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

Solvents01:12

Solvents

71.4K
A solvent is a substance, most often a liquid, that can dissolve other substances. Here, the substance being dissolved is called a solute. When a solvent and a solute combine, they form a solution - a homogenous mixture of both the solvent and the solute. Water is a universal biological solvent. Its polar structure allows it to dissolve many other polar compounds. The ability of water to dissolve is governed by a balance between water molecules binding to each other and binding to the solute.
A...
71.4K
Conservative Site-specific Recombination and Phase Variation02:53

Conservative Site-specific Recombination and Phase Variation

6.9K
Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...
6.9K
Implicit Differentiation01:25

Implicit Differentiation

72
In classical mechanics, motion is often described through relationships between spatial coordinates and time. A car moving along a straight highway with constant acceleration serves as a simple case where velocity is an explicit function of time. This scenario results in a linear equation, enabling straightforward analysis using basic differentiation techniques.In contrast, a satellite in circular orbit follows a path defined by an implicit function. The position of the satellite is constrained...
72
Implicit Memories01:24

Implicit Memories

472
Implicit memories, also known as non-declarative memories, are long-term memories that function outside of conscious awareness. These memories influence behavior and skills without explicit knowledge. This type of memory is evident in tasks like playing tennis, snowboarding, and texting. Implicit memory has three subsystems: procedural memory, conditioning, and priming. This type of memory is essential in various activities, from everyday tasks to specialized skills.
One key aspect of implicit...
472
What is Variation?01:14

What is Variation?

18.7K
Apart from the measures of central tendency, distribution, outliers, and the changing characteristics of data with time, an important characteristic of any data set is its variation or spread. In some data sets, the data values are concentrated closely near the mean; in others, the data values are more widely spread out from the mean.
The range, standard deviation, standard error, and variance are the different measures of variation.
Range: The range is the difference between its maximum and...
18.7K
Implicit Differentiation: Problem Solving01:29

Implicit Differentiation: Problem Solving

64
Curves defined implicitly, where variables cannot be separated algebraically, require specialized techniques for analysis. The conchoid of Nicomedes exemplifies such a case. Its equation links x and y in a way that prevents isolation of one variable, making implicit differentiation essential to determine the slope and behavior at any point on the curve.The implicit form of the conchoid can be expressed as:To differentiate this equation, y is treated as a function of x, and the chain rule is...
64

You might also read

Related Articles

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

Sort by
Same author

Identification of the gene cluster for the dithiolopyrrolone antibiotic holomycin in Streptomyces clavuligerus.

Proceedings of the National Academy of Sciences of the United States of America·2010
Same author

Safety evaluation of tea (Camellia sinensis (L.) O. Kuntze) flower extract: assessment of mutagenicity, and acute and subchronic toxicity in rats.

Journal of ethnopharmacology·2010
Same author

Influences of soil properties and leaching on nickel toxicity to barley root elongation.

Ecotoxicology and environmental safety·2010
Same author

Effects of CO2 insufflation on cerebrum during endoscopic thyroidectomy in a porcine model.

Surgical endoscopy·2010
Same author

Plants' use of different nitrogen forms in response to crude oil contamination.

Environmental pollution (Barking, Essex : 1987)·2010
Same author

Overexpression of p35 in Min6 pancreatic beta cells induces a stressed neuron-like apoptosis.

Journal of the neurological sciences·2010

Related Experiment Video

Updated: Feb 13, 2026

Formation of Ordered Biomolecular Structures by the Self-assembly of Short Peptides
07:26

Formation of Ordered Biomolecular Structures by the Self-assembly of Short Peptides

Published on: November 21, 2013

13.5K

Tailoring the Variational Implicit Solvent Method for New Challenges: Biomolecular Recognition and Assembly.

Clarisse Gravina Ricci1, Bo Li2,3, Li-Tien Cheng2

  • 1Department of Pharmacology and Department of Chemistry and Biochemistry, National Biomedical Computation Resource, University of California, San Diego, La Jolla, CA, United States.

Frontiers in Molecular Biosciences
|February 28, 2018
PubMed
Summary

The Variational Implicit Solvent Method (VISM) improves computational modeling of solvation free energies by allowing flexible water interfaces. This approach enhances the study of molecular recognition and biomolecular complex binding.

Keywords:
VISMbindingimplicit solvationmolecular recognitionsolvationsolvation free energysolvation free energy of bindingsolvent model

More Related Videos

Construction of Synthetic Phage Displayed Fab Library with Tailored Diversity
12:31

Construction of Synthetic Phage Displayed Fab Library with Tailored Diversity

Published on: May 1, 2018

14.8K
Variations on Negative Stain Electron Microscopy Methods: Tools for Tackling Challenging Systems
06:06

Variations on Negative Stain Electron Microscopy Methods: Tools for Tackling Challenging Systems

Published on: February 6, 2018

34.4K

Related Experiment Videos

Last Updated: Feb 13, 2026

Formation of Ordered Biomolecular Structures by the Self-assembly of Short Peptides
07:26

Formation of Ordered Biomolecular Structures by the Self-assembly of Short Peptides

Published on: November 21, 2013

13.5K
Construction of Synthetic Phage Displayed Fab Library with Tailored Diversity
12:31

Construction of Synthetic Phage Displayed Fab Library with Tailored Diversity

Published on: May 1, 2018

14.8K
Variations on Negative Stain Electron Microscopy Methods: Tools for Tackling Challenging Systems
06:06

Variations on Negative Stain Electron Microscopy Methods: Tools for Tackling Challenging Systems

Published on: February 6, 2018

34.4K

Area of Science:

  • Computational Chemistry
  • Biomolecular Modeling
  • Physical Chemistry

Background:

  • Accurately predicting solvation free energies is crucial for understanding biological processes.
  • Explicit solvent models are computationally expensive for large biomolecular systems.
  • Existing implicit solvent methods often fail to capture critical "dewetting" and hydration effects due to fixed interfaces.

Purpose of the Study:

  • To introduce and explore the Variational Implicit Solvent Method (VISM) for improved solvation free energy calculations.
  • To address the limitations of traditional implicit solvent models in capturing complex water behavior.
  • To adapt VISM for advanced applications, including molecular recognition and biomolecular complex binding.

Main Methods:

  • Formulating solvation free energy as a functional of all possible solvation interfaces, introducing solvent "plasticity".
  • Applying the Variational Implicit Solvent Method (VISM) to molecular recognition problems.
  • Developing VISM for enhanced accuracy and the inclusion of thermal fluctuations.

Main Results:

  • VISM offers a more flexible and accurate approach to modeling solvation compared to fixed-interface methods.
  • The method has shown promise in applications related to molecular recognition.
  • Ongoing research is extending VISM to handle more complex scenarios and thermal effects.

Conclusions:

  • The Variational Implicit Solvent Method (VISM) provides a powerful framework for characterizing complex solvation properties.
  • VISM advances are crucial for accurately modeling the recognition and binding of large-scale biomolecular complexes.
  • Future work aims to integrate thermal fluctuations, further enhancing VISM's predictive capabilities.