Introduction to Computational Biophysics
- A brief overview of computational biophysics and its applications in understanding the behavior of biological molecules and systems.
Molecular Dynamics Simulations
- Explanation of molecular dynamics simulations, a popular computational tool used in biophysics to study the motion and interactions of biomolecules.
- Key concepts such as atoms, force fields, and integration algorithms.
- Equations and formulas related to molecular dynamics simulations, including the Newtonian equations of motion and the Verlet algorithm.
- Examples of molecular dynamics simulations applied to biomolecules such as proteins, DNA, and lipid membranes.
- References for further learning on molecular dynamics simulations in biophysics.
Coarse-Grained Models
- Explanation of coarse-grained models, an efficient and simplified approach to studying the behavior of biological systems.
- Key concepts such as coarse-grained beads, potentials, and resolution.
- Equations and formulas related to coarse-grained models, including the Hamiltonian and free-energy functions.
- Examples of coarse-grained models applied to biomolecules such as proteins, nucleic acids, and carbohydrates.
- References for further learning on coarse-grained models in biophysics.
Free-Energy Calculations
- Explanation of free-energy calculations, a powerful computational tool used in biophysics to calculate the thermodynamic properties and energetics of biomolecular systems.
- Key concepts such as the potential of mean force, the umbrella sampling method, and the adaptive biasing force method.
- Equations and formulas related to free-energy calculations, including the Gibbs free energy and the Boltzmann distribution.
- Examples of free-energy calculations applied to biomolecules such as enzymes, ligand binding, and protein-protein interactions.
- References for further learning on free-energy calculations in biophysics.
Conclusion
- Summary of the main concepts covered in this article on computational biophysics, including molecular dynamics simulations, coarse-grained models, and free-energy calculations.
- Discussion of the potential future applications of these computational tools in biophysics and the growing importance of computational approaches for understanding biological systems.
