List of Publications

C60 in water: local microscopic structures v.s. quantum delocalization of atoms in space", Animesh Agarwal, Cecilia Clementi and Luigi Delle Site, submitted in Phys. Chem. Chem. Phys. (2017).

Computational Efficiency and Amdahl’s law for the Adaptive Resolution Simulation Technique", Christoph Junghans, Animesh Agarwal and Luigi Delle Site, Comp. Phys. Comm., 215, 20-25 (2017).

Grand-Canonical Adaptive Resolution Centroid Molecular Dynamics: Implementation and Application", Animesh Agarwal and Luigi Delle Site, Comp. Phys. Comm., 206, 26-34 (2016).

Adaptive Resolution Simulation as a Grand Canonical Molecular Dynamics Scheme: Principles, Applications, Perspectives" in: C. Clementi (Ed.), Multiscale Methods in Molecular Biophysics, Series in Computational Biophysics, CRC Press (2016), ISBN 1482225700

Path Integral Molecular Dynamics within the Grand Canonical-like Adaptive Resolution Technique: Simulation of Liquid Water", Animesh Agarwal and Luigi Delle Site, J. Chem. Phys., 143, 094102 (2015).

Adaptive Resolution Simulation in Equilibrium and Beyond", Han Wang and Animesh Agarwal, The European Physical Journal Special Topics, 224 (12), 2269-2287 (2015).

Molecular Dynamics in a grand ensemble: Bergmann-Lebowitz model and adaptive resolution simulation", Animesh Agarwal, Jinglong Zhu, Carsten Hartmann, Han Wang and Luigi Delle Site, New J. Phys., 17, 083042 (2015).

Chemical potential of liquids and mixtures via Adaptive Resolution Simulation", Animesh Agarwal, Han Wang, Christof Schütte, and Luigi Delle Site, J Chem. Phys., 141, 034102 (2014).

The Role of the Cation in the Solvation of Cellulose by Imidazolium-Based Ionic Liquids", Brooks D. Rabideau, Animesh Agarwal, and Ahmed E. Ismail, J. Phys. Chem. B, 118 (6), 1621 (2014).

Observed Mechanism for the Breakup of Small Bundles of Cellulose Iα and Iβ in Ionic Liquids from Molecular Dynamics Simulations" , Brooks D. Rabideau, Animesh Agarwal, and Ahmed E. Ismail, J. Phys. Chem. B, 117 (13), 3469 (2013)

Excess equimolar radius of liquid drops“, Martin Horsch, Hans Hasse, Alexander K. Shchekin, Animesh Agarwal, Stefan Eckelsbach, Jadran Vrabec, Erich A. Müller, and George Jackson, Phy. Rev. E., 85, 031605(2012)

Professional Experience

Sept 2016 -

Postdoctoral researcher, Free University of Berlin, Germany.
Application of Markov State Models to complex molecular systems in the presence of an external electric field.
Analysis of simulation data using various machine learning algorithms and tools built in Python, C++.

June 2013 – September 2016

PhD Graduate, Free University of Berlin, Germany.
Development of faster and efficient molecular dynamics algorithms by coupling coarse-grained dynamics with classical dynamics.
Implementation of algorithms in a massively parallel open source simulation software GROMACS.
Construction of markov state models to address the time-scale problem in molecular simulations.
Introduction of Feynman path-integral formalism to incorporate delocalisation of light nuclei.
Spectral analysis of simulation data using tools built in C++, Python.

November 2012 – May 2013

Master’s thesis, RWTH Aachen, Germany.
Development of coarse-graining scheme for molecular modeling of polymers at different granularity levels.
Development of programs for performing simulations of polymer systems in C++.
Implementation of various iterative methods for obtaining coarse-grained potentials.

October 2011 – May 2013

Research Assistant, RWTH Aachen, Germany.
Investigation of dissolution of cellulose in ionic liquids using molecular models using LAMMPS molecular dynamics package.
Development of analysis tools and scripts in Python.

May 2009 – August 2009

Summer Intern, University of Duisburg-Essen, Germany.
Investigation of morphology and dynamics in humidified Nafion polymer electrolytes, a key material in polymer electrolyte fuel cell technology
Setting up simulations of polymer systems of different size with various concentrations water content in GROMACS.
Development of shell scripts for an efficient analysis of simulation data.


June 2013 - September 2016

PhD in Biocomputing, Department of Mathematics and Computer Science, Free University of Berlin.
Title: Path Integral Techniques in Molecular Dynamics Simulations of Open Boundary Systems.
Grade: Magna Cum Laude

Oct. 2011 - May 2013

Master of Science, RWTH Aachen, Germany.
Subject area: Simulation Science (Aachen Institute for Advanced Study in Computational Engineering Science)
Thesis: Simulation of Polymer Solutions using Wavelet-Accelerated Monte Carlo
Grade: 1.3/5 (1.0 - highest)

July 2006 - May 2011

Indian Institute of Technology, BHU, Varanasi.
Degree: M.Tech (Dual Degree) in Industrial Chemistry
Thesis: Application of quantum chemical parameters in the inhibition of corrosion
Grade: 8.4/10 (10.0 - highest)

About Me

I have recently finished PhD in applied mathematics and computer science at Free University of Berlin. During my PhD, I have treated systems of condensed matter physics employing molecular simulation methodologies; my specific project concerned the inclusion of quantum effects in an algorithm designed for multi-resolution simulations. I developed novel software and used machine learning for analyzing large data systems with extremely high efficiency. I am now using my "scientific computing" background in the context of image processing and artificial intelligence.