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

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,...

Modeling and Similitude

Modeling and Similitude

Scaled modeling is a fundamental technique in engineering, enabling the study of large and complex systems by creating smaller, manageable replicas that recreate critical characteristics of the original. In hydrology and civil infrastructure, for example, scaled models of dams help analyze water flow, turbulence, and pressure. This method allows for accurate predictions of real-world behavior within a controlled environment, significantly reducing the cost and time involved in full-scale...

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...

You might also read

Related Articles

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

Sort by

Same author

Systematic selection of symmetry functions for transferable neural network potentials in coarse-grained molecular modeling.

The Journal of chemical physics·2026

Same author

Uncovering sequence effects in Titanium binding peptides adsorption on TiO<sub>2</sub>: A molecular dynamics study.

Scientific reports·2025

Same author

CG modeling of nucleosome arrays reveals the salt-dependent chromatin fiber conformational variability.

The Journal of chemical physics·2025

Same author

Exploring Carbamazepine Polymorph Crystal Growth in Water by Enhanced Sampling Simulations.

ACS omega·2024

Same author

Biomolecular Adsorption on Nanomaterials: Combining Molecular Simulations with Machine Learning.

Journal of chemical information and modeling·2024

Same author

Development of a bottom-up coarse-grained model for interactions of lipids with TiO <math> </math> nanoparticles.

Journal of computational chemistry·2024

Same journal

Knowledge Distillation of a Protein Language Model Yields a Foundational Implicit Solvent Model.

Journal of chemical theory and computation·2026

Same journal

Generalizable Protein Folding Pathway Exploration with DA2-GRASP: Extending Beyond Miniproteins.

Journal of chemical theory and computation·2026

Same journal

Improving PCM in Protic Media: Markov State Models for TD-DFT Calculations.

Journal of chemical theory and computation·2026

Same journal

Efficient Coupled-Cluster Python Frameworks for Next-Generation GPUs: A Comparative Study of CuPy and PyTorch on the Hopper and Grace Hopper Architecture.

Journal of chemical theory and computation·2026

Same journal

Extending the MARTINI 3 Coarse-Grained Force Field to Polypeptoids.

Journal of chemical theory and computation·2026

Same journal

Statistical Mechanics of Density- and Temperature-Dependent Potentials: Application to Condensed Phases within GenDPDE.

Journal of chemical theory and computation·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Mar 30, 2026

Subject-specific Musculoskeletal Model for Studying Bone Strain During Dynamic Motion

Subject-specific Musculoskeletal Model for Studying Bone Strain During Dynamic Motion

Published on: April 11, 2018

MagiC: Software Package for Multiscale Modeling.

Alexander Mirzoev¹, Alexander P Lyubartsev¹

¹Division of Physical Chemistry, Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, SE-10691, Sweden.

Journal of Chemical Theory and Computation

|November 21, 2015

Summary

This summary is machine-generated.

We developed MagiC software for systematic structure-based coarse graining of molecular models. It accurately reproduces structural distributions using effective potentials, enabling efficient simulations.

More Related Videos

Digital Hybrid Model Preparation for Virtual Planning of Reconstructive Dentoalveolar Surgical Procedures

Digital Hybrid Model Preparation for Virtual Planning of Reconstructive Dentoalveolar Surgical Procedures

Published on: August 5, 2021

Analysis of Multidimensional Microscopy Data Using Cell-ACDC

Analysis of Multidimensional Microscopy Data Using Cell-ACDC

Published on: November 7, 2025

Related Experiment Videos

Last Updated: Mar 30, 2026

Subject-specific Musculoskeletal Model for Studying Bone Strain During Dynamic Motion

Subject-specific Musculoskeletal Model for Studying Bone Strain During Dynamic Motion

Published on: April 11, 2018

Digital Hybrid Model Preparation for Virtual Planning of Reconstructive Dentoalveolar Surgical Procedures

Digital Hybrid Model Preparation for Virtual Planning of Reconstructive Dentoalveolar Surgical Procedures

Published on: August 5, 2021

Analysis of Multidimensional Microscopy Data Using Cell-ACDC

Analysis of Multidimensional Microscopy Data Using Cell-ACDC

Published on: November 7, 2025

Area of Science:

Computational chemistry
Molecular modeling
Biophysics

Background:

Coarse-graining reduces molecular complexity for large-scale simulations.
Accurate effective potentials are crucial for reliable coarse-grained models.
Reproducing structural distribution functions is key to model fidelity.

Purpose of the Study:

To introduce MagiC, a software package for systematic structure-based coarse graining.
To enable the construction of accurate effective potentials for coarse-grained molecular models.
To facilitate efficient and scalable simulations of molecular systems.

Main Methods:

Systematic structure-based coarse graining of molecular models.
Construction of effective pairwise potentials using iterative Boltzmann inversion or inverse Monte Carlo.
Metropolis Monte Carlo sampling with parallel execution and property averaging.
Treatment of long-range electrostatic forces via Ewald summation.

Main Results:

MagiC software package developed for coarse-grained molecular modeling.
Effective potentials reproduce structural distribution functions from atomistic models.
Implementation of iterative Boltzmann inversion and inverse Monte Carlo for potential refinement.
Parallel Monte Carlo engine ensures fast convergence and scalability.

Conclusions:

MagiC provides a robust framework for structure-based coarse graining.
The software enables accurate and efficient simulation of molecular systems at reduced resolution.
MagiC facilitates the study of complex molecular systems through scalable computational approaches.