Physical biology of bacterial motility

Si Tie-Yan; Yuan Jun-Hua; Wu Yi-Lin; Jay X. Tang

doi:10.7498/aps.65.178703

Abstract

Bacteria form a complex system. It consists of many components that cover broad size scales, including ions, small molecules, DNA, polymers, sub-micrometer sized organelles and compartments, micrometer sized cells, packs of cells in films of a few micrometers in thickness, large swarms or populations spanning plates over several centimeters in diameter, etc. The mechanisms to be explored span a wide range of time scales from micro-second or shorter for molecular interaction, to milli-second or longer times for diffusion and transport, up to minutes and hours for cellular metabolism, growth, and reproduction. An invisible colony of bacteria can grow rapidly and becomes visible to the human eye in several hours. Novel phenomena or behaviors emerge across these broad size and time scales. For example, the rotation direction and speed of a flagella motor, about 50 nm in diameter, are both tightly regulated by a signaling pathway within the cell. The fast rotation of the helical flagellum driven by the rotary motor is a key to explaining the bacterial swimming trajectory, chemo-taxis, accumulation, adhesion, or anchored body rotation near or at a solid surface. The activities of individual bacteria in response to their physicochemical environment give rise to their collective response such as quorum sensing, swarming, and growth of biofilms. The physical biology of bacteria is an interdisciplinary research covering micromechanics, micro-fluidics, non-equilibrium statistical physics, etc. This review covers several aspects of bacterial motility, including flagella motor behavior, bacterial swimming and accumulation near the surface, the self-organized patterns of bacterial swarms, and chemo-taxis regulated by the biochemical signaling network inside bacteria. Instead of presenting each aspect as a separate topic of microbiological study, we emphasize the strong relations among these topics, as well as the multidisciplinary perspective required to appreciate the strong relations among the topics covered. For instance, we point out the relevance of numerous phenomena in thin film fluid physics to bacterial swarming, such as capillary flow, surface tension reduction by surfactant, Marangoni flow, and viscous fingering. Another notable example is a recent application of a statistical mechanical theory called the first passage time theory to account for the intervals between the switches of bacterial motor rotation from clockwise to counter-clockwise, and vice versa. In concluding remarks, we point out a few open questions in the field of bacterial motility and likely advances that might transform the field. The central view conveyed through this review article is that further progress in the field demands interdisciplinary efforts. Therefore, a collaborative approach among those with both in depth knowledge and broad perspectives in biological and physical sciences will prove to be the most successful ones.

Keywords:

Authors and contacts

1.
Harbin Institute of Technology, Harbin 150001, China;
2.
University of Science and Technology of China, Hefei 230026, China;
3.
Chinese University of Hong Kong, Hong Kong, China;
4.
Brown University, Providence, Rhode Island, 02912, USA

Corresponding author: Jay X. Tang, jay_tang@brown.edu

Funds: Project is supported by the US National Science Foundation (Grant No. CBET 1438033), the National Natural Science Foundation of China (Grants 11374282, 21573214, and 21473152), the Research Grants Council of HKSAR (RGC Ref. No. CUHK 409713), and State Key Laboratory of Theoretical Physics in Institute of Theoretical Physics, Chinese Academy of Sciences, and China Scholarship Council.

References

[1]	Glud R N, Wenzhofer F, Middelboe M, Oguri K, Turnewitsch R, Canfield D E, Kitazato H 2013 Nat. Geosci. 6 284
[2]	Bardy S L, Ng S Y, Jarrell K F 2004 J. Mol. Microbiol. Biotechnol. 7 41
[3]	Driks A, Bryan R, Shapiro L, DeRosier D J 1989 J. Mol. Biol. 206 627
[4]	Turner L, Ryu W S, Berg H C 2000 J. Bacteriol. 182 2793
[5]	Costerton J W, Stewart P S, Greenberg E P 1999 Science 284 1318
[6]	Donlan R M 2002 Emerg. Infect. Dis. 8 881
[7]	Hall-Stoodley L, Costerton J W, Stoodley P 2004 Nat. Rev. Microbiol. 2 95
[8]	Lpez D, Vlamakis H, Kolter R 2010 Cold Spring Harb Perspect Biol. 2 a000398
[9]	Wilking J N, Angelini T E, Seminaraa A, Brennera M P, Weitz D A 2011 MRS Bulletin 36 385
[10]	Molin S, Tolker-Nielsen T 2003 Curr Opin Biotechnol 14 255
[11]	Kaewkamnerdpong B, Mongkut K 2009 Innovations in Swarm Intelligence, the series Studies in Computational Intelligence, Springer Berlin Heidelberg. 248 175
[12]	Yang A 2015 Thesis for Bachelor of Science, Brown University
[13]	Berg H C 2003 Annu. Rev. Biochem. 72 19
[14]	Kojima S, Blair D F 2001 Biochemistry 40 13041
[15]	Thomas D R, Morgan D G, DeRosier D J 1999 Proc. Nat. Acad. Sci. USA 96 10134
[16]	Turner L, Zhang R, Darnton N C, Berg H C 2010 J. Bacteriol. 192 3259
[17]	Leake M C, Chandler J H, Wadhams G H, Bai F, Berry R M, Armitage J P 2006 Nature 443 355
[18]	Yuan J, Branch R W, Hosu B G, Berg H C 2012 Nature 484 233
[19]	Lele P P, Hosu B G, Berg H C 2013 Proc. Natl. Acad. Sci. USA 110 11839
[20]	Tipping M J, Dalelez N J, Berry R M, Armitage J P 2013 mBio 4 00551
[21]	Atsumi T, Maekawa Y, Yamada T, Kawagishi I, Imae Y, Homma M 1996 J. Bacteriol. 178 5024
[22]	Sowa Y, Hotta H, Homma M, Ishijima A 2003 J. Mol. Biol. 327 1043
[23]	Kudo S, Imai N, Nishitoba M, Sugiyama S, Magariyama Y 2005 FEMS Microbiol. Lett. 242 221
[24]	Goto T, Nakata K, Baba K, Nishimura M, Magariyama Y 2005 Biophys. J. 893771
[25]	Carnazza S, Satriano C, Guglielmino S, Marletta G 2005 J. Colloid Interface Sci. 289 386
[26]	Sauer K, Camper A K, Ehrlich G D, Costerton J W, Davies D G 2002 J. Bacteriol. 184 1140
[27]	Skerker J M, Berg H C 2001 Proc. Nat. Acad. Sci. USA 98 6901
[28]	O'Toole G A, Kolter R 1998 Mol. Microbiol. 30 295
[29]	Brun Y V, Janakiraman R 2000 Dimorphic life cycles of Caulobacter and stalked bacteria. In: Yves VB, Larry S, editors. Prokaryotic Development: ASM Press; 2000. p. 297.
[30]	Li G L, Smith C S, Brun Y V, Tang J X 2005 J. Bacteriol. 187 257
[31]	Poindexter J S 1964 Bacteriol. Rev. 28 231
[32]	Wu M, Roberts J W, Kim S, Koch D L, DeLisa M P 2006 Appl. Environ. Microbiol. 72 4987
[33]	Lemelle L, Palierne J F, Chatre E, Place C 2010 J. Bacteriol. 192 6307
[34]	Hodges K, Hecht G 2013 Curr Opin Gastroenterol 29 159
[35]	Swiecicki J M, Sliusarenko O, Weibel D B 2013 Integr. Biol. 5 1490
[36]	Pratt L A, Kolter R 1998 Mol. Microbiol. 30 285
[37]	Mello B A, Tu Y 2007 Biophys. J. 92 2329
[38]	Hansen C H, Endres R G, Wingreen N S 2008 PLoS Comput. Biol. 4 e1
[39]	Xie L, Altindal T, Chattopadhyay S, Wu X L 2011 Proc. Natl. Acad. Sci. USA 108 2246
[40]	Son K, Guasto J S, Stocker R 2013 Nat. Phys. 9 5
[41]	Locsei J T 2007 J. Math. Biol. 55 41
[42]	Bodenmiller D, Toh E, Brun Y V 2004 J. Bacteriol. 186 1438
[43]	An Y H, Friedman R J 1998 J. Biomed. Mater. Res. 43 338
[44]	Busscher HJ, van Der Mei HC. Use of flow chamber devices and image analysis methods to study microbial adhesion. Meth. Enzym. Academic Press; 1995. p 455.
[45]	Lee L K, Ginsburg M A, Crovace C, Donohoe M, Stock D 2010 Nature 466 996
[46]	Bai F, Branch R W, Nicolau D V, Pilizota J T, Steel B C, Maini P K, Berry R M 2010 Science 327 685
[47]	Morse M, Bell J, Li G, Tang J X 2015 Phys. Rev. Lett. 115 198103
