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 Decoupled and DC Powerflow01:24

Fast Decoupled and DC Powerflow

916
The fast decoupled power flow method addresses contingencies in power system operations, such as generator outages or transmission line failures. This method provides quick power flow solutions, essential for real-time system adjustments. Fast decoupled power flow algorithms simplify the Jacobian matrix by neglecting certain elements, leading to two sets of decoupled equations:
916
The Power Flow Problem and Solution01:26

The Power Flow Problem and Solution

1.1K
Power flow problem analysis is fundamental for determining real and reactive power flows in network components, such as transmission lines, transformers, and loads. The power system's single-line diagram provides data on the bus, transmission line, and transformer. Each bus k in the system is characterized by four key variables: voltage magnitude Vk​, phase angle δk​, real power Pk​, and reactive power Qk​. Two of these four variables are inputs, while the power...
1.1K
Calculation of Electric Flux01:25

Calculation of Electric Flux

3.5K
Consider the electric field of an oppositely charged, parallel-plate system and an imaginary box between those plates. Let the bottom face of the box be ABCD, and the top face be FGHK. The electric field between the plates is uniform and points from the positive plate toward the negative plate. The calculation of this field's flux through the box's various faces shows that the net flux through the box is zero. Why does the flux cancel out here?
3.5K
Relation between Mathematical Equations and Block Diagrams01:20

Relation between Mathematical Equations and Block Diagrams

3.9K
In a spring-mass-damper system, the second-order differential equation describes the dynamic behavior of the system. When transformed into the Laplace domain under zero initial conditions, this equation can be effectively analyzed and manipulated. The transformation into the Laplace domain converts differential equations into algebraic equations, simplifying the process of isolating the output.
3.9K
Magnetostatic Boundary Conditions01:28

Magnetostatic Boundary Conditions

1.9K
An electric field suffers a discontinuity at a surface charge. Similarly, a magnetic field is discontinuous at a surface current. The perpendicular component of a magnetic field is continuous across the interface of two magnetic mediums. In contrast, its parallel component, perpendicular to the current, is discontinuous by the amount equal to the product of the vacuum permeability and the surface current. Like the scalar potential in electrostatics, the vector potential is also continuous...
1.9K
Boundary Conditions for Current Density01:25

Boundary Conditions for Current Density

1.5K
Current density becomes discontinuous across an interface of materials with different electrical conductivities. The normal component of the current density is continuous across the boundary.
1.5K

You might also read

Related Articles

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

Sort by
Same author

Modeling connectivity and sediment reduction with PROSEB: a study of prairie strips in agricultural catchments.

Journal of environmental management·2026
Same author

A Novel Eye- and Head-Tracking Interface for Digital Pathology Reduces Hand Movement and Improves Target Detection Accuracy.

Archives of pathology & laboratory medicine·2026
Same author

Biochemical phenotypes of acute kidney injury and their association with major adverse kidney events.

Renal failure·2026
Same author

Renal cell carcinoma with fibromyomatous stroma (RCC FMS) and with hemangioblastoma-like areas is part of the RCC FMS spectrum in patients with tuberous sclerosis complex.

Histopathology·2025
Same author

The Effect of Window Size on Pathologists' Search for Rare Elements in a Digital Pathology Setting.

Archives of pathology & laboratory medicine·2025
Same author

Identification of Distinct Visual Scan Paths for Pathologists in Rare-Element Search Tasks.

International journal of surgical pathology·2024
Same journal

OpenIMC: an open-source platform for analyzing single-cell and spatial proteomics by imaging mass cytometry.

BMC bioinformatics·2026
Same journal

NAP: an open source pipeline for cross-domain microbiome profiling using Nanopore sequencing-derived amplicon data.

BMC bioinformatics·2026
Same journal

SurvGME: an R package for survival analysis with graphical and measurement error models.

BMC bioinformatics·2026
Same journal

SimMapNet: a Bayesian framework for gene regulatory network inference using gene ontology similarities as external hint.

