Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Optimal Arousal Theory

Optimal Arousal Theory

The optimal arousal theory suggests that performance is maximized when an individual experiences a moderate level of arousal. This theory is closely tied to the Yerkes-Dodson law, which illustrates an inverted U-shaped relationship between arousal and performance. The law, formulated by psychologists Robert Yerkes and John Dodson, implies an ideal arousal level for optimal performance, and deviations from this level can lead to declines in effectiveness.
Inverted U-Shaped Performance Curve
The...

Band Theory

Band Theory

When two or more atoms come together to form a molecule, their atomic orbitals combine and molecular orbitals of distinct energies result. In a solid, there are a large number of atoms, and therefore a large number of atomic orbitals that may be combined into molecular orbitals. These groups of molecular orbitals are so closely placed together to form continuous regions of energies, known as the bands.
The energy difference between these bands is known as the band gap.
Conductor, Semiconductor,...

Scientific Laws and Theories

Scientific Laws and Theories

Scientific Laws

Optimal Foraging

Optimal Foraging

How animals obtain and eat their food is called foraging behavior. Foraging can include searching for plants and hunting for prey and depends on the species and environment.

Molecular Orbital Theory II

Molecular Orbital Theory II

Molecular Orbital Energy Diagrams

Valence Bond Theory

Valence Bond Theory

Overview of Valence Bond Theory

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Nonequilibrium Theory for Molecular Machine Design.

ArXiv·2026

Same author

Seeking Biology's Physics Stories: Simplify, Simplify.

Annual review of biophysics·2026

Same author

A principled basis for nonequilibrium network flows.

Nature communications·2026

Same author

Fluctuation-Response Design Rules for Nonequilibrium Flows.

ArXiv·2026

Same author

"Excluded phenotypes" restrict genetic paths toward adaptation in declining populations.

Proceedings of the National Academy of Sciences of the United States of America·2026

Same author

Modeling Protein-Protein and Protein-Ligand Interactions by the ClusPro Team in CASP16.

Proteins·2025

Same journal

A data-driven modeling study on the accurate identification of Doppler-free saturated absorption spectra in diatomic tellurium (130Te2).

The Journal of chemical physics·2026

Same journal

Anharmonic phonons via quantum thermal bath simulations.

The Journal of chemical physics·2026

Same journal

Quantum simulation of alignment dependent differential cross sections in co-propagating molecular beams at cold collision energies.

The Journal of chemical physics·2026

Same journal

Non-additive ion effects on the coil-globule equilibrium of a generic polymer in aqueous salt solutions.

The Journal of chemical physics·2026

Same journal

Insights into the unexpected small reduction of the temperature of maximum density of water by lithium chloride addition.

The Journal of chemical physics·2026

Same journal

Optical frequency comb double-resonance spectroscopy of the 9030-9175 cm-1 states of ethylene.

The Journal of chemical physics·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Jan 29, 2026

How to Build a Vacuum Spring-transport Package for Spinning Rotor Gauges

How to Build a Vacuum Spring-transport Package for Spinning Rotor Gauges

Published on: April 7, 2016

Building Markov state models using optimal transport theory.

Purushottam D Dixit¹, Ken A Dill²

¹Department of Systems Biology, Columbia University, New York, New York 10032, USA.

The Journal of Chemical Physics

|February 10, 2019

Summary

This summary is machine-generated.

This study presents an efficient method for Markov State Models (MSMs) by combining maximum caliber and optimal transport theory. This approach speeds up the estimation of biomolecular conformational dynamics from simulations.

More Related Videos

Building Finite Element Models to Investigate Zebrafish Jaw Biomechanics

Building Finite Element Models to Investigate Zebrafish Jaw Biomechanics

Published on: December 3, 2016

Author Spotlight: Advanced Techniques for Visualizing Endogenous Axonal Transport Dynamics

Author Spotlight: Advanced Techniques for Visualizing Endogenous Axonal Transport Dynamics

Published on: February 16, 2024

Related Experiment Videos

Last Updated: Jan 29, 2026

How to Build a Vacuum Spring-transport Package for Spinning Rotor Gauges

How to Build a Vacuum Spring-transport Package for Spinning Rotor Gauges

Published on: April 7, 2016

Building Finite Element Models to Investigate Zebrafish Jaw Biomechanics

Building Finite Element Models to Investigate Zebrafish Jaw Biomechanics

Published on: December 3, 2016

Author Spotlight: Advanced Techniques for Visualizing Endogenous Axonal Transport Dynamics

Author Spotlight: Advanced Techniques for Visualizing Endogenous Axonal Transport Dynamics

Published on: February 16, 2024

Area of Science:

Computational chemistry
Biophysics
Statistical mechanics

Background:

Markov State Models (MSMs) are crucial for understanding biomolecular conformational dynamics.
Estimating MSMs computationally is challenging due to the slow sampling of rare events in molecular simulations.

Purpose of the Study:

To develop an efficient and approximate method for determining MSM rate matrices.
To overcome the computational expense of traditional MSM estimation methods.

Main Methods:

Combining maximum caliber (maximizing path entropies) with optimal transport theory (minimizing path cost).
Patching together transient dynamical information from multiple non-equilibrium simulations.

Main Results:

An efficient approximate method for determining MSM rate matrices was developed.
The approach effectively combines information from multiple simulations to capture rare events.

Conclusions:

This novel method offers a computationally tractable way to estimate MSMs.
It facilitates a deeper understanding of biomolecular conformational dynamics by improving the efficiency of simulation analysis.