita and Bagchi, Biman. 2010."Enhanced pair hydrophobicity in the water-dimethylsulfoxide (DMSO) binary mixture at low DMSO concentrations.." J. Phys. Chem., B114, 12875

1. Roy, Susmita and Bagchi, Biman. 2010."Theoretical and computational analysis of static and dynamic anomalies in water-DMSO binary mixture at low DMSO concentrations.." J. Phys. Chem, B115, 685

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