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When done over a range of frequencies, a spectrum of dielectric (polarization) responses is obtained which serves to characterize a single living ell. In this manner, individual cells of several microorganisms,Saccharomyces cerevisiae andNetrium digitus, were investigated in the frequency range 102 to 106 Hz. These and related prior studies showed that the positive dielectrophoresis, i.e. where the suspended particle has a greater net polarization than the suspending medium, can be — used to show subtle differences between species, and even between cells of the same culture when using this technique.",{"EN":216},"Dynamic dielectrophoretic levitation of living individual cells",{"VOID":218},"[\"7494829825995771096\",\"5718206601021694727\"]",{"VOID":220},"H. A. Pohl, DIELECTROPHORESIS, Cambridge University Press, 1978.\nH. A. Pohl and K. Kaler, \"Continuous dielectrophoretic separation of cell mixtures\", Cell Biophysics (in press, 1979). Available as preprint, Quantum Theory Research Group Res. Note No. 76, Oklahoma State University, Stillwater, OK 74074.\nH. A. Pohl, K. Kaler and K. Pollock, \"Continuous positive and negative dielectrophoresis of microorganisms\", J. Biol. Phys. (in press, 1978). Available as preprint, QTRG Res. Note No. 75, Oklahoma State University, Stillwater, OK 74074.\nH. A. Pohl and J. S. Crane, Biophys. J.11, 711 (1971).\nJ. E. Rhoads, H. A. Pohl and R. G. Buckner, J. Biol. Phys.4, 93 (1976).\nH. A. Pohl and J. S. Crane, ELECTROSTATICS AND ITS APPLICATIONS, A. D. Moore, editor, Chap. 15, John Wiley and Sons, 1973.\nH. A. Pohl, J. Biol. Phys.1, 1 (1973).\nH. A. Pohl, METHODS OF CELL SEPARATION, N. Catsimpoolas, editor, Vol. I, pp. 67–169, Plenum Press, 1978.\nD. S. Parmar and A. K. Jalaluddin, Jap. J. Appl. Phys.13, 793 (1974).\nT. B. Jones and G. W. Bliss, J. Appl. Phys.48, 1419 (1977).\nC. S. Chen and H. A. Pohl, Trans. N. Y. Acad. Sci.238, 176 (1974).\nJ. S. Crane and H. A. Pohl, J. Electrostatics5, 11 (1978).\nH. A. Pohl, J. Appl. Phys.22, 869 (1951).\nH. A. Pohl, J. Appl. Phys.29, 1182 (1958).\nH. A. Pohl, J. Electrochem. Soc.107, 386 (1960).\nL. D. Sher, Nature220, 695 (1968).\nH. A. Pohl and J. S. Crane, J. Theor. Biol.37, 1 (1972).\nJ. S. Crane and H. A. Pohl, J. Theor. Biol.37, 15 (1972).\nP. Lorrain and D. Corson, ELECTROMAGNETIC FIELDS AND WAVES, Freeman and Co., San Francisco, 1970, p. 135.\nE. Durand, ELECTROSTATIQUE, Vol. 3, p. 258, Masson et Cie, Paris, 1966.\nT. B. Jones, \"Dielectrophoretic Force Calculation\", (in press, 1979).\nG. A. Kallio and T. B. Jones, \"Dielectrophoretic levitation of spheres and shells\", (in press, 1979).\nG. A. Kallio and T. B. Jones, \"Dielectric constant measurements using dielectrophoretic levitation\", Preprints of IEEE-IAS Meeting, Toronto, Oct., 1978.\nH. A. Pohl, K. Pollock and J. S. Crane, \"Dielectrophoretic force\", (MS submitted), Preprint available as QTRG Res. Note No. 78, Oct. 1978, Oklahoma State University, Stillwater, OK 74074.\nL. Benguigui and I. J. Lin, J. Appl. Phys.49, 2536 (1978).\nC. W. Einolf and E. L. Carstensen, J. Phys. Chem.75, 1091 (1971).\nS. S. Dukhin, Surface Colloid Sci.3, 83 (1973).\nG. J. Schwarz, J. Phys. Chem.66, 2636 (1962).\nC. T. O'Konski, J. Phys. Chem.64, 605 (1960).\nL. van Beek, Prog. 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have performed Langevin dynamics simulations of a coarse-grained model of ejection of dsDNA from Φ29 phage. Our simulation results show significant variations in the local ejection speed, consistent with experimental observations reported in the literature for both in vivo and in vitro systems. In efforts to understand the origin of such variations in the local speed of ejection, we have investigated the correlations between the local ejection kinetics and the packaged structures created at various motor forces and chain flexibility. At lower motor forces, the packaged DNA length is shorter with better organization. On the other hand, at higher motor forces typical of realistic situations, the DNA organization inside the capsid suffers from significant orientational disorder, but yet with long orientational correlation times. This in turn leads to lack of registry between the direction of the DNA segments just to be ejected and the direction of exit. As a result, a significant amount of momentum transfer is required locally for successful exit. Consequently, the DNA ejection temporarily slows down exhibiting pauses. This slowing down occurs at random times during the ejection process, completely determined by the particular starting conformation created by prescribed motor forces. In order to augment our inference, we have additionally investigated the ejection of chains with deliberately changed persistence length. For less inflexible chains, the demand on the occurrence of large momentum transfer for successful ejection is weaker, resulting in more uniform ejection kinetics. While being consistent with experimental observations, our