Article
Biophysics
Khadka B. Chhetri, Yun Hee Jang, Yves Lansac, Prabal K. Maiti
Summary: Phosphorylation of protamine-like cationic peptides reduces their binding efficiency with DNA duplexes, leading to less efficient DNA condensation. Phosphorylated protamines are speculated to easily intrude into chromatin and disrupt histone-histone and histone-DNA binding during spermatogenesis.
BIOPHYSICAL JOURNAL
(2022)
Article
Chemistry, Physical
Jeet Majumdar, Subhadeep Dasgupta, Soham Mandal, Mohd Moid, Manish Jain, Prabal K. Maiti
Summary: Graphene nanoslit pores are used for various nanofluidic devices, and the rotational misalignment between two parallel graphene sheets can affect the properties of the devices. The structure and dielectric constant of confined water molecules remain unchanged for different twist angles, while the ordering of water molecules shows differences between SPC/E and TIP4P/2005 water models. The friction coefficient of the confined water molecules varies for small twist angles, but becomes independent for twists greater than 5.1°.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Taylor M. Page, Chuanxiong Nie, Lenard Neander, Tatyana L. Povolotsky, Anil Kumar Sahoo, Philip Nickl, Julia M. Adler, Obida Bawadkji, Jorg Radnik, Katharina Achazi, Kai Ludwig, Daniel Lauster, Roland R. Netz, Jakob Trimpert, Benedikt Kaufer, Rainer Haag, Ievgen S. Donskyi
Summary: A combination of polyglycerol sulfates and hydrophobic C-60 fullerene can effectively inhibit the infection of SARS-CoV-2 variants in vitro. This research provides significant insights into antiviral strategies and holds promise for the development of effective treatments against viral outbreaks.
Article
Chemistry, Physical
Dharanish Rajendra, Jaydeep Mandal, Yashodhan Hatwalne, Prabal K. Maiti
Summary: The study of spatially ordered systems confined to surfaces such as spheres is important for understanding the interplay between geometry, topology, and elasticity. In this study, a numerical simulation of a spherical monolayer of soft repulsive spherocylinders (SRSs) was performed, and the packing and ordering transition of rods were investigated. The results showed the formation of a two-dimensional liquid crystalline phase at moderate densities, and a solid phase with topological defects and grain boundaries at higher densities.
Article
Chemistry, Multidisciplinary
Tarun Maity, Abhishek Aggarwal, Subhadeep Dasgupta, Vasumathi Velachi, Ashish Kumar Singha Deb, Sk Musharaf Ali, Prabal K. Maiti
Summary: Using MD simulations and experimental studies, we investigated the adsorption and removal of uranyl ions from aqueous solutions using PAMAM dendrimers. Our results show that PAMAM has a high adsorption capacity for uranyl ions, which increases with higher ion concentrations and dendrimer generations. This suggests that PAMAM is an effective adsorbent for removing uranyl ions.
Article
Chemistry, Multidisciplinary
Kingshuk Bag, Aditya Kumar Pal, Subhadip Basu, Mamta Singla, Biplab Sarkar, Dipankar Chatterji, Prabal Kumar Maiti, Anirban Ghosh, Narayanaswamy Jayaraman
Summary: The discovery of vitamin C as an inhibitor of Rel protein activities raises the prospect of tetronelactone derivatives to prevent biofilm and persister cell growth in mycobacteria. In this study, isotetronelactone derivatives were found to inhibit these processes in mycobacterium, with the isotetrone possessing a phenyl substituent at C-4 showing the strongest inhibition of biofilm formation, followed by moderate inhibition by the isotetrone with the p-hydroxyphenyl substituent. The latter isotetrone also inhibits the growth of persister cells.
