Dan Hu (胡丹)
Distinguished Research Fellow
Shanghai Jiao Tong University, Shanghai, China
Office: 519 Pao Yue-Kong Library
I have broad interests in understanding physical and biological systems by modeling, simulation, and analysis. Recently, my research mainly focuses on three topics: biological transport networks, pulse waves, and rare events in membrane dynamics including the mechanism of antimicrobial peptides.
Biological transport networks (BTN)
Life systems are able to achieve optimal biological transport networks. For example, blood vessels can adapt their diameters in response to the wall shear stress generated by the blood flow. This adaptation generally leads to the optimization of the whole vessel network.
Prediction of vessel pruning
Vessel pruning that means a few blood vessels disappear is observed in embryonic zebra-fish. Based on our modeling study, it turns out that the pruning effect is a consequence of the instability of loopy structures in the adaptation of blood vessels. The goal of the adaptation is to make the circulation system more efficient. (PLoS Biol. 10 e1001374 (2012).)
Adaptation and optimization of BTN
An adaptation model for generalized BTNs is constructed in which the local stimuli drive the optimization of the global structure. Strong fluctuations in flow distribution are shown to be able to stabilize the loops in the adaptation. (Phys. Rev. Lett., 111, 138701 (2013).)
Continuum modeling of the initiation process of BTNs.
Application of the optimization process in computer science problems.
Blood pulse phase
In Traditional Chinese Medicine, the blood pulse phase is believed to be an important indicator of the state of human body. Recent statistical studies really show clear correlations between the pulse phases and the diseases. Our works aim at a solid understanding from the viewpoint of the propagation of the blood pulse wave in the arterial vessel tree.
The origin of dicrotic wave and pre-dicrotic wave.
The wiry pulse in hypertension patients and smooth pulse in pregnant patients.
In this work, the main scientific problem is to understand the antimicrobial mechanisms of antimicrobial peptides (AMP) with molecular dynamics simulations. Rare event dynamics such as the translocation of the peptides in the membrane and the trans-membrane insertion of charged and highly hydrophilic groups are very important in these simulations.
Trans-membrane permeation of ions
By designing two tailored reaction coordinates, our two dimensional umbrella sampling reveals the water-bridge mechanism in the trans-membrane permeation of ions. Our free energy analysis suggests that this mechanism generally has smaller energy barrier than those without a water-bridge. The water-bridge mechanism is also frequently observed in our simulation of AMPs. (J. Chem. Theory Comput., 10 (4), pp 1717–1726, (2014).)
Antimicrobial mechanism of a few AMPs.