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Optimizing the Growth of Endothiapepsin Crystals for Serial Crystallography Experiments

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Computation of nucleation at a nonequilibrium first-order phase transition using a rare-event algorithm.

David A Adams¹, Robert M Ziff, Leonard M Sander

¹Department of Physics, University of Michigan, Ann Arbor, Michigan 48109-2136, USA. davidada@umich.edu

The Journal of Chemical Physics

|November 9, 2010

Summary

We developed a new algorithm to efficiently measure transition times in rare-event processes. This method accurately determines average transition times and critical points in complex systems.

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Area of Science:

* Statistical Physics
* Computational Chemistry
* Chemical Kinetics

Background:

* Rare-event processes in nonequilibrium systems are computationally challenging to study.
* Understanding transition times is crucial for predicting system behavior.
* First-order phase transitions in surface reactions require efficient simulation methods.

Purpose of the Study:

* To introduce a novel forward flux sampling in time algorithm.
* To efficiently measure transition times in rare-event processes.
* To apply the algorithm to the Ziff-Gulari-Barshad model.

Main Methods:

* Development of a forward flux sampling in time algorithm.
* Application to the Ziff-Gulari-Barshad model for catalytic surface reactions.
* Efficient measurement of average transition times and critical points.

Main Results:

* The new algorithm efficiently measures transition times in rare-event processes.
* Accurately determined the average time for transitions in the Ziff-Gulari-Barshad model.
* Successfully identified both spinodal and transition points.

Conclusions:

* The forward flux sampling in time algorithm is effective for studying nonequilibrium systems.
* This method provides an efficient way to analyze first-order kinetic transitions.
* The approach is valuable for determining critical parameters in surface reaction models.