Publications

Sk Habibullah, Lipika Baidya, Sunil Kumar, Govardhan Reddy (2024). Metal Ion Sensing by Tetraloop-like RNA Fragment: Role of Compact Intermediates with Non-Native Metal Ion–RNA Inner-Shell Contacts. J. Phys. Chem. B, 2024, 128, 11389-11401.

Subham Kumar Saha, Pritha Mondal, Dibyendu Mondal, Navyashree Vasudeva, Ashwini Anshu, Awadhesh Narayan, Govardhan Reddy, Anshu Pandey (2024). Physical Mechanisms of Improved Performance of Scaffolded Zinc–Silver Battery Cathodes. J. Phys. Chem. Lett., 2024, 15, 9474-9480.

S. A. M. Shamimul Ahsan, Govardhan Reddy, Smeer Durani, Yashonath Subramanian (2024). Hydrogen Bond Dynamics in Siliceous and Aluminated Faujasite: Comparison with Bulk Water. J. Phys. Chem. B, 2024, 128, 9229-9246.

Kushal Singh, Govardhan Reddy (2023). Excited States of apo-Guanidine-III Riboswitch Contribute to Guanidinium Binding through Both Conformational and Induced-Fit Mechanisms. J. Chem. Theory Comput., 2024, 20, 421-435.

Sunil Kumar, Govardhan Reddy (2023). Mechanism of Fluoride Ion Encapsulation by Magnesium Ions in a Bacterial Riboswitch. j. Phys. Chem. B, 2023, 127, 9267-9281.

Arvind Kumar Gupta, Kushal Singh, Yogesh Patidar, Ravish Sharma, Abhijit A. Sardesai, Govardhan Reddy, Gopal Balasubramanian (2023). Allosteric Determinants in High Temperature Requirement A Enzymes Are Conserved and Regulate the Population of Active Conformations. ACS Chem. Biol., 2023, 18, 1487-1499.

Kushal Singh, Aswathy N. Muttathukattil, Prashant Chandra Singh, Govardhan Reddy (2022). pH Regulates Ligand Binding to an Enzyme Active Site by Modulating Intermediate Populations. J. Phys. Chem. B, 2022, 126, 9759-9770.

Hiranmay Maity, Lipika Baidya, Govardhan Reddy (2022). Salt-Induced Transitions in the Conformational Ensembles of Intrinsically Disordered Proteins. J. Phys. Chem. B, 2022, 126, 5959-5971.

Lipika Baidya, Govardhan Reddy (2022). pH Induced Switch in the Conformational Ensemble of Intrinsically Disordered Protein Prothymosin-α and Its Implications for Amyloid Fibril Formation. J. Phys. Chem. Lett., 2022, 13, 9589-9598.

Antarip Halder, Sunil Kumar, Sk Habibullah, Govardhan Reddy (2022). Local RNA Structure, Ion Hydration Shell and the Energy Barrier for Water Exchange from the Ion Hydration Shell Determine the Mechanism of Ion Condensation on Specific RNA Sites. bioRxiv.

Sunil Kumar, Govardhan Reddy (2022). Mechanism of Mg2+ Mediated Encapsulation of an Anionic Cognate Ligand in a Bacterial Riboswitch. bioRxiv.

Sunil Kumar, Govardhan Reddy (2022). TPP Riboswitch Populates Holo-Form-like Structure Even in the Absence of Cognate Ligand at High Mg2+ Concentration. J. Phys. Chem. B, 2022, 126, 2369-2381.

Balaka Mondal, D. Thirumalai, Govardhan Reddy (2021). Energy Landscape of Ubiquitin is Weakly Multidimensional. J. Phys. Chem. B, 2021, 125, 8682-8689.

Govardhan Reddy, D Thirumalai (2021). Asymmetry in Histone Rotation in Forced Unwrapping and Force Quench Rewrapping in a Nucleosome. Nucleic Acids Res., 2021, 49, 4907–4918.

Balaka Mondal, Jayashree Nagesh, Govardhan Reddy (2021). Double Domain Swapping in Human γC and γD Crystallin Drives Early Stages of Aggregation. J. Phys. Chem. B, 2021, 125, 1705–1715.

Antarip Halder, Sunil Kumar, Omar Valsson, Govardhan Reddy (2020). Mg2+ Sensing by an RNA Fragment: Role of Mg2+-Coordinated Water Molecules. J. Chem. Theory Comput., 2020, 16, 6702–6715.

S. A. M. Shamimul Ahsan, Aninda J. Bhattacharyya, Govardhan Reddy, Smeer Durani, Yashonath Subramanian (2020). Mutual Diffusivity of an n‑Hexane-2,2-Dimethyl Butane Binary Mixture Confined to Zeolite Y. J. Phys. Chem. B, 2020, 124, 8618–8627.

