Tathagata Kundu

A highly enthusiastic Scientific Researcher working towards the development of MD force fields for the efficient all-atom simulation of DNA/RNA complexes. Have experience in molecular dynamics and Monte Carlo simulations along with parameterization of various classical force fields for residue introduction for classical MD simulation. Have worked vastly with GROMACS using AMBER force fields. In constant search of industrial applications and method development using the skills and knowledge of Biophysics, cellular biology and Data Science. 

In my PhD, I have been able to develop and reparametrize the popular AMBER force field for use with GROMACS. Where I have successfully introduced protonated cytosine residue by modelling and recalculating partial charges for successful simulation of DNA-RNA triple helices. I am also currently working on improving sequence-based prediction tools for certain genes and lncRNAs triple helix formation with the data obtained from our MD simulations. Further, I have written various bash and python scripts for analysis of the data derived from our simulations. I have also created Python notebooks for the automation of such simulation, from the creation of topologies to the extraction of data (also in form of plots) from the fitted trajectories using my experience with Python, Matplotlib, pandas, NumPy, etc. 

Currently, I work at the Papenfort laboratory at the Friedrich Schiller University of Jena (Germany) studying gene regulation in microbial pathogens. We focus on the molecular mechanisms underlying post-transcriptional gene control in bacteria and how these affect complex regulatory processes, such as quorum sensing, virulence, and biofilm formation. Our goal is to use this information to develop new approaches to treat and prevent microbial infections. I am working to develop and employ bioinformatic tools to analyse complex transcriptomic datasets focusing on the role of RNA-based regulation in bacteria. 

Specialities: DNA-RNA triple helices, Computational Biophysics, Computational Biology, Transcription factors, Long Non-Coding RNA, Molecular Dynamic Simulation, Classical MD, Force Fields, Cellular Biology, Data Science, Statistics, iPython, GROMACS, AMBER, NumPy, Matplotlib, Jupyter Notebooks, Team Work, Management and Leadership.

• (2022 - present) - Currently, I work at the Papenfort laboratory at the Friedrich Schiller University of Jena (Germany) studying gene regulation in microbial pathogens. We focus on the molecular mechanisms underlying post-transcriptional gene control in bacteria and how these affect complex regulatory processes, such as quorum sensing, virulence, and biofilm formation. Our goal is to use this information to develop new approaches to treat and prevent microbial infections. I am working to develop and employ bioinformatic tools to analyse complex transcriptomic datasets focusing on the role of RNA-based regulation in bacteria. 

• (2018 - 2022) Previously in my PhD, I worked at the Jülich Supercomputing centre, where I have been able to develop and reparametrize the popular AMBER force field for use with GROMACS. Where I have successfully introduced protonated cytosine residue by modelling and recalculating partial charges for successful simulation of DNA-RNA triple helices. I also worked on improving sequence-based prediction tools for certain genes and lncRNAs triple helix formation with the data obtained from our MD simulations. Further, I have written various bash and python scripts for analysis of the data derived from our simulations. I have also created Python notebooks for the automation of such simulation, from the creation of topologies to the extraction of data (also in form of plots) from the fitted trajectories using my experience with iPython, Matplotlib, pandas, NumPy, etc.

• (2017 - 2018) Prevention of thermal denaturation of proteins using amino acids as 
  osmolytes.
  
  Insulin was studied and its effect under thermal stress in both water in the presence of Sodium ions and also using the above six Binary Amino Acid Water Solutions under the supervision of Dr Madhurima Jana, National Institute of Technology, Rourkela to explore a more complex system for practical application.
  
  In this project, we computationally investigated the denaturation of Insulin under thermal stress, i.e. increase in surrounding temperature and their prevention using amino acid solutions which can prevent the protein from losing its shape, stability, and quality. The study is being carried out using GROMACS and NAMD simulation packages with the application of CHARMM27, and GROMOS43a1 force fields. Various analysis software like XMGRACE, VMD, PACKMOL, etc. has been used.

• (2016 - 2017) Systematic comparison of Empirical Force Fields for Molecular Dynamics Simulation Studies of Amino Acids on their Osmolytic behaviour. Master’s thesis project under the 
  supervision of Dr Madhurima Jana, National Institute of Technology, Rourkela.
  
  In this project, we have computationally investigated the various properties of binary amino acid solutions in water namely of Histidine, Phenyl Alanine, Proline, Glycine and Valine at various concentrations of 0.5M,1M and 2M which are the most commonly used amino acids and correlated the results with the experimental and computational value which can be used in future studies for preventing protein denaturation and aggregation. The study has been carried out using the GROMACS simulation package with the application of CHARMM27, AMBER99SB and GROMOS43a1 force fields. Various analysis software like XMGRACE, VMD, PACKMOL, etc. have been used for analysis such as Diffusion Coefficient, Radial Distribution 
  Function, Hydrogen Bonding, etc.

• PhD, RWTH Aachen University, Aachen, Germany (2018-2022)
• 5 years Integrated M.Sc. Chemistry, NIT Rourkela, Rourkela, Odisha, India
• 10, +2, St. Vincents Convent Sr. Sec. School, Balasore, Odisha, India