Publications 2018
1. The principle of X-ray free electron lasers and their applications in biological molecular structure determination
Yingchen Shi, Haiguang Liu, 物理, 47, 2018
2. How does supercoiling regulation on a battery of RNA polymerases impact on bacterial transcription bursting?
Xiaobo Jing, Pavel Loskot, Jin Yu, PHYSICAL BIOLOGY, 66007, 2018
3. IDPM: an online database for iondistribution in protein molecules
Xiang, Xilun; Liu, Haiguang, BMC BIOINFORMATICS, 19, 2018
4. A computational study of the chemokinereceptor CXCR1 bound with interleukin-8
Wang, Yang; Lupala, CecyliaSeverin; Wang, Ting; Li,Xuanxuan; Yun, Ji-Hye; Park, CHINESE PHYSICS B, 27, 3, 2018
5. Symmetric shear banding and swarming vortices in bacterial “superfluids”
S.Guo, D. Samanta, Y. Peng, X. L. Xu*, X. Cheng, PROC. NATL. ACAD. SCi, 115, 2018
6. Adapt to oscillate: a nonequilibrium thermodynamic view of dynamic quorum sensing
Shou-Wen Wang, Leihan Tang, BULLETIN OF THE AMERICAN PHYSICAL SOCIETY, 2018
7. Inferring energy dissipation from violation of the fluctuation-dissipation theorem
Shou-Wen Wang, PHYSICAL REVIEW E, 97, 2018
8. Balancing Non-Equilibrium Driving with Nucleotide Selectivity at Kinetic Checkpoints in Polymerase Fidelity Control
Chunhong Long; Jin Yu, ENTROPY, 20, 306, 2018
9. Maxwell’s demon in the quantum-Zeno regime and beyond
Georg Engelhardt, Gernot Schaller, NEW JOURNAL OF PHYSICS, 20, 2018
10. Thermoelectric performance of topological boundary modes
Sina Böhling, Georg Engelhardt, Gloria Platero, Gernot Schaller, PHYSICAL REVIEW B, 98, 2018
Publications 2017
1.T7 RNA polymerase translocation is facilitated by a helix opening on the fingers domain that may also prevent backtracking
Lintai Da; Chao E; Yao Shuai;Shaogui Wu; Xiao-Dong Su; Jin Yu， NUCLEIC ACIDS RESEARCH， 45，13，2017.
2.Nucleotide Selectivity at a Preinsertion Checkpoint of T7 RNA Polymerase Transcription Elongation
Chao E; Baogen Duan; Jin Yu，THE JOURNAL OF PHYSICAL CHEMISTRY B， 2017
3.Determining Complex Structures using Docking Method with Single Particle Scattering Data
Hongxiao Wang; Haiguang Liu， FRONTIERS IN MOLECULAR BIOSCIENCE， 2017
4.7 ! 7RMSD matrix: A new method for quantitative comparison of the transmembrane domain structures in the G-protein coupled receptors
Ting Wang; Yang Wang; Leihan Tang; Yong Duan; Haiguang Liu， JOURNAL OF STRUCTURAL BIOLOGY， 2017
5.Data Descriptor: Diffraction data of core-shell nanoparticles from an X-ray free electron laser
Xuanxuan Li; Chunya Chiu; Hsiang-Ju Wang; Stephan Kassemeyer; Sabine Botha; Robert L. Shoeman; Robert M. Lawrence; Christopher Kupitz;Richard Kirian; Daniel James;Dingjie Wang;Garrett Nelson;Marc Messerschmidt; Sébastien Boutet; Garth J. Williams;Elisabeth Hartmann;Aliakbar Jafarpour;Lutz M. Foucar; Anton Barty; Henry Chapman;Mengning Liang;Andreas Menzel; Fenglin Wang; Shibom Basu; Raimund Fromme; R. Bruce Doak; Petra Fromme; Uwe Weierstall; Michael H. Huang;John C. H. Spence; Ilme Schlichting;Brenda G. Hogue;Haiguang Liu，SCIENTIFIC DATA， 2017
6.SHREC’17 Track: Protein Shape Retrieval
Na Song; Daniela Craciun; Charles W. Christoffer; Xusi Han;Daisuke Kihara; Guillaume Levieux;Matthieu Montes; Hong Qin;Pranjal Sahu;Genki Terashi; Haiguang Liu， EUROGRAPHICS WORKSHOP ON 3D OBJECT RETRIEVAL， 2017
7.Application of cryo-electron microscopy in structure biology: current status and future perspectives
Lanqing Huang; Haiguang Liu， PHYSICS， 42 ,2, 2017
8.Merging single-shot XFEL diffraction data from inorganic nanoparticles: a new approach to size and orientation determination
