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Energy Diagrams - II

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Energy diagrams are important to understand the dynamics of a system. The topology of an energy diagram helps illustrate the equilibrium points of the system.
The point in the energy diagram at which the system’s potential energy is the lowest is known as the local minima. The system tends to stay in this position indefinitely unless acted upon by a net force. The slope of the potential energy diagram at the local minima is zero, indicating that zero net force is acting on the system. The slope...

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In the Carnot engine, which achieves the maximum efficiency between two reservoirs of fixed temperatures, the total change in entropy is zero. The observation can be generalized by considering any reversible cyclic process consisting of many Carnot cycles. Thus, it can be stated that the total entropy change of any ideal reversible cycle is zero.
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Entropy

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Related Experiment Video

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Nanomanipulation of Single RNA Molecules by Optical Tweezers

Nanomanipulation of Single RNA Molecules by Optical Tweezers

Published on: August 20, 2014

Hopping around an entropic barrier created by force.

Ronen Berkovich¹, Sergi Garcia-Manyes, Joseph Klafter

¹Department of Biological Sciences, Columbia University, New York, NY 10027, USA.

Biochemical and Biophysical Research Communications

|November 6, 2010

Summary

A force-induced entropic energy barrier explains two-state hopping in single RNA, DNA, and protein molecules. This barrier, absent at zero force, drives molecular conformational changes and is crucial for understanding single-molecule behavior.

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Area of Science:

Biophysics
Computational Biology
Molecular Dynamics

Background:

Single RNA, DNA, and protein molecules exhibit two-state hopping phenomena under stretching force.
This behavior is often interpreted as two-state folding/unfolding reactions, but the underlying mechanism at the single-molecule level requires further investigation.

Purpose of the Study:

To investigate the role of the force-induced entropic energy barrier in single-molecule two-state hopping.
To understand how applied force influences molecular conformations and transitions.

Main Methods:

Langevin dynamics simulations were employed to model molecular behavior under stretching force.
Free energy considerations were used to analyze the entropic barrier formation.

Main Results:

A force-induced entropic energy barrier was identified, separating collapsed and extended molecular states.
This barrier exhibits long transition state distances (up to tens of nanometers).
Langevin dynamics simulations reproduced the observed hopping behavior, demonstrating force-sensitive kinetics.

Conclusions:

The force-induced entropic energy barrier is a key factor driving the observed two-state hopping in single molecules.
This barrier mechanism explains phenomena not observed in bulk experiments due to the absence of force.
The study highlights the distinct behavior of single molecules under force compared to bulk conditions.