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 YuNUCLEIC ACIDS RESEARCH45132017.

2.Nucleotide Selectivity at a Preinsertion Checkpoint of T7 RNA Polymerase Transcription Elongation

Chao E; Baogen Duan; Jin YuTHE JOURNAL OF PHYSICAL CHEMISTRY B2017

3.Determining Complex Structures using Docking Method with Single Particle Scattering Data

Hongxiao Wang; Haiguang LiuFRONTIERS 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 LiuJOURNAL OF STRUCTURAL BIOLOGY2017

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 LiuSCIENTIFIC DATA2017

6.SHREC17 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 RETRIEVAL2017

7.Application of cryo-electron microscopy in structure biology: current status and future perspectives

Lanqing Huang; Haiguang LiuPHYSICS 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 LiuIUCrJ, 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)




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