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Trade-offs between effectiveness and cost in bifunctional enzyme circuit with concentration robustness 期刊论文
PHYSICAL REVIEW E, 2020, 卷号: 101, 期号: 1, 页码: 12409
Authors:  Guan, Shaohua;  Xu, Liufang;  Zhang, Qing;  Shi, Hualin
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CHEMICAL-SYSTEMS  GENE-EXPRESSION  PHOSPHORYLATION  NOISE  ORIGINS  GROWTH  SPEED  OMPR  ATP  
A Decrease in Transcription Capacity Limits Growth Rate upon Translation Inhibition 期刊论文
MSYSTEMS, 2020, 卷号: 5, 期号: 5, 页码: e00575-20
Authors:  Zhang, Qing;  Brambilla, Elisa;  Li, Rui;  Shi, Hualin;  Lagomarsino, Marco Cosentino;  Sclavi, Bianca
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RNA-POLYMERASE AVAILABILITY  ESCHERICHIA-COLI  RIBOSOMAL-RNA  GENE-EXPRESSION  PPGPP  EFFICIENCY  PROMOTERS  SUBUNITS  (P)PPGPP  REVEALS  
Template-specific fidelity of DNA replication with high-order neighbor effects: A first-passage approach 期刊论文
PHYSICAL REVIEW E, 2019, 卷号: 100, 期号: 1, 页码: 12131
Authors:  Li, Qiu-Shi;  Zheng, Pei-Dong;  Shu, Yao-Gen;  Ou-Yang, Zhong-Can;  Li, Ming
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MECHANISM  ENZYME  
Advances in the study of the mechanochemical coupling of kinesin 期刊论文
INTERNATIONAL JOURNAL OF MODERN PHYSICS B, 2018, 卷号: 32, 期号: 18, 页码: 1840001
Authors:  Li, M;  Ou-Yang, ZC;  Shu, YG
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SQUID GIANT-AXON  BOVINE BRAIN KINESIN  HAND-OVER-HAND  CRYSTAL-STRUCTURE  MOTOR DOMAIN  NECK LINKER  8-NM STEP  MOLECULAR MOTORS  OPTICAL-TRAP  FORCE  
Optimal Allocation of Bacterial Protein Resources under Nonlethal Protein Maturation Stress 期刊论文
BIOPHYSICAL JOURNAL, 2018, 卷号: 115, 期号: 5, 页码: 896-910
Authors:  Zhang, Q;  Li, R;  Li, JB;  Shi, HL
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ESCHERICHIA-COLI PROTEOME  SIGMA-FACTOR COMPETITION  GENE-EXPRESSION  RNA-POLYMERASE  OXIDATIVE STRESS  GROWTH-INHIBITION  CELL-GROWTH  TRANSLATION  RATES  OVERPRODUCTION  
Anchor Effect of Interactions Between Kinesin's Nucleotide-Binding Pocket and Microtubule 期刊论文
CELLULAR AND MOLECULAR BIOENGINEERING, 2017, 卷号: 10, 期号: 2, 页码: 162-173
Authors:  Jin, YM;  Geng, YZ;  Lu, LN;  Ma, YL;  Lu, G;  Zhang, H;  Ji, Q;  Geng, YZ (reprint author), Hebei Univ Technol, Sch Sci, Tianjin 300401, Peoples R China.;  Ji, Q (reprint author), Chinese Acad Sci, Inst Theoret Phys, State Key Lab Theoret Phys, Beijing 100190, Peoples R China.
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Kinesin  Microtubule  Nucleotide-binding Pocket  Anchor Effect  
Interacting networks of resistance, virulence and core machinery genes identified by genome-wide epistasis analysis 期刊论文
PLOS GENETICS, 2017, 卷号: 13, 期号: 2, 页码: e1006508
Authors:  Skwark, MJ;  Croucher, NJ;  Puranen, S;  Chewapreecha, C;  Pesonen, M;  Xu, YY;  Turner, P;  Harris, SR;  Beres, SB;  Musser, JM;  Parkhill, J;  Bentley, SD;  Aurell, E;  Corander, J;  Corander, J (reprint author), Wellcome Trust Sanger Inst, Pathogen Gen, Cambridge, England.;  Aurell, E (reprint author), KTH Royal Inst Technol, Dept Computat Biol, Stockholm, Sweden.;  Aurell, E (reprint author), Aalto Univ, Dept Appl Phys & Comp Sci, Espoo, Finland.;  Aurell, E (reprint author), Chinese Acad Sci, Inst Theoret Phys, Beijing, Peoples R China.;  Corander, J (reprint author), Univ Helsinki, Dept Math & Stat, Helsinki, Finland.;  Corander, J (reprint author), Univ Oslo, Dept Biostat, Oslo, Norway.;  Corander, J (reprint author), Univ Cambridge, Dept Vet Med, Cambridge, England.
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Molecular dynamics simulation study of the "stay or leave" problem for two magnesium ions in gene transcription 期刊论文
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2017, 卷号: 85, 期号: 6, 页码: 1002-1007
Authors:  Wu, SG;  Wu, SG (reprint author), Sichuan Normal Univ, Coll Chem & Mat Sci, Chengdu 610066, Peoples R China.
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Molecular Dynamics Simulation  T7 Rna Polymerase  Magnesium Ion  Transcription Mechanism  Free Energy  
Mechanism of NTP Binding to the Active Site of T7 RNA Polymerase Revealed by Free-Energy Simulation 期刊论文
BIOPHYSICAL JOURNAL, 2017, 卷号: 112, 期号: 11, 页码: 2253-2260
Authors:  Wu, SG;  Li, LC;  Li, Q;  Wu, SG (reprint author), Sichuan Normal Univ, Coll Chem & Mat Sci, Chengdu, Peoples R China.;  Wu, SG (reprint author), Chinese Acad Sci, Inst Theoret Phys, State Key Lab Theoret Phys, Beijing, Peoples R China.
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Feedback arcs and node hierarchy in directed networks 期刊论文
CHINESE PHYSICS B, 2017, 卷号: 26, 期号: 7, 页码: 78901
Authors:  Zhao, JH;  Zhou, HJ;  Zhou, HJ (reprint author), Chinese Acad Sci, Inst Theoret Phys, Key Lab Theoret Phys, Beijing 100190, Peoples R China.;  Zhou, HJ (reprint author), Univ Chinese Acad Sci, Sch Phys Sci, Beijing 100049, Peoples R China.
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Directed Graph  Feedback Arc  Hierarchy  Message-passing Algorithm