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Related Concept Videos

Entropy02:39

Entropy

Salt particles that have dissolved in water never spontaneously come back together in solution to reform solid particles. Moreover, a gas that has expanded in a vacuum remains dispersed and never spontaneously reassembles. The unidirectional nature of these phenomena is the result of a thermodynamic state function called entropy (S). Entropy is the measure of the extent to which the energy is dispersed throughout a system, or in other words, it is proportional to the degree of disorder of a...
Entropy01:18

Entropy

The first law of thermodynamics is quantitatively formulated via an equation relating the internal energy of a system, the heat exchanged by it, and the work done on it. A quantitative formulation of the second law of thermodynamics leads to defining a state function, the entropy.
When an ideal gas expands isothermally, the disorder in the gas increases. From the molecular perspective, the gas molecules have more volume to move around in.
Consider an infinitesimal step in the expansion, which...
Entropy Change in Reversible Processes01:10

Entropy Change in Reversible Processes

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.
The statement can be further generalized to prove that entropy is a state function. Take a cyclic process between any two points on a p-V diagram.
Entropy and the Second Law of Thermodynamics01:20

Entropy and the Second Law of Thermodynamics

The second law of thermodynamics can be stated quantitatively using the concept of entropy. Entropy is the measure of disorder of the system.
The relation  between entropy and disorder can be illustrated with the example of the phase change of ice to water. In ice, the molecules are located at specific sites giving a solid state, whereas, in a liquid form, these molecules are much freer to move. The molecular arrangement has therefore become more randomized. Although the change in average...
Entropy and the Second Law of Thermodynamics01:26

Entropy and the Second Law of Thermodynamics

Consider an isolated system in which a hot object is placed in contact with a cold one. This is an irreversible process that eventually leads both objects to reach the same equilibrium temperature. It is crucial to note that the constituents of any substance exhibit increased disorder at higher temperatures. As a cold substance absorbs heat, its constituents become more disordered. The energy transfer from a hotter object to a cooler one increases the system's disorder or randomness. This...
The Entropy as a State Function01:14

The Entropy as a State Function

Consider an arbitrary process that moves between two specific states (A and B) in a cyclic manner. This process is reversible and broken down into smaller parts that each follow a Carnot cycle. A Carnot cycle has two isothermal (constant temperature) processes. During these processes, the ratio of the amount of heat transferred to their respective temperature remains constant. The other two processes in the Carnot cycle are also reversible but adiabatic, which means they occur without any heat...

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Studying DNA Looping by Single-Molecule FRET
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Studying DNA Looping by Single-Molecule FRET

Published on: June 28, 2014

Modeling loop entropy.

Gregory S Chirikjian1

  • 1Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland, USA.

Methods in Enzymology
|December 29, 2010
PubMed
Summary
This summary is machine-generated.

This study introduces new mathematical models to quantify conformational entropy changes in protein folding. It explores the disorder in unfolded and folded protein states, offering insights into the protein folding process.

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Area of Science:

  • Biochemistry
  • Biophysics
  • Computational Biology

Background:

  • Protein folding transitions from disordered to ordered states.
  • The ensemble of unfolded protein forms may possess inherent order.
  • Native protein structures might be ensembles, not single conformations.

Purpose of the Study:

  • To quantify relative disorder in folded and unfolded protein ensembles via entropy differences.
  • To develop mathematical modeling tools for approximating conformational entropy changes during protein folding.
  • To investigate the conformational entropy of coil/loop regions in proteins.

Main Methods:

  • Utilizing kinematics for rigid-body motion analysis.
  • Applying classical statistical mechanics principles.
  • Employing information theory for entropy calculations.
  • Developing models for lower and upper bounds on conformational entropy for polymer models of polypeptide coils.

Main Results:

  • New mathematical modeling tools for approximating conformational entropy changes are introduced.
  • Models provide lower and upper bounds for entropy in polypeptide coil models.
  • The study clarifies the complex definitions and calculations of various entropy types relevant to protein folding.

Conclusions:

  • Quantifying conformational entropy differences offers insights into the protein folding process.
  • The developed models aid in understanding the transition from unfolded to folded ensembles.
  • Accurate entropy calculations are crucial for understanding protein structure and dynamics.