|
I'm a Research Scholar (PhD) in Computational (Bio)Physical Chemistry at the S. N. Bose National Centre for Basic Sciences (SNBNCBS), Kolkata. My research uses atomistic molecular dynamics and statistical mechanics to understand molecular aggregation pathways in disease-linked peptide and protein systems, and how small organic molecules and metal ions modulate them. I'm expanding toward machine-learning potentials and enhanced sampling to reach timescales beyond conventional MD. |
🔭 Currently
🎓 Education
|
|
Amyloid Aggregation & Inhibition Aggregation pathways of disease-linked peptides and proteins, and their modulation by small molecules and metal ions |
Enhanced Sampling & Free Energy Metadynamics, replica exchange, umbrella sampling and MBAR for free-energy landscapes |
Machine Learning ML-based molecular potentials and data-driven approaches for complex biological systems |
|
Solvation & Hydration How water structure and dynamics shape stability, aggregation and molecular recognition |
Protein–Ligand Interactions Docking, MD and free-energy analysis of inhibitors binding to aggregation-prone biomolecules |
Intrinsically Disordered Proteins Conformational ensembles, intermolecular contacts and aggregation propensity of IDPs |
flowchart LR
A["🧪 System setup<br/>GROMACS · Packmol"] --> B["🎯 Docking<br/>AutoDock"]
B --> C["⚙️ All-atom MD<br/>GROMACS · AMBER"]
C --> D["⛰️ Enhanced sampling<br/>PLUMED · Umbrella Sampling · MetaD"]
D --> E["📊 Analysis<br/>contacts · PMF · MM-PBSA"]
E --> F["🤖 ML<br/>DeePMD · models"]
F -. insight .-> C
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 2026, 130 (35), 8794–8804
| Date | Event | Type |
|---|---|---|
| Oct 2026 | Frontiers of Physical Chemistry (FPC 2026), SNBNCBS · poster | Poster |
| Sep 2026 | Frontier Research in Basic Sciences & Development of Advanced Technologies in India, IEM Gurukul · poster | Poster · 🏆 Best Poster Award |
| Mar 2026 | BOSE FEST 2026, SNBNCBS: Tannic acid-mediated inhibition of tryptophan amyloid aggregation | Oral |
- 🏆 Best Poster Award — Frontier Research in Basic Sciences, IEM Gurukul Campus (2026)
- 🎓 INSPIRE Fellowship (SRF) — for doctoral research at SNBNCBS (2023)
- ⭐ INSPIRE Scholarship — top 1% in the Higher Secondary Examination, West Bengal (2017)
| App | What it does | Try it |
|---|---|---|
| VAMD | Visual Analysis of Molecular Dynamics: a lightweight browser-based structure & trajectory viewer | Open ↗ |
| Figure Palette Lab | Accessible, publication-ready colour palettes for scientific figures | Open ↗ |
| VIBGYOR Color Studio | Explore, create and manage colour schemes in the browser | Open ↗ |
| azizsimx.github.io | My research website: publications, tools and curated MD tutorials | Visit ↗ |
⚙️ Simulation and sampling
🔍 Analysis and visualization
🤖 Scientific computing
💻 Languages
🧰 Operating Systems & Scientific Workflow
| Repository | What's inside | Language |
|---|---|---|
| Simulation_Methods | Advanced numerical methods and simulations | Jupyter Notebook |
| IDP_pdb | Structures and notebooks for intrinsically disordered proteins | Jupyter Notebook |
| Quantum-Computing-Qiskit | M.Sc. project: Quantum Cryptography — An IBMQ Experience | Qiskit Python |
| Python_Tutorial | Python from scratch to advanced, for students starting out | Jupyter Notebook |
Open to research collaborations and discussions on computational biophysical chemistry,
amyloid aggregation, enhanced sampling and ML for molecular systems.
