Computational Biophysical Chemistry · SNBNCBS · Est. 2023
Molecular Level
Understanding of Bio-Molecules
Abdul Aziz Mandal — Research Scholar
Working at the intersection of computational chemistry, biophysics, and machine learning
to unravel molecular aggregation pathways and interactions of complex biological systems at
S.N. Bose National Centre for Basic Sciences, Kolkata.
PhD Scholar, S. N. Bose National Centre for Basic Sciences
I am a Research Scholar in Computational Chemistry (MD Simulation) at the
S. N. Bose National Centre for Basic Sciences (SNBNCBS), Kolkata. My work sits
at the intersection of physical chemistry, biophysics, and computational science.
My research aims to unravel the molecular aggregation pathways and molecular
interactions of small molecules in complex biological systems — particularly disease-linked peptide
and protein aggregation processes and their modulation by small organic molecules and metal ions.
I am currently developing expertise in machine learning potentials and enhanced-sampling techniques
to push the boundaries of what classical MD simulations can reveal about biological systems.
S. N. Bose National Centre for Basic Sciences, Kolkata (Affiliation: Jadavpur University)
Supervisor: Prof. Ranjit Biswas Focus: Molecular Thermodynamics and Kinetics of Some Disease-
linked Peptide and Protein Aggregation Processes: Modulation by Small Organic
Molecules and Metal Ions.
2020– 2022
M.Sc. in Chemistry
University of Calcutta, Kolkata (Campus: Rajabazar Science College)
Specialization: Physical Chemistry
Supervisor: Prof. Swapan Chakrabarti Focus: This project is on “Quantum Cryptography: An IBMQ Experience”. This
Quantum Cryptography is a kind of encryption method uses quantum
mechanics properties to secure and transfer data in a way that can’t be
hacked. In current progress quantum computers will be able to break public
encryption key easily.
2017– 2020
B.Sc. in Chemistry (Hons.)
Maulana Azad College, Kolkata (Affiliation: University of Calcutta)
2016– 2017
Higher Secondary Education
Tapan High School, Tapan (Affiliation: WBCHSE)
2014– 2015
Secondary Education
Tapan High School, Tapan (Affiliation: WBBSE)
Achievements & Awards
Honours & Recognition
2023
Inspire Fellowship
Awarded junior research fellowship (JRF) for doctoral studies at SNBNCBS, Kolkata.
2017
Inspire Scholarship
Awarded for coming under top 1% students Higher Secondary Examination in West Bengal
Coming Soon
Conference Presentation
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Certification
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Research Themes
Core Focus Areas
🔬
Amyloid Aggregation & Inhibition
Exploring the aggregation pathways of disease-linked proteins and peptides (Alzheimer's, Parkinson's) and mechanistic inhibition by small molecules and metal ions using atomistic MD simulations.
Computational Biology
⚙️
Machine Learning & Enhanced Sampling
Developing expertise in ML-based force fields and enhanced sampling methods — metadynamics, replica exchange, OPES — to access timescales beyond classical MD.
ML / AI
💧
Solvation & Hydration
Investigating the role of water structure and solvation dynamics in modulating protein stability, aggregation, and small-molecule binding thermodynamics.
Physical Chemistry
📐
Protein–Ligand Interactions
Studying binding affinities and interaction mechanisms of small organic molecules with aggregation-prone proteins using docking and free-energy perturbation methods.
MD Simulations
🌀
Intrinsically Disordered Proteins
Characterising the conformational ensemble and aggregation propensity of intrinsically disordered regions using all-atom simulations.
Biophysics
🧮
Free Energy Methods
Learning and applying umbrella sampling, metadynamics, thermodynamic integration, and MBAR to compute binding free energies and conformational free energy landscapes.
Statistical Mechanics
Computational Tools & Software
⚡GROMACS
⚡AMBER
🐍Python
⚡Julia
📊MDAnalysis
🔭VMD
🧬PLUMED
🤖DeePMD
📐AutoDock
📈NumPy / SciPy
✏️ To update this page: edit the research-card blocks above to add/modify your focus areas.
Add new tools to the tools-grid div as you learn them.
✏️ To add a publication: copy a <li class="pub-item"> block, paste it inside <ul class="pub-list">,
and fill in year, title, authors, journal, and DOI link.
People
The Team
👤
Principal Investigator
Prof. Ranjit Biswas
Professor at S.N. Bose National Centre for Basic Sciences. Research interests span
ultrafast spectroscopy, ionic liquids, and biophysical chemistry of complex systems.
Guiding research direction and simulation methodology.
👤
Senior (Guidance)
Sudipta Mitra
Senior lab member providing methodological guidance.
👤
Me
Abdul Aziz Mandal
PhD student working on computational biophysical chemistry.
✏️ To add a team member: copy a team-card div, paste inside team-grid, and update name, role, initials/photo, and description.
To add a photo: place <img src="member.jpg" alt="Name"> inside the team-photo div.
Resources
Software & Tutorials
MD Simulations
GROMACS Tutorials
Step-by-step molecular dynamics tutorials for beginners and advanced users.
A curated collection of molecular simulation software, databases, tutorials, force fields, and computational chemistry resources frequently used in our research workflow.
✏️ To add a collaborator: copy a collab-card <a> block, paste inside collab-grid,
and update the initials, name, institution, and href link.
Find Me
Get in Touch
📍
Address
Department of Chemical & Biological Sciences
S. N. Bose National Centre for Basic Sciences
JD Block, Sector III, Salt Lake
Kolkata — 700 106, West Bengal, India
I am open to research collaborations, seminar invitations, and discussions on
computational biophysical chemistry. Graduate students and postdocs interested in
joining are also welcome to write.
Please include a brief description of your background and what you'd like to work on.
I typically respond within 3–5 working days.
