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

Gaussian Elimination: Problem Solving01:30

Gaussian Elimination: Problem Solving

162
Systems of linear equations in several variables are pivotal in modeling complex scenarios involving multiple unknowns and constraints. Such systems are widely used in various fields to represent relationships where several conditions must be simultaneously satisfied. Each variable in the system corresponds to an unknown quantity, while each equation imposes a linear constraint, leading to a structured approach for analyzing and solving real-world problems.A system of three equations with three...
162
One-Compartment Open Model: Wagner-Nelson and Loo Riegelman Method for ka Estimation01:24

One-Compartment Open Model: Wagner-Nelson and Loo Riegelman Method for ka Estimation

1.1K
This lesson introduces two critical methods in pharmacokinetics, the Wagner-Nelson and Loo-Riegelman methods, used for estimating the absorption rate constant (ka) for drugs administered via non-intravenous routes. The Wagner-Nelson method relates ka to the plasma concentration derived from the slope of a semilog percent unabsorbed time plot. However, it is limited to drugs with one-compartment kinetics and can be impacted by factors like gastrointestinal motility or enzymatic degradation.
On...
1.1K
Density and Archimedes' Principle01:05

Density and Archimedes' Principle

8.7K
When a lump of clay is dropped into water, it sinks. But if the same lump of clay is molded into the shape of a boat, it starts to float. Because of its shape, the clay boat displaces more water than the lump and experiences a greater buoyant force, even though its mass is the same. The same holds true for steel ships. The average density of an object majorly determines if the object will float. If an object's average density is less than that of the surrounding fluid, it will float. The...
8.7K
Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving01:29

Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving

290
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...
290
Hybridization of Atomic Orbitals II03:35

Hybridization of Atomic Orbitals II

48.0K
sp3d and sp3d 2 Hybridization
48.0K
Fermi Level Dynamics01:12

Fermi Level Dynamics

655
The vacuum level denotes the energy threshold required for an electron to escape from a material surface. It is usually positioned above the conduction band of a semiconductor and acts as a benchmark for comparing electron energies within various materials.
Electron affinity in semiconductors refers to the energy gap between the minimum of its conduction band and the vacuum level and it is a critical parameter in determining how easily a semiconductor can accept additional electrons.
The work...
655

You might also read

Related Articles

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

Sort by
Same author

Steric Mapping, Ligand Dynamics, and Cycloisomerization Catalysis with Redox Robust Mn<sup>I/0/‑I</sup> Dicarbenes.

Organometallics·2026
Same author

A Molecular "Thermometer" for Measuring Effective Non-Local Exchange.

Journal of computational chemistry·2026
Same author

Predicting the hydrogen bond strength from water reorientation dynamics at short timescales.

The Journal of chemical physics·2026
Same author

The CP-PAW Code Package for First-Principles Calculations from a User's Perspective.

The journal of physical chemistry. A·2026
Same author

A Ruthenium-(Ph-BPE) Catalyst for Asymmetric Alkynylation of Fluoral: Enantioselection From 1 of 12 Fluxional Stereogenic-at-Ruthenium Complexes.

Angewandte Chemie (International ed. in English)·2026
Same author

Quantifying Gibbs measures of disordered crystals up to the solid-liquid phase transition.

PNAS nexus·2026
Same journal

Revisiting crossed-correlated baths in open quantum systems simulated by HEOM or T-TEDOPA.

The Journal of chemical physics·2026
Same journal

Vesicle size and membrane composition control monomer transfer pathways in multicomponent lipid vesicles.

The Journal of chemical physics·2026
Same journal

Polaron-mediated exciton dynamics of P(NDI2OD-T2) unveiled by transient absorption spectroscopy under electrochemical conditions.

The Journal of chemical physics·2026
Same journal

Green-Kubo relation in a mesoscale odd fluid model.

The Journal of chemical physics·2026
Same journal

Nitrogenation of microscopic MoS2 surfaces by oxidation scanning probe lithography.

The Journal of chemical physics·2026
Same journal

Molecular structure, binding, and disorder in TDBC-Ag plexcitonic assemblies.

The Journal of chemical physics·2026
See all related articles

Related Experiment Video

Updated: Jan 16, 2026

Rapid in-silico Battery Electrolyte Electrochemical Reaction Generation using 3T-VASP Multi-Scale Energy Minimization
05:37

Rapid in-silico Battery Electrolyte Electrochemical Reaction Generation using 3T-VASP Multi-Scale Energy Minimization

Published on: August 22, 2025

612

Submatrix and GPU-accelerated implementation of density matrix tight-binding.

Abylay Katbashev1, Robert Schade2, Michael Lass2,3

  • 1Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany.

The Journal of Chemical Physics
|October 2, 2025
PubMed
Summary
This summary is machine-generated.

We developed faster tight-binding calculations using graphical processing units (GPUs) and a submatrix method. This accelerates simulations for larger systems, making advanced computational materials science more accessible.

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

8.7K
Excitonic Hamiltonians for Calculating Optical Absorption Spectra and Optoelectronic Properties of Molecular Aggregates and Solids
08:04

Excitonic Hamiltonians for Calculating Optical Absorption Spectra and Optoelectronic Properties of Molecular Aggregates and Solids

Published on: May 27, 2020

8.9K

Related Experiment Videos

Last Updated: Jan 16, 2026

Rapid in-silico Battery Electrolyte Electrochemical Reaction Generation using 3T-VASP Multi-Scale Energy Minimization
05:37

Rapid in-silico Battery Electrolyte Electrochemical Reaction Generation using 3T-VASP Multi-Scale Energy Minimization

Published on: August 22, 2025

612
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

8.7K
Excitonic Hamiltonians for Calculating Optical Absorption Spectra and Optoelectronic Properties of Molecular Aggregates and Solids
08:04

Excitonic Hamiltonians for Calculating Optical Absorption Spectra and Optoelectronic Properties of Molecular Aggregates and Solids

Published on: May 27, 2020

8.9K

Area of Science:

  • Computational Materials Science
  • Quantum Chemistry
  • Solid-State Physics

Background:

  • Single-particle theories like Hartree-Fock and DFT face computational limits due to the self-consistent field (SCF) procedure's cubic scaling.
  • Large-scale applications are impractical without advanced algorithms and hardware.
  • The PTB tight-binding potential is a key method in this field.

Purpose of the Study:

  • To implement and evaluate GPU-accelerated and submatrix methods for the PTB tight-binding potential.
  • To overcome the computational bottlenecks of traditional SCF procedures.
  • To enable simulations of larger and more complex material systems.

Main Methods:

  • Benchmarking traditional diagonalization-based SCF solvers against density-matrix purification approaches.
  • Implementing a decomposition-type submatrix method for efficient computation.
  • Utilizing graphical processing units (GPUs) for accelerated calculations.
  • Systematic variation of system size and computer hardware.

Main Results:

  • GPU acceleration achieved a 10-15-fold performance speedup, enabling simulations of larger systems.
  • The submatrix method reduced computational cost for systems with approximately 10^4 basis functions.
  • Acceptable numerical accuracy was maintained with the submatrix approach.

Conclusions:

  • The combination of GPU acceleration and the submatrix method significantly enhances the efficiency of tight-binding calculations.
  • This work pushes the boundaries of feasible system sizes in computational materials science.
  • The findings highlight the importance of hardware-algorithm interplay for future developments.