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

Molecular Models02:00

Molecular Models

45.2K
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.
45.2K
Three-Dimensional Force System:Problem Solving01:30

Three-Dimensional Force System:Problem Solving

1.5K
A three-dimensional force system refers to a scenario in which three forces act simultaneously in three different directions. This type of problem is commonly encountered in physics and engineering, where it is necessary to calculate the resultant force on the system, which can then be used to predict or analyze the behavior of the object or structure under consideration.
To solve a three-dimensional force system, first resolve each force into its respective scalar components. Do this using...
1.5K
Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving01:29

Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving

387
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...
387
Three-Dimensional Force System01:30

Three-Dimensional Force System

3.0K
In mechanical engineering, a three-dimensional force system is a system of forces acting in three dimensions, with forces applied along the x, y, and z coordinate axes. The three-dimensional force system is an important concept in mechanical engineering, as it allows engineers to understand and analyze the behavior of objects and structures in three dimensions. By understanding the forces acting on a system, engineers can design more efficient and effective mechanical systems that can withstand...
3.0K

You might also read

Related Articles

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

Sort by
Same author

Optimising the hygiene of a liquid feeding system to improve the quality of liquid feed for pigs.

Scientific reports·2024
Same author

Evaluation of monte carlo to support commissioning of the treatment planning system of new pencil beam scanning proton therapy facilities.

Physics in medicine and biology·2023
Same author

A portable primary-standard level graphite calorimeter for absolute dosimetry in clinical pencil beam scanning proton beams.

Physics in medicine and biology·2023
Same author

The spells of iatrogeny.

Netherlands heart journal : monthly journal of the Netherlands Society of Cardiology and the Netherlands Heart Foundation·2023
Same author

The spells of iatrogeny.

Netherlands heart journal : monthly journal of the Netherlands Society of Cardiology and the Netherlands Heart Foundation·2023
Same author

Development of optimised tissue-equivalent materials for proton therapy.

Physics in medicine and biology·2023

Related Experiment Video

Updated: Mar 18, 2026

Novel 3D/VR Interactive Environment for MD Simulations, Visualization and Analysis
11:29

Novel 3D/VR Interactive Environment for MD Simulations, Visualization and Analysis

Published on: December 18, 2014

12.3K

High performance computing for three-dimensional agent-based molecular models.

G Pérez-Rodríguez1, M Pérez-Pérez1, F Fdez-Riverola1

  • 1ESEI - Escuela Superior de Ingeniería Informática, Edificio Politécnico, Campus Universitario As Lagoas s/n, Universidad de Vigo, 32004 Ourense, Spain.

Journal of Molecular Graphics & Modelling
|July 4, 2016
PubMed
Summary

This study presents new 3D agent-based simulation methods for molecular-level cellular events. These cost-effective approaches accurately model spatial distribution and improve computational efficiency for complex biological systems.

Keywords:
Agent-based modellingCellular systemsDistributed computingIndividual molecule simulationThree-dimensional model representation

More Related Videos

Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry
12:11

Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry

Published on: April 8, 2020

8.8K
Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics
10:52

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

Published on: April 12, 2019

13.5K

Related Experiment Videos

Last Updated: Mar 18, 2026

Novel 3D/VR Interactive Environment for MD Simulations, Visualization and Analysis
11:29

Novel 3D/VR Interactive Environment for MD Simulations, Visualization and Analysis

Published on: December 18, 2014

12.3K
Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry
12:11

Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry

Published on: April 8, 2020

8.8K
Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics
10:52

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

Published on: April 12, 2019

13.5K

Area of Science:

  • Computational Biology
  • Biophysics
  • Systems Biology

Background:

  • Agent-based simulations are vital for understanding complex cellular systems.
  • Existing methods often lack cost-effectiveness and struggle with multi-level modeling.
  • Accurate spatial representation of molecules is crucial for studying cellular events.

Purpose of the Study:

  • To introduce novel sequential and distributed 3D agent-based simulation approaches for individual molecules.
  • To enable accurate modeling of molecular dimensions, position, and spatial distribution effects.
  • To provide computationally efficient and cost-effective simulation tools for cellular events.

Main Methods:

  • Developed sequential and distributed 3D agent-based simulation strategies.
  • Implemented multi-thread high-performance simulation capabilities for two approaches.
  • Designed platform-independent and computationally efficient distributed models.
  • Evaluated simulation accuracy, scalability, and adherence to biophysical/biochemical laws.

Main Results:

  • The novel approaches accurately simulate molecular dimensions and positions, enabling the study of spatial distribution.
  • Distributed approaches demonstrate enhanced performance for large agent populations.
  • The sequential approach is optimal for small to medium agent populations.
  • All three approaches faithfully simulate common biophysical and biochemical laws.

Conclusions:

  • The introduced methods offer a significant advancement in simulating 3D agent-based models at the molecular level.
  • These approaches reduce implementation effort and computational demands.
  • Their generic design allows broad applicability in various event-driven agent-based tools.