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

Molecular Models

Molecular Models

Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.

Mechanistic Models: Overview of Compartment Models

Mechanistic Models: Overview of Compartment Models

Mechanistic models, a category encompassing both physiological and compartmental modeling, differ from empirical models' approaches to incorporating known factors about the systems being modeled. Empirical models describe data with minimal assumptions, while mechanistic models aim to provide a robust description of available data by specifying assumptions and integrating known factors about the system. Compartmental analysis is a key example of a mechanistic model in pharmacokinetics and...

Model Approaches for Pharmacokinetic Data: Distributed Parameter Models

Model Approaches for Pharmacokinetic Data: Distributed Parameter Models

Pharmacokinetic models are mathematical constructs that represent and predict the time course of drug concentrations in the body, providing meaningful pharmacokinetic parameters. These models are categorized into compartment, physiological, and distributed parameter models.
The distributed parameter models are specifically designed to account for variations and differences in some drug classes. This model is particularly useful for assessing regional concentrations of anticancer or...

You might also read

Related Articles

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

Sort by

Same author

Antimicrobial Activity, Mechanism, and Future Prospects of Baicalin as an Antimicrobial Agent and Adjuvant.

Archiv der Pharmazie·2026

Same author

Lenacapavir-induced lattice hyperstabilization is central to HIV-1 capsid failure at the nuclear pore complex and in the cytoplasm.

eLife·2026

Same author

Systematic bottom-up coarse-graining of hydrated excess proton transport across scales.

Nature computational science·2026

Same author

Comprehensive analysis of pathogenic mechanisms of Enterobacter cancerogenus ECL9 in silkworms.

Developmental and comparative immunology·2026

Same author

Mechanism of HIV-1 Capsid Rupture and Uncoating by Reverse Transcription.

bioRxiv : the preprint server for biology·2026

Same author

Physical Confinement Modulates the Rate-Limiting Transition in the Release of Phosphate from Actin Filaments.

bioRxiv : the preprint server for biology·2026

Search research articles

Related Experiment Video

Updated: Oct 20, 2025

Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics

Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics

Published on: April 12, 2019

Accurate and Transferable Reactive Molecular Dynamics Models from Constrained Density Functional Theory.

Chenghan Li¹, Gregory A Voth¹

¹Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637, United States.

The Journal of Physical Chemistry. B

|September 14, 2021

Summary

This summary is machine-generated.

This study introduces accurate and transferable reactive molecular dynamics (MD) models for simulating chemical reactions. These models enable atomistic simulations of complex biomolecular processes, including accurate pKa predictions for amino acids in various environments.

More Related Videos

Author Spotlight: In Silico Creation and Impact of Carbonylated Amino Acids on Protein Structure and Function

Author Spotlight: In Silico Creation and Impact of Carbonylated Amino Acids on Protein Structure and Function

Published on: April 26, 2024

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

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

Published on: September 17, 2021

Related Experiment Videos

Last Updated: Oct 20, 2025

Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics

Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics

Published on: April 12, 2019

Author Spotlight: In Silico Creation and Impact of Carbonylated Amino Acids on Protein Structure and Function

Author Spotlight: In Silico Creation and Impact of Carbonylated Amino Acids on Protein Structure and Function

Published on: April 26, 2024

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

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

Published on: September 17, 2021

Area of Science:

Computational Chemistry
Molecular Dynamics
Biomolecular Simulations

Background:

Conventional molecular dynamics (MD) struggles with simulating chemical reactions due to fixed bonding topologies.
Ab initio MD is computationally expensive, limiting its application to shorter timescales.
Multiscale reactive molecular dynamics (MD) offers a promising approach for simulating complex chemical systems at atomistic detail.

Purpose of the Study:

To develop accurate and transferable reactive MD models for simulating chemical reactions.
To address the key barrier of model parametrization in reactive MD simulations.
To enable atomistic simulations of reactive systems and elucidate reaction mechanisms.

Main Methods:

Development of reactive MD models derived from constrained density functional theory.
Application of models to proton dissociation reactions of amino acids (glutamate and lysine).
Simulation of amino acids in both aqueous and protein environments (staphylococcal nuclease).

Main Results:

Accurate prediction of absolute pKa values for glutamate and lysine in water.
Accurate prediction of significantly shifted pKa values in staphylococcal nuclease without model modification.
Demonstration that residue deprotonation in proteins can couple with side chain rotations.

Conclusions:

Constrained density functional theory-derived reactive MD models are accurate and transferable.
The new methodology enables fully atomistic simulations of reactive systems, including pKa prediction.
The approach facilitates the determination of key reaction mechanisms in complex biomolecular systems.