Niladri Patra | Indian School of Mines, Dhanbad (original) (raw)

Papers by Niladri Patra

We propose a new strategy for robust high-quality self-assembly of non-trivial periodic structure... more We propose a new strategy for robust high-quality self-assembly of non-trivial periodic structures out of patchy particles, and investigate it with Brownian Dynamics (BD) simulations. Its first element is the use of specific patch-patch and shell-shell interactions between the particles, that can be implemented through differential functionalization of patched and shell regions with specific DNA strands. The other key element of our approach is the use of layer-by-layer protocol that allows to avoid a formations of undesired random aggregates. As an example, we design and self-assemble in silico a version of a Double Diamond (DD) lattice in which four particle types are arranged into BCC crystal made of four FCC sub-lattices. The lattice can be further converted to Cubic Diamond (CD) by selective removal of the particles of certain types. Our results demonstrate that by combining the directionality, selectivity of interactions and the layer-by-layer protocol, a high-quality robust s...

ChemPhysChem

MexAB-OprM efflux pumps, found in Pseudomonas aeruginosa, plays a major role in drug resistance b... more MexAB-OprM efflux pumps, found in Pseudomonas aeruginosa, plays a major role in drug resistance by extruding out drugs and antibiotic molecules from cells. Inhibitors are used to cease the potency of the efflux pumps. In this study, in-silico models are used to investigate the nature of the binding pocket of the MexAB-OprM efflux pump. First, we have performed Classical Molecular Dynamics (MD) simulations to shed light on different aspects of protein-inhibitor interaction in the binding pocket of the pump. Using classical molecular dynamics (MD) simulations, quantum mechanics/molecular mechanics QM/MM), and various types of analyses, we have shown that D13-9001 has a better binding affinity towards the binding pocket than D1 and D2 which was established experimentally. Two stable configurations of D13-9001 are discovered inside the distal pocket which could be one of the primary reason of the greater efficacy of D13-9001. Free energy barrier upon changing one state to another is calculated by employing umbrella sampling method. Finally, F178 is mutated to have the complete picture as it contributes a significant amount to the binding energy irrespective of the three inhibitors. The results of our study could be potentially used to design a new generation of inhibitors for such an efflux pump.

Applied Organometallic Chemistry

Photochemical & Photobiological Sciences

A coumarin–quinoline conjugated triazole based sensor has been developed for the selective detect... more A coumarin–quinoline conjugated triazole based sensor has been developed for the selective detection of Hg2+. The possible binding mode has been established via NMR, fluorescence spectroscopy and TDDFT calculations.

Proceedings of the International Astronomical Union

We investigate the nucleation of carbon and hydrogen atoms in the gas phase to form large carbon ... more We investigate the nucleation of carbon and hydrogen atoms in the gas phase to form large carbon chains, clusters and cages by reactive molecular dynamics simulations. We study how temperature, particle density, presence of hydrogen, and carbon inflow affect the nucleation of molecular moieties with different characteristics.

Proceedings of the International Astronomical Union, May 1, 2013

Lecture Notes in Nanoscale Science and Technology, 2013

Directed transport and self-assembly of nanomaterials can potentially be facilitated by water nan... more Directed transport and self-assembly of nanomaterials can potentially be facilitated by water nanodroplets, which could carry reactants or serve as a selective catalyst. We show by molecular dynamics simulations that water nanodroplets can be transported along and around the surfaces of vibrated carbon nanotubes. We show a second transport method where ions intercalated in carbon and boron- nitride nanotubes can be solvated at distance in polarizable nanodroplets adsorbed on their surfaces. When the ions are driven in the nanotubes by electric fields, the adsorbed droplets are dragged together with them. Finally, we demonstrate that water nanodroplets can activate and guide the folding of planar graphene nanostructures.

The Journal of chemical physics, Jan 14, 2014

We use classical molecular dynamics simulations to study nanofluidic properties of porous carbon ... more We use classical molecular dynamics simulations to study nanofluidic properties of porous carbon nanotubes. We show that saturated water vapor condenses on the porous nanotubes, can be absorbed by them and transported in their interior. When these nanotubes are charged and placed in ionic solutions, they can selectively absorb ions in their interior and transport them. Porous carbon nanotubes can also be used as selective molecular sieves, as illustrated on a room temperature separation of benzene and ethanol.

The Journal of Physical Chemistry C, 2013

We model the dynamics of ion binding to graphene nanostructures. In order to disclose the likely ... more We model the dynamics of ion binding to graphene nanostructures. In order to disclose the likely ion binding dynamics, we first perform scanned single-point DFT calculations of monovalent ions (Na + , Li + , Cl − , F −) at fixed distances above planar graphene-like H-passivated molecules of different shapes and sizes. The scans reveal intriguing details about the ion-nanostructure potential energy and charge transfer surfaces. We correlate these static results with our room-temperature quantum molecular dynamics simulations of the ion−molecule systems, performed in both vacuum and water. Our simulations show that anions either are physisorbed onto the nanostructures or covalently bind at their selected regions, depending on the initial conditions, while cations only physisorb onto them.

Nano Letters, 2009

We demonstrate by molecular dynamics simulations that water nanodroplets can activate and guide t... more We demonstrate by molecular dynamics simulations that water nanodroplets can activate and guide the folding of planar graphene nanostructures. Once the nanodroplets are deposited at selected spots on the planar nanostructure, they can act as catalytic elements that initiate conformational changes and help to overcome deformation barriers associated with them. Nanodroplets can induce rapid bending, folding, sliding, rolling, and zipping of the planar nanostructures, which can lead to the assembly of nanoscale sandwiches, capsules, knots, and rings.

Journal of the American Chemical Society, 2011

Journal of Computational Chemistry, 2011

We report here a new and fast approach (TPACM4: Transferable Partial Atomic Charge Model-up to 4 ... more We report here a new and fast approach (TPACM4: Transferable Partial Atomic Charge Model-up to 4 bonds) for deriving the partial atomic charges of small molecules for use in protein/DNA-ligand docking and scoring. In our method, we have used 5363 atom types to cover the chemical space of C, H, O, N, S, P, F, Cl and Br atoms in small molecules. Starting with a set of Cartesian coordinates, partial atomic charges are developed by considering diverse plausible chemical environments of each atom in a molecule. The model gives an average error ±1.16 kcal/mol and a correlation coefficient of 0.90 vis-à-vis an average error of ±1.02 kcal/mol and a correlation coefficient of 0.92 obtained with RESP fit charges in calculations of binding free energies of 161 protein-ligand complexes in comparison to experiment. This new method of charge derivation can also accurately predict hydrogen bond energetics, solvation free energies of small molecules. For a molecule containing 50-55 atoms, the method takes approximately 0.4 seconds to assign partial atomic charges. The TPACM4 programme has been web-enabled at http://scfbio-iitd.res.in/software/drug design/charge.jsp.

Chemical Communications, 2011