Sthitadhi Maiti

Sthitadhi Maiti

Computational Biophysics Postdoctoral Researcher at University of Genoa, Italy | Classical Molecular Dynamics Simulations, Multiscale Modeling & Enhanced Sampling

Publications

You can also find my articles on my Google Scholar profile.

Binding-induced folding of intrinsically disordered peptides

Published in Protein Dynamics: Experimental and Computational Approaches, 2026

This book chapter examines binding-induced folding in intrinsically disordered peptides, with a focus on alpha-helical molecular recognition features and the energetic effects of residual structure. Atomistic umbrella-sampling simulations are used to quantify folding free energies, while coarse-grained simulations examine the binding free energies of PUMA and NOXA-A peptides interacting with MCL-1. The results clarify how prefolding, sequence variation, and conformational penalties influence coupled folding and binding, with implications for peptide and small-molecule design.

Recommended citation: Heyden, M.; Maiti, S. "Binding-induced folding of intrinsically disordered peptides." In Protein Dynamics: Experimental and Computational Approaches; Bondar, A.-N.; Sengupta, D., Eds.; Elsevier, 2026; Chapter 8, pp. 215-240. http://smaiti7.github.io/files/paper6.pdf

Fast sampling of protein conformational dynamics

Published in Sci. Adv., 2026

Here we demonstrate that anharmonic low-frequency vibrations extracted from short molecular dynamics simulations provide effective collective variables for enhanced sampling of protein conformational dynamics. Across five proteins of varying complexity, FRESEAN-guided metadynamics reproduced known conformational transitions and generated consistent free-energy landscapes without requiring prior knowledge of those transitions. This approach enables the rapid generation of accurate protein conformational ensembles for studying relationships between protein sequence, structure, and dynamics. My contributions included investigation, data curation, and visualization.

Recommended citation: Sauer, M. A.; Mondal, S.; Neff, B.; Maiti, S.; Heyden, M. "Fast sampling of protein conformational dynamics." Sci. Adv. 2026, 12, 13, eaea4617. http://smaiti7.github.io/files/paper5.pdf

Linear and Nonlinear Dielectric Response of Intrinsically Disordered Proteins

Published in J. Phys. Chem. Lett., 2024

Here we investigated how different alterations to force fields influence the conformational ensembles of intrinsically disordered proteins in simulations. Our findings indicate that various approaches to adjusting intra-protein and protein-water interactions distinctly affect protein solvation, especially concerning the hydration of polar and nonpolar functional groups. These variations are not completely reflected by global metrics such as the radius of gyration, yet they are essential for understanding the protein’s propensity to aggregate or form phase-separated droplets. Here we explored the dielectric responses of intrinsically disordered proteins (IDPs) in solutions were through molecular dynamics (MD) simulations and theoretical frameworks. My contribution here was conducting all the simulations to produce the necessary trajectories. We observed a significant increase in the linear dielectric function of IDPs compared to the solvent, attributed to their large dipole moments. IDPs exhibit a pronounced nonlinear dielectric effect (NDE) that surpasses that of standard electrolytes, providing insights into their conformational and rotational dynamics. The IDPs’ conformational flexibility aligns the dipole moment statistics with gamma/log-normal distributions, enhancing the NDE. This effect, influenced by the dipole moment’s intrinsic non-Gaussian parameter, interacts with protein osmotic compressibility to affect the nonlinear dielectric susceptibility, particularly under conditions of reduced electrolyte screening.

Recommended citation: Sauer, M.; Colburn, T.; Maiti, S.; Heyden, M.; Matyushov, D. "Linear and Nonlinear Dielectric Response of Intrinsically Disordered Proteins." J. Phys. Chem. Lett. 2024, 15, 20, 5420–5427. http://smaiti7.github.io/files/paper4.pdf

Solvation Thermodynamics and Free Energy Surfaces of Intrinsically Disordered Proteins in Aqueous Solutions

Published in Arizona State University, 2024

My doctoral research employed classical molecular dynamics simulations and enhanced-sampling techniques to characterize the solvation thermodynamics, conformational landscapes, and folding and binding free energies of intrinsically disordered proteins.