results show the nonergodic nature of the ejection kinetics and call for better theoretical models to portray the kinetics of genome ejection from phages.",{"EN":338},"Langevin dynamics simulation of DNA ejection from a phage",{"VOID":340},"[\"2961939122845006097\"]",{"VOID":342},"10.1007\u002Fs10867-013-9316-x","2024-04-29T01:51:47.661+00:00","https:\u002F\u002Flink.springer.com\u002Farticle\u002F10.1007\u002Fs10867-013-9316-x",[346,363,376],{"id":347,"sortIndex":23,"researcher":22,"roles":348,"affiliations":349,"properties":358,"displayName":360,"givenName":22,"familyName":22},"bc0669fa-46bc-41a1-ab5d-f5452ff68df5",[232],[350],{"id":351,"sortIndex":23,"affiliation":352,"properties":22},"4f2b0531-e678-47f5-91c0-a663f5278652",{"id":351,"createTime":22,"updateTime":22,"relativeEntities":353,"slug":22,"properties":354,"entityType":22,"verifyStatus":22,"verifyTime":22,"verifyNote":22,"languages":22,"translateLanguages":22,"viewCount":22,"url":22,"parentIds":357,"statistic":22},[],{"title":355},{"VI":356},"Department of Polymer Science and Engineering, Department of Physics, University of Massachusetts, Amherst, USA",[],{"title":359,"gsAuthor":361},{"VI":360},"J. 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Biol. Phys. 34, 511–519, 2018) is studied. We report on the presence of the modulational instability (MI) of a plane wave for charge migration in DNA and the generation of soliton-like excitations in DNA nucleotides. We show that the original differential-difference equation for the DNA dynamics can be reduced in the continuum approximation to a set of three coupled nonlinear equations. The linear stability analysis of continuous wave solutions of the coupled systems is performed and the growth rate of instability is found numerically. Numerical simulations show the validity of the analytical approach with the generation of wave packets provided that the wave numbers fall in the instability domain.",{"EN":693},"Charge transport in DNA model with vibrational and rotational coupling motions",{"VOID":695},"[\"18430184443880457627\"]",{"VOID":697},"10.1007\u002Fs10867-017-9455-6","2024-05-04T17:28:09.423+00:00","http:\u002F\u002Flink.springer.com\u002F10.1007\u002Fs10867-017-9455-6",[701,716,731],{"id":702,"sortIndex":23,"researcher":22,"roles":703,"affiliations":704,"properties":713,"displayName":715,"givenName":22,"familyName":22},"28372b7b-dbef-41a0-82d6-61d473fccb49",[232],[705],{"id":706,"sortIndex":23,"affiliation":707,"properties":22},"584dba32-2271-45dd-8899-adeaaaa15408",{"id":706,"createTime":22,"updateTime":22,"relativeEntities":708,"slug":22,"properties":709,"entityType":22,"verifyStatus":22,"verifyTime":22,"verifyNote":22,"languages":22,"translateLanguages":22,"viewCount":22,"url":22,"parentIds":712,"statistic":22},[],{"title":710},{"VI":711},"Laboratory of Biophysics, Department of Physics, Faculty of Science, University of Yaounde I, Yaounde, Cameroon",[],{"title":714},{"VI":715},"H. 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Ben-Bolie",{"id":732,"sortIndex":135,"researcher":22,"roles":733,"affiliations":734,"properties":743,"displayName":745,"givenName":22,"familyName":22},"388d932b-5e0e-4a2a-bf74-7456fed7409e",[232],[735],{"id":736,"sortIndex":23,"affiliation":737,"properties":22},"92706de7-76eb-473f-ac54-5befc2193610",{"id":736,"createTime":22,"updateTime":22,"relativeEntities":738,"slug":22,"properties":739,"entityType":22,"verifyStatus":22,"verifyTime":22,"verifyNote":22,"languages":22,"translateLanguages":22,"viewCount":22,"url":22,"parentIds":742,"statistic":22},[],{"title":740},{"VI":741},"Laboratory of Mechanics, Department of Physics, Faculty of Science, University of Yaounde I, Yaounde, Cameroon",[],{"title":744,"gsAuthor":746},{"VI":745},"T. C. Kofané",{"VOID":747},"[\"TH3a8EAAAAAJ\"]",{"url":699,"publisher":749,"properties":803},{"id":6,"createTime":7,"updateTime":8,"relativeEntities":750,"slug":10,"properties":751,"entityType":20,"verifyStatus":21,"verifyTime":22,"verifyNote":22,"languages":22,"translateLanguages":22,"viewCount":23,"subjectFields":755,"manageAffiliations":772,"indexDatabases":783,"url":22,"thumbnailPath":22,"statistic":798,"gsStatistic":22,"type":201,"analyzePriority":22},[],{"issn":752,"title":753,"eissn":754},{"VOID":15},{"EN":17},{"VOID":13},[756,760,764,768],{"id":26,"createTime":22,"updateTime":22,"relativeEntities":757,"label":758,"description":759,"parentId":22,"standard":22,"scholarHubFieldId":22},[],{"EN":29},{},{"id":32,"createTime":22,"updateTime":22,"relativeEntities":761,"label":762,"description":763,"parentId":22,"standard":22,"scholarHubFieldId":22},[],{"EN":35},{},{"id":38,"createTime":22,"updateTime":22,"relativeEntities":765,"label":766,"description":767,"parentId":22,"standard":22,"scholarHubFieldId":22},[],{"EN":41},{},{"id":44,"createTime":22,"updateTime":22,"relativeEntities":769,"label":770,"description":771,"parentId":22,"standard":22,"scholarHubFieldId":22},[],{"EN":47},{},[773,778],{"id":51,"createTime":22,"updateTime":22,"relativeEntities":774,"slug":22,"properties":775,"entityType":22,"verifyStatus":22,"verifyTime":22,"verifyNote":22,"languages":22,"translateLanguages":22,"viewCount":22,"url":22,"parentIds":777,"statistic":22},[],{"title":776},{"EN":55},[57],{"id":59,"createTime":22,"updateTime":22,"relativeEntities":779,"slug":22,"properties":780,"entityType":22,"verifyStatus":22,"verifyTime":22,"verifyNote":22,"languages":22,"translateLanguages":22,"viewCount":22,"url":22,"parentIds":782,"statistic":22},[],{"title":781},{"EN":63},[],[784,791],{"id":67,"indexDatabase":785,"url":80,"indexYears":22,"academicFieldIds":790,"indexDatabaseRanking":22},{"id":69,"createTime":22,"updateTime":22,"relativeEntities":786,"label":787,"description":788,"key":76,"publicationTags":789,"standard":22},[],{"EN":72,"VI":72},{"EN":74,"VI":75},[78,79],[82],{"id":84,"indexDatabase":792,"url":95,"indexYears":96,"academicFieldIds":797,"indexDatabaseRanking":102},{"id":86,"createTime":22,"updateTime":22,"relativeEntities":793,"label":794,"description":795,"key":92,"publicationTags":796,"standard":22},[],{"EN":89,"VI":89},{"EN":89,"VI":91},[94],[98,99,100,101],{"impactFactor":23,"impactFactorByYear":799,"i10Index":117,"i10IndexLast5Year":118,"totalPublication":119,"totalPublicationByYear":800,"totalCitation":153,"totalCitationByYear":801,"totalCitationPerPublication":167,"totalCitationPerPublicationByYear":802,"hindexLast5Year":151,"hindex":151},{"2012":105,"2013":106,"2014":107,"2015":108,"2016":109,"2017":110,"2018":111,"2019":112,"2020":113,"2021":114,"2022":115,"2023":116},{"1973":121,"1974":122,"1975":123,"1976":124,"1977":122,"1978":122,"1979":125,"1980":126,"1981":122,"1982":127,"1983":128,"1984":129,"1985":130,"1986":131,"1987":124,"1988":123,"1989":123,"1990":130,"1991":132,"1992":124,"1993":133,"1994":115,"1995":134,"1996":131,"1997":132,"1998":135,"1999":136,"2000":137,"2001":132,"2002":138,"2003":139,"2004":140,"2005":141,"2006":139,"2007":142,"2008":143,"2009":144,"2010":128,"2011":136,"2012":145,"2013":146,"2014":128,"2015":147,"2016":148,"2017":149,"2018":150,"2019":137,"2020":151,"2021":139,"2022":137,"2023":152,"2024":135},{"1977":115,"1978":140,"1980":125,"1982":151,"1983":155,"1984":124,"1985":135,"1986":140,"1988":126,"1989":125,"1990":121,"1991":137,"1993":142,"1995":150,"1996":156,"2004":135,"2005":157,"2006":158,"2007":135,"2008":159,"2009":150,"2010":160,"2011":130,"2012":151,"2013":161,"2014":152,"2015":159,"2016":162,"2017":163,"2018":164,"2019":165,"2020":152,"2021":166,"2022":118,"2023":135},{"1977":169,"1978":170,"1980":171,"1982":172,"1983":173,"1984":174,"1985":175,"1986":176,"1988":177,"1989":174,"1990":178,"1991":179,"1993":180,"1995":181,"1996":182,"2004":183,"2005":184,"2006":185,"2007":186,"2008":187,"2009":180,"2010":188,"2011":108,"2012":189,"2013":190,"2014":191,"2015":192,"2016":193,"2017":194,"2018":195,"2019":196,"2020":197,"2021":198,"2022":199,"2023":200},{"pages":804,"volume":806},{"VOID":805},"341-353",{"VOID":807},"43",{"total":23,"publishYear":809,"statisticByYear":810},2017,{},"2017-07-20","2026-07-24T23:18:01.564+00:00",[102,78],[815,818,821,824,830,833,836,839,845,848,854,857,860,863,866,872,875,878,881,884,887,890,893,896,899,902,905,908,911,914],{"id":22,"text":816,"url":22,"identifiers":817},"Benjamin, T.B., Feir, J.E.: The disintegration of wave trains on deep water I. J. Fluid Mech. 27, 417 (1967)",{},{"id":22,"text":819,"url":22,"identifiers":820},"Benjamin, T.B.: Instability of periodic wave trains in non linear systems. Proc. Roy. Soc. A 299, 59 (1967)",{},{"id":460,"text":822,"url":462,"identifiers":823},"Zagryadskaya, L.I., Ostrovskii, L.A.: Observed self influence of modulated waves in a non linear lines. Radiofizika 11, 948 (1968). [Transl. Radiophys. and Quantum Electronics 11, 548 (1969)]",{"doi":464},{"id":825,"text":826,"url":827,"identifiers":828},"ce8699aa-d96b-4a86-86a3-ff28a60494d0","Ostrovskii, L.A., Soustov, L.V., Izvestiya, V.U.Z.: Self modulation of electromagnetic waves in non linear transmission lines. Radiofizika 15, 242 (1972). [Transl. Radiophys. and Quantum Electronics 15, 182 (1973)]","https:\u002F\u002Flink.springer.com\u002Farticle\u002F10.1007\u002FBF02209115",{"doi":829},"10.1007\u002FBF02209115",{"id":460,"text":831,"url":462,"identifiers":832},"Kogelman, S., Di Prima, R.C.: Stability of spatially periodic supercritical flows in hydrodynamics. Phys. Fluids 13, 1 (1970)",{"doi":464},{"id":460,"text":834,"url":462,"identifiers":835},"Hasegawa, A., Brinkman, W.F.: Tunable coherent IR and FIR sources utilizing modulational instability. IEEE J. Quant. Elect. QE 16, 694 (1980)",{"doi":464},{"id":460,"text":837,"url":462,"identifiers":838},"Tai, K., Hasegawa, A., Tomita, A.: Observation of modulational instability in optics fibers. Phys. Rev. Lett. 56, 135 (1986)",{"doi":464},{"id":840,"text":841,"url":842,"identifiers":843},"ccbc7916-9440-420c-98ae-8af8e24428f2","Dauxois, T., Peyrard, M., Bishop, A.R.: Entropy -driven DNA denaturation. Phys. Rev. E 47, R44 (1993)","https:\u002F\u002Flink.aps.org\u002Fdoi\u002F10.1103\u002FPhysRevE.47.R44",{"doi":844},"10.1103\u002Fphysreve.47.r44",{"id":22,"text":846,"url":22,"identifiers":847},"Zamora-Sillero, E., Shapovalov, A.V., Esteban, F.J.: Formation, control and dynamics of N localized structures in the Peyrard-Bishop model. Phys. Rev. E 76, 066603 (2007)",{},{"id":849,"text":850,"url":851,"identifiers":852},"0a5fddf6-448c-436e-9b8d-5f4eb9849c21","Peyrard, M., Bishop, A.R.: Statistical mechanics of a non linear model for DNA denaturation. Phys. Rev. Lett. 62, 2755 (1989)","https:\u002F\u002Flink.aps.org\u002Fdoi\u002F10.1103\u002FPhysRevLett.62.2755",{"doi":853},"10.1103\u002Fphysrevlett.62.2755",{"id":460,"text":855,"url":462,"identifiers":856},"Zdravkovic, S., Sataric, M.: Resonance mode in DNA dynamics. Europhys. Lett. 80, 38003 (2007)",{"doi":464},{"id":460,"text":858,"url":462,"identifiers":859},"Zdravkovic, S., Sataric, M.: Nonlinear Schrodinger equation and DNA dynamics. Phys. Lett. A 373, 126 (2008)",{"doi":464},{"id":460,"text":861,"url":462,"identifiers":862},"Tabi, C.B., Mohamadou, A., Kofané, T.C.: Soliton-like excitation in a non linear model of DNA dynamics with viscosity. Math. Biosci. Eng. 5, 205 (2008)",{"doi":464},{"id":460,"text":864,"url":462,"identifiers":865},"Tabi, C.B., Mohamadou, A., Kofané, T.C.: Soliton excitation in the DNA double helix. Phys. Scr. 77, 045002 (2008)",{"doi":464},{"id":867,"text":868,"url":869,"identifiers":870},"9f659369-b353-4fcd-9762-b65c4233d22b","Barbi, M., Cocco, S., Peyrard, M.: Helicoidal model for DNA opening. Phys. Lett. A 253, 358 (1999)","https:\u002F\u002Flinkinghub.elsevier.com\u002Fretrieve\u002Fpii\u002FS0375960199000596",{"doi":871},"10.1016\u002Fs0375-9601(99)00059-6",{"id":460,"text":873,"url":462,"identifiers":874},"Cocco, S., Monasson, R.: Statistical mechanics of Torque induced denaturation of DNA. Phys. Rev. Lett. 83, 5178 (1999)",{"doi":464},{"id":460,"text":876,"url":462,"identifiers":877},"Yomosa, S.: Solitary excitations in deoxyribonucleic acid (DNA) double helices. Phys. Rev. A 30, 474 (1984)",{"doi":464},{"id":460,"text":879,"url":462,"identifiers":880},"Takeno, S., Homma, S.: Kinks and breathers associated with collective sugar puckering in DNA. Prog. Theor. Phys. 77, 548 (1987)",{"doi":464},{"id":460,"text":882,"url":462,"identifiers":883},"Chun-Ting, Z.: Solitons excitations in deoxyribonucleic acid (DNA) double helices. Phys. Rev. A 35, 886 (1987)",{"doi":464},{"id":460,"text":885,"url":462,"identifiers":886},"Fialko, N.S., Lakhno, V.D.: Nonlinear dynamics of excitations in DNA. Phys. Lett. A 278, 108 (2000)",{"doi":464},{"id":460,"text":888,"url":462,"identifiers":889},"Fialko, N.S., Lakhno, V.D.: Long range charge transfer in DNA. Regul. Chaotic Dyn. 7(3), 299–313 (2002)",{"doi":464},{"id":460,"text":891,"url":462,"identifiers":892},"Dauxois, T., Peyrard, M.: Energy localization in nonlinear lattices. Phys. Rev. Lett. 70, 3935 (1993)",{"doi":464},{"id":460,"text":894,"url":462,"identifiers":895},"Silva, R.A.S., Drigo Filho, E., Ruggiero, J.R.: A model coupling vibrational and rotational motion for the DNA molecule. J. Biol. Phys. 34, 511–519 (2008)",{"doi":464},{"id":460,"text":897,"url":462,"identifiers":898},"Tabi, C.B., Mohamadou, A., Kofane, T.C.: Modulational instability of charge transport in Peyrard-Bishop-Holstein. J. Phys. Condens. Matter 21, 335101 (2009)",{"doi":464},{"id":460,"text":900,"url":462,"identifiers":901},"Bruinsma, R., Gruner, G., D’Orsogna, M., Rudnick, J.: Fluctuation-facilitated charge migration along DNA. Phys. Rev. Lett. 85, 4393 (2000)",{"doi":464},{"id":460,"text":903,"url":462,"identifiers":904},"Kaloskas, G., Aubry, S., Tsironis, G.P.: Polaron solutions and normal-model analysis in the semi classical Holstein model. Phys. Rev. B 58, 3094 (1998)",{"doi":464},{"id":460,"text":906,"url":462,"identifiers":907},"Su, W.P., Schrieffer, J.R., Heeger, A.J.: Solitons excitations in polyacetylene. Phys. Rev. B 22, 2099 (1980)",{"doi":464},{"id":22,"text":909,"url":22,"identifiers":910},"Holstein, T.: The effect of coupling to multiple-phonon modes. Ann. Phys. (N. Y) 8, 325 (1959)",{},{"id":460,"text":912,"url":462,"identifiers":913},"Dauxois, T., Peyrard, M., Willis, C.R.: Localized breathers- like solution in a discrete Klein-Gordon model and application to DNA. Physica D 56, 267 (1992)",{"doi":464},{"id":460,"text":915,"url":462,"identifiers":916},"Berashevich, J., Bookatz, A., Chakraborty, T.: The electric field effect and conduction in the Peyrard-Bishop-Holstein model. J. Phys. Condens. Matter 20, 035207 (2008)",{"doi":464},{"id":918,"createTime":919,"updateTime":920,"relativeEntities":921,"slug":922,"properties":923,"entityType":223,"verifyStatus":224,"verifyTime":934,"verifyNote":226,"languages":22,"translateLanguages":22,"viewCount":23,"primaryUrl":935,"fullTextUrl":22,"authors":936,"publicationType":258,"publisherRelationship":993,"citationCount":122,"citationInfo":1053,"publishDate":1056,"publishYear":1054,"citationAnalyzeStatus":21,"lastCitationAnalyze":1057,"indexDatabases":1058,"openAccess":22,"references":22,"isForceReanalyzing":327},"b092c098-c7b7-4487-8108-61394cb04b5c","2024-01-15T16:50:29.767+00:00","2026-07-24T22:17:06.461+00:00",[],"Imaging-and-determining-friction-forces-of-specific-interactions-between-human-IgG-and-rat-anti-human-IgG",{"abstract":924,"title":926,"gsPaper":928,"references":930,"doi":932},{"EN":925},"Covalently