Wenjin Li, Personal Home Page

Interested Fields

• Mechanochemistry

Like humans, Cell can adjust their behavior while interacting with the environment. The interaction between cell and their environment was proposed to generate mechanical stimuli and coupled with some vital functions of the cell. How do cell sense, conduct and response to those mechanical stimuli? One of mechanism could be that (bio)chemical reactions within the cell can be regulated by the external mechanical force and then the cell behavior. Here, we mainly focus on the theoretical description of how force regulate (bio)chemical reactions.

• The mechanism of GTP hydrolysis

How is the GTP hydrolyzed under different environments? There are two major hypotheses: associative pathway and dissociative pathway.

• Force Distribution Analysis in Quantum System

Force distribution analysis (FDA) was developed to see how the external force distributed within a molecule, which provide an alternative way analysis the response of a system to mechanical force. However, the current version of FDA can only be applied to classic molecular system. In some cases, FDA is asked to be applied to a quantum system and the development of FDA in QM system is necessary.

• Multi-dimensional Pontential of Mean Constraint Force

Potential of Mean Constraint Force (PMCF) is one of the methods for free energy calculation. For it can only be used to evaluate the free energy landscape along one reaction coordinate, one-dimential free energy landscape, its application was largely limited. Here we extended the method and allow it to get the multi-dimensional free energy landscape.

Introductions to Methods

• Gromacs and Gaussian

Gromacs and Gaussian are two of the main methods used at present in classical molecular simualtion and quantum molecular simulation, respectively. Beginners are recommanded to visit there website for more information.

• QM/MM Simulations

How to setup a simple system for QM/MM simulation using GROMACS.

• Transition Path Sampling

Transition Path Sampling (TPS) was developed in David Chandler's group in 1998 and aimed to enhance sampling during molecular simulations. Here I will provide the code of TPS implemented in gromacs and show how to use it.

Friend's Links

• Prof. Dr. Klaus Gerwert
• Dr. Frauke Graeter
• Prof. Dr. Helmut Grubmueller

My Hobbys

• Reading
• Biking
• Bodybuilding
• Swimming