Research
Research
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The objective of my research is actomyosin network, a biological active network composed of actin, myosin and other actin-binding proteins that is ubiquitous in animal cells as cytoskeleton while especially rich in neural cells. Dendritic spine is an important postsynaptic part of the neural cell, the morphology of which has been proven to be closely related to the formation of memory and ability of learning. Therefore, the particular case that interests me is how the actomyosin network dynamics inside a dendritic spine modulate the spine development which underlies the basis of memory. I use computational coarse-grained models to simulate actomyosin network evolvement and actin-binding protein structures.
The objective of my research is actomyosin network, a biological active network composed of actin, myosin and other actin-binding proteins that is ubiquitous in animal cells as cytoskeleton while especially rich in neural cells. Dendritic spine is an important postsynaptic part of the neural cell, the morphology of which has been proven to be closely related to the formation of memory and ability of learning. Therefore, the particular case that interests me is how the actomyosin network dynamics inside a dendritic spine modulate the spine development which underlies the basis of memory. I use computational coarse-grained models to simulate actomyosin network evolvement and actin-binding protein structures.
A diagram of simulated actomyosin dynamics flow which mainly contains four steps:
A diagram of simulated actomyosin dynamics flow which mainly contains four steps:
1. Chemical model: Evolve network by stochastic chemical reaction-diffusion simulations.
1. Chemical model: Evolve network by stochastic chemical reaction-diffusion simulations.
2. Update of mechanochemical configurations: Chemical reactions cause local deformations and new mechanical configuration is formed.
2. Update of mechanochemical configurations: Chemical reactions cause local deformations and new mechanical configuration is formed.
3. Mechanical model: Total energy of new mechanical configuration is minimized by conjugate gradient method to reach new equilibrium.
3. Mechanical model: Total energy of new mechanical configuration is minimized by conjugate gradient method to reach new equilibrium.
4. Update of chemical reaction rates: Chemical reaction rates are mechanochemically updated in the new equilibrium state.
4. Update of chemical reaction rates: Chemical reaction rates are mechanochemically updated in the new equilibrium state.
The four steps serve as a loop and continuously update the simulated system. For detailed information about the active network model, please visit MEDYAN website.
The four steps serve as a loop and continuously update the simulated system. For detailed information about the active network model, please visit MEDYAN website.
The protein complex that I am currently working on is the actin-related proteins 2/3 (Arp2/3) complex, which is also known as the ‘brancher’ for its function to form branches in actomyosin networks.
The protein complex that I am currently working on is the actin-related proteins 2/3 (Arp2/3) complex, which is also known as the ‘brancher’ for its function to form branches in actomyosin networks.
Arp2/3 mediated actomyosin networks show a very interesting phenomenon called ‘avalanche’, reflected as drastic structural changes in a short period of time (left figure: tension snapshots of actins). Such dynamics may underlie the ‘cytoquakes’ observed experimentally.
Arp2/3 mediated actomyosin networks show a very interesting phenomenon called ‘avalanche’, reflected as drastic structural changes in a short period of time (left figure: tension snapshots of actins). Such dynamics may underlie the ‘cytoquakes’ observed experimentally.
The alteration of Arp2/3 concentration in actomyosin networks also influences the network dynamics from various scales and perspectives.
The alteration of Arp2/3 concentration in actomyosin networks also influences the network dynamics from various scales and perspectives.
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