Biophysics

Where membranes, molecules and thermodynamics meet biology

Biophysics sits at the intersection of physics and biology. My focus is on lipid membrane physics — understanding how the thin bilayer membranes that surround every cell behave, deform and interact at the molecular level.

Membrane Physics Theory

The theoretical framework behind membrane elasticity, curvature, phase behaviour and the Helfrich Hamiltonian.

Molecular Dynamics

Principles of MD simulations — force fields, integration algorithms, ensembles and how to set up a membrane simulation.

GROMACS Guide

Practical, step-by-step tutorials for running lipid bilayer simulations in GROMACS, from system preparation to analysis.

CHARMM-GUI Guide

How to use CHARMM-GUI's Membrane Builder to generate simulation-ready lipid bilayer systems with custom compositions.

Thermodynamics

Statistical mechanics and thermodynamics as they apply to biological membranes — free energy, entropy and phase transitions.

Membrane Physics Theory

Biological membranes are remarkable structures. Just 5 nanometres thick, they are fluid, flexible and self-assembling. Understanding their physics requires ideas from elasticity theory, statistical mechanics and soft matter physics.

Key topics in this section:

  • The lipid bilayer as a two-dimensional fluid
  • Bending rigidity and the Helfrich free energy
  • Gaussian curvature and membrane topology
  • Phase behaviour: gel, liquid-ordered and liquid-disordered phases
  • Membrane fluctuations and the role of thermal energy
  • Protein-membrane interactions and curvature sensing

The bending energy of a membrane is described by the Helfrich Hamiltonian, which captures how much energy it costs to deform a flat bilayer into a curved shape.

Detailed notes and derivations are in preparation.

Molecular Dynamics

Molecular dynamics (MD) simulation is a computational method that lets us study the motion of atoms and molecules over time by numerically solving Newton’s equations of motion.

In the context of membrane biophysics, MD allows us to:

  • Watch individual lipid molecules diffuse and interact
  • Measure mechanical properties like bending modulus and area compressibility
  • Study how cholesterol modulates membrane properties
  • Observe spontaneous membrane curvature and vesicle formation

Key concepts covered:

  • Force fields for lipids (CHARMM36, Martini, OPLS)
  • Periodic boundary conditions and minimum image convention
  • Temperature and pressure coupling (thermostats and barostats)
  • Ewald summation for long-range electrostatics
  • Coarse-grained vs all-atom simulations

Tutorials and walkthroughs coming soon.

GROMACS Guide

GROMACS is one of the most widely used MD simulation engines, particularly for biomolecular systems. This guide walks through the complete workflow for lipid bilayer simulations.

Planned tutorial topics:

  1. Installing GROMACS and verifying the build
  2. Preparing a lipid bilayer system with CHARMM-GUI
  3. Energy minimisation: steepest descent and conjugate gradient
  4. Equilibration: NVT and NPT ensembles
  5. Production MD runs and checkpoint management
  6. Basic analysis: density profiles, order parameters, area per lipid
  7. Advanced analysis: membrane thickness, curvature, lateral diffusion
  8. Troubleshooting common errors

Step-by-step guides with example commands are being written.

CHARMM-GUI Guide

CHARMM-GUI is a web-based tool that simplifies the preparation of complex molecular systems. Its Membrane Builder module is particularly useful for setting up lipid bilayer simulations.

What this guide covers:

  • Navigating the Membrane Builder interface
  • Choosing lipid composition and bilayer size
  • Adding water, ions and setting up the simulation box
  • Selecting the right force field and output format
  • Downloading input files for GROMACS, NAMD or OpenMM
  • Common mistakes and how to avoid them

Guide under development — first sections will appear shortly.

Thermodynamics

Thermodynamics provides the framework for understanding why membranes behave the way they do. From phase transitions to free energy calculations, the statistical mechanics of lipid assemblies is both rich and beautiful.

Topics planned:

  • Free energy perturbation and thermodynamic integration
  • Umbrella sampling for potential of mean force calculations
  • The role of entropy in lipid self-assembly
  • Critical behaviour near phase transitions in membranes
  • Connecting simulation results to experimental observables (DSC, X-ray scattering)

Content in preparation.