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Related Concept Videos

Energy Diagrams - II01:10

Energy Diagrams - II

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...
Energy Diagrams, Transition States, and Intermediates02:13

Energy Diagrams, Transition States, and Intermediates

Free-energy diagrams, or reaction coordinate diagrams, are graphs showing the energy changes that occur during a chemical reaction. The reaction coordinate represented on the horizontal axis shows how far the reaction has progressed structurally. Positions along the x-axis close to the reactants have structures resembling the reactants, while positions close to the products resemble the products.  Peaks on the energy diagram represent stable structures with measurable lifetimes, while other...
Transition State Theory01:25

Transition State Theory

Transition-state theory, also known as activated-complex theory, provides a molecular-level explanation of reaction rates in both gas-phase and solution-phase reactions. It extends earlier kinetic models by considering the formation of a short-lived, high-energy configuration during a reaction.The progress of a chemical reaction can be represented using a reaction profile, which plots potential energy against the reaction coordinate. As two reactant molecules approach one another, their...
Phase Transitions: Melting and Freezing02:39

Phase Transitions: Melting and Freezing

Heating a crystalline solid increases the average energy of its atoms, molecules, or ions, and the solid gets hotter. At some point, the added energy becomes large enough to partially overcome the forces holding the molecules or ions of the solid in their fixed positions, and the solid begins the process of transitioning to the liquid state or melting. At this point, the temperature of the solid stops rising, despite the continual input of heat, and it remains constant until all of the solid is...
Free Energy Changes for Nonstandard States03:25

Free Energy Changes for Nonstandard States

The free energy change for a process taking place with reactants and products present under nonstandard conditions (pressures other than 1 bar; concentrations other than 1 M) is related to the standard free energy change according to this equation:
Energy Diagrams - I01:14

Energy Diagrams - I

The dynamics of a mechanical system can be easily understood by interpreting a potential energy diagram. Since energy is a scalar quantity, the interpretation of the dynamics of the system becomes even simpler.
Take the example of a skater on a parabolic ramp. The potential energy at different points along the ramp will be proportional to the height of the ramp, which varies quadratically with the horizontal position on the ramp. As the skater moves down the ramp from the highest position,...

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Related Experiment Video

Updated: Jun 23, 2026

Orientational Transition in a Liquid Crystal Triggered by the Thermodynamic Growth of Interfacial Wetting Sheets
06:26

Orientational Transition in a Liquid Crystal Triggered by the Thermodynamic Growth of Interfacial Wetting Sheets

Published on: May 15, 2017

Characterizing structural transitions using localized free energy landscape analysis.

Nilesh K Banavali1, Alexander D Mackerell

  • 1Laboratory of Computational and Structural Biology, Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, USA. banavali@wadsworth.org

Plos One
|May 14, 2009
PubMed
Summary
This summary is machine-generated.

This study quantifies DNA base flipping energetics using molecular dynamics simulations. Free energy landscapes reveal backbone changes, aiding understanding of DNA structural dynamics.

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Area of Science:

  • Biophysics
  • Computational Biology
  • Molecular Dynamics

Background:

  • Macromolecular structural changes are key to biological processes like replication and transcription.
  • These changes often stem from distortions in molecular backbones.
  • Quantitative energy analysis of these distortions enhances atomic-level understanding of biological dynamics.

Purpose of the Study:

  • To quantitatively characterize localized structural changes during DNA base flipping.
  • To understand the energetic landscape of DNA backbone and sugar pucker during base flipping.
  • To develop a method for pinpointing determinants of structural change in macromolecules.

Main Methods:

  • Employed molecular dynamics simulations.
  • Utilized Weighted Histogram Analysis Method for potential of mean force determination.
  • Simplified base flipping into a two-state model for free energy difference calculation.

Main Results:

  • Characterized cytosine base flipping in a DNA duplex.
  • Calculated free energy landscapes for backbone torsion and sugar pucker.
  • Quantified a free energy difference of up to 14 kcal/mol for the flipped base state.

Conclusions:

  • Free energy landscapes pinpoint structural change determinants at the atomic scale.
  • Delocalized effects of base flipping extend up to four nucleotide positions.
  • Methodology applicable to conformational changes in nucleic acids, carbohydrates, lipids, and proteins.