[48]	Kim M, Powers T R 2004 Phys. Rev. E 69 061910
[49]	Morse M, Huang A, Li G, Maxey M R, Tang J X 2013 Biophys. J. 105 21
[50]	Vigeant M A S, Ford R M 1997 Appl. Environ. Microbiol. 63 3474
[51]	Vigeant M A S, Roseanne M F, Michael W, Tamm L K 2002 Appl. Environ. Microbiol. 68 2794
[52]	Vigeant M A S, Wagner M, Tamm L K, Ford R M 2001 Langmuir 17 2235
[53]	Li G, Tang J X 2009 Phys. Rev. Lett. 103 078101
[54]	Berke A P, Turner L, Berg H C, Lauga E 2008 Phys. Rev. Lett. 101 038102
[55]	Marchetti M C, Joanny J F, Ramaswamy S, Liverpool T B, Prost J, Rao M, Simha R A 2013 Rev. Mod. Phys. 85 1143
[56]	Li G, Bensson J, Nisimova L, Munger D, Mahautmr P, Tang J X, Maxey M R, Brun Y V 2011 Phys. Rev. E 84041932
[57]	Drescher K, Dunkel J, Cisneros L H, Ganguly S, Goldstein R E 2011 Proc. Natl. Acad. Sci. USA 108 10940
[58]	Frymier P D, Ford R M, Berg H C, Cummings P T 1995 Proc. Natl. Acad. Sci. USA 92 6195
[59]	Magariyama Y, Ichiba M, Nakata K, Baba K, Ohtani T, Kudo S, Goto T 2005 Biophys. J. 88 3648
[60]	Li G L, Tam L K, Tang J X 2008 Proceedings of the National Academy of Sciences of the United States of America 105 18355
[61]	Li G, Brown P J, Tang J X, Xu J, Quardokus E M, Fuqua C, Brun Y V 2012 Mol Microbiol 83 41
[62]	Pushkar P L, Thibault R, Abhishek S, Chen Y, Berg H C 2016 Nat. Phys. 12 175
[63]	Li G L, Tam L K, Tang J X 2008 Proc. Natl. Acad. Sci. USA 105 18355
[64]	Costerton J W, Cheng K J, Geesey G G, Ladd T I, Nickel J C, Dasgupta M, Marrie T J 1987 Annu Rev Microbiol 41 435
[65]	VanGestel J, Vlamakis H, Kolter R 2015 PLOS Biol. 13 e1002141
[66]	Parsek M, Singh P 2003 Annu. Rev. Microbiol. 57 677
[67]	Wu Y L 2015 Quant. Biol. 3 199
[68]	Copeland M F, Weibel D B 2009 Soft Matter 5 1174
[69]	Ramaswamy S 2010 Annu. Rev. Cond. Mat. Phys. 1 323
[70]	Jimenez P N, Koch G, Papaioannou E, Wahjudi M, Krzeslak J, Coenye T, et al. 2010 Microbiology 156 49
[71]	Prigent-Combaret C, Prensier G, Le Thi T T, Vidal O, Lejeune P, Dorel C 2000 Environ. Microbiol. 2 450
[72]	Wolfe A J, Visick K L 2008 J. Bacteriol. 190 463
[73]	Danese P N, Pratt L A, Kolter R 2000 J. Bacteriol. 182 3593
[74]	Vlamakis H, Aguilar C, Losick R, Kolter R 2008 Genes. Dev. 22 945
[75]	Allison C, Lai H C, Gygi D, Hughes C 1993 Mol. Microbiol. 8 53
[76]	Harshey R M, Matsuyama T 1994 Proc. Natl. Acad. Sci. USA 91 8631
[77]	Allison C, Hughes C 1991 Sci. Prog. 75 403
[78]	Harshey R M 2003 Annu. Rev. Microbiol. 57 249
[79]	Henrichsen J 1972 Bacteriol. Rev. 36 478
[80]	Kearns D B 2010 Nat. Rev. Microbiol. 8 634
[81]	McCarter L L 2004 J. Mol. Microbiol. Biotechnol. 7 18
[82]	Verstraeten N, Braeken K, Debkumari B, Favart M, Fransaer J, Vermant J, Michiels J 2008 Trends Microbiol. 16 496
[83]	Hamze K, Autret S, Hinc K, Laalami S, Julkowska D, Briandet R, Renault M, Absalon C, Holland IB, Putzer H, Sror SJ 2011 Microbiology 157 2456
[84]	Kaiser D 2007 Curr. Biol. 17 R561
[85]	Kerr B, Riley M A, Feldman M W, Bohannan B J M 2002 Nature 418 171
[86]	Struthers J K, Westran R P. Clinical Bacteriology: CRC Press; 2003.
[87]	Zhang H P, Be'er A, Smith R S, Florin E L, Swinney H L 2009 EPL 87 48011
[88]	Darnton N C, Turner L, Rojevsky S, Berg H C 2010 Biophys. J. 98 2082
[89]	Zhang H P, Be'er A, Florin E L, Swinney H L 2010 Proc. Natl. Acad. Sci. USA 107 13626
[90]	Be'er A, Strain SK, Hernndez R A, Ben-Jacob E, Florin E L 2013 J. Bacteriol. 195 2709
[91]	Wu Y, Hosu B G, Berg H C 2011 Proc. Natl. Acad. Sci. USA 108 4147
[92]	Mariconda S, Wang Q, Harshey R M 2006 Mol. Microbiol. 60 1590
[93]	Peruani F, Deutsch A, Br M 2006 Phys. Rev. E 74 030904
[94]	F. B, Minamino T, Wu Z, Namba K, Xing J 2012 Phys. Rev. Lett. 108 178105
[95]	Ping L, Wu Y, Hosu Basarab G, Tang Jay X, Berg Howard C 2014 Biophys. J. 107 871