immobilized rat anti-human immunoglobulin (IgG) monolayers on thiol-modified gold substrates and human IgG linked with the tips were fabricated using the self-assembled monolayer method, and interactions between these systems were studied by friction force microscopy (FFM). In addition to observation of distinct nanostructures of protein monolayers due to recognition events, FFM also quantified the friction force due to protein–protein-specific interactions. The average friction force due to interactions between the antigen functionalized tip and the antibody monolayer was determined as 200–250 pN, significantly greater than that between either the bare tip and the antibody monolayer (0–50 pN), or the blocked antigen tip and the antibody monolayer (50–100 pN), indicative of antigen\u002Fantibody-specific interactions. These results, taken together, suggest that FFM is not only capable of tracking recognition events, but also quantifying the friction force due to specific interactions between biological molecules, such as antigen and antibody.",{"EN":927},"Imaging and determining friction forces of specific interactions between human IgG and rat anti-human IgG",{"VOID":929},"[\"5745229248785815771\"]",{"VOID":931},"Kwong, P.D., Wyatt, R., Robinson, J., Sweet, R.W., Sodroski, J., Hendrickson, W.A.: Structure of an HIV gp120 envelope glycoprotein in complex with the CD4 receptor and a neutralizing human antibody. Nature 393, 648–659 (1998)\nCalarese, D.A., Scanlan, C.N., Zwick, M.B., Deechongkit, S., Mimura, Y., Kunert, R., Zhu, P., Wormald, M.R., Stanfield, R.L., Roux, K.H., Kelly, J.W., Rudd, P.M., Dwek, R.A., Katinger, H., Burton, D.R., Wilson, I.A.: Antibody domain exchange is an immunological solution to carbohydrate cluster recognition. Science 300, 2065–2071 (2003)\nCarroll, M.C.: The complement system in regulation of adaptive immunity. Nat. Immunol. 5, 981–986 (2004)\nPeretz, D., Williamson, R.A., Kaneko, K., Vergara, J., Leclerc, E., Schmitt-Ulms, G., Mehlhorn, I.R., Legname, G., Wormald, M.R., Rudd, P.M., Dwek, R.A., Burton, D.R., Prusiner, S.B.: Antibodies inhibit prion propagation and clear cell cultures of prion infectivity. Nature 412, 739–743 (2001)\nLi, H., Sethuraman, N., Stadheim, T.A., Zha, D., Prinz, B., Ballew, N., Bobrowicz, P., Choi, B.K., Cook, W.J., Cukan, M., Houston-Cummings, N.R., Davidson, R., Gong, B., Hamilton, S.R., Hoopes, J.P., Jiang, Y., Kim, N., Mansfield, R., Nett, J.H., Rios, S., Strawbridge, R., Wildt, S., Gerngross, T.U.: Optimization of humanized IgGs in glycoengineered Pichia pastoris. Nat. Biotechnol. 24, 210–215 (2006)\nZhu, H., Bilgin, M., Snyder, M.: Proteomics. Annu. Rev. Biochem. 72, 783–812 (2003)\nKusnezow, W., Jacob, A., Walijew, A., Diehl, F., Hoheisel, J.D.: Antibody microarrays: an evaluation of production parameters. Proteomics 3, 254–264 (2003)\nSheth, S.R., Leckband, D.: Measurements of attractive forces between proteins and end-grafted poly(ethylene glycol) chains. Proc. Natl. Acad. Sci. U.S.A. 94, 8399–8404 (1997)\nKarisson, R., Falt, A.: Experimental design for kinetic analysis of protein–protein interactions with surface plasmon resonance biosensors. J. Immunol. Methods 200, 121–133 (1997)\nLin, S., Chen, J.L., Huang, L.S., Li, H.W.: Measurements of the forces in protein interactions with atomic force microscopy. Curr. Proteomics. 2, 55–81 (2005)\nFotiadis, D., Scheuring, S., Muller, S.A., Engel, A., Muller, D.J.: Imaging and manipulation of biological structures with the AFM. Micron 33, 385–397 (2002)\nLeggett, G.J., Brewer, N.J., Chonga, K.S.L.: Friction force microscopy: towards quantitative analysis of molecular organisation with nanometre spatial resolution. Phys. Chem. Chem. Phys. 7, 1107–1120 (2005)\nColburn, T.J., Leggett, G.J.: Influence of solvent environment and tip chemistry on the contact mechanics of tip-sample interactions in friction force microscopy of self-assembled monolayers of mercaptoundecanoic acid and dodecanethiol. Langmuir 23, 4959–4964 (2007)\nLeggett, G.J.: Friction force microscopy of self-assembled monolayers: probing molecular organisation at the nanometre scale. Anal. Chim. Acta. 479, 17–38 (2003)\nAhimou, F., Semmens, M.J., Novak, P.J., Haugstad, G.: Biofilm cohesiveness measurement using a novel atomic force microscopy methodology. Appl. Environ. Microbiol. 