Physician
Radiology
Dr. Vijay S. Pande, MD
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Vijay Pande works in the field of Radiology. He studied medicine at Indira Gandhi Medical College. Vijay Pande is a published doctor and has 101 publications published. The lastest was: 'Automated Discovery and Refinement of Reactive Molecular Dynamics Pathways.'
Publications
- Automated Discovery and Refinement of Reactive Molecular Dynamics Pathways.
- MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories.
- Potential-Based Dynamical Reweighting for Markov State Models of Protein Dynamics.
- Conserve Water: A Method for the Analysis of Solvent in Molecular Dynamics.
- Modeling Molecular Kinetics with tICA and the Kernel Trick.
- Markov state models provide insights into dynamic modulation of protein function.
- Revised Parameters for the AMOEBA Polarizable Atomic Multipole Water Model.
- Automatic Selection of Order Parameters in the Analysis of Large Scale Molecular Dynamics Simulations.
- Discovering chemistry with an ab initio nanoreactor.
- Perspective: Markov models for long-timescale biomolecular dynamics.
- Complex pathways in folding of protein g explored by simulation and experiment.
- Dynamical Phase Transitions Reveal Amyloid-like States on Protein Folding Landscapes.
- Observation of correlated X-ray scattering at atomic resolution.
- Statistical model selection for markov models of biomolecular dynamics.
- A Molecular Interpretation of 2D IR Protein Folding Experiments with Markov State Models.
- Bayesian energy landscape tilting: towards concordant models of molecular ensembles.
- Activation pathway of Src kinase reveals intermediate states as targets for drug design.
- Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways.
- Ventriculoperitoneal shunt malfunction: cumulative effect of cost, radiation, and turnaround time on the patient and the health care system.
- Calculations of the electric fields in liquid solutions.
- SCISSORS: Practical Considerations.
- Finite domain simulations with adaptive boundaries: Accurate potentials and nonequilibrium movesets.
- Accelerated Molecular Dynamics Simulations with the AMOEBA Polarizable Force Field on Graphics Processing Units.
- Probing the origins of two-state folding.
- Inclusion of persistence length-based secondary structure in replica field theoretic models of heteropolymer freezing.
- Long Timestep Molecular Dynamics on the Graphical Processing Unit.
- Systematic Improvement of a Classical Molecular Model of Water.
- Functional understanding of solvent structure in GroEL cavity through dipole field analysis.
- Emergence of Glass-like Behavior in Markov State Models of Protein Folding Dynamics.
- MSMExplorer: visualizing Markov state models for biomolecule folding simulations.
- Molecular dynamics simulations for the ranking, evaluation, and refinement of computationally designed proteins.
- Building Markov state models with solvent dynamics.
- Derivation and assessment of phase-shifted, disordered vector field models for frustrated solvent interactions.
- OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation.
- A-Site Residues Move Independently from P-Site Residues in all-Atom Molecular Dynamics Simulations of the 70S Bacterial Ribosome.
- Simbios: an NIH national center for physics-based simulation of biological structures.
- MSMBuilder2: Modeling Conformational Dynamics at the Picosecond to Millisecond Scale.
- Characterization and rapid sampling of protein folding Markov state model topologies.
- Markov State Model Reveals Folding and Functional Dynamics in Ultra-Long MD Trajectories.
- Error Bounds on the SCISSORS Approximation Method.
- Calculation of rate spectra from noisy time series data.
- Anatomy of High-Performance 2D Similarity Calculations.
- (Compressed) sensing and sensibility.
- Splitting probabilities as a test of reaction coordinate choice in single-molecule experiments.
- The social network (of protein conformations).
- Quantitative comparison of villin headpiece subdomain simulations and triplet-triplet energy transfer experiments.
- Dynamical reweighting: Improved estimates of dynamical properties from simulations at multiple temperatures.
- Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamics.
- CAMPAIGN: An open-source Library of GPU-accelerated Data Clustering Algorithms.
