Structure and Dynamics of Biological Molecules Experimental and Theoretical Approaches

Chapter 1: Biolayer interferometry and microscale thermophoresis: friends or foes? Chapter 2: Biophysical Methods for the Study of Lipid Droplet Models. Chapter 3: G-quadruplex DNA: Structure, Stability, and Significance. Chapter 4: Macromolecular Crowding: Impact on Protein Dynamics and Aggregation. Chapter 5: Metal Ion-regulated Biomolecular Conformational Dynamics: Implications for Health and Disease. Chapter 6: Enhanced conformational and solute sampling in molecular simulations of nucleic acids, carbohydrates, and proteins using the additive CHARMM36 and polarizable classical Drude oscillator force fields. Chapter 7: Molecular Dynamics (MD) Simulation: Background and Applications. Chapter 8: Molecular Dynamics Simulations of Ion Channels. Chapter 9: Lipid Bilayer Dynamics from Molecular Simulation: Impact of Small Saccharides. Chapter 10: Molecular Dynamics Simulations of Integral and Peripheral Membrane Proteins. Chapter 11: In silico repurposing of drugs: A case study targeting the methyltransferase complex of SARS-CoV-2. Chapter 12: Molecular Dynamics Simulation Study of Cooperative Binding of Thyroid Receptor to a Thyroid Response Element. Chapter 13: Validation of biomolecular simulation results by their comparison with the experimental data. Chapter 14: Modulation of Structural Dynamics in DNA Duplex and G-Quadruplex by Natural Alkaloids and Flavonoids: Integrative Insights from Spectroscopy, Calorimetry, and Molecular Modelling. 

Biography

Harekrushna Sahoo is a Professor at the National Institute of Technology Rourkela (NIT Rourkela), India. He completed his doctoral studies in biophysical chemistry at International University Bremen (now Constructor University, Bremen), Germany, in 2006, focusing on peptide conformation and dynamics using fluorescence spectroscopy. In 2012, he joined the Department of Chemistry at NIT Rourkela as an assistant professor. Before this appointment, he amassed a rich postdoctoral experience: he spent three years (2007–2009) at the University of Massachusetts–Amherst, USA, working on protein kinetics and dynamics; two years (2010–2011) at the Technical University Dresden, Germany, focusing on membrane dynamics; and a six-month tenure in 2012 as a guest scientist at the Max-Bergmann Center in Dresden, Germany. He has been awarded multiple international research fellowships, including NAWA (Poland, 2022), DAAD (Germany, 2021), and ICMR-DHR (Germany, 2022), recognizing his contributions to advanced research. Notably, he has been recognized as a top 2% researcher globally by Stanford University, USA, a distinction he has held consecutively from 2021 to 2023. Dr. Sahoo’s research group is primarily focused on protein kinetics, dynamics, and conformation as functions of environmental stress, along with examining the protein structure-function correlation using various experimental techniques. He has successfully managed several sponsored projects funded by the Science and Engineering Research Board (SERB), Government of India; the Board of Research in Nuclear Sciences (BRNS); the Department of Science and Technology (DST, Odisha); and through Indo-German collaborative research efforts. Additionally, Dr. Sahoo has served as a reviewer for numerous international peer-reviewed and renowned journals. With over 14 years of teaching experience, he has educated undergraduate and postgraduate students in general chemistry, physical chemistry, supramolecular chemistry, biophysical chemistry, and spectroscopy. He is also an active member of several scientific societies and organizations, including the Indian Photobiology Society (IPS) and the Orissa Chemical Society (OCS).

Madhurima Jana is currently serving as a Professor at the National Institute of Technology Rourkela (NIT Rourkela), India. She completed her doctoral studies in computational physical chemistry with a focus on carbohydrate dynamics at IIT Kharagpur in 2012. Her thesis earned the Eli Lily & Company Asia Outstanding Thesis Award (1st prize, 2012). She joined the Department of Chemistry at NIT Rourkela as an Assistant Professor in 2011. Concurrently with her role there, from 2013 to 2014, she spent a year at the University of Maryland, Baltimore, as an INDO-US fellowship award (IUSSTF Fellow) recipient, where she contributed to the development of a polarizable force field for carbohydrates. She was honored with the Fast Track Scheme for Young Scientist Award by DST (2012) and the DAE-BRNS Young Scientist award (2018) in India and is a Fellow of the Indian Chemical Society. Additionally, she is the recipient of the CRSI Bronze Medal for 2023. Dr. Jana’s research group is dedicated to modeling biomolecules and materials in the condensed phase. Their work aims to understand the microscopic properties of molecules associated with various chemical and biophysical processes, utilizing advanced molecular dynamics, enhanced sampling techniques, and quantum mechanical tools. She has led several sponsored projects funded by the Science and Engineering Research Board (SERB), Government of India; Board of Research in Nuclear Sciences (BRNS), Department of Atomic Energy (DAE), Government of India; and Indo-US collaborative research initiatives. Furthermore, Dr. Jana has served as a reviewer for numerous international peer-reviewed and renowned journals. With over 11 years of teaching experience, she has educated undergraduate and postgraduate students in General Chemistry, Physical Chemistry, Statistical Thermodynamics, and Computational Chemistry. She is an active member of various scientific societies and organizations, including the Indian Chemical Society (ICS), the Chemical Research Society of India (CRSI), the Indian Photobiology Society (IPS), and the Orissa Chemical Society (OCS).