Molecular Motors

<h2 align=center> Welcome to the Molecular Motors Home at Northwestern University!</h2> <br><br> <table width="100%"><tr width="100%"><td><font size=4> <p> This site is devoted to the modeling and study of the dynamics and kinematics of molecular motors. Molecular motors are characterized by "the ability to convert chemical energy into mechanical force," hence providing motion or power for additional reactions. This site is being developed in conjunction with "Molecular Machines in Biology," a course offered each spring quarter by <a href="http://othello.mech.northwestern.edu/lichter/" target="_top">Professor Seth Lichter</a> of the Mechanical Engineering Department at Northwestern University.</td> <td><img src="images/top1.JPG" name="Top1" alt="Field of F0F1 Rotors"></td></tr></table> <br><p> The models are based, in part, on problem sets from the two chapters "Molecular Motors: Theory" and "Molecular Motors: Examples," by A. Mogilner, T. Elston, H.-Y. Wang, and G. Oster in <i>Computational Cell Biology</i>, by C. P. Fall, E. Marland, J. Tyson, and J. Wagner, Eds., Springer, N.Y. (2002). These two chapters are an excellent introduction to numerical modeling of molecular motors. <br><p> At the bottom of this page you will find our main menu; your browser does not support frames, or they are not enabled at the moment, so you will have to use your browser's back button to navigate back to this page. The subsequent five links will bring you to the main computational models of the listed processes. All models use Java applets, so you will need a Java-capable web browser to view them. The ATPase link will take you to a full explanation of both the processes involved in ATP Synthase, including the details of the simulation on this website, and the final link will provide a list of webpages which are interesting and helpful to those desiring more information about Molecular Motors in Biology. Please keep your browser updated; check for updates at the homepages for <a href="http://www.netscape.com/" target="_blank">Netscape</a>, <a href="http://www.microsoft.com/" target="_blank">Microsoft</a>, or <a href="http://www.mozilla.org/" target="_blank">Mozilla</a>. At this time the models have been tested on the most recent versions of Netscape for Linux, Mozilla for Linux, and MSIE for Mac OSX and Windows XP. There is a known bug in Netscape which results in difficulty to recognize the Java applet's class. This bug is fixed in versions 5 and higher, so please be sure to update your browser. <br><p>For the programmer and non-programmer alike, two heavily commented versions of the models' code have been printed: one in Java, one in MATLAB. The Java code can be pasted into any text editor and compiled as an applet, and the MATLAB code can be pasted into a new MATLAB .m file and run immediately. Often examining the code is more helpful to understanding than an explanation of the models themselves. <br><h3>News:</h3> <p>Stop buttons have now been added to the final two models to assist those with slower computers. Due to the calling of an external function, the simulation cannot be stopped during the inverting of any matrices. It will, however, break immediately afterwards if the stop button is pressed. <br><table width="100%"><tr width="100%"><td><img src="images/top2.GIF" name="ATPase1" alt="ATPase Motor Up Close"></td> <td><p><font size=4> The models are all are functioning, and are being tested at the moment. If you encounter any problems while using them or if you find any broken links please <a href="mailto:zmarshal@uclink.berkeley.edu">notify the webmaster</a>. Thank you for your patience with the developement of both the models and the site. Enjoy using all of the working models!! These pages are best viewed in the highest resolution your monitor allows, however the models will function on quite small screens. <br><h3>Thanks:</h3> <p> The final two models, the F0 ATPase rotor engine and the polymerization ratchet, both use the JAMA linear algebra package. The package was written to be "the standard matrix class for Java", and is being proposed as such to Sun. It is currently available <a href="http://math.nist.gov/javanumericas/jama/" target="_blank">here</a>.</td></tr></table> <br><p> Special thanks to Yong Chen, <a href="http://pubweb.nwu.edu/~jap183/index.html" target="_top">John Pedersen</a>, and <a href="http://www.fluids.mech.nwu.edu/~n-sharma/" target="_top">Nitin Sharma</a> for their help, especially for making the MATLAB codes. Further course acknowledgements are <a href="#" onClick="window.open('credits.html','credits');return false;">here</a>. <br><p> This site was constructed by Zach Marshall, under a Research Experience for Undergraduates (REU) grant from the NSF and the generosity of the <a href="http://www.mccormick.northwestern.edu/giving/givingsociety.html" target="_top">Walter P. Murphy Society at Northwestern University</a>. <a href="mailto:zmarshal@uclink.berkeley.edu">Contact the webmaster</a>. <br><br><p><font size=3> The above pictures are copyrighted by the Montemagno Research Group and Cornell University, 2000. The original page on F0F1 motors from which they came is available <a href="http://univrelations.cornell.edu/NewSciLife/ss-molecules_of_life.html" target="_top">here</a>. Java is a trademark of <a href="http://java.sun.com" target="_blank">Sun Microsystems</a>. The counter on this page is courtesy of <a href="http://www.digits.com/" target="_blank">Digits</a>. <br> <br> <h3 align="center">Main Menu</h3> <br><font size=3> <p align=center><a href="pgm.html">Polymer Growth</a> <br><p align=center><a href="wall.html">Polymerization Ratchet</a> <br><p align=center><a href="pmm.html">Protein Motion in a Potential Well</a> <br><p align=center><a href="pot.html">Diffusion Against a Constant Force</a> <br><p align=center><a href="f0model.html">F0-ATPase</a> <br><p align=center><a href="intro.html">ATPase Intro</a> <br><p align=center><a href="links.html">Links</a> <br> <br> <p align=center>You are visitor <IMG SRC="http://counter.digits.com/wc/-d/4/MotorCounter" align=middle width=60 height=20 border=0 hspace=4 vspace=2> <br><br><p align=center><a href="http://www.webmonkey.com/" target="_blank"><img height=22 width=136 src="images/webmonkey.gif"></a> <a href="http://www.digits.com" target="_blank"><img height=28 width=267 src="images/wc.gif"></a>