Govardhan Reddy, Aswathy N. Muttathukattil, Balaka Mondal (2020). Cosolvent Effects on the Growth of Amyloid Fibrils. Curr. Opin. Struct. Biol., 2020, 60, 101-109.

SAM Shamimul Ahsan, Smeer Durani, Govardhan Reddy, Yashonath Subramanian (2019). Shared Hydrogen Bonds: Water in Aluminated Faujasite. Phys. Chem. Chem. Phys., 2019, 22, 1632-1639.

Aswathy N. Muttathukattil, Sriraksha Srinivasan, Antarip Halder, Govardhan Reddy (2019). Role of Guanidinium-Carboxylate Ion Interaction in Enzyme Inhibition with Implications for Drug Design. J. Phys. Chem. B, 2019, 123, 9302-9311.

Balaka Mondal, Govardhan Reddy (2019). A Transient Intermediate Populated in Prion Folding Leads to Domain Swapping. Biochemistry, 2019, 59, 114-124.

D. Thirumalai, Himadri S. Samanta, Hiranmay Maity, Govardhan Reddy (2019). Universal Nature of Collapsibility in the Context of Protein Folding and Evolution. Trends Biochem. Sci., 2019, 44, 675-687.

Hiranmay Maity, Govardhan Reddy (2019). Transition State Ensemble in Salt Induced Protein Folding Follows Hammond's Postulate. J. Indian Chem. Soc., 2019, 96, 981-990.

Govardhan Reddy (2019). An example preprint / working paper.

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Aswathy N. Muttathukattil, Prashant Chandra Singh, Govardhan Reddy (2019). Role of Disulfide Bonds and Topological Frustration in the Kinetic Partitioning of Lysozyme Folding Pathways. J. Phys. Chem. B, 2019, 123, 3232-3241.

Balaka Mondal, Govardhan Reddy (2019). Cosolvent Effects on the Growth of Protein Aggregates Formed by a Single Domain Globular Protein and an Intrinsically Disordered Protein. J. Phys. Chem. B, 2019, 123, 1950-1960.

Biswajit Biswas, Aswathy N. Muttathukattil, Govardhan Reddy, Prashant Chandra Singh (2018). Contrasting Effects of Guanidinium Chloride and Urea on the Activity and Unfolding of Lysozyme. ACS Omega, 2018, 3, 14119-14126.

Hiranmay Maity, Aswathy N. Muttathukattil,, Govardhan Reddy (2018). Salt Effects on Protein Folding Thermodynamics. J. Phys. Chem. Lett., 2018, 9, 5063-5070.

Hiranmay Maity, Govardhan Reddy (2018). Transient Intermediates are Populated in the Folding Pathways of Single-Domain Two-State Folding Protein L. J. Chem. Phys., 2018, 148, 165101.

Hiranmay Maity, Govardhan Reddy (2018). Thermodynamics and Kinetics of Single-Chain Monellin Folding with Structural Insights into Specific Collapse in the Denatured State Ensemble. J. Mol. Biol., 2018, 430, 465-478.

Atreya Dey, Govardhan Reddy (2017). Toroidal Condensates by Semiflexible Polymer Chains: Insights into Nucleation, Growth and Packing Defects. J. Phys. Chem. B, 2017, 121, 9291-9301.

Shyamashis Das, Atreya Dey, Govardhan Reddy, D. D. Sarma (2017). Suppression of the Coffee-Ring Effect and Evaporation-Driven Disorder to Order Transition in Colloidal Droplets. J. Phys. Chem. Lett., 2017, 8, 4704-4709.

Govardhan Reddy, D. Thirumalai (2017). Collapse Precedes Folding in Denaturant-Dependent Assembly of Ubiquitin. J. Phys. Chem. B, 2017, 121, 995-1009.

Aswathy N. Muttathukattil, Govardhan Reddy (2016). Osmolyte Effects on the Growth of Amyloid Fibrils. J. Phys. Chem. B, 2016, 120, 10979-10989.

Zhenxing Liu, Govardhan Reddy, D. Thirumalai (2016). Folding PDZ2 Domain Using the Molecular Transfer Model. J. Phys. Chem. B, 2016, 120, 8090–8101.

Hiranmay Maity, Govardhan Reddy (2016). Folding of Protein L with Implications for Collapse in the Denatured State Ensemble. J. Am. Chem. Soc., 2016, 138, 2609-2616.

Govardhan Reddy, Robert Ford (2015). An example journal article. Journal of Source Themes, 1(1).

Govardhan Reddy, D. Thirumalai (2015). Dissecting Ubiquitin Folding Using the Self-Organized Polymer Model. J. Phys. Chem. B, 2015, 119, 11358–11370.

V. Navratna, Govardhan Reddy, B. Gopal (2015). Structural Basis for the Catalytic Mechanism of Homoserine Dehydrogenase. Acta Cryst., 2015, D71, 1216–1225.

