Dr. Suman Samantray
Computational Scientist · Ph.D.
I am very passionate about harnessing data and Machine Learning techniques to tackle the complex problems in the overlapping realms of Chemistry, Molecular Simulations and Protein Science by developing cutting edge learning algorithms. I was a former AICES fellow, at RWTH Aachen University and jointly worked at Forschungszentrum Jülich GmbH in Germany. Currently, I am a Research Associate at PNNL, a DOE laboratory in United States.
Experience
Postdoctoral Research Associate
Development and implementation of simulation methods for studying structural characteristics of bifunctional enzymes in fixating fossil fuel byproducts.
Postdoctoral Researcher / Project Leader
Development of rational engineering approaches to understand the binding kinetics of anchor peptides (or, adhesion promoting peptides) on polymer surfaces using computational tools and molecular simulations.
Developing semi-rational methods concurrently with directed evolution techniques and biophysical experiments to reveal detailed mechanisms of enzyme function and elucidate/explore the sequence-structure-function paradigm of proteins.
Development of simulation methods for studying amyloid aggregation under the influence of glycosaminoglycans.
Co-mentoring of Ph.D. and M.Sc. students as Project leader in the Computational Biotechnology division.
Scientific (PhD) Researcher
Determination of molecular mechanics parameters and building kinetic transition models to elucidate the amyloid-β aggregation pathways.
Classification of rare dynamical transitions from long time scale Molecular Dynamics simulations of protein systems by building statistical frameworks like Markov state models.
Identification of bio-mimetic molecules inhibiting amyloid-β aggregation.
Development of simulation methods for studying amyloid aggregation under the influence of glycosaminoglycans.
Co-organiser of hands-on workshop on Molecular Dynamics Simulations of Proteins at IHRS BioSoft.
Co-supervision of Strodel group online code databases on GitHub.
Maintenance of Strodel group computing clusters and cloud storage services.
Co-mentoring of HiWi and M.Sc. students in the Strodel group.
ISS Computing Assistant
Responsible for the management, development, physical upkeep and maintenance of the ISS and departmental PC suites across NUIG campus.
Assist the Desktop Services, Provisioning and Support Manager, ensuring efficient operationally of all PC suites.
Senior Application Developer
Lead a team of Dev’s and QA’s to develop MPS mobile SDK and built a Test App to displays ads fetch SDK users (NBC native apps) and configure it for vendor purposes during Rio Olympics 2016.
Developed the NBCUView iOS app, an exclusive viewing platform of NBC media products to its private clients. Documented the app architecture including identification of the service end points.
Contributed to bi-monthly scrum project databases and attended internal research seminars to stay up-to-date with exciting research.
Education
RWTH Aachen University, Aachen, DE
Dissertation: Essays on the interplay between glycosaminoglycans and amyloid-β peptides.
Supervisor(s): Prof. (Dr.) Birgit Strodel and Prof. (Dr.) Arne Lüchow
State University of New York, Buffalo, US
Dissertation: Calculation of Saturation and Interfacial properties of model Carbon Dioxide-Water system using Monte Carlo Simulation.
Supervisor: Prof. (Dr.) Jeffrey R. Errington.
Indira Gandhi Institute of Technology, Sarang, IN
Dissertation: Synthesis of Activated Carbon from Agricultural waste for Purification of water.
Supervisor: Prof. (Dr.) Satyabrata Mohanta.
Skills
- Familiarity with MATLAB, C++, Fortran 2003, Aspen HYSYS, OpenMP, MPI, R.
- Strong ability to build algorithms with Python, Bash, Objective C, Swift, Xcode IDE.
- Understanding of the theory of Neural Networks especially CNNs and their application to Protein Interactions.
- Strong knowledge of the VMD, QTGrace, PyMOL, GROMACS, PLUMEDv2.2 .
- Knowledge of and experience with Gaussian, LAMMPS, CHARMM-GUI.
Awards & Honors
- Reviewer for : ACS Molecular Pharmaceutics, ACS applied materials & interfaces, MDPI Molecules, MDPI Life, MDPI Biomolecules, MDPI Cancers MDPI IJMS, MDPI IJERPH (2021- present).
- Graduated doctoral degree with magna cum laude honors from RWTH Aachen University, DE (2021).
- Awarded Aachen Institute of computational engineering science (AICES) fellowship, RWTH Aachen University, DE (2018).
- Awarded 120k Class C project CPU hours from Irish High End Computing Centre (ICHEC), NUI Galway, IE (2017-18).
- Stokes Modelling Workshop NUIG 2017
- Awarded College of Science and Engineering (CoSE) postgraduate research scholarship, NUI Galway, IE (2017).
- Selected for Invitational Internship Program (DAE) at Variable Energy Cyclotron Centre, Kolkata, IN (2012).
- Selected for Summer Internship Scholarship Program, NIT Rourkela, IN (2011).
- Selected for the 2nd level of Indian National Astronomy Olympiad, IN (2005).
Interests
When not coding or studying I spend my time travelling around Europe to embrace new culture and collect unique food recipes. I also enjoy watching movies and reading biographies.
