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

Simplified Synchronous Machine Model01:30

Simplified Synchronous Machine Model

924
The Synchronous Machine Model is a fundamental tool in analyzing and ensuring the transient stability of power systems. This model simplifies the representation of a synchronous machine under balanced three-phase positive-sequence conditions, assuming constant excitation and ignoring losses and saturation. The model is pivotal for understanding the behavior of synchronous generators connected to a power grid, particularly during transient events.
In this model, each generator is connected to a...
924
Neural Circuits01:25

Neural Circuits

3.3K
Neural circuits and neuronal pools are two of the main structures found in the nervous system. Neural circuits are networks of neurons that work together to carry out a specific task or process. They consist of interconnected neurons and glial cells, which provide structural and metabolic support.
Neuronal pools are collections of nerve cells with similar functions and interact through chemical and electrical signals. These pools include both interneurons (the central neural circuit nodes that...
3.3K
Synthetic Biology02:55

Synthetic Biology

5.8K
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...
5.8K
Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving01:29

Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving

411
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...
411
Second-Order Circuits01:17

Second-Order Circuits

4.9K
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...
4.9K
Assembly of Signaling Complexes01:30

Assembly of Signaling Complexes

7.2K
Multiprotein signaling complexes are formed in a dynamic process involving protein-protein interactions at the cytoplasmic domain of transmembrane receptors or enzymatic and non-enzymatic proteins associated with the receptor. These complexes ensure the activation and propagation of intracellular signals that regulate cell functions.
Interaction domains in cell signaling
Interaction domains recognize exposed features of their binding partners containing post-translationally modified sequences,...
7.2K

You might also read

Related Articles

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

Sort by
Same author

Estimating genotype-tissue specific gene expression using hybrid deep learning.

Communications biology·2026
Same author

Optimal solution to the set cover problem with a vicinity constraint for estimating genotype tissue expression profiles.

Bioinformatics advances·2025
Same author

Nearby and non-nested genes in the human genome have more similar genotype tissue expression.

PloS one·2024
Same author

Design of Synthetic Mammalian Promoters Using Highly Palindromic Subsequences.

ACS synthetic biology·2022
Same author

Design of a synthesis-friendly hypoxia-responsive promoter for cell-based therapeutics.

Engineering in life sciences·2021
Same author

Creation of a synthesis-friendly inflammation-inducible promoter suitable for cell therapy.

Integrative biology : quantitative biosciences from nano to macro·2021
Same journal

A Multitask Prediction Framework for CircRNAs, Drugs, and Diseases Based on Multi-View Information Integration and Graph Contrastive Learning.

ACS synthetic biology·2026
Same journal

Engineering Modular Cargo Loading Strategies for Carboxysome-Derived Protein Particles.

ACS synthetic biology·2026
Same journal

Suppression of Salmonella Effectors with CRISPRi Controls the Immune Response to Bacterial Therapies.

ACS synthetic biology·2026
Same journal

Rational Design of Linalool Dehydratase-Isomerase Enables Efficient Conversion of Phytol to Neophytadiene.

ACS synthetic biology·2026
Same journal

<i>De Novo</i> Biosynthesis of Polyphyllin V in <i>Nicotiana benthamiana</i> through Pathway Reconstruction and UDP-Sugar Engineering.

ACS synthetic biology·2026
Same journal

Rapid and Continuous Directed Evolution in <i>Vibrio natriegens</i> Utilizing an <i>In Vivo</i> Hypermutation System.

ACS synthetic biology·2026
See all related articles

Related Experiment Video

Updated: Apr 14, 2026

Synaptic Microcircuit Modeling with 3D Cocultures of Astrocytes and Neurons from Human Pluripotent Stem Cells
08:48

Synaptic Microcircuit Modeling with 3D Cocultures of Astrocytes and Neurons from Human Pluripotent Stem Cells

Published on: August 16, 2018

12.9K

Prompt-Only Gene-Circuit Modeling with a Large Language Model Simulates the synNotch Spheroids.

Kaiwen Chen1, Kevin Truong1,2

  • 1Edward S. Rogers, Sr. Department of Electrical and Computer Engineering, University of Toronto, 10 King's College Circle, Toronto, Ontario M5S 3G4, Canada.

ACS Synthetic Biology
|April 13, 2026
PubMed
Summary
This summary is machine-generated.

Large language models (LLMs) can now generate complex biological simulations from natural language prompts, simplifying computational modeling. This approach accelerates the exploration of developmental biology principles by non-specialists.

Keywords:
CompuCell3Dcellular Potts modelcomputational modelinglarge language modelsynNotchsynthetic morphogenesis

More Related Videos

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

10.9K
Computational Modeling of Retinal Neurons for Visual Prosthesis Research - Fundamental Approaches
10:50

Computational Modeling of Retinal Neurons for Visual Prosthesis Research - Fundamental Approaches

Published on: June 21, 2022

2.3K

Related Experiment Videos

Last Updated: Apr 14, 2026

Synaptic Microcircuit Modeling with 3D Cocultures of Astrocytes and Neurons from Human Pluripotent Stem Cells
08:48

Synaptic Microcircuit Modeling with 3D Cocultures of Astrocytes and Neurons from Human Pluripotent Stem Cells

Published on: August 16, 2018

12.9K
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

10.9K
Computational Modeling of Retinal Neurons for Visual Prosthesis Research - Fundamental Approaches
10:50

Computational Modeling of Retinal Neurons for Visual Prosthesis Research - Fundamental Approaches

Published on: June 21, 2022

2.3K

Area of Science:

  • Computational Biology
  • Developmental Biology
  • Systems Biology

Background:

  • Quantitative simulations of morphogenesis are crucial for understanding gene regulatory circuits.
  • Constructing these simulations is technically demanding, posing a barrier for many researchers.

Purpose of the Study:

  • To develop a prompt-only pipeline using large language models (LLMs) to automatically generate CompuCell3D (CC3D) simulations from natural-language biological specifications.
  • To assess the LLM's ability to capture key biological dynamics in simulations without manual programming.

Main Methods:

  • Utilized a large language model (LLM) to generate CompuCell3D (CC3D) code from natural language descriptions.
  • Employed the synNotch spheroid assay as a benchmark for validating simulation accuracy.
  • Iteratively refined simulation parameters, such as incorporating a cumulative contact-duration threshold, to address observed discrepancies.

Main Results:

  • LLM-generated CC3D code successfully simulated contact-dependent signaling, cadherin-mediated adhesion, and multicellular sorting dynamics.
  • Initial simulations showed spheroid fragmentation, indicating premature signaling as a failure mode.
  • Implementing a contact-duration threshold rescued single-spheroid formation, highlighting the importance of sustained cell-cell interactions.

Conclusions:

  • Conversational LLM guidance significantly accelerates multiscale modeling by simplifying the CompuCell3D (CC3D) workflow.
  • This framework empowers nonspecialists to test gene-circuit hypotheses in silico.
  • The approach offers a generalizable method for rapid, mechanism-level exploration of developmental design principles.