1. Project By: Itai Sanders Directed By: Dr. Chen Keasar Toy Proteins and Molecular Dynamics

2. Discreet Proteins http://en.wikipedia.org/wiki/Thermodynamic_temperature#/media/File:Thermally_Agitated_Molecule.gif http://www0.cs.ucl.ac.uk/staff/d.jones/T42morphs.gif

3. Implementing a system allowing: Temporary existence outside the “grid”. Upholding the HP-Model concept. Implementing a continuous algorithm: Molecular Dynamics. The Challenge

4. The available HP-Model system: Discreet in essence. Does NOT support continuous algorithms. The “Meshi” system: Supports continuous algorithms. Does NOT implement the HP-Model. Does NOT implement molecular dynamics features. Available Systems

5. HP residues. HP interactions. Grid configuration : Angles and planes - found to be numerically unstable. Egg box implementation. Implementing HP-Model in “Meshi”

6. Velocities. Verlet algorithm - a numeric integration of Newton's Laws. Implementing Molecular Dynamics in “Meshi”

7. Adiabatic environment. Simulated Annealing Implementing Molecular Dynamics in “Meshi” https://upload.wikimedia.org/wikipedia/commons/d/d5/Hill_Climbing_with_Simulated_Annealing.gif

8. Simulation example

9. Simulation Example

11. Conclusions The challenge of diving into existing intensive code. Implementing continuous HP-Model. Implementing Molecular Dynamics algorithm. Future work: Testing long runs. Testing parameter combinations.