Ruijun Zhao</titile> </head> <body text="#000000" link="#B1946C" vlink="#6F6F6F" alink="#818501" bgcolor="#FFFFFF" topmargin="1"> <HR> <H1> Maximum Flux Transition Paths of Conformational Change </H1> <H2>Project description</H2> Given two metastable states A and B of a biomolecular system, the problem is to calculate the likely paths of the transition from A to B. Such a calculation is more informative and more manageable if done for a reduced set of collective variables chosen so that paths cluster in collective variable space. The maximum flux transition path (MFTP) is defined as a path that crosses each isocommittor at a point which (locally) has the highest crossing rate of distinct reactive trajectories. Such a path is nearer to an ideal path than others that have been proposed with the possible exception of the finite-temperature string method path. <br><br> In particular, the MFTP is a finite-temperature correction to the minimum free energy path. <H2> Python code for the MFTP </H2> <ul> <li> The main module mftp.py can be downloaded from <a href = "mftp.py">here</a> <br> <li> Please refer to <a href = "README.txt">README.txt</a> to learn more about how to use this module. <br> <li> Click <a href="example.html"> here </a> to see examples </ul> <H2> Paper </H2> <ul> <li> Click <a href = "0yZhSS.pdf"> here</a> to download the paper. </ul> <HR> </body> </html>