Recommended citation: Maiti, S. (2024). Solvation Thermodynamics and Free Energy Surfaces of Intrinsically Disordered Proteins in Aqueous Solutions. Ph.D. dissertation, Arizona State University. https://smaiti7.github.io/files/SM_PhD_Thesis.pdf

Model-Dependent Solvation of the K-18 Domain of the Intrinsically Disordered Protein Tau

Published in J. Phys. Chem. B., 2023

Here we investigated how different alterations to force fields influence the conformational ensembles of intrinsically disordered proteins in simulations. Our findings indicate that various approaches to adjusting intra-protein and protein-water interactions distinctly affect protein solvation, especially concerning the hydration of polar and nonpolar functional groups. These variations are not completely reflected by global metrics such as the radius of gyration, yet they are essential for understanding the protein’s propensity to aggregate or form phase-separated droplets.

Recommended citation: Maiti, S.; Heyden, M. "Model-Dependent Solvation of the K-18 Domain of the Intrinsically Disordered Protein Tau." J. Phys. Chem. B. 2023, 127, 33, 7220–7230. http://smaiti7.github.io/files/paper3.pdf

Electric-field induced entropic effects in liquid water

Published in J. Chem. Phys., 2023

In our research, we examined how externally applied electric fields affect the entropy of bulk water through classical TIP4P/2005 and ab initio molecular dynamics simulations. My role involved conducting the classical molecular dynamics simulations using the TIP4P/2005 model and analyzing the results. We found that while strong electric fields can align water molecules, they only cause slight reductions in entropy, indicating that electrofreezing is improbable in bulk water at room temperature. Additionally, we employed an analysis method of 3D-2PT, which allows for the spatial resolution of local entropy and number density of water in an electric field, offering comprehensive insights into the entropic and structural alterations at the atomic level.

Recommended citation: Nibali, V. C.; Maiti, S.; Saija, F.; Heyden, M.; Cassone, G. "Electric-field induced entropic effects in liquid water." J. Chem. Phys. 2023, 158, 184501. http://smaiti7.github.io/files/paper2.pdf

Two Keggin-Based Isostructural POMOF Hybrids: Synthesis, Crystal Structure, and Catalytic Properties

Published in Inorg. Chem., 2018

In this study, we synthesized two novel isostructural twin hybrids, Comp1: [H(C10H10N2)Cu2][PMo12O40] and Comp2: [H(C10H10N2)Cu2][PW12O40], using Keggin ions, Cu(I) cations, and 4,4′-bipyridine. My role involved the hydrothermal synthesis of both compounds, successful isolation of pure, homogeneous crystals, and their application as catalysts in the oxidation of various organic compounds like ethylbenzene, cyclohexanol, and cyclooctene. Both compounds formed crystals in the monoclinic P21/c space group with closely matching lattice parameters and crystal structures. Despite their structural similarity, Comp2 exhibited superior catalytic performance, particularly in the oxidation of ethylbenzene and cyclooctene, as well as in the photocatalytic degradation of methylene blue. Furthermore, studies on their electrochemical pseudocapacitance suggest potential applications of these polyoxometalate-based metal-organic frameworks (POMOFs) in charge storage and conducting devices, contingent upon enhancements in their electrochemical stability.

Recommended citation: Roy, S.; Vemuri, V.; Maiti, S.; Manoj, K. S.; Subbarao, U.; Peter, S. C. "Two Keggin-Based Isostructural POMOF Hybrids: Synthesis, Crystal Structure, and Catalytic Properties." Inorg. Chem. 2018, 57, 19, 12078–12092. http://smaiti7.github.io/files/paper1.pdf