[96]	McBride M J 2004 J. Mol. Microbiol. Biotechnol. 7 63
[97]	Wu Y, Kaiser D, Jiang Y, Alber M 2009 Proc. Natl. Acad. Sci. USA 106 1222
[98]	Berleman J E, Scott J, Chumley T, Kirby J R 2008 Proc. Natl. Acad. Sci. USA 105 17127
[99]	Thutupalli S, Sun M, Bunyak F, Palaniappan K, Shaevitz J W 2015 J. Royal. Society. Inter. 12 0049
[100]	Be'er A, Ariel G, Kalisman O, Helman Y, Sirota-Madi A, Zhang H P, Florin E L, Payne S M, Ben-Jacob E, Swinney H L 2010 Proc. Natl. Acad. Sci. USA 107 6258
[101]	Davies D G, Parsek M R, Pearson J P, Iglewski B H, Costerton J W, Greenberg E P 1998 Science 280 295
[102]	Matsushita M W J, Itoha H, Watanabea K, Araia T, Matsuyamab T S H, Mimura M 1999 Physica A 274 10
[103]	Mezanges X, Regeard C, Gerin C, Deroulers C, Grammaticos B, Badoual M 2012 Phys. Rev. E 85 041913
[104]	Fauvart M, Phillips P, Bachaspatimayum D, Verstraeten N, Fransaer J, Michiels J, Vermant J 2012 Soft Matter 8 70
[105]	Sempels W, De Dier R, Mizuno H, Hofkens J, Vermant J 2013 Nat. Comm. 4 1757
[106]	Vicsek T, Zafeiris A 2012 Phys. Rep. 517 71
[107]	Koch D L, Subramanian G 2010 Annu. Rev. Flui. Mech. 43 637
[108]	Ghosh P K, Li Y, Marchesoni F, Nori F 2015 Phys. Rev. E 92 012114
[109]	Wang Y, Hernandez R M, Bartlett D J, Bingham J M, Kline T R, Sen A, Mallouk T E 2006 Langmuir 22 10451
[110]	Wu Z, Lin X, Wu Y, Si T, Sun J, He Q 2014 ACS nano 8 9
[111]	Shao J, Xuan M, Dai L, Si T, Li J, He Q 2015 Angew. Chem. 54 12782
[112]	Dombrowski C, Cisneros L, Chatkaew S, Goldstein RE, Kessler JO 2004 Phys. Rev. Lett. 93 098103
[113]	Discher D E, Janmey P, Wang Y L 2005 Science 310 1139
[114]	Prigent-Combaret C, Vidal O, Dorel C, Lejeune P 1999 J. Bacteriol. 181 5993
[115]	Wang Q, Frye J G, McClelland M, Harshey R M 2004 Mol. Microbiol. 52 169
[116]	Inoue T, Shingaki R, Hirose S, Waki K, Mori H, Fukui K 2007 J. Bacteriol. 189 950
[117]	Girgis H S, Liu Y, Ryu W S, Tavazoie S 2007 PLoS Genet. 3 1644
[118]	Vogel V 2012 Nat. Mater. 11 841
[119]	Yuan J H 2014 44 5 (in Chinese) [袁军华 2014 中国科学技术大学学报 44 5]
[120]	Hazelbauer G L, Falke J J, Parkinson J S 2008 Trends Biochem. Sci. 33 9
[121]	kollmann M, Lovdok L, Bartholome K, Timmer J, Sourjik V 2005 Nature 438 504
[122]	Alon U, Surette M G, Barkai N, Leibler S 1999 Nature 397 168
[123]	Segall J E, Block S M, Berg H C 1986 Proc. Natl. Acad. Sci. USA 83 8987
[124]	Duke T A J, Bray D 1999 Proc. Natl. Acad. Sci. USA 96 10104
[125]	Sourjik V, Berg H C 2002 Proc. Natl. Acad. Sci. USA 99 123
[126]	Tu Y 2013 Annu. Rev. Biophys. 42 337
[127]	Oleksiuk O, Jakovljevic V, Vladimirov N, Carvalho R, Paster E 2011 Cell 145 312
[128]	Si G, Wu T, Ouyang Q, Tu Y 2012 Phys. Rev. Lett. 109 048101
[129]	Yuan J, Berg H C 2008 Proc. Natl. Acad. Sci. USA 105 1182
[130]	Yuan J, Fahrner K A, Berg H C 2009 J. Mol. Biol. 390 394
[131]	Morse M, Colin R, Wilson L G, Tang J X 2016 Biophys. J. 110 2076
[132]	Schnitzer M J 1993 Phys. Rev. E 48 2553
[133]	Xie L, Wu X L 2014 Biophys. J. 107 1712
[134]	Xie L, Lu C, Wu X L 2015 Biophys J. 108 766
[135]	Yang Y, He J, Altindal T, Xie L, Wu X L 2015 Biophys. J. 109 1058
[136]	Chat H, Ginelli F, Montagne R 2006 Phys. Rev. Lett. 96 180602
[137]	McCandlish S R, Baskaran A, Hagan M F 2012 Soft Matter 8 2527
[138]	Nagai K H, Sumino Y, Montagne R, Aranson I S, Chat H 2015 Phys. Rev. Lett. 114 168001
[139]	Berdahl A, Torney C J, Ioannou C C, Faria J, Couzin I D 2013 Science 339 574
[140]	Torellaa J P, Gagliardib C J, Chena J S, Bediakob D K, Colna B, Wayc J C, Silvera P A, Nocerab D G 2014 Proc. Natl. Acad. Sci. USA 112 2337
[141]	Darnton N T L, Breuer K, Berg H C 2004 Biophys. J. 86 1863
[142]	Vogel V, Hess H 2007 Controlled Nanoscale Motion, Nobel Symposium 131 711 367

