Our collaborative efforts with Prof. Sai Li at Tsinghua University to model and simulate SARS-CoV-2 have been published in Quantitative Biology. Undertaking the challenging task of intricately modeling SARS-CoV-2, we have gained extensive experience in dealing with such complex systems, drawing from our own investigations as well as the research papers of other teams. Dali and Jiaxuan dedicated significant time and effort to modeling the virion structure as accurately as possible, leading to the discovery of interesting dynamics of viral proteins and lipids during coarse-grained Martini simulations. Additionally, we were fortunate to utilize China's E-scale Tianhe-3 supercomputer, conducting all-atom simulations on the massive system comprising 274,193,494 atoms.
Cav paper online
We have been collaborating with Prof. Yan's team to study the structures and functions of Cav1.2, and Lingfeng has done a wonderful job in identifying the functional state of a novel Cav1.2 structure by using all-atom MD simulations. Our collaborative paper has been published in Cell, and we anticipate sharing more interesting stories in the future.
Conference at Daegu
Conference at Qingdao
Lingfeng passed qualifying exam
Congrats to Lingfeng! He has passed his qualifying exam, and will continue to pursue his PhD in the group.
Visiting Göttingen
Chen was invited to visit the Max Planck Institute for Multidisciplinary Sciences at Göttingen, which was called the Max Planck Institute for Biophysical Chemistry previously. The academic meeting was to celebrate the 20th anniversary of the Department of Theoretical and Computational Biophysics. It was a wonderful event that stimulated lots of old memories and new ideas.
TRPV paper online
The TRPV paper is online in the Journal of General Physiology! Congrats to Chunhong and Lingfeng! They used our multisite calcium model to simulate the ion permeation and binding patterns in TRPV1 and TRPV6, uncovering distinct features for these two channels. Chunghong had to work on weekends to finish this project, as she left the group a year ago and worked in a company. Lingfeng made a substantial contribution to conducting all the PMF calculations for the revision. Great teamwork! Special thanks go to Dr. Ives and Prof. Zachariae at the University of Dundee for their insightful discussions and invaluable advice.
RIKEN Visit
Chen and Song were invited to visit Dr. Yuji Sugita's Theoretical Molecular Science Laboratory at RIKEN (Wako, Japan) on 13-16 Sep, 2023. During the visit, Chen shared our team's recent advancements in predicting alternative protein conformations, while Song presented his research on Switching Go-Martini simulations. Interestinly, Professor Ben Corry from the Australian National University happened to be in Tokyo at the same time and also participated in the seminars!
Dali left for a new faculty job
After dedicating eight years to studying and contributing to our group, Dali has embarked on a new professional adventure. Dali has accepted a position as a faculty member at Binzhou Medical University, Yantai Campus.
Dali's journey with our group began in 2015 when he joined as our first graduate student. Over the years, he excelled, earning his Ph.D. in 2020 and subsequently dedicating three years to postdoctoral research within our team. Dali consistently proved himself to be an invaluable asset, not only a diligent member but also a dependable and helpful friend to all.
As Dali moves forward in his career, we extend our warmest wishes for his success and happiness in all his future endeavors!
Jiaxuan and Chang attended EBSA Congress 2023
Jiaxuan and Chang attended the EBSA Congress in Stockholm, Sweden, on July 31-August 4, 2023. Jiaxuan presented her work on the prediction of the alternative conformations of proteins, and Chang presented her work on asymmetrical Ca2+-membrane interactions.