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

Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving

Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving

Mechanistic models play a crucial role in algorithms for numerical problem-solving, particularly in nonlinear mixed effects modeling (NMEM). These models aim to minimize specific objective functions by evaluating various parameter estimates, leading to the development of systematic algorithms. In some cases, linearization techniques approximate the model using linear equations.
In individual population analyses, different algorithms are employed, such as Cauchy's method, which uses a...

Multimachine Stability

Multimachine Stability

Multimachine stability analysis is crucial for understanding the dynamics and stability of power systems with multiple synchronous machines. The objective is to solve the swing equations for a network of M machines connected to an N-bus power system.
In analyzing the system, the nodal equations represent the relationship between bus voltages, machine voltages, and machine currents. The nodal equation is given by:

One-Compartment Open Model: Wagner-Nelson and Loo Riegelman Method for ka Estimation

One-Compartment Open Model: Wagner-Nelson and Loo Riegelman Method for k_a Estimation

This lesson introduces two critical methods in pharmacokinetics, the Wagner-Nelson and Loo-Riegelman methods, used for estimating the absorption rate constant (ka) for drugs administered via non-intravenous routes. The Wagner-Nelson method relates ka to the plasma concentration derived from the slope of a semilog percent unabsorbed time plot. However, it is limited to drugs with one-compartment kinetics and can be impacted by factors like gastrointestinal motility or enzymatic degradation.
On...

Mechanistic Models: Compartment Models in Individual and Population Analysis

Mechanistic Models: Compartment Models in Individual and Population Analysis

Mechanistic models are utilized in individual analysis using single-source data, but imperfections arise due to data collection errors, preventing perfect prediction of observed data. The mathematical equation involves known values (Xi), observed concentrations (Ci), measurement errors (εi), model parameters (ϕj), and the related function (ƒi) for i number of values. Different least-squares metrics quantify differences between predicted and observed values. The ordinary least squares (OLS)...

Multicompartment Models: Overview

Multicompartment Models: Overview

Multicompartment models are mathematical constructs that depict how drugs are distributed and eliminated within the body. They segment the body into several compartments, symbolizing various physiological or anatomical areas connected through drug transfer processes such as absorption, metabolism, distribution, and elimination.
These models offer a more comprehensive representation of drug behavior in the body than one-compartment models. They accommodate the complexity of drug distribution,...

You might also read

Related Articles

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

Sort by

Same author

A lattice Monte Carlo model for amyloid fibril formation.

Biophysics and physicobiology·2026

Same author

Molecular dynamics simulations of amyloid-β(29-42) aggregation in bulk water and at the air-water interface.

Biophysics and physicobiology·2026

Same author

Oligomerization Mechanism of Amyloid-<b>β</b> Peptides at Hydrophobic Interfaces Revealed by Molecular Dynamics Simulations.

The journal of physical chemistry. B·2025

Same author

Why do histone monomethylation and dimethylation cause a significant difference in binding to LEDGF?

The Journal of chemical physics·2025

Same author

Cell position-based evaluation of mechanical features of cells in multicellular systems.

Journal of theoretical biology·2025

Same author

Nonequilibrium Molecular Dynamics Method to Generate Poiseuille-Like Flow between Lipid Bilayers.

Journal of chemical theory and computation·2024

Search research articles

Related Experiment Video

Updated: Jun 27, 2026

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

Partial multicanonical algorithm for molecular dynamics and Monte Carlo simulations.

Hisashi Okumura¹

¹Department of Physics, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku Nagoya, Aichi 464-8602, Japan. okumura@biomaps.rutgers.edu

The Journal of Chemical Physics

|December 3, 2008

Summary

A new partial multicanonical algorithm enhances molecular simulations by focusing on key energy terms. This method improves conformational sampling efficiency compared to traditional multicanonical and canonical approaches.

More Related Videos

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

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

Related Experiment Videos

Last Updated: Jun 27, 2026

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

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

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

Area of Science:

Computational Chemistry
Molecular Dynamics
Statistical Mechanics

Background:

Efficient conformational sampling is crucial for understanding molecular behavior.
Traditional methods like canonical and multicanonical simulations have limitations in exploring the full conformational space.

Purpose of the Study:

To introduce and evaluate a novel Partial Multicanonical (PMMC) algorithm for molecular dynamics and Monte Carlo simulations.
To assess the PMMC algorithm's efficiency in sampling conformational space compared to existing methods.

Main Methods:

Development of the Partial Multicanonical (PMMC) simulation technique.
Application of PMMC, multicanonical, and canonical molecular dynamics algorithms to an alanine dipeptide in explicit water.
Analysis of sampled conformational states and dihedral angle rotations.

Main Results:

PMMC simulations sampled a wider range of conformational states, including the C(7) (ax) state, compared to multicanonical and canonical simulations.
Backbone dihedral angles (phi and psi) exhibited more frequent rotations in PMMC simulations.
The PMMC algorithm demonstrated superior sampling efficiency over multicanonical and canonical methods.

Conclusions:

The Partial Multicanonical algorithm offers enhanced sampling efficiency for molecular simulations.
PMMC allows for focused determination of weight factors on critical energy terms.
This improved efficiency facilitates broader exploration of molecular conformational space.