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

Synthetic Biology02:55

Synthetic Biology

5.2K
Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
Golden rice
Golden rice is a genetically modified...
5.2K
Second-Order Circuits01:17

Second-Order Circuits

2.8K
Integrating two fundamental energy storage elements in electrical circuits results in second-order circuits, encompassing RLC circuits and circuits with dual capacitors or inductors (RC and RL circuits). Second-order circuits are identified by second-order differential equations that link input and output signals.
Input signals typically originate from voltage or current sources, with the output often representing voltage across the capacitor and/or current through the inductor. For example, in...
2.8K
First-Order Circuits01:15

First-Order Circuits

3.0K
First-order electrical circuits, which comprise resistors and a single energy storage element - either a capacitor or an inductor, are fundamental to many electronic systems. These circuits are governed by a first-order differential equation that describes the relationship between input and output signals.
One common example of a first-order circuit is the RC (resistor-capacitor) circuit. These circuits are used in relaxation oscillators such as neon lamp oscillator circuits. When voltage is...
3.0K
Transformers with Off-Nominal Turns Ratios01:25

Transformers with Off-Nominal Turns Ratios

323
In scenarios involving parallel transformers with disparate ratings, developing per-unit models requires accommodating off-nominal turns ratios. This situation arises when the selected base voltages are not proportional to the transformer’s voltage ratings. Consider a transformer where the rated voltages are related by the term a. If the chosen voltage bases satisfy a relationship involving term b, term c is defined as the ratio of these bases. This ratio is then substituted into the...
323
Source Transformation for AC Circuits01:11

Source Transformation for AC Circuits

870
The process of source transformation in the frequency domain entails the conversion of a voltage source, positioned in series with an impedance, into a current source that is parallel to an impedance, or the other way around. It is essential to maintain the following relationships while transitioning from one source type to another.
870
Block Diagram Reduction01:22

Block Diagram Reduction

394
The process of deriving the transfer function of a control system often involves reducing its block diagram to a single block. This simplification can be achieved through a series of strategic operations, including relocating branch points and comparators. These operations preserve the overall function of the system while allowing for easier manipulation and combination of blocks.
The first step in this process is the identification and relocation of a branch point. A branch point, where a...
394

You might also read

Related Articles

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

Sort by
Same author

A Bacteroides synthetic biology toolkit to build an in vivo malabsorption biosensor.

Cell·2026
Same author

Basic Science and Pathogenesis.

Alzheimer's & dementia : the journal of the Alzheimer's Association·2025
Same author

In mouse and in vitro models, bowel preparation promotes pathogen colonization, translocation, and exacerbation of inflammation.

Cell reports. Medicine·2025
Same author

Exploiting fluctuations in gene expression to detect causal interactions between genes.

eLife·2025
Same author

Open-space microfluidics as a tool to study signaling dynamics.

Lab on a chip·2025
Same author

<i>In Vitro</i> Enzyme Self-Selection Using Molecular Programs.

ACS synthetic biology·2024
Same journal

Isolation of Mesenchymal Stem Cell-Derived Extracellular Vesicles.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Modeling Melanoma Immune Surveillance by CAR-T Cells in Human Skin Organoids.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Stepwise Optimization of a Matrigel-Based In Vitro Angiogenesis Assay for Reproducible and Quantifiable 2D-Tube Formation Using HUVECs.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Quantifying Mechanical Properties of Fresh Ovarian Tissue with Optical Brillouin Microscopy.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

3D Chromatin Architecture During Early Development: New Methods and New Findings.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Metabolic Plasticity in Embryogenesis Throughout the Lens of NAD<sup></sup>.

Methods in molecular biology (Clifton, N.J.)·2026
See all related articles

Related Experiment Video

Updated: Nov 22, 2025

A Multilayer Microfluidic Platform for the Conduction of Prolonged Cell-Free Gene Expression
11:23

A Multilayer Microfluidic Platform for the Conduction of Prolonged Cell-Free Gene Expression

Published on: October 6, 2019

10.5K

Using Models to (Re-)Design Synthetic Circuits.

Giselle McCallum1, Laurent Potvin-Trottier2,3,4

  • 1Department of Biology, Concordia University, Montreal, QC, Canada.

Methods in Molecular Biology (Clifton, N.J.)
|January 6, 2021
PubMed
Summary
This summary is machine-generated.

This guide helps biologists create mathematical models for synthetic gene circuits, accounting for molecule numbers and stochastic gene expression. It details simulation methods and shows how modeling and experiments improve synthetic circuit design for precision and robustness.

Keywords:
Biological oscillationsDynamical gene networkGillespie algorithmMathematical modelingStochastic simulationsSynthetic biologySynthetic gene circuitsSynthetic oscillator

More Related Videos

Gene Digital Circuits Based on CRISPR-Cas Systems and Anti-CRISPR Proteins
10:46

Gene Digital Circuits Based on CRISPR-Cas Systems and Anti-CRISPR Proteins

Published on: October 18, 2022

2.1K
Modeling Biological Membranes with Circuit Boards and Measuring Electrical Signals in Axons: Student Laboratory Exercises
13:56

Modeling Biological Membranes with Circuit Boards and Measuring Electrical Signals in Axons: Student Laboratory Exercises

Published on: January 18, 2011

23.0K

Related Experiment Videos

Last Updated: Nov 22, 2025

A Multilayer Microfluidic Platform for the Conduction of Prolonged Cell-Free Gene Expression
11:23

A Multilayer Microfluidic Platform for the Conduction of Prolonged Cell-Free Gene Expression

Published on: October 6, 2019

10.5K
Gene Digital Circuits Based on CRISPR-Cas Systems and Anti-CRISPR Proteins
10:46

Gene Digital Circuits Based on CRISPR-Cas Systems and Anti-CRISPR Proteins

Published on: October 18, 2022

2.1K
Modeling Biological Membranes with Circuit Boards and Measuring Electrical Signals in Axons: Student Laboratory Exercises
13:56

Modeling Biological Membranes with Circuit Boards and Measuring Electrical Signals in Axons: Student Laboratory Exercises

Published on: January 18, 2011

23.0K

Area of Science:

  • Systems Biology
  • Synthetic Biology
  • Computational Biology

Background:

  • Mathematical models are crucial for designing synthetic gene circuits.
  • Understanding gene network dynamics requires considering stochastic gene expression due to low molecule numbers in cells.
  • Previous models often assumed high molecule counts, neglecting cellular stochasticity.

Purpose of the Study:

  • To provide a guide for biologists on building and using gene network models.
  • To analyze dynamical properties of synthetic and natural gene networks.
  • To incorporate stochastic gene expression into modeling for more accurate predictions.

Main Methods:

  • Describing model construction and determining appropriate levels of detail.
  • Demonstrating deterministic differential equation simulations for high molecule counts.
  • Providing a tutorial on stochastic Gillespie simulations, including algorithm coding and examples.

Main Results:

  • A comprehensive guide for modeling gene networks, including stochastic effects.
  • Demonstration of how quantitative experiments combined with modeling can guide iterative circuit redesign.
  • Successful redesign of a synthetic oscillator (repressilator) for enhanced precision and robustness.

Conclusions:

  • The presented toolkit enables synthetic biologists to build more precise and robust synthetic circuits.
  • This approach deepens the understanding of gene regulatory network dynamics.
  • Mathematical modeling, especially stochastic simulations, is essential for advancing synthetic biology.