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

Parallel Resonance01:23

Parallel Resonance

557
The parallel RLC circuit is an arrangement where the resistor (R), inductor (L), and capacitor (C) are all connected to the same nodes and, as a result, share the same voltage across them. The parallel RLC circuit is analyzed in terms of admittance (Y), which reflects the ease with which current can flow. The admittance is given by:
557
Parallel Processing01:20

Parallel Processing

713
The brain processes sensory information rapidly due to parallel processing, which involves sending data across multiple neural pathways at the same time. This method allows the brain to manage various sensory qualities, such as shapes, colors, movements, and locations, all concurrently. For instance, when observing a forest landscape, the brain simultaneously processes the movement of leaves, the shapes of trees, the depth between them, and the various shades of green. This enables a quick and...
713
Inertial Frames of Reference01:03

Inertial Frames of Reference

8.8K
Newton’s first law is usually considered to be a statement about reference frames. It provides a method for identifying a special type of reference frame: the inertial reference frame. In principle, we can make the net force on a body zero. If its velocity relative to a given frame is constant, then that frame is said to be inertial. So, by definition, an inertial reference frame is a reference frame where Newton's first law holds valid. Newton's first law applies to objects with...
8.8K
Non-inertial Frames of Reference01:27

Non-inertial Frames of Reference

7.2K
A reference frame accelerating or decelerating relative to an inertial frame is a non-inertial frame. To help understand this, consider what taking off in an airplane, turning a corner in a car, riding a merry-go-round, and the circular motion of a tropical cyclone all have in common. All these systems are accelerating, decelerating, or rotating relative to the Earth; hence, they all are non-inertial frames. All these systems exhibit inertial forces, which merely seem to arise from motion,...
7.2K
Resistors In Parallel01:23

Resistors In Parallel

6.1K
Resistors are in parallel when one end of all the resistors are connected to a continuous wire of negligible resistance and the other end of all the resistors are also connected to one another through a continuous wire of negligible resistance. In the case of a parallel configuration, the potential drop across each resistor is the same. Current through each resistor can be found using Ohm’s law, I = V/R, where the voltage is constant across each resistor. The sum of the individual currents...
6.1K
Vector Components in the Cartesian Coordinate System01:29

Vector Components in the Cartesian Coordinate System

27.5K
Vectors are usually described in terms of their components in a coordinate system. Even in everyday life, we naturally invoke the concept of orthogonal projections in a rectangular coordinate system. For example, if someone gives you directions for a particular location, you will be told to go a few km in a direction like east, west, north, or south, along with the angle in which you are supposed to move. In a rectangular (Cartesian) xy-coordinate system in a plane, a point in a plane is...
27.5K

You might also read

Related Articles

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

Sort by
Same author

Author Correction: Biophysical prediction of protein-peptide interactions and signaling networks using machine learning.

Nature methods·2026
Same author

AlphaFold as a prior: experimental structure determination conditioned on a pretrained neural network.

Nature methods·2026
Same author

AlphaFold as a Prior: Experimental Structure Determination Conditioned on a Pretrained Neural Network.

bioRxiv : the preprint server for biology·2025
Same author

From Mechanistic Interpretability to Mechanistic Biology: Training, Evaluating, and Interpreting Sparse Autoencoders on Protein Language Models.

bioRxiv : the preprint server for biology·2025
Same author

Mapping variant effects on anti-tumor hallmarks of primary human T cells with base-editing screens.

Nature biotechnology·2024
Same author

OpenFold: retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization.

Nature methods·2024

Related Experiment Video

Updated: Jan 31, 2026

Massively Parallel Reporter Assays in Cultured Mammalian Cells
11:03

Massively Parallel Reporter Assays in Cultured Mammalian Cells

Published on: August 17, 2014

22.4K

Parallelized Natural Extension Reference Frame: Parallelized Conversion from Internal to Cartesian Coordinates.

Mohammed AlQuraishi1,2

  • 1Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, 02115.

Journal of Computational Chemistry
|January 8, 2019
PubMed
Summary

A new algorithm, parallelized Natural Extension Reference Frame (pNeRF), significantly speeds up polymer simulations by enabling parallel processing along polymer chains. This enhances computational efficiency in molecular modeling and machine learning workflows.

Keywords:
internal coordinatesmachine learningmolecular dynamicsmolecular mechanicsprotein structure

More Related Videos

Terahertz Microfluidic Sensing Using a Parallel-plate Waveguide Sensor
07:28

Terahertz Microfluidic Sensing Using a Parallel-plate Waveguide Sensor

Published on: August 30, 2012

11.2K
Ubiquitin Chain Analysis by Parallel Reaction Monitoring
08:33

Ubiquitin Chain Analysis by Parallel Reaction Monitoring

Published on: June 17, 2020

4.0K

Related Experiment Videos

Last Updated: Jan 31, 2026

Massively Parallel Reporter Assays in Cultured Mammalian Cells
11:03

Massively Parallel Reporter Assays in Cultured Mammalian Cells

Published on: August 17, 2014

22.4K
Terahertz Microfluidic Sensing Using a Parallel-plate Waveguide Sensor
07:28

Terahertz Microfluidic Sensing Using a Parallel-plate Waveguide Sensor

Published on: August 30, 2012

11.2K
Ubiquitin Chain Analysis by Parallel Reaction Monitoring
08:33

Ubiquitin Chain Analysis by Parallel Reaction Monitoring

Published on: June 17, 2020

4.0K

Area of Science:

  • Computational chemistry
  • Polymer science
  • Molecular modeling

Background:

  • Converting polymer parameterization from internal to Cartesian coordinates is crucial for molecular modeling.
  • The Natural Extension Reference Frame (NeRF) algorithm is commonly used but not parallelizable along a polymer's length.
  • This limits computational efficiency for long polymer chains.

Purpose of the Study:

  • Introduce a mathematically equivalent algorithm to NeRF that is parallelizable along a polymer's length.
  • Demonstrate the performance improvements of the new algorithm.
  • Assess its impact on machine learning workflows.

Main Methods:

  • Derived the parallelized Natural Extension Reference Frame (pNeRF) algorithm.
  • Performed empirical analysis comparing pNeRF to NeRF on modern GPUs and CPUs.
  • Evaluated the computational cost reduction in machine learning workflows involving backpropagation.

Main Results:

  • pNeRF achieves an order-of-magnitude speedup compared to NeRF on modern hardware.
  • The fractional computational cost of coordinate conversion in machine learning workflows is reduced from over two-thirds to approximately 10%.
  • An optimized TensorFlow implementation of pNeRF is publicly available.

Conclusions:

  • pNeRF offers significant computational advantages for polymer simulations.
  • The algorithm enhances efficiency in molecular modeling and machine learning applications.
  • pNeRF represents a substantial improvement over the standard NeRF algorithm for parallelizable polymer simulations.