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

DNA Packaging00:58

DNA Packaging

112.6K
Overview
112.6K
Chromatin Packaging01:32

Chromatin Packaging

19.3K
Each human somatic cell contains 6 billion base pairs of DNA. Each base pair is 0.34 nm long, meaning each diploid cell contains a staggering 2 meters of DNA. This long DNA strand is packed inside a nucleus measuring only 10-20 microns in diameter with the help of specialized DNA-binding proteins called histones. Together they form a compact DNA-protein complex called chromatin. The chromatin is further compacted into higher-order structures. The highest level of compaction is achieved during...
19.3K
Chromatin Packaging02:21

Chromatin Packaging

22.1K
Each human somatic cell contains 6 billion base-pairs of DNA. Each base-pair is 0.34 nm long, which means that each diploid cell contains a staggering 2 meters of DNA. How is such a long DNA strand packed inside a nucleus measuring only 10 - 20 microns in diameter? 
The chromatin
In combination with specialized DNA binding protein called Histones, the DNA double helix forms a compact DNA: protein complex called chromatin. The chromatin itself is further compacted into higher-order...
22.1K
Chromatin Packaging02:21

Chromatin Packaging

9.8K
9.8K
Molecular Models02:00

Molecular Models

43.7K
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.
43.7K
Interfacial Electrochemical Methods: Overview01:06

Interfacial Electrochemical Methods: Overview

879
Interfacial electrochemical methods focus on the phenomena occurring at the boundary between an electrode and a solution, as opposed to bulk methods that concentrate on the solution's overall properties. These interfacial methods are classified as either static or dynamic based on the presence of a nonzero current in the electrochemical cell and the consistency of analyte concentrations. Static methods, such as potentiometry, measure the cell's potential without any significant current...
879

You might also read

Related Articles

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

Sort by
Same author

Anisotropic compressibility in inhomogeneous fluids.

The Journal of chemical physics·2026
Same author

The Early Trauma Inventory Self Report-Short Form (ETISR-SF): Validation and Psychometric Properties of the Hungarian Version.

Neuropsychopharmacologia Hungarica : a Magyar Pszichofarmakologiai Egyesulet lapja = official journal of the Hungarian Association of Psychopharmacology·2026
Same author

Arc mediates intercellular tau transmission via extracellular vesicles.

Cell·2026
Same author

pH-dependent activation of the Na<sup>+</sup>/H<sup>+</sup> antiporter NhaA and conformational dynamics of its N-terminus.

Nature communications·2026
Same author

Solvation of Inorganic Salts in <i>N</i>,<i>N</i>-Dimethylformamide: A Computer Simulation Investigation.

The journal of physical chemistry. B·2026
Same author

Nucleation of NaCl crystals from solution: Rate prediction and influence of noisy order parameters on the committor.

The Journal of chemical physics·2026

Related Experiment Video

Updated: Feb 4, 2026

Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package
06:37

Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package

Published on: September 17, 2021

5.1K

Pytim: A python package for the interfacial analysis of molecular simulations.

Marcello Sega1, György Hantal1, Balázs Fábián2,3

  • 1Faculty of Physics, University of Vienna, Boltzmangasse 5, Vienna A-1090, Austria.

Journal of Computational Chemistry
|October 12, 2018
PubMed
Summary

Pytim is a Python framework for analyzing molecular simulation interfaces. It offers tools for identifying arbitrary interfaces and calculating properties like intrinsic profiles, enhancing interfacial studies.

Keywords:
interfacial analysismolecular simulationspython

More Related Videos

Vibrational Spectra of a N719-Chromophore/Titania Interface from Empirical-Potential Molecular-Dynamics Simulation, Solvated by a Room Temperature Ionic Liquid
08:54

Vibrational Spectra of a N719-Chromophore/Titania Interface from Empirical-Potential Molecular-Dynamics Simulation, Solvated by a Room Temperature Ionic Liquid

Published on: January 25, 2020

6.0K
Interfacial Molecular-level Structures of Polymers and Biomacromolecules Revealed via Sum Frequency Generation Vibrational Spectroscopy
09:43

Interfacial Molecular-level Structures of Polymers and Biomacromolecules Revealed via Sum Frequency Generation Vibrational Spectroscopy

Published on: August 13, 2019

9.9K

Related Experiment Videos

Last Updated: Feb 4, 2026

Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package
06:37

Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package

Published on: September 17, 2021

5.1K
Vibrational Spectra of a N719-Chromophore/Titania Interface from Empirical-Potential Molecular-Dynamics Simulation, Solvated by a Room Temperature Ionic Liquid
08:54

Vibrational Spectra of a N719-Chromophore/Titania Interface from Empirical-Potential Molecular-Dynamics Simulation, Solvated by a Room Temperature Ionic Liquid

Published on: January 25, 2020

6.0K
Interfacial Molecular-level Structures of Polymers and Biomacromolecules Revealed via Sum Frequency Generation Vibrational Spectroscopy
09:43

Interfacial Molecular-level Structures of Polymers and Biomacromolecules Revealed via Sum Frequency Generation Vibrational Spectroscopy

Published on: August 13, 2019

9.9K

Area of Science:

  • Computational chemistry and materials science.
  • Development of open-source software for molecular simulations.

Background:

  • Molecular simulations generate vast amounts of data requiring specialized tools for interfacial analysis.
  • Existing tools may lack flexibility for arbitrary interface shapes or specific property calculations.

Discussion:

  • Pytim provides algorithms for identifying instantaneous interfaces of any shape.
  • It includes analysis tools for interfacial properties, such as intrinsic profiles.
  • The framework leverages NumPy and SciPy for high computational performance.

Key Insights:

  • Pytim integrates with MDAnalysis to support various simulation package formats (GROMACS, CHARMM, NAMD, LAMMPS, Amber).
  • It can steer OpenMM simulations and output surface data to VTK, Cube, and PDB files for visualization.
  • The open-source nature and customizable classes facilitate extension and adoption.

Outlook:

  • Potential for Pytim to become a standard tool in interfacial molecular simulation research.
  • Further development could incorporate advanced machine learning techniques for interface analysis.
  • Broader applications in fields requiring detailed understanding of molecular interfaces.