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

Shape and Texture of Coarse Aggregate01:25

Shape and Texture of Coarse Aggregate

696
Aggregate shape is classified based on the relative sharpness or roundness of the edges and corners. This classification includes categories like rounded, angular, elongated, and flaky, each with specific characteristics. Rounded aggregates, fully shaped by attrition, are typical of river or seashore gravel, while angular aggregates, such as crushed rock, have well-defined edges. Aggregates that are elongated and flaky are less desirable, as they can reduce the workability and strength of...
696
Second Order systems II01:18

Second Order systems II

412
In an underdamped second-order system, where the damping ratio ζ is between 0 and 1, a unit-step input results in a transfer function that, when transformed using the inverse Laplace method, reveals the output response. The output exhibits a damped sinusoidal oscillation, and the difference between the input and output is termed the error signal. This error signal also demonstrates damped oscillatory behavior. Eventually, as the system reaches a steady state, the error diminishes to zero.
412
Dynamic Equilibrium02:20

Dynamic Equilibrium

63.0K
A reversible chemical reaction represents a chemical process that proceeds in both forward (left to right) and reverse (right to left) directions. When the rates of the forward and reverse reactions are equal, the concentrations of the reactant and product species remain constant over time and the system is at equilibrium. A special double arrow is used to emphasize the reversible nature of the reaction. The relative concentrations of reactants and products in equilibrium systems vary greatly;...
63.0K
First Order Systems01:21

First Order Systems

433
First-order systems, such as RC circuits, are foundational in understanding dynamic systems due to their straightforward input-output relationship. Analyzing their responses to different input functions under zero initial conditions reveals significant insights into system behavior.
When a first-order system is subjected to a unit-step input, its response is characterized by its transfer function. By applying the Laplace transform of the unit-step input to the transfer function, expanding the...
433
Second Order systems I01:20

Second Order systems I

603
A servo system exemplifies a second-order system, featuring a proportional controller and load elements that ensure the output position aligns with the input position. The relationship between these components is described by a second-order differential equation. Applying the Laplace transform under zero initial conditions yields the transfer function, showing how inputs are converted to outputs in the system.
By reinterpreting the system, one can derive the closed-loop transfer function, which...
603
Thermodynamic Systems01:06

Thermodynamic Systems

8.2K
A thermodynamic system is a set of objects whose thermodynamic properties are of interest. The system is considered to be embedded in its surroundings or the environment. The system and its environment can exchange heat and do work on each other through a boundary that separates them. However, the immediate surroundings of the system interact with it directly and therefore have a much stronger influence on its behavior and properties.
Consider an example of  tea boiling in a kettle. The...
8.2K

You might also read

Related Articles

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

Sort by
Same author

Realistic transition paths for large biomolecular systems: A Langevin bridge approach.

The Journal of chemical physics·2026
Same author

Analyzing the Geometry and Dynamics of Viral Structures: A Review of Computational Approaches Based on Alpha Shape Theory, Normal Mode Analysis, and Poisson-Boltzmann Theories.

Viruses·2023
Same author

Computing the Volume, Surface Area, Mean, and Gaussian Curvatures of Molecules and Their Derivatives.

Journal of chemical information and modeling·2023
Same author

Sampling constrained stochastic trajectories using Brownian bridges.

The Journal of chemical physics·2022
Same author

Parameterizing elastic network models to capture the dynamics of proteins.

Journal of computational chemistry·2021
Same author

Simultaneous Identification of Multiple Binding Sites in Proteins: A Statistical Mechanics Approach.

The journal of physical chemistry. B·2021

Related Experiment Video

Updated: Feb 9, 2026

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
09:17

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

3.6K

Large Eigenvalue Problems in Coarse-Grained Dynamic Analyses of Supramolecular Systems.

Patrice Koehl1

  • 1Department of Computer Sciences and Genome Center , University of California , Davis , California 95616 , United States.

Journal of Chemical Theory and Computation
|June 7, 2018
PubMed
Summary
This summary is machine-generated.

This study introduces a novel tensor product method for calculating normal modes in large molecular systems, overcoming computational limits. The block Chebyshev-Davidson method proved most efficient for analyzing viral capsids.

More Related Videos

Synthesis and Characterization of Supramolecular Colloids
09:26

Synthesis and Characterization of Supramolecular Colloids

Published on: April 22, 2016

10.5K
Controlling the Size, Shape and Stability of Supramolecular Polymers in Water
16:24

Controlling the Size, Shape and Stability of Supramolecular Polymers in Water

Published on: August 2, 2012

19.3K

Related Experiment Videos

Last Updated: Feb 9, 2026

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
09:17

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

3.6K
Synthesis and Characterization of Supramolecular Colloids
09:26

Synthesis and Characterization of Supramolecular Colloids

Published on: April 22, 2016

10.5K
Controlling the Size, Shape and Stability of Supramolecular Polymers in Water
16:24

Controlling the Size, Shape and Stability of Supramolecular Polymers in Water

Published on: August 2, 2012

19.3K

Area of Science:

  • Computational biology
  • Biophysics
  • Structural biology

Background:

  • Molecular dynamics simulations and normal mode analyses are key for studying molecular motion.
  • Current computational methods face limitations with very large molecular systems on standard hardware.

Purpose of the Study:

  • To address computational challenges in calculating coarse-grained normal modes for large molecular systems.
  • To develop and implement improved algorithms for analyzing the Hessian matrix.

Main Methods:

  • A new tensor product-based method for handling the Hessian matrix was developed and implemented.
  • Four eigenpair computation methods were tested: Lanczos, polynomial filtering, functional-based, and block Chebyshev-Davidson.
  • The focus was on calculating eigenpairs of the Hessian for normal mode computation.

Main Results:

  • The tensor product formulation reduced space requirements and improved parallelization.
  • The block Chebyshev-Davidson method demonstrated superior efficiency for extremely large Hessian matrices, such as those from viral capsids.
  • Thousands of eigenpairs were found to be necessary for viral capsid analysis, representing a small fraction of the total.

Conclusions:

  • The developed tensor product method and block Chebyshev-Davidson algorithm significantly enhance the computational feasibility of normal mode analysis for large molecular systems.
  • This advancement enables more in-depth studies of large biological structures like viral capsids.