Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

lncRNA - Long Non-coding RNAs

lncRNA - Long Non-coding RNAs

In humans, more than 80% of the genome gets transcribed. However, only around 2% of the genome codes for proteins. The remaining part produces non-coding RNAs which includes ribosomal RNAs, transfer RNAs, telomerase RNAs, and regulatory RNAs, among other types. A large number of regulatory non-coding RNAs have been classified into two groups depending upon their length – small non-coding RNAs, such as microRNA, which are less than 200 nucleotides in length, and long non-coding RNA...

lncRNA - Long Non-coding RNAs

lncRNA - Long Non-coding RNAs

Accelerators

Accelerators

Accelerators in concrete serve as admixtures to speed up the hardening process, enabling the concrete to achieve early strength faster. Although accelerators do not necessarily impact the time it takes concrete to set, they reduce this time in practice. A common accelerator is calcium chloride, which is particularly useful for hastening early strength development in cold weather or for rapid repair jobs that require quick heat generation after mixing.
The effectiveness of calcium chloride can...

Nursing Code of Ethics

Nursing Code of Ethics

The Nursing Code of Ethics sets the ethical benchmark for the profession, and guides nurses in ethical analysis and decision making at the societal, organizational, and clinical levels. The code encompasses showing compassion and respect for the patient, their families, and communities in all circumstances while committing to providing patient-centered care. In addition, the code states that nurses must advocate for the patient by defending a cause or recommendation to protect their rights,...

Average Acceleration

Average Acceleration

The importance of understanding acceleration spans our day-to-day experiences, as well as the vast reaches of outer space and the tiny world of subatomic physics. In everyday conversation, to accelerate means to speed up. For instance, we are familiar with the acceleration of our car; the harder we apply our foot to the gas pedal, the faster we accelerate. The greater the acceleration, the greater the change in velocity over a given time. Acceleration is widely seen in experimental physics. In...

Instantaneous Acceleration

Instantaneous Acceleration

Acceleration is in the direction of the change in velocity, but it is not always in the direction of motion. When an object slows down, its acceleration is opposite to the direction of its motion. Although commonly referred to as deceleration, this causes confusion in our analysis as deceleration is not a vector, and does not point to a specific direction with respect to a coordinate system. Therefore, the term deceleration is not used. For example, when a subway train slows down, it...

You might also read

Related Articles

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

Sort by

Same author

High-Performance Mixed Models Based Genome-Wide Association Analysis with omicABEL software.

F1000Research·2015

Same author

Multilevel summation for dispersion: a linear-time algorithm for r(-6) potentials.

The Journal of chemical physics·2014

See all related articles

Search research articles

Related Experiment Video

Updated: Jan 28, 2026

Identification of Coding and Non-coding RNA Classes Expressed in Swine Whole Blood

Identification of Coding and Non-coding RNA Classes Expressed in Swine Whole Blood

Published on: November 28, 2018

Accelerating AIREBO: Navigating the Journey from Legacy to High-Performance Code.

Markus Höhnerbach¹, Paolo Bientinesi¹

¹High Performance and Automatic Computing Group, RWTH Aachen University, Aachen, Germany.

Journal of Computational Chemistry

|February 21, 2019

Summary

This summary is machine-generated.

This study refactored legacy scientific software, the AIREBO potential in LAMMPS, for improved performance and maintainability. The optimized code achieved significant speedups on modern hardware, demonstrating the value of complexity reduction and hardware abstraction.

Keywords:

AIREBO many-body potential molecular dynamics testing vectorization

More Related Videos

Dynamic Navigation in Endodontics: Guided Access Cavity Preparation by Means of a Miniaturized Navigation System

Dynamic Navigation in Endodontics: Guided Access Cavity Preparation by Means of a Miniaturized Navigation System

Published on: May 5, 2022

Dynamic Navigation for Dental Implant Placement

Dynamic Navigation for Dental Implant Placement

Published on: September 13, 2022

Related Experiment Videos

Last Updated: Jan 28, 2026

Identification of Coding and Non-coding RNA Classes Expressed in Swine Whole Blood

Identification of Coding and Non-coding RNA Classes Expressed in Swine Whole Blood

Published on: November 28, 2018

Dynamic Navigation in Endodontics: Guided Access Cavity Preparation by Means of a Miniaturized Navigation System

Dynamic Navigation in Endodontics: Guided Access Cavity Preparation by Means of a Miniaturized Navigation System

Published on: May 5, 2022

Dynamic Navigation for Dental Implant Placement

Dynamic Navigation for Dental Implant Placement

Published on: September 13, 2022

Area of Science:

Computational materials science
Scientific software engineering

Background:

Legacy scientific software often prioritizes domain-specific features over maintainability and performance.
Architecture-specific optimizations can lead to code that is difficult to maintain and port.

Purpose of the Study:

To optimize the AIREBO potential within LAMMPS, addressing its complex computational kernels.
To demonstrate an approach for improving scientific software through complexity-reducing refactoring and hardware abstraction.

Main Methods:

Refactoring a C++ port of a Fortran code for the AIREBO potential.
Implementing hardware abstraction, KNC-hybridization, vectorization, and scalability.
Supporting both full and reduced precision calculations.
Conducting extensive testing to identify and fix bugs in the original code.

Main Results:

Achieved performance-portable, optimized code supporting full and reduced precision.
Identified and fixed bugs within the original AIREBO potential code through rigorous testing.
Sustained speedups of over 4x on KNL and 3x on Skylake architectures for large-scale, full-precision runs.

Conclusions:

Complexity-reducing refactoring and hardware abstraction are effective strategies for optimizing legacy scientific software.
The optimized AIREBO potential offers significant performance gains, enhancing its usability in large-scale simulations.
Systematic optimization of complex computational kernels is feasible and yields substantial improvements.