KMC-KaiC

This code is a dedicated Kinetic Monte Carlo (KMC) algorithm which simulates a model of the post-translational Kai circadian clock.
The code allows you to simulate the Kai system at the level of individual KaiC hexamers and monomers and explicitly tracks the turnover of every ATP nucleotide. Apart from ATP hydrolysis, all reactions obey detailed balance.

The application of the code is described in our article titled "A Thermodynamically consistent model of the post-translational Kai circadian clock", which is freely available at the open access journal PLOS Computational Biology:

https://doi.org/10.1371/journal.pcbi.1005415

*UPDATE* We made a fully reversible version of our model, including the inverse reactions for ATP hydrolysis. This makes it possible to run the model at thermodynamic equilibrium. This version of the model can be downloaded under KMC_KaiC_Rev.zip.

If you like to use our model for your own research, please cite our PLoS Computational Biology paper.

Project Samples

Project Activity

See All Activity >

License

GNU General Public License version 3.0 (GPLv3)

Follow KMC-KaiC

KMC-KaiC Web Site

Other Useful Business Software

Gen AI apps are built with MongoDB Atlas

The database for AI-powered applications.

MongoDB Atlas is the developer-friendly database used to build, scale, and run gen AI and LLM-powered apps—without needing a separate vector database. Atlas offers built-in vector search, global availability across 115+ regions, and flexible document modeling. Start building AI apps faster, all in one place.

Start Free

Rate This Project

User Reviews

Be the first to post a review of KMC-KaiC!

Additional Project Details

Operating Systems

Linux

Languages

English

Intended Audience

Science/Research

User Interface

Command-line

Programming Language

C++

Related Categories

C++ Simulation Software

Registered

2017-02-07

Similar Business Software

Innoslate

SPEC Innovations’ flagship model-based systems engineering solution can help your team reduce time-to-market, cost, and risk on even some of the most complex systems. This cloud or on-premise application uses a modern web browser, with an intuitive graphical user interface. Innoslate’s full...

See Software
Azore CFD

AzoreCFD has been a trusted, cutting-edge software tool since 2007. Azore focuses on analysis, design, engineering, and on obtaining precise, and quick results. Customers use Azore for applications that include: industrial flows, aerodynamics, thermal mixing, conjugate heat transfer, gas species...

See Software
OpenModelica

OpenModelica is an open source modeling and simulation environment based on the Modelica language, intended for industrial and academic use. Its development is supported by the Open Source Modelica Consortium (OSMC), a non-profit organization. The platform aims to provide a comprehensive...

See Software
MapleSim

From digital twins for virtual commissioning to system-level models for complex engineering design projects, MapleSim is an advanced modeling tool that helps you reduce development time, lower costs, and diagnose real-world performance issues. Remove vibrations with better control code, not...

See Software
Simulink

Design and simulate your system in Simulink before moving to hardware. Explore and implement designs that you wouldn’t otherwise consider – without having to write C, C++, or HDL code. Explore a wide design space by modeling the system under test and the physical plant. Your entire team can use...

See Software
Analytic Solver

Analytic Solver Optimization - 100% upward compatible from the Excel Solver - handles every type and size of the conventional optimization problem (without uncertainty). Unlike other optimization software, it algebraically analyzes your model structure and maximally exploits multiple cores in...

See Software