/* My Website */ Abdul Aziz Mandal — Computational (Bio)physical Chemistry

Computational (Bio)physical Chemistry · SNBNCBS · Est. 2023

Decode Life
at the
Molecular Level

Abdul Aziz Mandal — Research Scholar

Working at the intersection of Computational (Bio)physical Chemistry, Biophysics, and Machine Learning (ML) to unravel Molecular Aggregation pathways and Interactions of complex biological systems at S. N. Bose National Centre for Basic Sciences, Kolkata.

Abdul Aziz Mandal
PhD Scholar, S. N. Bose National Centre for Basic Sciences
Kolkata, India
MD Simulation · ML · Enhanced Sampling
Scroll

About Me

At the Interface of Chemistry,
Physics & Biology

Abdul Aziz Mandal
Abdul Aziz Mandal
Research Scholar — PhD
✉ abdulazizcaluniv@gmail.com ✉ abdulaziz.mandal@bose.res.in
RG
Computational (Bio)Physical Chemistry · MD Simulation

Love to Explore Molecular Processes Through Computation

I am a Research Scholar in Computational (Bio)Physical Chemistry (Molecular Dynamics Simulation) at the S. N. Bose National Centre for Basic Sciences (SNBNCBS), Kolkata. My work lies at the interface of physical chemistry, biophysics, and computational science.

My research focuses on understanding molecular aggregation pathways and molecular interactions in complex biological systems, particularly disease-linked peptide and protein aggregation processes and their modulation by small organic molecules and metal ions.

◉
Current Focus
Amyloid Aggregation
Molecular mechanisms of disease-linked peptide and protein aggregation.
⌬
Core Method
Molecular Dynamics
Atomistic simulations for studying molecular interactions, thermodynamics, and kinetics.
✦
Expanding Toward
AI / ML & Enhanced Sampling
Machine-learning potentials and advanced sampling approaches for complex biological systems.
Research Profile

Research Interests

Amyloid Aggregation Molecular Dynamics Free Energy Methods Machine Learning / AI Enhanced Sampling Small Molecule Inhibition Biophysics
Education

Academic Qualifications

2023Present
Doctoral Research
CURRENT
Ph.D. in Computational (Bio)Physical Chemistry
S. N. Bose National Centre for Basic Sciences, Kolkata
Affiliation: Jadavpur University
SupervisorProf. Ranjit Biswas
Research FocusMolecular Thermodynamics and Kinetics of Some Disease-linked Peptide and Protein Aggregation Processes: Modulation by Small Organic Molecules and Metal Ions.
20202022
Postgraduate
M.Sc. in Chemistry
University of Calcutta, Kolkata
Campus: Rajabazar Science College
SpecializationPhysical Chemistry
SupervisorProf. Swapan Chakrabarti
ProjectQuantum Cryptography: An IBMQ Experience
20172020
Undergraduate
B.Sc. in Chemistry (Hons.)
Maulana Azad College, Kolkata
Affiliation: University of Calcutta
20162017
Higher Secondary
Higher Secondary Education
Tapan High School, Tapan
Affiliation: WBCHSE
20142015
Secondary
Secondary Education
Tapan High School, Tapan
Affiliation: WBBSE
Achievements & Awards

Honours & Recognition

2017
Scholarship
INSPIRE Scholarship
Awarded for ranking among the top 1% of students in the Higher Secondary Examination, West Bengal.
2023
Fellowship
INSPIRE Fellowship
Awarded Junior Research Fellowship (JRF) for doctoral studies at SNBNCBS, Kolkata.
2025
Certification
Python Bootcamp
The Complete Python Bootcamp — From Zero to Hero, Udemy course.
Scientific Meetings

Conferences & Presentations

24 MAR 2026
Conference Presentation
BOSE FEST 2026
Molecular Dynamics Unravel Tannic Acid-Mediated Inhibition of Tryptophan Amyloid Aggregation: A Comparative Efficacy with Polyols.
⌖ SNBNCBS

Research Themes

Core Focus Areas

Using Atomistic Molecular Dynamics Simulations, Statistical Mechanics, and emerging Machine-Learning (ML) approaches to understand Biomolecular Aggregation, Molecular Recognition, and Inhibition.

