Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Extraction: Advanced Methods00:56

Extraction: Advanced Methods

1.2K
Metal ions can be separated from one another by complexation with organic ligands–the chelating agent– to form uncharged chelates. Here, the chelating agent must contain hydrophobic groups and behave as a weak acid, losing a proton to bind with the metal. Since most organic ligands used in this process are insoluble or undergo oxidation in the aqueous phase, the chelating agent is initially added to the organic phase and extracted into the aqueous phase. The metal-ligand complex is...
1.2K
Sample Preparation for Analysis: Advanced Techniques01:08

Sample Preparation for Analysis: Advanced Techniques

1.5K
Accurate analysis of complex samples often requires advanced preparation techniques to achieve reliable and reproducible results. Samples containing inorganic or organic materials can be challenging to dissolve or decompose effectively. Standard sample preparation methods include acid digestion, fusion, dry ashing, and wet digestion.
Acid digestion with strong acids is commonly used to dissolve inorganic materials that are insoluble (do not dissolve) in water. This method can be useful for...
1.5K
Inductively Coupled Plasma Atomic Emission Spectroscopy: Principle01:19

Inductively Coupled Plasma Atomic Emission Spectroscopy: Principle

1.9K
Inductively coupled plasma (ICP) is the most widely used plasma source in atomic emission spectroscopy (AES), also known as Inductively Coupled Plasma Optical Emission Spectroscopy (ICP-OES). The ICP source, or torch, consists of three concentric quartz tubes with argon gas flowing through them. A spark from a Tesla coil initiates the ionization of argon, generating a high-temperature plasma.
The ions and electrons produced interact with the fluctuating magnetic field created by a water-cooled...
1.9K
Sampling Methods: Sample Types01:18

Sampling Methods: Sample Types

3.3K
Sampling materials are classified into three main types: solid, liquid, and gas.
Solid samples include a variety of substances, such as sediments from water bodies, soil, metals, and biological tissues. Two standard methods for extracting sediments from water bodies are grab sampling and piston coring. Grab sampling involves using a device to collect a discrete sediment sample from the bottom of a water body with minimal disturbance. Grab samples do not always represent the entire area due to...
3.3K
The Uncertainty Principle04:08

The Uncertainty Principle

33.1K
Werner Heisenberg considered the limits of how accurately one can measure properties of an electron or other microscopic particles. He determined that there is a fundamental limit to how accurately one can measure both a particle’s position and its momentum simultaneously. The more accurate the measurement of the momentum of a particle is known, the less accurate the position at that time is known and vice versa. This is what is now called the Heisenberg uncertainty principle. He...
33.1K
Le Chatelier's Principle: Changing Concentration02:27

Le Chatelier's Principle: Changing Concentration

66.1K
A system at equilibrium is in a state of dynamic balance, with forward and reverse reactions taking place at equal rates. If an equilibrium system is subjected to a change in conditions that affects these reaction rates differently (a stress), then the rates are no longer equal and the system is not at equilibrium. The system will subsequently experience a net reaction in the direction of a greater rate (a shift) that will re-establish the equilibrium. This phenomenon is summarized by Le...
66.1K

You might also read

Related Articles

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

Sort by
Same author

Strategies to Predict and Design Spin Defects for Quantum Technologies.

Journal of chemical theory and computation·2026
Same author

Harnessing the Spin-Flip Radiative Lifetimes of Optically Addressable Molecular Qubits.

JACS Au·2026
Same author

Effect of ensemble averaging on Green-Kubo estimation of short-time stress relaxation modulus in all-atom molecular dynamics simulations of an unentangled polymer melt.

The Journal of chemical physics·2026
Same author

Impact of Small-Alkane Solvents on Polyolefin Hydrogenolysis over a Ruthenium Catalyst.

Industrial & engineering chemistry research·2026
Same author

Sequential chemo-durvalumab, reduced-dose RT, and consolidation durvalumab for unresectable stage III NSCLC unfit for PACIFIC regimen (DEDALUS trial).

JNCI cancer spectrum·2026
Same author

Characterizing Defect Dynamics in Silicon Carbide Using Symmetry-Adapted Collective Variables and Machine Learning Interatomic Potentials.

Journal of chemical theory and computation·2026

Related Experiment Video

Updated: Feb 11, 2026

Analyses of Actin Dynamics, Clutch Coupling and Traction Force for Growth Cone Advance
07:53

Analyses of Actin Dynamics, Clutch Coupling and Traction Force for Growth Cone Advance

Published on: October 21, 2021

3.9K

Hierarchical Coupling of First-Principles Molecular Dynamics with Advanced Sampling Methods.

Emre Sevgen1, Federico Giberti1, Hythem Sidky2

  • 1University of Chicago , 5801 S. Ellis Ave. , Chicago , Illinois 60637 , United States.

Journal of Chemical Theory and Computation
|April 26, 2018
PubMed
Summary

First-principles molecular dynamics (MD) simulations reveal significant differences in free energy surfaces compared to classical force fields. These discrepancies impact transition pathways and molecular structure predictions for peptides.

More Related Videos

Visualizing Single Molecular Complexes In Vivo Using Advanced Fluorescence Microscopy
11:26

Visualizing Single Molecular Complexes In Vivo Using Advanced Fluorescence Microscopy

Published on: September 8, 2009

9.8K
Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package
06:37

Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package

Published on: September 17, 2021

5.1K

Related Experiment Videos

Last Updated: Feb 11, 2026

Analyses of Actin Dynamics, Clutch Coupling and Traction Force for Growth Cone Advance
07:53

Analyses of Actin Dynamics, Clutch Coupling and Traction Force for Growth Cone Advance

Published on: October 21, 2021

3.9K
Visualizing Single Molecular Complexes In Vivo Using Advanced Fluorescence Microscopy
11:26

Visualizing Single Molecular Complexes In Vivo Using Advanced Fluorescence Microscopy

Published on: September 8, 2009

9.8K
Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package
06:37

Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package

Published on: September 17, 2021

5.1K

Area of Science:

  • Computational chemistry
  • Molecular dynamics simulations
  • Biophysics

Background:

  • Advanced sampling simulations are crucial for understanding molecular behavior.
  • First-principles molecular dynamics (MD) offers high accuracy but is computationally expensive.
  • Classical force fields are efficient but may lack accuracy for complex systems.

Purpose of the Study:

  • To couple advanced sampling codes with a first-principles MD engine.
  • To investigate the free energy and potential surfaces of alanine dipeptide using various computational methods.
  • To compare the accuracy of first-principles calculations with classical force fields.

Main Methods:

  • Seamless integration of advanced sampling codes with a first-principles MD engine.
  • Utilized local and hybrid density functionals (DFT) for first-principles calculations.
  • Employed hierarchical sampling to enhance the efficiency of hybrid DFT calculations.
  • Applied the string method to analyze transition pathways.

Main Results:

  • First-principles MD calculations using DFT revealed differences in free energy surfaces compared to the Amber99sb classical force field.
  • The classical force field overestimated internal energy in high free energy states and underestimated entropic contributions.
  • Distinct transition pathways were identified between metastable minima for alanine dipeptide.

Conclusions:

  • First-principles MD with DFT provides a more accurate representation of molecular free energy surfaces than classical force fields.
  • The observed discrepancies can lead to qualitatively different predictions for peptide structure and dynamics.
  • This integrated approach enables more reliable simulations of complex molecular systems.