Pavel I.Zhuravlev, Govardhan Reddy, John E.Straub, D.Thirumalai (2014). Propensity to Form Amyloid Fibrils Is Encoded as Excitations in the Free Energy Landscape of Monomeric Proteins. J. Mol. Biol., 2014, 426, 2653-2666.

Govardhan Reddy, Robert Ford (2013). An example conference paper. In ICW.

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D. Thirumalai, Zhenxing Liu, Edward PO’Brien, Govardhan Reddy (2013). Protein Folding: From Theory to Practice. Curr. Opin. Struct. Biol., 2013, 23, 22–29.

Govardhan Reddy, Zhenxing Liu, D. Thirumalai (2012). Denaturant-Dependent Folding of GFP. Proc. Natl. Acad. Sci., 2012, 109, 17832-17838.

Zhenxing Liu, Govardhan Reddy, D. Thirumalai (2012). Theory of the Molecular Transfer Model for Proteins with Applications to the Folding of the src-SH3 Domain. J. Phys. Chem. B, 2012, 116, 6707–6716.

D. Thirumalai, Govardhan Reddy (2011). Are Native Proteins Metastable?. Nat. Chem., 2011, 3, 910–911.

Samuel S. Cho, Govardhan Reddy, John E. Straub, D. Thirumalai (2011). Entropic Stabilization of Proteins by TMAO. J. Phys. Chem. B, 2011, 45, 13401–13407.

D. Thirumalai, Govardhan Reddy, John E. Straub (2011). Role of Water in Protein Aggregation and Amyloid Polymorphism. Acc. Chem. Res., 2011, 45, 83–92.

Zhenxing Liu, Govardhan Reddy, Edward P. O’Brien, D. Thirumalai (2011). Collapse Kinetics and Chevron Plots from Simulations of Denaturant-Dependent Folding of Globular Proteins. Proc. Natl. Acad. Sci., 2011, 108, 7787-7792.

Govardhan Reddy, John E. Straub, D. Thirumalai (2010). Dry Amyloid Fibril Assembly in a Yeast Prion Peptide is Mediated by Long-Lived Structures Containing Water Wires. Proc. Natl. Acad. Sci., 2010, 107, 21459-21464.

Mai Suan Li, Nguyen Truong Co, Govardhan Reddy, Chin-Kun Hu, J. E. Straub, D. Thirumalai (2010). Factors Governing Fibrillogenesis of Polypeptide Chains Revealed by Lattice Models. Phys. Rev. Lett., 2010, 105, 218101.

Govardhan Reddy, Arun Yethiraj (2010). Solvent Effects in Polyelectrolyte Adsorption: Computer Simulations with Explicit and Implicit Solvent. J. Chem. Phys., 2010, 132, 074903.

Govardhan Reddy, John E. Straub, D. Thirumalai (2009). Dynamics of Locking of Peptides onto Growing Amyloid Fibrils. Proc. Natl. Acad. Sci., 2009, 106, 11948-11953.

S. Vaitheeswaran, Govardhan Reddy, D. Thirumalai (2009). Water-Mediated Interactions Between Hydrophobic and Ionic Species in Cylindrical Nanopores. J. Chem. Phys., 2009, 130, 094502.

Govardhan Reddy, John E. Straub, D. Thirumalai (2009). Influence of Preformed Asp23−Lys28 Salt Bridge on the Conformational Fluctuations of Monomers and Dimers of Aβ Peptides with Implications for Rates of Fibril Formation. J. Phys. Chem. B, 2009, 113, 1162–1172.

Ruxandra Dima, Bogdan Tarus, Govardhan Reddy, John E. Straub, D. Thirumalai (2008). Protein Folding, Misfolding and Aggregation: Classical Themes and Novel Approaches. The Royal Society of Chemistry, 2008, Chapter 11, 241-265.

Govardhan Reddy, Arun Yethiraj (2006). Implicit and Explicit Solvent Models for the Simulation of Dilute Polymer Solutions. Macromolecules, 2006, 39, 8536–8542.

Govardhan Reddy, Rakwoo Chang, Arun Yethiraj (2006). Adsorption and Dynamics of a Single Polyelectrolyte Chain near a Planar Charged Surface: Molecular Dynamics Simulations with Explicit Solvent. J. Chem. Theory Comput., 2006, 2, 630–636.

Kamakshi Jagannathan, Govardhan Reddy, Arun Yethiraj (2005). Integral Equation Theory for Symmetric Nonadditive Hard Sphere Mixtures. J. Phys. Chem. B, 2005, 109, 6764–6768.

Govardhan Reddy, Arun Yethiraj (2004). The Behavior of Fluids Near Solutes: A Density Functional Theory and Computer Simulation Study. J. Chem. Phys., 2004, 121, 4203-4209.

Govardhan Reddy, C. P. Lawrence, J. L. Skinner, Arun Yethiraj (2003). Liquid State Theories for the Structure of Water. J. Chem. Phys., 2003, 119, 13012-13016.