BMC bioinformatics·2026
Same journal

Dual channel drug-drug interactions extraction based on cross attention.

BMC bioinformatics·2026
Same journal

FeSseqdb: a curated sequence-level database and interpretable machine learning framework for identifying iron-sulfur proteins.

BMC bioinformatics·2026
See all related articles

Related Experiment Video

Updated: Apr 19, 2026

Surrogate Model Development for Digital Experiments in Welding
09:17

Surrogate Model Development for Digital Experiments in Welding

Published on: March 28, 2025

2.1K

DFBAlab: a fast and reliable MATLAB code for dynamic flux balance analysis.

Jose A Gomez1, Kai Höffner2, Paul I Barton3

  • 1Process Systems Engineering Laboratory, Massachusetts Institute of Technology, Cambridge, 02139, MA, USA. jagomezr@mit.edu.

BMC Bioinformatics
|December 19, 2014
PubMed
Summary
This summary is machine-generated.

DFBAlab, a new MATLAB simulator, reliably simulates complex dynamic cultures using unique exchange fluxes and an extended system to avoid common simulation failures. Its performance scales linearly with species models, outperforming other simulators.

More Related Videos

Particle Image Velocimetry Investigation of Hemodynamics via Aortic Phantom
06:26

Particle Image Velocimetry Investigation of Hemodynamics via Aortic Phantom

Published on: February 25, 2022

5.1K
Author Spotlight: Understanding Riverine Nitrogen Impacts and Primary Productivity for Effective Nutrient Management
05:04

Author Spotlight: Understanding Riverine Nitrogen Impacts and Primary Productivity for Effective Nutrient Management

Published on: July 14, 2023

854

Related Experiment Videos

Last Updated: Apr 19, 2026

Surrogate Model Development for Digital Experiments in Welding
09:17

Surrogate Model Development for Digital Experiments in Welding

Published on: March 28, 2025

2.1K
Particle Image Velocimetry Investigation of Hemodynamics via Aortic Phantom
06:26

Particle Image Velocimetry Investigation of Hemodynamics via Aortic Phantom

Published on: February 25, 2022

5.1K
Author Spotlight: Understanding Riverine Nitrogen Impacts and Primary Productivity for Effective Nutrient Management
05:04

Author Spotlight: Understanding Riverine Nitrogen Impacts and Primary Productivity for Effective Nutrient Management

Published on: July 14, 2023

854

Area of Science:

  • Biochemical Engineering
  • Computational Biology
  • Systems Biology

Background:

  • Dynamic Flux Balance Analysis (DFBA) is a key framework for simulating biochemical processes.
  • Existing DFBA simulators struggle with nonunique exchange fluxes and infeasible linear programs (LPs), leading to failures.
  • Static optimization (SOA), dynamic optimization (DOA), and direct approaches (DA) are common DFBA methods.

Purpose of the Study:

  • To present DFBAlab, a novel MATLAB-based simulator designed to overcome common challenges in DFBA.
  • To address issues of nonunique exchange fluxes and infeasible LPs in dynamic simulations.
  • To provide a reliable and efficient tool for simulating complex dynamic cultures.

Main Methods:

  • DFBAlab employs an LP feasibility problem to create an extended system.
  • Lexicographic optimization is utilized to ensure unique exchange fluxes.
  • The simulator handles differential-algebraic equation (DAE) systems and scales linearly with the number of species.

Main Results:

  • DFBAlab successfully simulates complex dynamic cultures with multiple species rapidly and reliably.
  • The simulator avoids failures caused by infeasible LPs during numerical integration.
  • DFBAlab demonstrates superior performance compared to COBRA and DyMMM in benchmark examples.

Conclusions:

  • Lexicographic optimization is crucial for defining unique exchange fluxes in dynamic systems.
  • DFBAlab's extended system provides a penalty function applicable to optimization algorithms.
  • The DFBAlab simulator offers a robust solution for DFBA, enhancing reliability and efficiency.