Cited By

[1]	Glud R N, Wenzhofer F, Middelboe M, Oguri K, Turnewitsch R, Canfield D E, Kitazato H 2013 Nat. Geosci. 6 284
[2]	Bardy S L, Ng S Y, Jarrell K F 2004 J. Mol. Microbiol. Biotechnol. 7 41
[3]	Driks A, Bryan R, Shapiro L, DeRosier D J 1989 J. Mol. Biol. 206 627
[4]	Turner L, Ryu W S, Berg H C 2000 J. Bacteriol. 182 2793
[5]	Costerton J W, Stewart P S, Greenberg E P 1999 Science 284 1318
[6]	Donlan R M 2002 Emerg. Infect. Dis. 8 881
[7]	Hall-Stoodley L, Costerton J W, Stoodley P 2004 Nat. Rev. Microbiol. 2 95
[8]	Lpez D, Vlamakis H, Kolter R 2010 Cold Spring Harb Perspect Biol. 2 a000398
[9]	Wilking J N, Angelini T E, Seminaraa A, Brennera M P, Weitz D A 2011 MRS Bulletin 36 385
[10]	Molin S, Tolker-Nielsen T 2003 Curr Opin Biotechnol 14 255
[11]	Kaewkamnerdpong B, Mongkut K 2009 Innovations in Swarm Intelligence, the series Studies in Computational Intelligence, Springer Berlin Heidelberg. 248 175
[12]	Yang A 2015 Thesis for Bachelor of Science, Brown University
[13]	Berg H C 2003 Annu. Rev. Biochem. 72 19
[14]	Kojima S, Blair D F 2001 Biochemistry 40 13041
[15]	Thomas D R, Morgan D G, DeRosier D J 1999 Proc. Nat. Acad. Sci. USA 96 10134
[16]	Turner L, Zhang R, Darnton N C, Berg H C 2010 J. Bacteriol. 192 3259
[17]	Leake M C, Chandler J H, Wadhams G H, Bai F, Berry R M, Armitage J P 2006 Nature 443 355
[18]	Yuan J, Branch R W, Hosu B G, Berg H C 2012 Nature 484 233
[19]	Lele P P, Hosu B G, Berg H C 2013 Proc. Natl. Acad. Sci. USA 110 11839
[20]	Tipping M J, Dalelez N J, Berry R M, Armitage J P 2013 mBio 4 00551
[21]	Atsumi T, Maekawa Y, Yamada T, Kawagishi I, Imae Y, Homma M 1996 J. Bacteriol. 178 5024
[22]	Sowa Y, Hotta H, Homma M, Ishijima A 2003 J. Mol. Biol. 327 1043
[23]	Kudo S, Imai N, Nishitoba M, Sugiyama S, Magariyama Y 2005 FEMS Microbiol. Lett. 242 221
[24]	Goto T, Nakata K, Baba K, Nishimura M, Magariyama Y 2005 Biophys. J. 893771
[25]	Carnazza S, Satriano C, Guglielmino S, Marletta G 2005 J. Colloid Interface Sci. 289 386
[26]	Sauer K, Camper A K, Ehrlich G D, Costerton J W, Davies D G 2002 J. Bacteriol. 184 1140
[27]	Skerker J M, Berg H C 2001 Proc. Nat. Acad. Sci. USA 98 6901
[28]	O'Toole G A, Kolter R 1998 Mol. Microbiol. 30 295
[29]	Brun Y V, Janakiraman R 2000 Dimorphic life cycles of Caulobacter and stalked bacteria. In: Yves VB, Larry S, editors. Prokaryotic Development: ASM Press; 2000. p. 297.
[30]	Li G L, Smith C S, Brun Y V, Tang J X 2005 J. Bacteriol. 187 257
[31]	Poindexter J S 1964 Bacteriol. Rev. 28 231
[32]	Wu M, Roberts J W, Kim S, Koch D L, DeLisa M P 2006 Appl. Environ. Microbiol. 72 4987
[33]	Lemelle L, Palierne J F, Chatre E, Place C 2010 J. Bacteriol. 192 6307
[34]	Hodges K, Hecht G 2013 Curr Opin Gastroenterol 29 159
[35]	Swiecicki J M, Sliusarenko O, Weibel D B 2013 Integr. Biol. 5 1490
[36]	Pratt L A, Kolter R 1998 Mol. Microbiol. 30 285
[37]	Mello B A, Tu Y 2007 Biophys. J. 92 2329
[38]	Hansen C H, Endres R G, Wingreen N S 2008 PLoS Comput. Biol. 4 e1
[39]	Xie L, Altindal T, Chattopadhyay S, Wu X L 2011 Proc. Natl. Acad. Sci. USA 108 2246
[40]	Son K, Guasto J S, Stocker R 2013 Nat. Phys. 9 5
[41]	Locsei J T 2007 J. Math. Biol. 55 41
[42]	Bodenmiller D, Toh E, Brun Y V 2004 J. Bacteriol. 186 1438
[43]	An Y H, Friedman R J 1998 J. Biomed. Mater. Res. 43 338
[44]	Busscher HJ, van Der Mei HC. Use of flow chamber devices and image analysis methods to study microbial adhesion. Meth. Enzym. Academic Press; 1995. p 455.
[45]	Lee L K, Ginsburg M A, Crovace C, Donohoe M, Stock D 2010 Nature 466 996
[46]	Bai F, Branch R W, Nicolau D V, Pilizota J T, Steel B C, Maini P K, Berry R M 2010 Science 327 685
[47]	Morse M, Bell J, Li G, Tang J X 2015 Phys. Rev. Lett. 115 198103