Interactive Molecular Structure

Lysozyme Protein in 3D

Interactive cartoon representation of lysozyme (PDB: 1AKI) rendered in real time using 3Dmol.js. Molecular visualization tools such as this are useful for inspecting protein structures, simulation trajectories, intermolecular interactions, and aggregation intermediates.

Drag to rotate Scroll to zoom
LIVE STRUCTURE
loading molecular structure…
What I Study

Research Directions

My research interests span molecular aggregation, biomolecular interactions, solvation, enhanced sampling, and computational free-energy methods.

01
Molecular Aggregation

Amyloid Aggregation & Inhibition

Investigating molecular pathways associated with disease-linked peptide and protein aggregation and understanding how small organic molecules and metal ions modulate these processes using atomistic molecular dynamics simulations.

AmyloidsAggregationInhibition
02
Emerging Methods

Machine Learning & Enhanced Sampling

Developing expertise in machine-learning-based molecular potentials and advanced sampling approaches such as metadynamics, replica-exchange methods, and OPES to explore configurational spaces beyond conventional molecular dynamics timescales.

AI / MLMetadynamicsOPES
03
Molecular Environment

Solvation & Hydration

Exploring how hydration structure, solvent dynamics, and water-mediated interactions influence biomolecular stability, aggregation pathways, and small-molecule recognition.

HydrationSolvationWater Dynamics
04
Molecular Recognition

Protein–Ligand Interactions

Characterising interactions between small organic molecules and aggregation-prone biomolecules through molecular docking, molecular dynamics, structural analysis, and free-energy-based approaches.

BindingDockingMD Simulation
05
Conformational Ensembles

Intrinsically Disordered Proteins

Investigating heterogeneous conformational ensembles, intermolecular contacts, and aggregation propensities of intrinsically disordered peptides and protein regions using all-atom simulations.

IDPsEnsemblesBiophysics
06
Statistical Mechanics

Free Energy Methods

Learning and applying umbrella sampling, metadynamics, thermodynamic integration, and reweighting approaches to characterise conformational free-energy landscapes and molecular association processes.

PMFUmbrella SamplingMBAR
Computational Toolkit

Tools & Software

Software and programming environments used for molecular simulation, trajectory analysis, visualization, and scientific computing.

GGROMACSMolecular Dynamics
AAMBERMD Simulation
</>PythonScientific Computing
JJuliaScientific Computing
MDMDAnalysisTrajectory Analysis
VMDVisualization
PPLUMEDEnhanced Sampling
DeePMDMachine Learning
ADAutoDockMolecular Docking
NNumPy / SciPyData Analysis

Selected Work

Publications & Preprints

24 AUG 2026
★ First Author J. Phys. Chem. B

Mechanistic Role of Different Functional Groups in Inhibiting Tryptophan Self-Assembly: Comparison between Aromatic and Nonaromatic Hydroxyl Moiety-Rich Chemical Compounds

Abdul Aziz Mandal · Sudipta Mitra · Suman Chakrabarty · Ranjit Biswas*
The Journal of Physical Chemistry B 130(35) : 8794-8804
View Publication ↗
Soon
Upcoming Paper Journal Name

Title Will Appear Here

Author · Author*
Journal Name Volume(Issue) · Pages
DOI ↗
View on Google Scholar ↗

People

The Team

Abdul Aziz Mandal
Me
Abdul Aziz Mandal
PhD student working on Computational (Bio)physical Chemistry.
Visit Me →
Ranjit Biswas
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.
Lab Website →
Suman Chakrabarty
Mentor
Prof. Suman Chakrabarty
Guiding on research direction and simulation methodology.
Lab Website →
Sudipta Mitra
Senior
Dr. Sudipta Mitra
Senior lab member providing methodological guidance.

