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

Fast Fourier Transform01:10

Fast Fourier Transform

230
The Fast Fourier Transform (FFT) is a computational algorithm designed to compute the Discrete Fourier Transform (DFT) efficiently. By breaking down the calculations into smaller, manageable sections, the FFT significantly reduces the computational complexity involved. Direct computation of an N-point DFT requires N2 complex multiplications, whereas the FFT algorithm needs only (N/2)log⁡2N multiplications, offering a much faster performance.
The computational efficiency of the FFT becomes...
230
Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving01:29

Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving

34
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...
34
Next-generation Sequencing03:00

Next-generation Sequencing

86.3K
The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
86.3K

You might also read

Related Articles

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

Sort by
Same author

Mechanistic Understanding of Protein-MOF Integration Through Surfactant-Driven Interfacial Design.

Advanced science (Weinheim, Baden-Wurttemberg, Germany)·2026
Same author

Multiscale Free-Energy Methods for Protonation-Coupled Light-Responsive Binding of Ionizable Photoswitchable eDHFR Inhibitors.

bioRxiv : the preprint server for biology·2026
Same author

Adam13 interacts with large protein complexes to regulate histone modification and gene expression.

Frontiers in cell and developmental biology·2026
Same author

A Systematic Benchmark Study of Free Energy Methods for Quantifying Light-Responsive Binding Affinities of Photoswitchable Antagonists of Beta-Adrenergic Receptors.

Journal of medicinal chemistry·2026
Same author

Allosteric effects of the coupling cation in melibiose transporter MelB.

eLife·2026
Same author

Mechanistic Understanding of Protein-MOF Integration through Surfactant-Driven Interfacial Design.

bioRxiv : the preprint server for biology·2025
Same journal

Electron Alchemy with Machine-Learned Interatomic Potentials: Case Studies of Local Charge in Bond Dissociation Curves.

Journal of chemical theory and computation·2026
Same journal

Multilevel Fragmentation and Boundary Corrections for Accurate Vibrational Spectra of Large Molecules.

Journal of chemical theory and computation·2026
Same journal

Special Topics: Developments of Theoretical and Computational Chemistry Methods in Asia.

Journal of chemical theory and computation·2026
Same journal

Predicting Excited-State Energies from Ground-State Descriptors in Thermally Fluctuating π-Conjugated Molecules.

Journal of chemical theory and computation·2026
Same journal

Many-Body Theory Predictions of Positron Binding Energies in Five-Membered Heterocycles Involving N, O, S, and NH Substituents.

Journal of chemical theory and computation·2026
Same journal

<i>opt</i>-DDAP: Optimizable Density-Derived Atomic Point Charges via Automatic Differentiation.

Journal of chemical theory and computation·2026
See all related articles

Related Experiment Video

Updated: May 17, 2025

Large Scale Energy Efficient Sensor Network Routing Using a Quantum Processor Unit
05:30

Large Scale Energy Efficient Sensor Network Routing Using a Quantum Processor Unit

Published on: September 8, 2023

462

Development of Parallel On-the-Fly Crystal Algorithm for Reaction Discovery in Large and Complex Molecular Systems.

Ankit Pandey1, Gustavo J Costa1, Mushfiq Alam1

  • 1Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States.

Journal of Chemical Theory and Computation
|May 1, 2025
PubMed
Summary
This summary is machine-generated.

A new parallel algorithm, Crystal, efficiently explores molecular configurations to discover reactions in complex photoswitches like bilirubin. This method works even in condensed phases, revealing new reaction pathways and environmental influences.

More Related Videos

Author Spotlight: Introduction to Active Probe Atomic Force Microscopy with Quattro-Parallel Cantilever Arrays
05:04

Author Spotlight: Introduction to Active Probe Atomic Force Microscopy with Quattro-Parallel Cantilever Arrays

Published on: June 13, 2023

1.4K
Optimization of Radiochemical Reactions using Droplet Arrays
10:54

Optimization of Radiochemical Reactions using Droplet Arrays

Published on: February 12, 2021

3.4K

Related Experiment Videos

Last Updated: May 17, 2025

Large Scale Energy Efficient Sensor Network Routing Using a Quantum Processor Unit
05:30

Large Scale Energy Efficient Sensor Network Routing Using a Quantum Processor Unit

Published on: September 8, 2023

462
Author Spotlight: Introduction to Active Probe Atomic Force Microscopy with Quattro-Parallel Cantilever Arrays
05:04

Author Spotlight: Introduction to Active Probe Atomic Force Microscopy with Quattro-Parallel Cantilever Arrays

Published on: June 13, 2023

1.4K
Optimization of Radiochemical Reactions using Droplet Arrays
10:54

Optimization of Radiochemical Reactions using Droplet Arrays

Published on: February 12, 2021

3.4K

Area of Science:

  • Computational Chemistry
  • Chemical Dynamics
  • Molecular Modeling

Background:

  • Exploring potential energy surfaces and conical intersections is crucial for understanding molecular reactions.
  • Applying global search algorithms to complex systems, especially in condensed phases, presents significant computational challenges due to high dimensionality.

Purpose of the Study:

  • To extend the applicability of the parallel on-the-fly Crystal algorithm to reaction discovery in large, complex molecular photoswitches.
  • To investigate the influence of molecular environments, including explicit solvent, on reaction pathways.

Main Methods:

  • Developed an enhanced Crystal algorithm for explicit exploration of configurational subspaces in complex molecules.
  • Implemented an automated workflow for reaction discovery and characterization in vacuum and aqueous solutions.
  • Applied the algorithm to study bilirubin and donor-acceptor Stenhouse adducts.

Main Results:

  • Successfully applied the Crystal algorithm to discover and characterize new minima and low-energy reaction pathways in complex photoswitches.
  • Demonstrated the algorithm's efficiency in exploring configuration space and identifying kinetically accessible products.
  • Provided insights into the role of molecular environments on reaction pathways.

Conclusions:

  • The enhanced Crystal algorithm effectively addresses challenges in exploring complex molecular systems, including condensed phases.
  • The findings highlight the potential of parallelized global exploration methods for reaction discovery in biomolecular systems.
  • This work offers new perspectives on the reactivity of molecular photoswitches and environmental effects.