[48]	Kim M, Powers T R 2004 Phys. Rev. E 69 061910
[49]	Morse M, Huang A, Li G, Maxey M R, Tang J X 2013 Biophys. J. 105 21
[50]	Vigeant M A S, Ford R M 1997 Appl. Environ. Microbiol. 63 3474
[51]	Vigeant M A S, Roseanne M F, Michael W, Tamm L K 2002 Appl. Environ. Microbiol. 68 2794
[52]	Vigeant M A S, Wagner M, Tamm L K, Ford R M 2001 Langmuir 17 2235
[53]	Li G, Tang J X 2009 Phys. Rev. Lett. 103 078101
[54]	Berke A P, Turner L, Berg H C, Lauga E 2008 Phys. Rev. Lett. 101 038102
[55]	Marchetti M C, Joanny J F, Ramaswamy S, Liverpool T B, Prost J, Rao M, Simha R A 2013 Rev. Mod. Phys. 85 1143
[56]	Li G, Bensson J, Nisimova L, Munger D, Mahautmr P, Tang J X, Maxey M R, Brun Y V 2011 Phys. Rev. E 84041932
[57]	Drescher K, Dunkel J, Cisneros L H, Ganguly S, Goldstein R E 2011 Proc. Natl. Acad. Sci. USA 108 10940
[58]	Frymier P D, Ford R M, Berg H C, Cummings P T 1995 Proc. Natl. Acad. Sci. USA 92 6195
[59]	Magariyama Y, Ichiba M, Nakata K, Baba K, Ohtani T, Kudo S, Goto T 2005 Biophys. J. 88 3648
[60]	Li G L, Tam L K, Tang J X 2008 Proceedings of the National Academy of Sciences of the United States of America 105 18355
[61]	Li G, Brown P J, Tang J X, Xu J, Quardokus E M, Fuqua C, Brun Y V 2012 Mol Microbiol 83 41
[62]	Pushkar P L, Thibault R, Abhishek S, Chen Y, Berg H C 2016 Nat. Phys. 12 175
[63]	Li G L, Tam L K, Tang J X 2008 Proc. Natl. Acad. Sci. USA 105 18355
[64]	Costerton J W, Cheng K J, Geesey G G, Ladd T I, Nickel J C, Dasgupta M, Marrie T J 1987 Annu Rev Microbiol 41 435
[65]	VanGestel J, Vlamakis H, Kolter R 2015 PLOS Biol. 13 e1002141
[66]	Parsek M, Singh P 2003 Annu. Rev. Microbiol. 57 677
[67]	Wu Y L 2015 Quant. Biol. 3 199
[68]	Copeland M F, Weibel D B 2009 Soft Matter 5 1174
[69]	Ramaswamy S 2010 Annu. Rev. Cond. Mat. Phys. 1 323
[70]	Jimenez P N, Koch G, Papaioannou E, Wahjudi M, Krzeslak J, Coenye T, et al. 2010 Microbiology 156 49
[71]	Prigent-Combaret C, Prensier G, Le Thi T T, Vidal O, Lejeune P, Dorel C 2000 Environ. Microbiol. 2 450
[72]	Wolfe A J, Visick K L 2008 J. Bacteriol. 190 463
[73]	Danese P N, Pratt L A, Kolter R 2000 J. Bacteriol. 182 3593
[74]	Vlamakis H, Aguilar C, Losick R, Kolter R 2008 Genes. Dev. 22 945
[75]	Allison C, Lai H C, Gygi D, Hughes C 1993 Mol. Microbiol. 8 53
[76]	Harshey R M, Matsuyama T 1994 Proc. Natl. Acad. Sci. USA 91 8631
[77]	Allison C, Hughes C 1991 Sci. Prog. 75 403
[78]	Harshey R M 2003 Annu. Rev. Microbiol. 57 249
[79]	Henrichsen J 1972 Bacteriol. Rev. 36 478
[80]	Kearns D B 2010 Nat. Rev. Microbiol. 8 634
[81]	McCarter L L 2004 J. Mol. Microbiol. Biotechnol. 7 18
[82]	Verstraeten N, Braeken K, Debkumari B, Favart M, Fransaer J, Vermant J, Michiels J 2008 Trends Microbiol. 16 496
[83]	Hamze K, Autret S, Hinc K, Laalami S, Julkowska D, Briandet R, Renault M, Absalon C, Holland IB, Putzer H, Sror SJ 2011 Microbiology 157 2456
[84]	Kaiser D 2007 Curr. Biol. 17 R561
[85]	Kerr B, Riley M A, Feldman M W, Bohannan B J M 2002 Nature 418 171
[86]	Struthers J K, Westran R P. Clinical Bacteriology: CRC Press; 2003.
[87]	Zhang H P, Be'er A, Smith R S, Florin E L, Swinney H L 2009 EPL 87 48011
[88]	Darnton N C, Turner L, Rojevsky S, Berg H C 2010 Biophys. J. 98 2082
[89]	Zhang H P, Be'er A, Florin E L, Swinney H L 2010 Proc. Natl. Acad. Sci. USA 107 13626
[90]	Be'er A, Strain SK, Hernndez R A, Ben-Jacob E, Florin E L 2013 J. Bacteriol. 195 2709
[91]	Wu Y, Hosu B G, Berg H C 2011 Proc. Natl. Acad. Sci. USA 108 4147
[92]	Mariconda S, Wang Q, Harshey R M 2006 Mol. Microbiol. 60 1590
[93]	Peruani F, Deutsch A, Br M 2006 Phys. Rev. E 74 030904
[94]	F. B, Minamino T, Wu Z, Namba K, Xing J 2012 Phys. Rev. Lett. 108 178105
[95]	Ping L, Wu Y, Hosu Basarab G, Tang Jay X, Berg Howard C 2014 Biophys. J. 107 871
