Programs are available here for analysis and simulation of movement of flagella. All are Macintosh programs; some have accompanying source code. These are not set up for anonymous FTP, but can be downloaded with Netscape 3.0. These files are sea.hqx files that will need Stufit Expander to translate after downloading.
Flagsim is a program for simulating the movement of a model flagellum in which the direction of active sliding is controlled by the curvature of the flagellum. It is described in detail in publication #84. Only the PPC version is currently maintained.
Download FlagsimPPC (381kb. May 27, 1997)
Download Flagsim partial source code (62kb. May 27, 1997)
MacCB is a program for simulating the operation of motor enzymes such as myosin and dynein. It is described in detail in publication #116. Macintosh PowerPC and 68K versions are available, and partial source code listings are provided.
Download MacCB for PowerPC (424kb. May 27, 1997)
Download MacCB partial source code (46kb. May 27, 1997)
These programs are the ones used for modeling dynein cross-bridge behavior and a flagellar model with different inner and outer arm dynein models, in "Computer Simulation of Flagellar Movement VII" (publication # 125). They are Macintosh Power PC programs. They have been running most recently on Mac Power PC 7600 and 9500 with 233 mHz 604e accelerator cards, using OS 8.5.
Download crossbridge modelling program (969kb. September 1, 1998)
Download flagellar modelling program and required dynein model files (1.3mb. September 1, 1998)
FlagFitter is a program for parameter extraction from shear curves obtained from a sequence of images of a moving flagellum. It is based on the methods in publication #79.The only version available is for Macintosh PowerPC. Partial source files are supplied for the Symantec C++ IDE (v. 8.5) and compiler.
Download FlagFitter (381 kb. July 3, 1997)
Download FlagFitter source code (309 kb. July 3, 1997)
A modified version of the public domain NIH Image program, which includes routines for tracing images of flagella (see publication #102) and outputting data for analysis by FlagFitter, is available, for Macintosh PowerPC only. Source code with my modifications is available, for use with the Metrowerks Pascal compiler. The January 29 version has been improved for working with free axonemes, where the fitting is started from a manually entered point. This version was compiled with the MW Pro4 Pascal Compiler.
Download modified NIHImage (527kb. January 29, 1999)
Download Pascal source code for modified NIHImage (651kb. January 29, 1999)
Two-headed motor model used in publication #126 "Stochastic simulation of processive and oscillatory sliding using a two-headed model for axonemal dynein." Cell Motil.
Download TwoHeads program file(February 3, 2000)
Modified cross-bridge modelling program for easier computation of two parallel models. Used for "Protein-protein ratchets: Stochastic simulation and application to processive enzymes", 2001.
Download CB2Models program file(January 29, 2001)
Flagsim3D is a flagellar simulation program for a flagellum that is able to bend in three dimensions, rather than being restricted to a plane. This is the version that was used for Publication #129, to demonstrate that local curvature control of active sliding is sufficient to generate quasi-helical bending waves. It has not been updated to give accurate results with external viscous resistances. This version is for Classic Mac PPC only.
Download Flagsim3D application.(March 22, 2002)
FlagsimX is a flagellar simulation program for a flagellum that is able to bend in three dimensions, rather than being restricted to a plane. This is the version that was used for Publication #130, to investigate oscillation and symmetry breaking in short flagella, using a mathematical formulation for active moment generation, and control by shear velocity to produce oscillation. This version is for MacOSX 10.3 "Panther"
Download FlagsimX application as Apple .zip file.
Download FlagsimX application as Stuffit .sitx file (smaller: save result to desktop and then use Stuffit to expand it.).(December 16, 2004)