Zongyang QIU/邱宗仰

Physics methods evaluation in protein engineer and collaborate with AI specialists to explore the combination with AI models.

in Dr. Jing Huang group, working on MD simulation of protein and force field development

supervised by Prof. Zhenyu Li, working on multiscale simulation of graphene growth and cutting.

Awards: Secondary, First and Third Scholar in freshman, sophomore and junior year

• AI + Molecular Simulation of Protein:    Physical methods evalution and expore the combination with AI methods. Start to learn AI models and improve my coding skills.

• Molecular Simulation of Biomolecules:   MD Simulation of Protein, Polarizable Drude Force Field Parameter Development, Biomolecular Docking and Binding Affinity Estimation.

Cell Res. 31, 126–140 (2021) doi: 10.1038/s41422-020-00460-y
(collaborated with Shuai Wang in Dr. Xu Li group@Westlake University and other groups, listed as second co-author for docking and binding affinity estimation part work)

As molecular simulation part of this work, we build a work flow to idetify potential receptors which may help ConV19 spike protein infect human cells. In this work flow, the complex struture of receptors and full-length spike protein were determined with Haddock, then filtered via aligned full-length receptors. Selected strutures with top-ranking score were performed MD simulation and MM/PBSA method was adopted for binding affinity estimation. Following ACE2, AXL had stronger binding affinity than other calculated receptors which was consistent with Li's experimental observation.

Angew. Chem. Int. Ed. 60, 6733(2021) doi: 10.1002/anie.202015129
(collaborated with prof. Zhou Nie group@Hunan University, listed as second author for MD simulation part work)

Similarly, we also studied the docking of single-strand DNA aptamer with MET protein as collaborators with prof. Zhou Nie group. In this work, DNA aptamer's structure were prediced via MFold with sequence from prof. Nie group. MET docking with HGF and DNA aptamer were performed with Haddock,repectively. Prediced MET/HGF complex struture was consistent with that in PDB database and shared the interface with predicted MET/DNA aptamer complex structure. This indicated the compition binding between HGF and DNA aptamer with MET, consistent with experimental observation.

• Molecular Simulation of Material:    Multiscale Simulation(DFT, MD and Kinetic Monte Carlo) and Free Energy Calculation(thermodynamics integration, umbrella sampling and metadynamics simulation) in Graphene.

Angew. Chem. Int. Ed. 55, 9918-9921(2016) doi: 10.1002/anie.201602541

In this work, we carried out mutilscale simulation to investigate how Ni nanoparticle etching graphene into graphene nanoribbon. Starting from MD simulation with ReaxFF force field, we obtained the understanding of how Ni nanoparticle break graphene C-C bond at high temperature at atomic level. Then, energy barrier of Ni atoms breaking C-C bond were quantitied with DFT calculation whose data comfirmed the transferability of ReaxFF force field. Furthermore, the free energy barries of the corresponding elemental etching processes were determined by metadynamics simualtion with ReaxFF force field. All these simulation indicated zigzag edge was much more difficult to be etched than armchair edge by Ni nanoparticle. In the last, the change of etching rate with nanoparticle size was studied with KMC simulation, obtaining R^2 dependent etching rate. A new explaination for this dependence was proposed, originating from the different ethcing rate of zigzag and armchair edge.

CCS Chemistry, 2, 460-467(2020) doi: 10.1002/anie.201602541
(worked with Xiongzhi, Pai under the supervision of prof. Zhenyu Li; listed as co-author for extending code function, conducting most calculations and writing a draft.)

Methane dissociation on Cu at high temperature is the first step of graphene growth. Many works discussed the dissociation kinetics with static strcuture calculation. In this work, we used ab initial MD simulation to review how the free energy of methane and its unsaturated radicals dissociation on Cu surface at 300 K and 1300 K. Our results showed new CH dissociation path at 300K with lattice motion. And CHx radicals dissociation have lower energy barrier than that from calculation with perfect surface.

ACS Earth Space Chem. 2019, 3, 1, 62–69(2019) doi: 10.1021/acsearthspacechem.8b00136
(worked with Dr. Xin Ding who launched this work and initiated simulations; listed as second author for running simulations, data analysis and participating in responding to reviewers.)

This is one of topics in geochemistry/geophysics where Dr. Ding worked in. In this work, we used MD simulation with CLAYFF force field to investigate the distribution of water and noble gas along with their diffusion in the silica nanopore.