73, 2897–2904 (2007)\nLo, Y.S., Zhu, Y.J., Beebe, T.P.: Loading-rate dependence of individual ligand-receptor bond-rupture forces studied by atomic force microscopy. Langmuir 17, 3741–3748 (2001)\nFlorin, E.L., Moy, V.T., Gaub, H.E.: Adhesion forces between individual ligand–receptor pairs. Science 264, 415–417 (1994)\nChoi, J.W., Park, S.J., Nam, Y.S., Lee, W.H., Fujihira, M.: Molecular pattern formation using chemically modified cytochrome. Colloids Surf. B, Biointerfaces 23, 295–303 (2002)\nLekka, M., Kulik, A.J., Jeney, S., Raczkowska, J., Lekki, J., Budkowski, A., Forro, L.: Friction force microscopy as an alternative method to probe molecular interactions. J. Chem. Phys. 123, 014702 (2005)\nFerretti, S., Paynter, S., Russell, D.A., Sapsford, K.E., Richardson, D.J.: Self-assembled monolayers: a versatile tool for the formulation of bio-surfaces. Trends. Analyt. Chem. 19, 530–540 (2000)\nLove, J.C., Estroff, L.A., Kriebel, J.K., Nuzzo, R.G., Whitesides, G.M.: Self-assembled monolayers of thiolates on metals as a form of nanotechnology. Chem. Rev. 105, 1103–1169 (2005)\nLv, Z., Wang, J., Deng, L., Chen, G.: Preparation and characterization of covalent binding of rat anti-human IgG monolayer on thiol-modified gold surface. Nanoscale Res. Lett. 4, 1403–1408 (2009)\nWakayama, J., Sekiguchi, H., Akanuma, S., Ohtani, T., Sugiyama, S.: Methods for reducing nonspecific interaction in antibody–antigen assay via atomic force microscopy. Anal. Biochem. 380, 51–58 (2008)\nLuthi, R., Meyer, E., Haefke, H., Howald, L., Gutmannsbauer, W., Guggisberg, M., Bammerlin, M., Guntherodt, H.J.: Nanotribology: an UHV-SFM study on thin films of C60 and AgBr. Surf. Sci. 338, 247–260 (1995)\nNonnenmacher, M., Greschner, J., Wolter, O., Kassing, R.: Scanning force microscopy with micromachined silicon sensors. J. Vac. Sci. Technol. B9, 1358–1362 (1991)\nSader, J.E., Sader, R.C.: Susceptibility of atomic force microscope cantilevers to lateral forces: experimental verification. Appl. Phys. Lett. 83, 3195–3197 (2003)\nSadaie, M., Nishikawa, N., Ohnishi, S., Tamada, K., Yase, K., Hara, M.: Studies of human hair by friction force microscopy with the hair-model-probe. Colloids Surf. B. Biointerfaces 51, 120–129 (2006)\nLv, Z., Wang, J., Chen, G., Deng, L.: Probing specific interaction forces between human IgG and rat anti-human IgG by self-assembled monolayer and atomic force microscopy. Nanoscale Res. Lett. 5, 1032–1038 (2010)\nChen, L.W., Cheung, C.L., Ashby, P.D., Lieber, C.M.: Single-walled carbon nanotube AFM probes: optimal imaging resolution of nanoclusters and biomolecules in ambient and fluid environments. Nano Lett. 4, 1725–1731 (2004)\nClear, S.C., Nealey, P.F.: Chemical force microscopy study of adhesion and friction between surfaces functionalized with self-assembled monolayers and immersed in solvents. J. Colloid Interface Sci. 213, 238–250 (1999)\nDerjaguin, B.V., Muller, V.M., Toporov, Yu.P.: Effect of contact deformations on the adhesion of particles. J. 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Springer-Verlag, New York (1980)",{"doi":464},{"id":1218,"text":1219,"url":1220,"identifiers":1221},"2aea60b2-2c58-4ffb-8d50-2e6bf7b7cc6c","Crum, L.A.: Nucleation and stabilization of micro-bubbles in liquids. Appl. Sci. Res. 38, 101–115 (1982)","https:\u002F\u002Flink.springer.com\u002Farticle\u002F10.1007\u002FBF00385941",{"doi":1222},"10.1007\u002FBF00385941",{"id":1218,"text":1224,"url":1220,"identifiers":1225},"Crum, L.A.: Nucleation and stabilization of microbubbles in liquids. In: van Wijngaarden, L. (ed.) Mechanics and Physics of Bubbles in Liquids, pp. 101–115. Martinus Nijhoff Publishers, The Hague (1982)",{"doi":1222},{"id":460,"text":1227,"url":462,"identifiers":1228},"Sirotyuk, M.G.: Experimental investigations of ultrasonic cavitation. In: Rozenberg, L.D. (ed.) High Intensity Ultrasonic Fields, pp. 319–337. Plenum Press, New York (1971)",{"doi":464},{"id":22,"text":1230,"url":22,"identifiers":1231},"Washburn, E.W. (ed.): International Critical Tables, vol. 4. 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Lett. 46, 454–460 (1999)",{"doi":464},{"id":1512,"text":1513,"url":1514,"identifiers":1515},"4da74040-670b-4fb1-8dd1-d9dd3d8d8689","Joanny, J.F.: Polyelectrolyte adsorption and charge inversion. Eur. J. Phys. B 9, 117–122 (1999)","http:\u002F\u002Flink.springer.com\u002F10.1007\u002Fs100510050747",{"doi":1516},"10.1007\u002Fs100510050747",{"id":1518,"text":1519,"url":1520,"identifiers":1521},"115ca564-cc1c-4010-a2ea-ba7aab3abd80","Perel, V.I., Shklovskii, B.I.: Screening of a macroion by multivalent ions: a new boundary condition for the Poisson-Boltzmann equation and charge inversion. Physica A (Amsterdam) 274, 446–453 (1999)","https:\u002F\u002Fwww.sciencedirect.com\u002Fscience\u002Farticle\u002Fpii\u002FS0378437199003799",{"doi":1522},"10.1016\u002Fs0378-4371(99)00379-9",{"id":460,"text":1524,"url":462,"identifiers":1525},"Shklovskii, B.I.: Screening of a macroion by multivalent ions: correlation-induced inversion of charge. Phys. Rev. E 60, 5802–5811 (1999)",{"doi":464},{"id":460,"text":1527,"url":462,"identifiers":1528},"Nguyen, T.T., Grosberg, F.Yu., Shklovskii, B.I.: Screening of a charged particle by multivalent counterions in salty water: strong charge inversion. J. Chem. Phys. 113, 1110–1125 (2000)",{"doi":464},{"id":460,"text":1530,"url":462,"identifiers":1531},"Nguyen, T.T., Grosberg, F.Yu., Shklovskii, B.I.: Macroions in salty water with multivalent ions: giant inversion of charge. Phys. Rev. Lett. 85, 1568–1571 (2000)",{"doi":464},{"id":460,"text":1533,"url":462,"identifiers":1534},"Levin, Y.: Electrostatic correlations: from plasma to biology. Rep. Prog. Phys. 65, 1577–1632 (2002)",{"doi":464},{"id":460,"text":1536,"url":462,"identifiers":1537},"Quesada-Perez, M., Gonzalez-Tovar, E., Martin-Molina, A., Lozada-Cassou, M., Hidalgo-Alvarez, R.: Overcharging in colloids: beyond the Poisson-Boltzmann approach. ChemPhysChem 4, 235–248 (2003)",{"doi":464},{"id":460,"text":1539,"url":462,"identifiers":1540},"Grosberg, F.Yu., Nguyen, T.T., Shklovskii, B.I.: Colloquium: the physics of charge inversion in chemical and biological systems. Rev. Mod. Phys. 74, 329–345 (2002)",{"doi":464},{"id":460,"text":1542,"url":462,"identifiers":1543},"Zhang, R.; Shklovskii, B.I.: Long-range polarization attraction between two different like-charged macroions. Phys. Rev. E 72, 021405 (2005)",{"doi":464},{"id":460,"text":1545,"url":462,"identifiers":1546},"Pittler, J., Bu, W., Vakhnin, D., Travesset, A., McGillivray, D.J., Losche, M.: Charge inversion at minute electrolyte concentrations. Phys. Rev. Lett. 97, 046102 (2006)",{"doi":464},{"id":460,"text":1548,"url":462,"identifiers":1549},"Gracheva, M.E., Leburton, J.P.: Electrolytic charge inversion at the liquid-solid interface in a nanopore in a doped semiconductor membrane. Nanotechnology 18, 145704 (2007)",{"doi":464},{"id":460,"text":1551,"url":462,"identifiers":1552},"Faraudo, J., Travesset, A.: The many origins of charge inversion in electrolyte solutions: effects of discrete interfacial charges. J. Phys. Chem. C 111, 987–994 (2007)",{"doi":464},{"id":460,"text":1554,"url":462,"identifiers":1555},"Calero, C., Faraudo, J.: Enhancement of charge inversion by multivalent interfacial groups. Phys. Rev. E 80, 042601 (2009)",{"doi":464},{"id":460,"text":1557,"url":462,"identifiers":1558},"Terao, T., Nakayama, T.: Charge inversion of colloidal particles in an aqueous solution: screening by multivalent ions. Phys. Rev. E 63, 041401 (2001)",{"doi":464},{"id":460,"text":1560,"url":462,"identifiers":1561},"Wang, Z.Y., Ma, Y.Q.: Monte Carlo determination of mixed electrolytes next to a planar dielectric interface with different surface charge distributions. J. Chem. Phys. 131, 244715 (2009)",{"doi":464},{"id":460,"text":1563,"url":462,"identifiers":1564},"Wang, Z.Y., Ma, Y.Q.: Insights from Monte Carlo simulations on charge inversion of planar electric double layers in mixtures of asymmetric electrolytes. J. Chem. Phys. 133, 064704 (2010)",{"doi":464},{"id":22,"text":1566,"url":22,"identifiers":1567},"Dukhin, S.S., Deryaguin, B.V.: Electrophoresis. Nauka, Moscow (1976, in Russian)",{},{"id":22,"text":1569,"url":22,"identifiers":1570},"Landau, L.D., Lifshitz, E.M.: Fluid Mechanics. Pergamon Press, Oxford (1987)",{},{"id":22,"text":1572,"url":22,"identifiers":1573},"Langevin, P.: Sur la théorie du mouvement brownien. Coptes Rendus (Paris) 146, 530–533 (1908)",{},{"id":22,"text":1575,"url":22,"identifiers":1576},"Tikhonov, V.I.: Outliers in Random Processes. Nauka, Moscow (1970, in Russian)",{},{"id":460,"text":1578,"url":462,"identifiers":1579},"Jullien, R.: Aggregation phenomena and fractal aggregates. Cont. Phys. 28, 477–493 (1987)",{"doi":464},{"id":1581,"createTime":1582,"updateTime":1583,"relativeEntities":1584,"slug":1585,"properties":1586,"entityType":223,"verifyStatus":224,"verifyTime":1597,"verifyNote":226,"languages":22,"translateLanguages":22,"viewCount":23,"primaryUrl":1598,"fullTextUrl":22,"authors":1599,"publicationType":258,"publisherRelationship":1638,"citationCount":22,"citationInfo":22,"publishDate":1697,"publishYear":1054,"citationAnalyzeStatus":324,"lastCitationAnalyze":1583,"indexDatabases":1698,"openAccess":22,"references":22,"isForceReanalyzing":327},"460c2f2b-7b18-4bb8-8120-51a34aa1808b","2024-01-20T13:23:57.626+00:00","2026-07-23T12:35:42.885+00:00",[],"Studying-the-evolutionary-relationships-and-phylogenetic-trees-of-21-groups-of-tRNA-sequences-based-on-complex-networks",{"abstract":1587,"title":1589,"gsPaper":1591,"references":1593,"doi":1595},{"EN":1588},"To find out the evolutionary relationships among different tRNA sequences of 21 amino acids, 22 networks are constructed. One is constructed from whole tRNAs, and the other 21 networks are constructed from the tRNAs which carry the same amino acids. A new method is proposed such that the alignment scores of any two amino acids groups are determined by the average degree and the average clustering coefficient of their networks. The anticodon feature of isolated tRNA and the phylogenetic trees of 21 group networks are discussed. We find that some isolated tRNA sequences in 21 networks still connect with other tRNAs outside their group, which reflects the fact that those tRNAs might evolve by intercrossing among these 21 groups. We