- Scientific computing, rare events and saddle point algorithm
- Math Biology, computational systems
News and Events
- 2022/4, Congratulations to Dr. Xiaolu Guo for her paper “The Nonequilibrium Mechanism of Noise Enhancer synergizing with Activator in HIV Latency Reactivation" being accepted by iScience. This is a joint work with Prof. Hao Ge (PKU).
- 2022/4, Congratulations to Dr. Lingxia Qiao for her paper “Coactivation of antagonistic genes stabilizes polarity patterning during shoot organogenesis" being accepted by Science Advances. This is a joint work with Prof. Yuling Jiao (Life Science, PKU).
- 2022/4, Congratulations to Dr. Yucen Han for her paper “Elastic anisotropy in the reduced Landau-de Gennes model" being accepted by Proceedings of the Royal Society A. This is a joint work with Prof. Apala Majumdar (University of Strathclyde).
- 2022/4, Congratulations to Dr. Xiaomei Yao for her paper “Transition pathways in Cylinder-Gyroid interface" being accepted by Commun. Comput. Phys.. This is a joint work with Prof. Jie Xu (CAS).
- 2022/3, Congratulations to Dr. Xiaomei Yao for her paper “Defect patterns of two-dimensional nematic liquid crystals in confinement" being accepted by Physical Review E. This is a joint work with Prof. Jeff Chen (University of Waterloo).
- 2022/3, Congratulations to Dr. Jianyuan Yin and Zhen Huang for their paper “Constrained high-index saddle dynamics for the solution landscape with equality constraints" being accepted by Journal of Scientific Computing.
- 2022/01, Congratulations to Xiangyu Kuang for his paper “Computable early Caenorhabditis elegans embryo with a phase field model" being publised by PLOS Computational Biology. A cell is the smallest unit of life. Cells of different species, organs, and tissues have different morphologies, and morphology characterizes their mechanical properties and functions. What kind of mathematical/physical equations can accurately describe cell morphology and mechanics is an important and fascinating problem for biomechanics, cell biology, and developmental biology. We proposed a phase field model coupled with experimental data to accurately compute the morphological evolution of C. elegans embryo in vivo. The model can infer the underlying cellular mechanical properties and was utilized to analyze the early C. elegans embryogenesis.
This is a joint work with Prof. Chao Tang (PKU).
- 2021/12, Congratulations to Dr. Jianyuan Yin for his paper “Transition pathways connecting crystals and quasicrystals" being published in PNAS. Despite the fact that tremendous efforts have been made on the study of quasicrystals since their discovery in 1984, nucleation of quasicrystals, viz. the emergence of a quasicrystal from a crystalline phase, still presents an unsolved problem. The difficulties lie in that quasicrystals and crystals are incommensurate structures in general, so there are no obvious epitaxial relations between them. We solved this problem by applying an Saddle Dynamics method to Landau theory of phase transitions and obtained the accurate critical nuclei and transition pathways connecting crystalline and quasicrystalline phases. The proposed computational methodology not only reveals the mechanism of nucleation of quasicrystals, but also paves the way to investigate a wide range of physical problems undergoing the first-order phase transitions. This is a joint work with Prof. Pingwen Zhang (PKU), Prof. An-Chang Shi (McMaster University), and Prof. Kai Jiang (Xiangtan University).(PKU News)
- 2021/11, Congratulations to Dr. Jianyuan Yin for his paper “Solution Landscape of the Onsager Model Identifies Non-axisymmetric Critical Points" being published in Physica D: Nonlinear Phenomena. We proposed a solution landscape approach to investigate the critical points of the three-dimensional Onsager model on a sphere with different interaction potentials, and numerically answered some open questions, including finding the unstable non-axisymmetric critical points. This is a joint work with Prof. Pingwen Zhang (PKU).
- 2021/09, Welcome Dr. ZHANG He (PhD at Penn State University, US) join our group！
- 2021/8, Congratulations to Dr. Yuzhe Zhang for his paper “Construction of a minimum energy path for the VT flash model by the string method coupled with the exponential time differencing scheme" being accepted by Commun. Comput. Phys.. This is a joint work with Prof. Shuyu Sun (KAUST).
- 2020/08, we published a review paper “Modelling and Computation of Liquid Crystals” in Acta Numerica, joint with Prof. Pingwen Zhang (PKU) and Wei Wang (Zhejiang University).Liquid crystals are a type of soft matter that is intermediate between crystalline solids and isotropic fluids. The study of liquid crystals has made tremendous progress over the past four decades, which is of great importance for fundamental scientific research and has widespread applications in industry. In this paper we review the mathematical models and their connections to liquid crystals, and survey the developments of numerical methods for finding rich configurations of liquid crystals.(PKU News)
- 2021/8, Congratulations to Dr. Yucen Han and Dr. Jianyuan Yin for the paper “Solution Landscapes of the Simplified Ericksen-Leslie Model and its Comparison with the Reduced Landau-de Gennes Model" being accepted by Proceedings of the Royal Society A. This is a joint work with Prof. Apala Majumdar (University of Strathclyde) and Prof. Yucheng Hu (Capital Normal University).
- 2021/6, Congratulations to Dr. Zhen Xu for the paper “Solution landscapes of the diblock copolymer-homopolymer model under two-dimensional confinement" being accepted by Physical Review E. This is a joint work with Prof. Yasumasa Nishiura (Hokkaido University).
