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

Fermi Level Dynamics

Fermi Level Dynamics

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...

Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving

Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving

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...

Parallel Processing

Parallel Processing

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...

Ampere-Maxwell's Law: Problem-Solving

Ampere-Maxwell's Law: Problem-Solving

A parallel-plate capacitor with capacitance C, whose plates have area A and separation distance d, is connected to a resistor R and a battery of voltage V. The current starts to flow at t = 0. What is the displacement current between the capacitor plates at time t? From the properties of the capacitor, what is the corresponding real current?
To solve the problem, we can use the equations from the analysis of an RC circuit and Maxwell's version of Ampère's law.
For the first part of the problem,...

Multimachine Stability

Multimachine Stability

Multimachine stability analysis is crucial for understanding the dynamics and stability of power systems with multiple synchronous machines. The objective is to solve the swing equations for a network of M machines connected to an N-bus power system.
In analyzing the system, the nodal equations represent the relationship between bus voltages, machine voltages, and machine currents. The nodal equation is given by:

Distribution of Molecular Speeds

Distribution of Molecular Speeds

The motion of molecules in a gas is random in magnitude and direction for individual molecules, but a gas of many molecules has a predictable distribution of molecular speeds. This predictable distribution of molecular speeds is known as the Maxwell-Boltzmann distribution. The distribution of molecular speeds in liquids is comparable to that of gases but not identical and can help to understand the phenomenon of the boiling and vapor pressure of a liquid. Consider that a molecule requires a...

You might also read

Related Articles

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

Sort by

Same author

Large-scale multi-site study shows no association between musical training and early auditory neural sound encoding.

Nature communications·2025

Same author

Musical training does not enhance neural sound encoding at early stages of the auditory system: A large-scale multisite investigation.

bioRxiv : the preprint server for biology·2024

Same author

Real-time data analysis for medical diagnosis using FPGA-accelerated neural networks.

BMC bioinformatics·2018

Same author

3D FFTs on a Single FPGA.

Proceedings IEEE International Symposium on Field-Programmable Custom Computing Machines : FCCM 2011 : 1-3 May 2011, Salt Lake City, Utah, USA. IEEE Symposium on FPGAs for Custom Computing Machines (19th : 2011 : Salt Lake City, Utah)·2015

Same author

GPU Optimizations for a Production Molecular Docking Code.

... IEEE conference on high performance extreme computing. IEEE Conference on High Performance Extreme Computing·2015

Same author

Parallel Discrete Molecular Dynamics Simulation With Speculation and In-Order Commitment.

Journal of computational physics·2011

Same journal

Mercury BLASTP: Accelerating Protein Sequence Alignment.

ACM transactions on reconfigurable technology and systems·2009

See all related articles

Search research articles

Related Experiment Video

Updated: Jun 1, 2026

Novel 3D/VR Interactive Environment for MD Simulations, Visualization and Analysis

Novel 3D/VR Interactive Environment for MD Simulations, Visualization and Analysis

Published on: December 18, 2014

Molecular Dynamics Simulations on High-Performance Reconfigurable Computing Systems.

Matt Chiu¹, Martin C Herbordt

¹Computer Architecture and Automated Design Laboratory; Department of Electrical and Computer Engineering; Boston University; Boston, MA 02215; Web: http://www.bu.edu/caadlab.

ACM Transactions on Reconfigurable Technology and Systems

|June 11, 2011

Summary

This summary is machine-generated.

High-performance reconfigurable computing (HPRC) can accelerate molecular dynamics (MD) simulations. This study shows FPGAs achieve an 80-fold speed-up for short-range force calculations, making them competitive for MD.

More Related Videos

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

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

Published on: August 22, 2025

Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package

Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package

Published on: September 17, 2021

Related Experiment Videos

Last Updated: Jun 1, 2026

Novel 3D/VR Interactive Environment for MD Simulations, Visualization and Analysis

Novel 3D/VR Interactive Environment for MD Simulations, Visualization and Analysis

Published on: December 18, 2014

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

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

Published on: August 22, 2025

Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package

Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package

Published on: September 17, 2021

Area of Science:

Computational Physics
High-Performance Computing
Reconfigurable Computing

Background:

Molecular Dynamics (MD) simulations are computationally intensive.
High-performance reconfigurable computing (HPRC) offers potential for MD acceleration.
The competitiveness of HPRC against multicore processors and GPUs for MD is under investigation.

Purpose of the Study:

To evaluate the feasibility and performance of using FPGAs for MD simulations.
To optimize the short-range force calculation kernel, a critical component of MD.
To investigate novel filtering techniques for particle pairs with negligible forces.

Main Methods:

Systematic exploration of the force pipeline design space, including arithmetic algorithms, modes, and precision.
Implementation and evaluation of a novel particle space partitioning method for efficient filtering.
Mapping computational work onto FPGA pipelines for optimized performance.

Main Results:

Optimizations and simplifications were explored, with some found to have minimal impact on simulation quality.
A highly efficient zero-force particle pair filtering method was developed, utilizing a small fraction of FPGA resources.
Eight force pipelines operating at ~200 MHz were successfully implemented on an Altera Stratix-III EP3ES260 FPGA, achieving 95% efficiency.

Conclusions:

FPGAs can achieve significant speed-ups for the critical short-range force calculation in MD simulations.
The developed methods demonstrate the potential for FPGAs to be highly competitive for accelerating MD.
This research contributes to advancing the use of HPRC in scientific computing.