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An Unbiased Approach of Sampling TEM Sections in Neuroscience

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Published on: April 13, 2019

Equilibrium sampling by reweighting nonequilibrium simulation trajectories.

Cheng Yang¹, Biao Wan¹, Shun Xu¹

¹School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.

Physical Review. E

|April 15, 2016

Summary

This summary is machine-generated.

This study introduces Reweighted Nonequilibrium Ensemble Dynamics (RNED), a novel method for efficiently sampling complex molecular conformations. RNED overcomes limitations of existing techniques, enabling accurate equilibrium distribution analysis from nonequilibrium simulations.

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Area of Science:

Computational Chemistry
Statistical Mechanics
Molecular Dynamics

Background:

Equilibrium molecular simulations struggle to explore complex systems with high free energy barriers.
Nonequilibrium simulations can enhance transitions between metastable states.
The Jarzynski equality (JE) can remove nonequilibrium effects to sample equilibrium distributions.

Purpose of the Study:

To develop a systematic method for efficiently sampling equilibrium conformations in complex systems.
To combine the strengths of the Jarzynski equality and Reweighted Ensemble Dynamics (RED).

Main Methods:

Introduction of Reweighted Nonequilibrium Ensemble Dynamics (RNED).
RNED combines the Jarzynski equality (JE) with the Reweighted Ensemble Dynamics (RED) method.
RNED utilizes nonequilibrium simulation trajectories with an arbitrary initial conformational distribution.

Main Results:

RNED successfully reproduces equilibrium distributions from nonequilibrium simulations.
The method was validated on a toy model and a Lennard-Jones fluid.
RNED demonstrated its capability in detecting liquid-solid phase coexistence.

Conclusions:

RNED offers an efficient approach for equilibrium sampling of complex systems.
The method extends the applicability of the Jarzynski equality and RED.
RNED enhances the exploration of conformational space in molecular simulations.