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...

Three-Dimensional Analysis of Strain

Three-Dimensional Analysis of Strain

Three-dimensional strain analysis is crucial for understanding how materials deform under stress, particularly in elastic, homogeneous materials. This method employs principal stress axes to simplify complex stress states into more understandable forms. Subjected to stress, a small cubic element within a material either expands or contracts along these axes, transforming into a rectangular parallelepiped. This transformation effectively illustrates the material's deformation. The principal...

You might also read

Related Articles

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

Sort by

Same author

Downregulation of fibroblast growth factor 7 impairs endometrial receptivity and decidualisation via extracellular signal-regulated kinase and C-Jun N-Terminal kinase pathways, contributing to recurrent spontaneous abortion.

Journal of molecular histology·2026

Same author

High-Precision MEMS Resonant Pressure Sensor for Real-Time Barometric Monitoring.

Micromachines·2026

Same author

Comparison of food allergic immune responses in sensitized female and male Balb/c mouse induced by Lateolabrax japonicus tropomyosin.

Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association·2026

Same author

A unified analysis of global riverine eDNA reveals common associations of fish biodiversity with drainage characteristics.

Nature ecology & evolution·2026

Same author

LncRNA CDIPTOSP-induced destabilization of KLF17 promotes ovarian cancer progression through STAU1-mediated mRNA decay.

American journal of translational research·2026

Same author

Depositional architecture and post-depositional alteration of the Toutunhe Formation (J2t) in the Louzhuangzi area, Southern Junggar Basin: Implications for uranium mineralization.

PloS one·2026

Same journal

Nuclear Gradients from Auxiliary-Field Quantum Monte Carlo and Their Applications in ML-Driven Geometry Optimization and Transition State Search.

Journal of chemical theory and computation·2026

Same journal

Correction to "Cluster-in-Molecule Local Correlation Method with an Accurate Distant Pair Correction for Large Systems".

Journal of chemical theory and computation·2026

Same journal

Machine-Learned Force Fields for Lattice Dynamics at Coupled-Cluster Level Accuracy.

Journal of chemical theory and computation·2026

Same journal

Systematic Molecularity-Dependent Entropy Errors in Continuum/RRHO Solution Thermochemistry: Origin and Correction.

Journal of chemical theory and computation·2026

Same journal

After 100 Years of Quantum Mechanics: Toward a Constructive Observation-Centered Perspective.

Journal of chemical theory and computation·2026

Same journal

Sample-Based Quantum Diagonalization Methods for Modeling the Photochemistry of Diazirine and Diazo Compounds.

Journal of chemical theory and computation·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Mar 29, 2026

Visualization of Failure and the Associated Grain-Scale Mechanical Behavior of Granular Soils under Shear using Synchrotron X-Ray Micro-Tomography

Visualization of Failure and the Associated Grain-Scale Mechanical Behavior of Granular Soils under Shear using Synchrotron X-Ray Micro-Tomography

Published on: September 29, 2019

Multiscale Coarse-Graining via Normal Mode Analysis.

Fei Xia¹, Lanyuan Lu¹

¹School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore.

Journal of Chemical Theory and Computation

|November 26, 2015

Summary

This summary is machine-generated.

A new multiscale coarse-graining method, normal-mode analysis based fluctuation matching (NMA-FM), efficiently models biomolecular systems. This approach accurately captures low-frequency motions, enabling conformational and mechanical property analyses for large biomolecules.

More Related Videos

Examining Local Network Processing using Multi-contact Laminar Electrode Recording

Examining Local Network Processing using Multi-contact Laminar Electrode Recording

Published on: September 8, 2011

Two Algorithms for High-throughput and Multi-parametric Quantification of Drosophila Neuromuscular Junction Morphology

Two Algorithms for High-throughput and Multi-parametric Quantification of Drosophila Neuromuscular Junction Morphology

Published on: May 3, 2017

Related Experiment Videos

Last Updated: Mar 29, 2026

Visualization of Failure and the Associated Grain-Scale Mechanical Behavior of Granular Soils under Shear using Synchrotron X-Ray Micro-Tomography

Visualization of Failure and the Associated Grain-Scale Mechanical Behavior of Granular Soils under Shear using Synchrotron X-Ray Micro-Tomography

Published on: September 29, 2019

Examining Local Network Processing using Multi-contact Laminar Electrode Recording

Examining Local Network Processing using Multi-contact Laminar Electrode Recording

Published on: September 8, 2011

Two Algorithms for High-throughput and Multi-parametric Quantification of Drosophila Neuromuscular Junction Morphology

Two Algorithms for High-throughput and Multi-parametric Quantification of Drosophila Neuromuscular Junction Morphology

Published on: May 3, 2017

Area of Science:

Computational Biology
Biophysics
Molecular Modeling

Background:

Developing accurate coarse-grained models is crucial for simulating large biomolecular systems.
Existing methods often require computationally expensive atomistic simulations.
Capturing essential low-frequency motions in coarse-grained models remains a challenge.

Purpose of the Study:

To introduce a novel multiscale coarse-graining method, normal-mode analysis based fluctuation matching (NMA-FM).
To enable systematic conversion of fine-grained models to coarse-grained models while preserving key dynamics.
To provide an efficient approach for analyzing large biomacromolecules and biomaterials.

Main Methods:

The study develops and applies the normal-mode analysis based fluctuation matching (NMA-FM) method.
This method utilizes fluctuation matching, previously used for elastic network models.
It systematically converts fine-grained models to coarse-grained models using normal-mode analysis.

Main Results:

The NMA-FM method successfully constructs coarse-grained models that reproduce low-frequency motions.
The approach avoids costly atomistic molecular dynamics simulations.
Demonstrated efficacy on systems including amyloid dimers, lysozyme, adenylate kinase, and myosin S2 subdomain.

Conclusions:

NMA-FM offers an efficient and accurate strategy for coarse-grained biomolecular modeling.
The method is suitable for conformational and mechanical property analyses of large systems.
This technique advances the simulation capabilities for complex biological macromolecules and materials.