- A smoothly decoupled particle interface: New methods for coupling explicit and implicit solvent.
- Reintroducing electrostatics into macromolecular crystallographic refinement: application to neutron crystallography and DNA hydration.
- Water ordering at membrane interfaces controls fusion dynamics.
- A bundling of viral fusion mechanisms.
- Atomistic folding simulations of the five-helix bundle protein λ(6−85).
- Calculation of local water densities in biological systems: a comparison of molecular dynamics simulations and the 3D-RISM-KH molecular theory of solvation.
- Rationally Designed Turn Promoting Mutation in the Amyloid-? Peptide Sequence Stabilizes Oligomers in Solution.
- Simple theory of protein folding kinetics.
- Everything you wanted to know about Markov State Models but were afraid to ask.
- Bayesian inference for Brownian dynamics.
- SCISSORS: a linear-algebraical technique to rapidly approximate chemical similarities.
- Polarizable atomic multipole x-ray refinement: hydration geometry and application to macromolecules.
- Protein folded states are kinetic hubs.
- Atomic-resolution simulations predict a transition state for vesicle fusion defined by contact of a few lipid tails.
- Efficient nonbonded interactions for molecular dynamics on a graphics processing unit.
- SIML: a fast SIMD algorithm for calculating LINGO chemical similarities on GPUs and CPUs.
- Unfolded-state dynamics and structure of protein L characterized by simulation and experiment.
- Current status of the AMOEBA polarizable force field.
- Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39).
- CCMA: A Robust, Parallelizable Constraint Method for Molecular Simulations.
- PAPER--accelerating parallel evaluations of ROCS.
- Bayesian detection of intensity changes in single molecule and molecular dynamics trajectories.
- Non-bulk-like solvent behavior in the ribosome exit tunnel.
- Do conformational biases of simple helical junctions influence RNA folding stability and specificity?
- Rapid equilibrium sampling initiated from nonequilibrium data.
- Using generalized ensemble simulations and Markov state models to identify conformational states.
- Progress and challenges in the automated construction of Markov state models for full protein systems.
- Bayesian single-exponential kinetics in single-molecule experiments and simulations.
- Combining molecular dynamics with bayesian analysis to predict and evaluate ligand-binding mutations in influenza hemagglutinin.
- Comparison of computational approaches for predicting the effects of missense mutations on p53 function.
- Accelerating molecular dynamic simulation on graphics processing units.
- The Fip35 WW domain folds with structural and mechanistic heterogeneity in molecular dynamics simulations.
- Topological methods for exploring low-density states in biomolecular folding pathways.
- Simulated tempering yields insight into the low-resolution Rosetta scoring functions.
- Accelerating molecular dynamic simulation on the cell processor and Playstation 3.
- The roles of entropy and kinetics in structure prediction.
- Assessment of the protein-structure refinement category in CASP8.
- Simulating oligomerization at experimental concentrations and long timescales: A Markov state model approach.
- Side-chain recognition and gating in the ribosome exit tunnel.
- Potential for modulation of the hydrophobic effect inside chaperonins.
- Structural basis for influence of viral glycans on ligand binding by influenza hemagglutinin.
- Critical assessment of nucleic acid electrostatics via experimental and computational investigation of an unfolded state ensemble.
- Chemical denaturants inhibit the onset of dewetting.
- A role for confined water in chaperonin function.
- Molecular simulation of multistate peptide dynamics: a comparison between microsecond timescale sampling and multiple shorter trajectories.
- The Simbios National Center: Systems Biology in Motion.
- Structural insight into RNA hairpin folding intermediates.
- Convergence of folding free energy landscapes via application of enhanced sampling methods in a distributed computing environment.
- Solvent viscosity dependence of the protein folding dynamics.
- Effects of long-range electrostatic forces on simulated protein folding kinetics.
- Normal mode partitioning of Langevin dynamics for biomolecules.
Doctors Specialties
- Neuroradiology
- Radiology
Accepted Insurances
Education
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Penn State University -
Indira Gandhi Medical College
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