235 citations · 394 across the 16 of their papers we have counts for
17 papers
Kinetics of Barrier Crossing Events from Temperature Accelerated Sliced Sampling Simulations
Sameer Saurav, Debjit Das, Ramsha Javed +1
Temperature-accelerated sliced sampling (TASS) is a well-established enhanced sampling method that facilitates exhaustive exploration of high-dimensional collective variable (CV) s…
Nature of Hydrated Electron in Varied Solvation Environments
Ritama Kar, Nisanth N. Nair
Understanding the nature of solvated electrons is important in studying a range of chemical and biological phenomena. This study investigates the structural and dynamical behavior…
Speeding-up Hybrid Functional based Ab Initio Molecular Dynamics using Multiple Time-stepping and Resonance Free Thermostat
Ritama Kar, Sagarmoy Mandal, Vaishali Thakkur +2
Ab initio molecular dynamics (AIMD) based on density functional theory (DFT) has become a workhorse for studying the structure, dynamics, and reactions in condensed matter systems.…
Computational Study of pKa shift of Aspartate residue in Thioredoxin: Role of Configurational Sampling and Solvent Model
Shivani Verma, Nisanth N. Nair
Alchemical free energy calculations are widely used in predicting pKa, and binding free energy calculations in biomolecular systems. These calculations are carried out using either…
Hybrid Functional and Plane Waves based Ab Initio Molecular Dynamics Study of the Aqueous Fe/Fe Redox Reaction
Sagarmoy Mandal, Ritama Kar, Bernd Meyer +1
Kohn-Sham density functional theory and plane wave basis set based ab initio molecular dynamics (AIMD) simulation is a powerful tool for studying complex reactions in solutions, su…
Improving the Scaling and Performance of Multiple Time Stepping based Molecular Dynamics with Hybrid Density Functionals
Sagarmoy Mandal, Ritama Kar, Tobias Kloeffel +2
Density functionals at the level of the Generalized Gradient Approximation (GGA) and a plane-wave basis set are widely used today to perform ab initio molecular dynamics (AIMD) sim…
Boosting the Conformational Sampling by Combining Replica Exchange with Solute Tempering and Well-Sliced Metadynamics
Anji Babu Kapakayala, Nisanth N. Nair
Methods that combine collective variable (CV) based enhanced sampling and global tempering approaches are used in speeding-up the conformational sampling and free energy calculatio…
Mean Force Based Temperature Accelerated Sliced Sampling: Efficient Reconstruction of High Dimensional Free Energy Landscapes
Asit Pal, Subhendu Pal, Shivani Verma +2
Temperature Accelerated Sliced Sampling (TASS) is an efficient method to compute high dimensional free energy landscapes. The original TASS method employs the Weighted Histogram An…
Achieving an Order of Magnitude Speed-up in Hybrid Functional and Plane Wave based Ab Initio Molecular Dynamics: Applications to Proton Transfer Reactions in Enzymes and in Solution
Sagarmoy Mandal, Vaishali Thakkur, Nisanth N. Nair
Ab initio molecular dynamics (AIMD) with hybrid density functionals and plane wave basis is computationally expensive due to the high computational cost of exact exchange energy ev…
Improving the Exploration of High Dimensional Free Energy Landscape by a Combination of Temperature Accelerated Sliced Sampling and Parallel Biasing
Abhinav Gupta, Shivani Verma, Nisanth N. Nair
Biased sampling methods such as the Temperature Accelerated Sliced Sampling (TASS), which can explore high dimensional collective variable (CV) space, is of great interest in free…
Efficient Computation of Free Energy Surfaces of Chemical Reactions using Ab Initio Molecular Dynamics with Hybrid Functionals and Plane Waves
Sagarmoy Mandal, Nisanth N. Nair
Ab initio molecular dynamics (AIMD) simulations employing density functional theory (DFT) and plane waves are routinely carried out using density functionals at the level of Genera…
Speeding-up Ab Initio Molecular Dynamics with Hybrid Functionals using Adaptively Compressed Exchange Operator based Multiple Timestepping
Sagarmoy Mandal, Nisanth N. Nair
Ab initio molecular dynamics (AIMD) simulations using hybrid density functionals and plane waves are of great interest owing to the accuracy of this approach in treating condensed…
Hydrolysis of Cephalexin and Meropenem by New Delhi Metallo -Lactamase: Substrate Protonation Mechanism is Drug Dependent
Chandan Kumar Das, Nisanth N. Nair
Emergence of antibiotic resistance due to New Delhi Metallo -lactamase (NDM-1) bacterial enzymes is of great concern due to their ability to hydrolyze wide range of antibiotics.…
Exploring High Dimensional Free Energy Landscapes: Temperature Accelerated Sliced Sampling
Shalini Awasthi, Nisanth N. Nair
Biased sampling of collective variables is widely used to accelerate rare events in molecular simulations and to explore free energy surfaces. However, computational efficiency of…
CPMD/GULP QM/MM Interface for Modeling Periodic Solids: Implementation and its Application in the Study of Y-Zeolite Supported Rh Clusters
Sudhir K. Sahoo, Nisanth N. Nair
We report here the development of hybrid quantum mechanics/molecular mechanics (QM/MM) interface between the plane-wave density functional theory based CPMD code and the empirical…
Sampling Free Energy Surfaces as Slices by Combining Umbrella Sampling and Metadynamics
Shalini Awasthi, Venkat Kapil, Nisanth N. Nair
Metadynamics (MTD) is a very powerful technique to sample high-dimensional free energy landscapes, and due to its self-guiding property, the method has been successful in studying…
Charge Localization Dynamics induced by Oxygen Vacancies on the Titania TiO(110) Surface
Piotr M. Kowalski, Matteo Farnesi Camellone, Nisanth N. Nair +2
The dynamics of an F--center created by an oxygen vacancy on the rutile surface has been investigated using {\it ab initio} molecular dynamics. These simula…