- 2021/6, Congratulations to Dr. Wei Zhao for the paper “Modeling of histone modifications reveals formation mechanism and function of bivalent chromatin" being accepted by iScience. This is a joint work with Prof. Qing Nie (UC Irvine).
- 2021/06, Congratulations to Jianyuan Yin and Ruotai Li for successfully passing the Ph.D. thesis defense! Congratulations to Shiyu Yan and Di Xie for successfully passing the Master thesis defense!
- 2020/10, Congratulations to Yucen Han and Jianyuan Yin for the paper “Solution landscape of a reduced Landau-de Gennes model on a hexagon" being accepted by Nonlinearity. This is a joint work with Prof. Pingwen Zhang and Prof. Apala Majumdar (University of Strathclyde).
- 2020/10, Congratulations to our group members, WANG Haoran and HUANG Zhen for their excellent achievements in S. T. YAU College Student Mathematics Contest 2020. WANG Haoran 1 Goald (individual all-around) and 2 Silvers (Applied and Computational Math, Analysis and Differential equations) , HUANG Zhen 1 Bronze (Applied and Computational Math) [Link]。
- 2020/10, Welcome Dr. YAO Xiaomei (PhD at Beijing Normal University) join our group！
- 2020/09, Congratulations to Dr. HAN Yucen for her award “Newton International Fellowship" by the Royal Society, UK. She will work with Prof. Apala Majumdar (University of Strathclyde).
- 2020/08, Congratulations to Ruotai Li for his paper “Numerical discretization of variational phase field model for phase transitions in ferroelectric thin films" has been accepted by Commun. Comput. Phys.. This is a joint work with Prof. Qiang Du (Columbia University).
- 2020/07, Welcome Dr. Donghang ZHANG (PhD at AMSS, CAS) join our group！
- 2020/07, Congratulations to Bing Yu and Jianyuan Yin for their paper “Searching the solution landscape by generalized high-index saddle dynamics" has been accepted by SCIENCE CHINA Mathematics.
- 2020/06, Congratulations to QIAO Lingxia, GUO Xiaolu, HAN Yucen, ZHAO Wei for successfully passing the thesis defense! They will be postdocs at UCSD，UCLA，U. of Strathclyde, UCI, respectively.
- 2020/04, Congratulations to Dr. Kuan Tao for his paper “Tuning cell motility via cell tension with a mechanochemical cell migration model” has been accepted by Biophysical Journal. This is a joint work with Prof. Feng Liu (CQB, PKU).
- 2020/04, Congratulations to Ruotai Li for his paper “Variational Phase Field Formulations of Polarization and Phase Transition in Ferroelectric Thin Films” has been accepted by SIAM Journal on Applied Mathematics. This is a joint work with Prof. Qiang Du (Columbia University).
- 2020/04, Congratulations to Yucen Han for her paper “A Reduced Study for Nematic Equilibria on Two-Dimensional Polygons” has been accepted by SIAM Journal on Applied Mathematics. This is a joint work with Prof. Apala Majumdar (University of Strathclyde).
- 2020/03, Congratulations to Bing Yu for his paper “Global optimization-based dimer method for finding saddle points” has been accepted by Discrete Contin. Dyn. Syst. Ser. B.
- 2020/03, Congratulations to Jianyuan Yin for publishing the paper “Construction of a pathway map on a complicated energy landscape” in Phys. Rev. Lett.. This work is joint with Prof. Pingwen Zhang and Prof. Jeff Z.Y. Chen in University of Waterloo.
- 2019/12, Congratulations to Yucen Han and Zirui Xu for publishing the paper “Pathways connecting two opposed bilayers with a fusion pore: a molecularly-informed phase field approach” in Soft Matter. This work is joint with Prof. An-Chang Shi in McMaster University.
- 2019/11, Congratulations to Jianyuan Yin for publishing the paper “High-index Optimization-based Shrinking Dimer Method for Finding High-Index Saddle Points” in SIAM Journal on Scientific Computing. This work is joint with Prof. Pingwen Zhang.
- 2019/09, Welcome Dr. Yuzhe ZHANG (Poly. University of Hong Kong) join our group！
- 2019/09, We published the paper “Network topologies that can achieve dual function of adaptation and noise attenuation” in Cell Systems. Lingxia Qiao and Wei ZHAO are the co-first authors
- 2019/07, Welcome Dr. Lu (Lucy) Klinger (University of Sydney), Dr. Zhen Xu (Beijing Normal University) join our group！
- 2019/06, Congratulations to Yucen Han to publish the paper "Transition Pathways between Defect Patterns in Confined Nematic Liquid Crystals" in Journal of Computational Physics. This work is joint with Prof. Pingwen Zhang and Yucheng Hu (Tsinghua University).
- 2019/06, Congratulations to TAO Kuan succesfully passed the thesis defense. He will join the Beijing Sports University in Fall.
- 2019/05, We succesfully held the Fourth A3 Workshop on Mathematical Life Science in BICMR, Peking University.
Graduate students and Postdocs Position
- We are constantly recruiting diligent and bright Ph.D. students.
- We have postdoc positions available! Candidates with recently awarded Ph.D. degrees from all countries in the area of computational math and math biology are encouraged to apply. These are two-year full-time positions, with salary 250,000+ Chinese Yuan (RMB) per year (before tax). Once accepted, they are also qualified for all other benefits of Peking University postdoctoral fellows, including health insurance and subsidized housing arrangements.
- If you are interested in working with us, please send your CV to me directly.