[96]	McBride M J 2004 J. Mol. Microbiol. Biotechnol. 7 63
[97]	Wu Y, Kaiser D, Jiang Y, Alber M 2009 Proc. Natl. Acad. Sci. USA 106 1222
[98]	Berleman J E, Scott J, Chumley T, Kirby J R 2008 Proc. Natl. Acad. Sci. USA 105 17127
[99]	Thutupalli S, Sun M, Bunyak F, Palaniappan K, Shaevitz J W 2015 J. Royal. Society. Inter. 12 0049
[100]	Be'er A, Ariel G, Kalisman O, Helman Y, Sirota-Madi A, Zhang H P, Florin E L, Payne S M, Ben-Jacob E, Swinney H L 2010 Proc. Natl. Acad. Sci. USA 107 6258
[101]	Davies D G, Parsek M R, Pearson J P, Iglewski B H, Costerton J W, Greenberg E P 1998 Science 280 295
[102]	Matsushita M W J, Itoha H, Watanabea K, Araia T, Matsuyamab T S H, Mimura M 1999 Physica A 274 10
[103]	Mezanges X, Regeard C, Gerin C, Deroulers C, Grammaticos B, Badoual M 2012 Phys. Rev. E 85 041913
[104]	Fauvart M, Phillips P, Bachaspatimayum D, Verstraeten N, Fransaer J, Michiels J, Vermant J 2012 Soft Matter 8 70
[105]	Sempels W, De Dier R, Mizuno H, Hofkens J, Vermant J 2013 Nat. Comm. 4 1757
[106]	Vicsek T, Zafeiris A 2012 Phys. Rep. 517 71
[107]	Koch D L, Subramanian G 2010 Annu. Rev. Flui. Mech. 43 637
[108]	Ghosh P K, Li Y, Marchesoni F, Nori F 2015 Phys. Rev. E 92 012114
[109]	Wang Y, Hernandez R M, Bartlett D J, Bingham J M, Kline T R, Sen A, Mallouk T E 2006 Langmuir 22 10451
[110]	Wu Z, Lin X, Wu Y, Si T, Sun J, He Q 2014 ACS nano 8 9
[111]	Shao J, Xuan M, Dai L, Si T, Li J, He Q 2015 Angew. Chem. 54 12782
[112]	Dombrowski C, Cisneros L, Chatkaew S, Goldstein RE, Kessler JO 2004 Phys. Rev. Lett. 93 098103
[113]	Discher D E, Janmey P, Wang Y L 2005 Science 310 1139
[114]	Prigent-Combaret C, Vidal O, Dorel C, Lejeune P 1999 J. Bacteriol. 181 5993
[115]	Wang Q, Frye J G, McClelland M, Harshey R M 2004 Mol. Microbiol. 52 169
[116]	Inoue T, Shingaki R, Hirose S, Waki K, Mori H, Fukui K 2007 J. Bacteriol. 189 950
[117]	Girgis H S, Liu Y, Ryu W S, Tavazoie S 2007 PLoS Genet. 3 1644
[118]	Vogel V 2012 Nat. Mater. 11 841
[119]	Yuan J H 2014 44 5 (in Chinese) [袁军华 2014 中国科学技术大学学报 44 5]
[120]	Hazelbauer G L, Falke J J, Parkinson J S 2008 Trends Biochem. Sci. 33 9
[121]	kollmann M, Lovdok L, Bartholome K, Timmer J, Sourjik V 2005 Nature 438 504
[122]	Alon U, Surette M G, Barkai N, Leibler S 1999 Nature 397 168
[123]	Segall J E, Block S M, Berg H C 1986 Proc. Natl. Acad. Sci. USA 83 8987
[124]	Duke T A J, Bray D 1999 Proc. Natl. Acad. Sci. USA 96 10104
[125]	Sourjik V, Berg H C 2002 Proc. Natl. Acad. Sci. USA 99 123
[126]	Tu Y 2013 Annu. Rev. Biophys. 42 337
[127]	Oleksiuk O, Jakovljevic V, Vladimirov N, Carvalho R, Paster E 2011 Cell 145 312
[128]	Si G, Wu T, Ouyang Q, Tu Y 2012 Phys. Rev. Lett. 109 048101
[129]	Yuan J, Berg H C 2008 Proc. Natl. Acad. Sci. USA 105 1182
[130]	Yuan J, Fahrner K A, Berg H C 2009 J. Mol. Biol. 390 394
[131]	Morse M, Colin R, Wilson L G, Tang J X 2016 Biophys. J. 110 2076
[132]	Schnitzer M J 1993 Phys. Rev. E 48 2553
[133]	Xie L, Wu X L 2014 Biophys. J. 107 1712
[134]	Xie L, Lu C, Wu X L 2015 Biophys J. 108 766
[135]	Yang Y, He J, Altindal T, Xie L, Wu X L 2015 Biophys. J. 109 1058
[136]	Chat H, Ginelli F, Montagne R 2006 Phys. Rev. Lett. 96 180602
[137]	McCandlish S R, Baskaran A, Hagan M F 2012 Soft Matter 8 2527
[138]	Nagai K H, Sumino Y, Montagne R, Aranson I S, Chat H 2015 Phys. Rev. Lett. 114 168001
[139]	Berdahl A, Torney C J, Ioannou C C, Faria J, Couzin I D 2013 Science 339 574
[140]	Torellaa J P, Gagliardib C J, Chena J S, Bediakob D K, Colna B, Wayc J C, Silvera P A, Nocerab D G 2014 Proc. Natl. Acad. Sci. USA 112 2337
[141]	Darnton N T L, Breuer K, Berg H C 2004 Biophys. J. 86 1863
[142]	Vogel V, Hess H 2007 Controlled Nanoscale Motion, Nobel Symposium 131 711 367

