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Nest Building Behavior as an Early Indicator of Behavioral Deficits in Mice

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Nested Transition Path Sampling.

Peter G Bolhuis¹, Gábor Csányi²

¹Van 't Hoff Institute for Molecular Sciences, Universiteit van Amsterdam, Science Park 904, Amsterdam 1098 XH, The Netherlands.

Physical Review Letters

|July 7, 2018

Summary

This summary is machine-generated.

We developed a new transition path sampling method using nested sampling. This technique efficiently explores all possible trajectories, enabling calculation of rare event rates at low temperatures by linking them to high-temperature rates.

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Area of Science:

Computational Chemistry
Statistical Mechanics
Chemical Kinetics

Background:

Transition path sampling (TPS) is crucial for studying rare events in complex systems.
Existing TPS methods can be computationally expensive, limiting their application.
Efficiently sampling trajectory space is key to understanding chemical processes.

Purpose of the Study:

Introduce a novel nested sampling approach for transition path sampling.
Enable simultaneous calculation of thermodynamic and path observables.
Develop a method to compute rare process rates at low temperatures.

Main Methods:

Employed nested sampling to create a novel transition path sampling (TPS) scheme.
Developed a method to sample the entire trajectory space in a single simulation.
Constructed thermodynamic and path observables a posteriori.

Main Results:

Demonstrated that nested TPS explores the entire available trajectory space.
Showcased the ability to compute observables for all temperatures simultaneously.
Successfully computed rare process rates at low temperatures by coupling to high-temperature rates.

Conclusions:

The novel nested TPS method offers a more efficient way to study rare events.
This approach allows for flexible and accurate calculation of rates across various temperatures.
The method is validated on several model systems, showing its broad applicability.