The rapid growth of computational power and simulation methodologies has revolutionized the study of biological systems, enabling researchers to investigate biomolecular structure, dynamics, and function at atomic resolution. Molecular dynamics simulations, electronic structure methods, statistical mechanics, and machine learning have become indispensable tools in modern biophysics, structural biology, drug discovery, and biomaterials research.
This five-day Summer School aims to provide undergraduate students, postgraduate researchers, and early-career academics with a comprehensive introduction to the theoretical foundations and practical applications of computational biophysics. Through a combination of lectures, hands-on computational laboratories, and interactive discussions, participants will gain practical experience in molecular dynamics simulations, biomolecular modelling, statistical mechanics, free-energy calculations, density functional theory, ab initio molecular dynamics, and emerging machine learning approaches for molecular simulations.
The programme places particular emphasis on developing practical computational skills using widely adopted open-source software and Python-based scientific computing tools. Participants will learn to perform molecular simulations, analyse biomolecular trajectories, conduct basic electronic structure calculations, and apply modern data analysis techniques to biological systems.

Main Topics
The scientific programme will include lectures on

• Fundamentals of Computational Biophysics and Statistical Mechanics
• Classical Molecular Dynamics Simulations of Biomolecular Systems
• Enhanced Sampling and Free Energy Methods
• Quantum Mechanical Methods for Biomolecular Simulations
• Scientific Computing and Molecular Dynamics Analysis with Python
• Machine Learning for Molecular Simulations

Hands-on Computational Laboratories
Participants will gain practical experience through guided computational exercises including

• Scientific programming and molecular dynamics simulations using Python and GROMACS, including the development of simple molecular dynamics algorithms.
• Analysis of biomolecular simulations, including trajectory analysis, free-energy calculations, and visualization using modern computational tools such as MDAnalysis.
• Advanced computational methods, including electronic structure calculations with CP2K and introductory machine learning techniques for molecular simulation data.

 Programme Structure
The school consists of five thematic days each day consisting of lectures and hands-on laboratory sessions. 

Who Can Apply?
The school is intended for

• Final-year undergraduate students
• MSc, MPhil and PhD students
• Early-career researchers
• Academic staff from Sri Lankan universities

Applicants should have a background in Physics, Chemistry, Biology, Computer Science, Engineering, or related disciplines, together with an interest in computational molecular science.
A total of 25 participants will be selected.
 
Speakers
Dr. Marta Monti
University of Amsterdam, Netherlands
Dr. Vittorio Del Tatto
Laboratorio de Procesado de Imágenes, University of Valencia, Spain
Dr. W. A. Monika Madhavi
Department of Physics, University of Colombo, Sri Lanka

Coordinator
Dr. W. A. Monika Madhavi
Department of Physics, University of Colombo

Partner Institutions

• Department of Physics, University of Colombo
• IT Service Centre, Faculty of Science, University of Colombo
• SLAAS Section E1 (Physical Sciences)
• Physics Society, University of Colombo

Applications
Applications are invited from eligible participants from Sri Lankan universities.
Selection will be based on academic background, current level of study, and the relevance of the applicant's research interests to computational biophysics.
Application deadline: 1 September 2026

Registration
https://docs.google.com/forms/d/e/1FAIpQLSdXXOLaJrKbBNB53Cliq7MSWDJ98mCrN5DCiR981x6HmY3R7Q/viewform?usp=header