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Burkhard Heim's Mass Formula - A collection of programs that calculate the mass of a variety of sub-atomic particles, based on work by the late Burkhard Heim.
http://www.heim-theory.com/
OpenTAU is a physics simulation package written in Java. It is intended for scientifical application as it incorporates FEM, FDM and MD and other simulation techniques. Also contains a fast math library.
ODE for Java is a binding between C dynamics library ODE (Open Dynamics Engine, http://ode.org) and Java. Separate packages provide among other things a Java3D integration and thus a scenegraph representation of selected ODE objects.
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A flexible and easy-to-use physics engine for 2d written in java. A similar engine for 3d in c++, and a AI able to interact with the physics engine, affecting the world, written in c++ using neural nets and genetic algorithms.
Computational modelling is a interdisciplinary field spanning many techniques and programming languages. AgenTools is a project dedicated to establishing increased modularity in scientific computing packages and a portal linking to other existing project