[1]	Shi Yan, Zhang Tian-Hui. Control of self-organization: From equilibrium to non-equilibrium. Acta Physica Sinica, 2020, 69(14): 140503. doi: 10.7498/aps.69.20200161
[2]	Shang Xiang-Jun, Ma Ben, Chen Ze-Sheng, Yu Ying, Zha Guo-Wei, Ni Hai-Qiao, Niu Zhi-Chuan. Physics and devices of quanutm light emission from semicoductor self-assembled quantum Dots. Acta Physica Sinica, 2018, 67(22): 227801. doi: 10.7498/aps.67.20180594
[3]	Wu Xiao-Wa, Qin Si-Qing, Xue Lei, Yang Bai-Cun, Zhang Ke. Behavior characteristics from self-organization to criticality caused by cumulative damage leading to instability of locked segments in seismogenic fault system. Acta Physica Sinica, 2018, 67(20): 206401. doi: 10.7498/aps.67.20180614
[4]	Sun Bao-An, Wang Li-Feng, Shao Jian-Hua. Self-organized critical behavior in plastic flow of amorphous solids. Acta Physica Sinica, 2017, 66(17): 178103. doi: 10.7498/aps.66.178103
[5]	Yu Xu-Tao, Xu Jin, Zhang Zai-Chen. Routing protocol for wireless ad hoc quantum communication network based on quantum teleportation. Acta Physica Sinica, 2012, 61(22): 220303. doi: 10.7498/aps.61.220303
[6]	Dong Li-Fang, Xie Wei-Xia, Zhao Hai-Tao, Fan Wei-Li, He Ya-Feng, Xiao Hong. Experimental study on self-organized hexagonal superlattice pattern in dielectric barrier discharge in argon/air. Acta Physica Sinica, 2009, 58(7): 4806-4811. doi: 10.7498/aps.58.4806
[7]	Huang Li-Qing, Pan Hua-Qiang, Wang Jun, Tong Hui-Min, Zhu Ke, Ren Guan-Xu, Wang Yong-Chang. Spontaneous formation of ordered Sn nanodot array on porous anodic alumina membrane. Acta Physica Sinica, 2007, 56(11): 6712-6716. doi: 10.7498/aps.56.6712
[8]	Zhou Hai-Ping, Cai Shao-Hong, Wang Chun-Xiang. Self-organized criticality in one-dimensional sandpile model with avalanche probability included. Acta Physica Sinica, 2006, 55(7): 3355-3359. doi: 10.7498/aps.55.3355
[9]	Zhang Lin, Kong Hong-Yan, Yang Guo-Jian. Self-organization of light driven atoms induced by recoil effect in a harmonic trap. Acta Physica Sinica, 2006, 55(10): 5122-5128. doi: 10.7498/aps.55.5122
[10]	Dong Qing-Rui, Niu Zhi-Chuan. Excitonic energy of vertically stacked self-assmbled InAs quantum dots. Acta Physica Sinica, 2005, 54(4): 1794-1798. doi: 10.7498/aps.54.1794
[11]	Zhang Yong-Ju, Yu Sen-Jiang. Self-organization of ordered surface patterns in nearly free sustained Al films. Acta Physica Sinica, 2005, 54(10): 4867-4873. doi: 10.7498/aps.54.4867
[12]	Dong Li-Fang, Mao Zhi-Guo, Ran Jun-Xia. Study on the electrical characteristic of different modes of dielectric barrier discharge in argon. Acta Physica Sinica, 2005, 54(7): 3268-3272. doi: 10.7498/aps.54.3268
[13]	Yin Zeng-Qian, Chai Zhi-Fang, Dong Li-Fang, Li Xue-Chen. Pattern formation in the dielectric barrier discharge in argon at atmospheric pressure. Acta Physica Sinica, 2003, 52(4): 925-928. doi: 10.7498/aps.52.925
[14]	Zhang Yong-Peng, Yan Long, Xie Si-Shen, Pang Shi-Jin, Gao Hong-Jun. . Acta Physica Sinica, 2002, 51(2): 296-299. doi: 10.7498/aps.51.296
[15]	. . Acta Physica Sinica, 2002, 51(2): 310-314. doi: 10.7498/aps.51.310
[16]	Dong Li-Fang, Li Xue-Chen, Yin Zeng-Qian, Wang Long. . Acta Physica Sinica, 2002, 51(10): 2296-2301. doi: 10.7498/aps.51.2296
[17]	HE SHENG-TAI, YAO JIAN-NIAN, WANG YU-PING, JIANG PENG, SHI DONG-XIA, XIE SI-SHEN, PANG SHI-JIN, GAO HONG-JUN. SELF-ASSEMBLED TWO-DIMENSIONAL ORDERED ARRAYOF SILVER NANOPARTICLES. Acta Physica Sinica, 2001, 50(4): 765-768. doi: 10.7498/aps.50.765
[18]	SI JUN-JIE, YANG QIN-QING, TENG DA, WANG HONG-JIE, YU JIN-ZHONG, WANG QI-MING, GUO LI-WEI, ZHOU JUN-MING. MORPHOLOGY AND PHOTOLUMINESCENCE OF GeSi SELF-ASSEMBLED QUANTUM DOT ON Si(113). Acta Physica Sinica, 1999, 48(9): 1745-1750. doi: 10.7498/aps.48.1745
[19]	LV ZHEN-DONG, LI QING, XU JI-ZONG, ZHENG BAO-ZHEN, XU ZHONG-YING, GE WEI-KUN. EXCITON DYNAMICS IN SELF-ORGANIZED InAs/GaAs QUANTUM DOTS. Acta Physica Sinica, 1999, 48(4): 744-750. doi: 10.7498/aps.48.744
[20]	WANG ZHI-MING, FENG SONG-LIN, Lv ZHEN-DONG, YANG XIAO-PING, CHEN ZONG-GUI, SONG CHUN-YING, XU ZHONG-YING, ZHENG HOU-ZHI, WANG FENG-LIAN, HAN PAI-DE, DUAN XIAO-FENG. STUDY OF VERTICALLY ALIGNING GROWTH OF SELF-ASSEMBLED InAs/GaAs QUANTUM DOTS. Acta Physica Sinica, 1998, 47(1): 89-93. doi: 10.7498/aps.47.89

Catalog

Vol. 65, Issue 17 - 2016-09-05

Metrics

Abstract views: 6762
PDF Downloads: 550
Cited By: 0

姓名
邮箱
手机号码
标题
留言内容
验证码

Search

Article

留言板