Article
Chemistry, Physical
J. Hingies Monisha, Vasumathi Velachi, Prabal K. Maiti
Summary: We investigated the aggregation behavior of AuNPs on graphene at different temperatures using molecular dynamic simulations. The results showed that the size of AuNPs and temperature have significant effects on the aggregation behavior. Smaller AuNPs exhibited more shape changes due to aggregation, while larger AuNPs showed higher charge transfer. The quantity of Au atoms in direct contact with graphene during aggregation primarily facilitated the charge transfer between AuNPs and graphene. Our findings will contribute to the development of AuNPs-graphene composites for sensor applications.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Materials Science, Multidisciplinary
Hemant Kumar, Saheb Bera, Subhadeep Dasgupta, A. K. Sood, Chandan Dasgupta, Prabal K. Maiti
Summary: The flow of water through nanochannels shows potential in various applications such as desalination, energy conversion, and nanomedicine. Through molecular dynamics simulations, we demonstrate that water molecules passing through wide single-walled carbon nanotubes (CNTs) get aligned by the flow to have a net dipole moment along the flow direction. This behavior is similar to an Ising chain with the flow velocity acting as an effective aligning field, and is attributed to the preferential entry of water molecules with their dipole vectors pointing inward along the CNT axis.
Article
Physics, Fluids & Plasmas
Nayana Venkatareddy, Shiang-Tai Lin, Prabal K. Maiti
Summary: Phase separation in a mixture of hot and cold three-dimensional dumbbells interacting with Lennard-Jones potential was investigated. The asymmetry of dumbbells and the ratio of hot and cold dumbbells were found to affect the phase separation. The high kinetic pressure of hot dumbbells led to the formation of dense clusters of cold dumbbells and solidlike ordering.
Article
Physics, Fluids & Plasmas
Jayeeta Chattopadhyay, Sriram Ramaswamy, Chandan Dasgupta, Prabal K. Maiti
Summary: In this study, it is found that soft repulsive spherocylinders under active driving can exhibit various liquid crystalline phases, including a nematic phase and a smectic phase that are not observed in equilibrium.
Article
Chemistry, Physical
Supriyo Naskar, Dhiraj Bhatia, Shiang-Tai Lin, Prabal K. Maiti
Summary: The uniqueness of DNA sequence specificity makes it an ideal building block for constructing precise and accurate nanoscale arrays and devices. In this study, DNA nanostars with three, four, and five arms were self-assembled into a gel phase using a simplified bead-spring model. Simulations showed that the DNA nanostars formed a thermodynamically stable gel phase from an unstructured liquid phase at lower temperatures. The phase transition was characterized by calculating various structural features and quantifying the thermodynamics of gelation.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Subhadeep Dasgupta, K. S. Arun, K. Ganapathy Ayappa, Prabal K. Maiti
Summary: With the renewed interest in CO2 separations, this study focuses on evaluating the performance of carbon molecular sieving (CMS) membranes by determining diffusion coefficients. By implementing the trajectory-extending kinetic Monte Carlo (TEKMC) technique, molecular dynamics trajectories were extended to accurately estimate diffusion coefficients and permeability of gases in CMS and polymeric membranes. The study revealed the linear increase of pure CO2 self-diffusion coefficient in CMS membranes under different pressures and also evaluated mixture diffusivities of CO2 in binary mixtures. The importance of using mixture diffusivity data for accurate evaluation of membrane performance was highlighted.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Chemistry, Physical
Khadka B. Chhetri, Yun Hee Jang, Yves Lansac, Prabal K. Maiti
Summary: This study investigated the DNA groove preference of a short protamine-like cationic peptide before and after phosphorylation using molecular dynamics simulations. The results showed that the non-phosphorylated peptide preferred the minor groove, but phosphorylation reduced the binding affinity and deformed the minor groove. The binding of the peptide to DNA was enthalpy-driven.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Nayana Venkatareddy, Jaydeep Mandal, Prabal K. Maiti
Summary: 2-TIPS investigates the phase separation phenomenon in mixtures of active and passive particles under different confinement conditions. The study shows that the extent of phase separation is heavily influenced by the type of confinement. Under parallel wall confinement, the phase separation is reduced, while under spherical cavity confinement, the phase separation is enhanced. In addition, at high densities, the phase separation is decreased due to the trapping of active particles inside the passive clusters.
Article
Chemistry, Physical
Soham Mandal, Indrajit Maity, Anindya Das, Manish Jain, Prabal K. Maiti
Summary: In this study, the thermal conductivity of layered MoS2 was investigated using molecular dynamics simulations and first principles methods. It was found that the thermal conductivity decreases with increasing twist angle and lattice constant of the moire superlattice. The decrease in thermal conductivity was explained by anharmonic phonon scattering events through first principles calculations based on the BTE.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