Resources

Software & Tutorials

MD Simulations

GROMACS Tutorials

Step-by-step molecular dynamics tutorials for beginners and advanced users.

Open Resource
MD Simulations

AmberTools Tutorials

Amber is a suite of biomolecular simulation programs.

Open Resource
MD Simulations

LAMMPS Tutorials

Official tutorials, examples, and user guides for molecular dynamics simulations using LAMMPS.

Open Resource
MD Simulations

OpenMM Tutorials

Step-by-step molecular dynamics tutorials and documentation for beginners and advanced OpenMM users.

Open Resource
GROMACS

All GROMACS Versions

Official archive containing all released versions of GROMACS.

Download
Visualization

VMD / QwikMD Tutorials

Learn molecular visualization, trajectory analysis, and simulation setup.

Open Tutorial
MD Analysis

MDAnalysis Tutorials

Python module for post-processing, analyzing, and visualizing molecular dynamics trajectories and simulation data.

Open Resource
Force Field Generation

Force Field

Generate topology and parameter files for small molecules using AMBER, OPLS-AA, CHARMM, and GROMOS force fields.

ACPYPE (AMBER)AmberToolsLigParGen (OPLS-AA)CHARMMCHARMM-GUI Ligand ReaderCGenFF (CHARMM)ATB (GROMOS)
System Preparation

Packmol

Generate initial configurations for molecular dynamics simulations by packing molecules into simulation boxes using geometric optimization.

Open Resource
gmx_MMPBSA

gmx_MMPBSA Tutorials

gmx_MMPBSA is a tool based on AMBER's MMPBSA.py, built to perform end-state free energy calculations with GROMACS files.

Open Resource
Amino Acid Mutation

PMX Tutorials

Generate hybrid structures and topologies for amino acid mutations and perform alchemical free energy calculations using PMX.

Open Resource
Coarse-Grained MD

MARTINI Tutorials

Tutorials and examples for MARTINI coarse-grained simulations.

Open Tutorial
RCSB Protein Data Bank

RCSB PDB

Single worldwide archive of structural data of biological macromolecules.

Open Tutorial
System Builder

CHARMM-GUI

Web-based platform for preparing simulation-ready biomolecular systems.

Open Website
Protein Structure

AlphaFold Database

Predicted protein structures generated using AlphaFold.

Browse Database
Chemistry News

C&EN

Latest news and developments in chemistry and related sciences.

Read News
LaTeX

Tables Generator

Create publication-quality LaTeX tables online.

Open Tool
LaTeX

Special Characters Guide

Reference for LaTeX symbols and special character formatting.

View Guide
Nucleic Acids

Build DNA/RNA Structures

Create custom DNA and RNA PDB structures from user-defined sequences.

NAFlex
Nucleic Acids

DNA Builder

Generate canonical DNA structures for simulations and modeling.

Open Tool
Protein Analysis

MetaDisorder

Predict intrinsically disordered regions in proteins.

Run Prediction
Phase Separation

PSPredictor

Predict liquid–liquid phase separation propensity of proteins.

Run Prediction
Force Fields

CHARMM FF for GROMACS

Official CHARMM force-field distributions compatible with GROMACS.

Download FF
Enhanced Sampling

PLUMED Documentation

Comprehensive documentation for collective variables and enhanced sampling methods.

Read Docs

Network

Collaborators & Partners

——
Coming Soon
Institution · Country
——
Coming Soon
Institution · Country
——
Coming Soon
Institution · Country
——
Coming Soon
Institution · Country

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
✉️
Email (Personal)
abdulazizcaluniv@gmail.com
✉️
Email (Institute)
abdulaziz.mandal@bose.res.in
📞
Phone
+91-XX-XXXX-XXXX
🔬
Institution
www.bose.res.in
👁️
Profile Views
Visitor Count

Interested in Collaborating?

I am open to research collaborations, and discussions on computational biophysical chemistry.

For research-related inquiries, please include a brief introduction and a short description of the topic you would like to discuss. I typically respond within 3–5 working days.

Send an Email