Xuanxuan Li,John C. H. Spence,Brenda G. Hogued and Haiguang Liu， IUCrJ, 2017
9.Deciphering Intrinsic Inter-subunit Couplings that Lead to Sequential Hydrolysis of F1-ATPase Ring
Liqiang Dai, Holger Flechsig, Jin Yu, BIOPHYSICAL JOURNAL, 2017
10.Dynamics of the excised base release in thymine DNA glycosylase during DNA repair process
Lin-Tai Da, Yi Shi, Guodong Ning, Jin Yu, NUCLEIC ACIDS RESEARCH, 2017
11.Protein crystal quality oriented disulfide bond engineering
Mengchen Pu, Zhijie Xu, Yao Peng, Yaguang Hou, Dongsheng Liu, Yang Wang, Haiguang Liu, Gaojie Song, Zhi-Jie Liu, Protein & Cell, 2017
Publications 2016
1 Computational investigations on polymerase actions in gene transcription and replication: Combining physical modeling and atomistic simulations
Jin Yu*; Chinese Physics B; 25 (1) 018706, (2016)
2 Facilitating model reconstruction for single-particle scattering using small-angle X-ray scattering methods
Ma, S. & *Liu, HG; J. Appl. Cryst; 49, 665-671, (2016)
3 XFEL data analysis for structural biology
*Liu HG. & *J.C.H. Spence; Quantitative Biology; Published online, (2016)
4 Diffusion of Ellipsoids in Bacterial Suspensions
Y. Peng, L. Lai, Y. Tai, K. Zhang, X. L. Xu*, X. Cheng*; Physical Review Letters; volume 116, 068303, selected as Editors’ suggestion; (2016)
5 Entropy Production of Nanosystems with Time Scale Separation
Wang, Shouwen，K Kawaguchi，S Sasa，Tang, Leihan; Physical Review Letters; 117, 7 (2016)
6 Analytic Solution of the Ornstein-Zernike Relation for Inhomogeneous Liquids
He, Yan, Stuart A Rice, Xu Xinliang; Journal of Chemical Physics; 145, 23 (2016)
Publications 2015
1 Protein denaturation at a single-molecule level: the effect of nonpolar environments and its implications on the unfolding mechanism by proteases†
Bo Cheng, Shaogui Wu, Shixin Liu, Piere Rodriguez-Aliaga, Jin Yu and Shuxun Cui; Nanoscale; 2970 (2015)
2 Computational modeling to elucidate molecular mechanisms of epigenetic memory
Jianhua Xing, Jin Yu, Hang Zhang, Xiao-Jun Tian; TRANSLATIONAL EPIGENETICS; (2015)
3 Sample dependent first-passage time distribution in a disordered medium
Liang Luo, Lei-Han Tang; Phys. Rev. E 92; 042137 (2015).
4 A jump-from-cavity pyrophosphate ion release assisted by a key lysine residue in T7 RNA polymerase transcription elongation
Lin-Tai Da, Chao E, Baogen Duan, Chuanbiao Zhang, Xin Zhou, Jin Yu*; PLoS Computational Biology; 11 (11), e1004624, (2015)
Publications 2014
1 Constructing kinetic models to elucidate structural dynamics of a complete RNA polymerase II elongation cycle
Yu, Jin; Da, Lin-Tai; Huang, Xuhui; Physical Biology; 12 (2014)
2 Efficient fidelity control by stepwise nucleotide selection in polymerase elongation
Yu, Jin; Molecular Based Mathematical Biology; 2 (2014)
3 Coordination and control inside simple biomolecular machines
Jin Yu; Protein Conformational Dynamics, Advances in Experimental; (2014)
4 A Critical residue selectively recruits nucleotides for T7 RNA polymerase transcription fidelity control
Baogen Duan, Shaogui Wu,Lin-Tai Da,and Jin Yu; Biophysical Journal; 107, 9 (2014)
5 Sub-diffusive scaling with power-law trapping times
Luo Liang and Tang Lei-Han; Chin. Phys. B; 23, 7 (2014)
6 Stochastic heat engine with the consideration of inertial effects and shortcuts to adiabaticity
Zhanchun Tu; PHYSICAL REVIEW E; 8, 95, 52148 (2014)
Publications 2013
1 Phase transitions of the q-state Potts model on multiply-laced Sierpinski gaskets
Tian, Liang; Ma, Hui; Guo, Wenan; Tang, Lei-Han; EUROPEAN PHYSICAL JOURNAL B; 86, 5, 197 (2013)
2 新发现接通了基因组调控的一条逻辑链
汤雷翰; Physics Today; 10, 10 (2013)