also find that most anticodons among the same cluster are only one base different in the same sites when S ≥ 70, and they stay in the same rank in the ladder of evolutionary relationships. Those observations seem to agree on that some tRNAs might mutate from the same ancestor sequences based on point mutation mechanisms.",{"EN":1590},"Studying the evolutionary relationships and phylogenetic trees of 21 groups of tRNA sequences based on complex networks",{"VOID":1592},"[\"2934028534693726559\"]",{"VOID":1594},"Barabási, A.L., Albert, R.: Emergence of scaling in random networks. Science 286, 509–511 (1999)\nWatts, D.J., Strogatz, S.H.: Collective dynamics of ‘small-world’ networks. Nature 393, 440–442 (1998)\nStrogatz, S.H.: Exploring complex networks. Nature 410, 268–276 (2001)\nVázquez, A., Pastor-Satorras, R., Vespignani, A.: Large-scale topological and dynamical properties of the Internet. Phys. Rev. E 65, 066130 (2002)\nAlbert, R., Jeong, H., Barabási, A.L.: Diameter of the world-wide web. Nature 401, 130 (1999)\nBarabási, A.L., Albert, R., Jeong, H.: Scale-free characteristics of random networks: the topology of the world-wide web. Physica A 281, 69–77 (2000)\nJeong, H., Mason, S.P., Barabási, A.L., Oltvai, Z.N.: Lethality and centrality in protein networks. Nature 411, 41–42 (2001)\nGoh, K., Cusick, M.E., Valle, D., Childs, B., Vidal, M., Barabási, A.L.: The human disease network. Proc. Natl. Acad. Sci. U. S. A. 104, 8685–8690 (2007)\nChen, B., Xian, Y., Wei, F.: The evolutionary network study of tRNA sequences. Acta Biophysica Sinica 25, 117 (2009). In Chinese\nWei, F., Li, S., Ma, H.: Network of tRNA gene sequences. J. Shanghai Jiaotong Univ. (Sci.) 13, 611–616 (2008)\nSong, N., Joseph, J.M., Davis, G.B., Durand, D.: Sequence similarity network reveals common ancestry of multidomain proteins. Comput. Biol. 4, 1–19 (2008)\nEigen, M., Winkler-Oswatitsch, R.: Transfer-RNA: the early adaptor. Naturwissenschaften 68, 217–228 (1981)\nSaks, M.E., Sampson, J.R., Abelson, J.: Evolution of a transfer RNA gene through a point mutation in the anticodon. Science 279, 1665–1667 (1998)\nRodriguez-Vargas, A.M., Fajardo, J.E., Ramirez, B.C.: Phylogeny of transfer RNA. Orig. Life 14, 547–555 (1984)\nSoto, M.A., Toha, J.: Phylogenetic tree of tRNAs using a simple algorithm. Orig. Life Evol. Biosph. 20, 161–166 (1990)\nFarias, S.T., Guimaraes, R.C.: Aminoacyl-tRNA synthetase classes and groups in prokaryotes. J. Theor. Biol. 250, 221–229 (2008)\nWei, F., Meng, M., Li, S., Ma, H.: Comparing two evolutionary mechanisms of modern tRNAs. Mol. Phylogenet. Evol. 38, 1–11 (2006)\nSprinzl, M., Horn, C., Brown, M., Steinberg, S.: Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res. 26, 148–153 (1998)\nSprinzl, M., Vassilenko, K.S.: Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res. 33, 139–140 (2005)\nJühling, F., Mörl, M., Hartmann, R.K., Sprinzl, M., Stadler, P.F., Pütz, J.: tRNAdb 2009: compilation of tRNA sequences and tRNA genes. Nucleic Acids Res. 37, 159–162 (2009)\nSaitou, N., Nei, M.: The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406–425 (1987)\nWei, F., Li, S., Ma, H.: Computer simulation of tRNA evolution. J. Phys. A: Math. Theor. 42, 345101 (2009)",{"VOID":1596},"10.1007\u002Fs10867-011-9236-6","2024-06-23T01:53:33.204+00:00","https:\u002F\u002Flink.springer.com\u002Farticle\u002F10.1007\u002Fs10867-011-9236-6",[1600,1615],{"id":1601,"sortIndex":23,"researcher":22,"roles":1602,"affiliations":1603,"properties":1612,"displayName":1614,"givenName":22,"familyName":22},"c86e90c3-fe39-48e4-a053-278d4ce40385",[232],[1604],{"id":1605,"sortIndex":23,"affiliation":1606,"properties":22},"2a702cbd-ef3f-4343-a6f4-0fc3cf723af3",{"id":1605,"createTime":22,"updateTime":22,"relativeEntities":1607,"slug":22,"properties":1608,"entityType":22,"verifyStatus":22,"verifyTime":22,"verifyNote":22,"languages":22,"translateLanguages":22,"viewCount":22,"url":22,"parentIds":1611,"statistic":22},[],{"title":1609},{"VI":1610},"Physical Science & Technology College, Guangxi University, Nanning, China",[],{"title":1613},{"VI":1614},"Fangping 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Communications, Ministry of Education, Beijing University of Posts and Telecommunications, Beijing, China",[],{"title":1634,"gsAuthor":1636},{"VI":1635},"Bowen 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numerical study of the energy landscape of the space of model proteinsequences is carried out. As a consequence of the heterogeneity of thecontact energies among amino acids, the energy landscape displays a veryrough profile, a behaviour typical of frustrated systems. This givesraise to a hierarchical clustering of low-energy sequences and can have evolutionary consequences.",{"EN":1709},"Energy Profile of the Space of Model Protein Sequences",{"VOID":1711},"[\"6825871542077298877\"]",{"VOID":1713},"10.1023\u002FA:1013151530254","2024-05-04T13:19:04.834+00:00","https:\u002F\u002Flink.springer.com\u002Farticle\u002F10.1023\u002FA:1013151530254",[1717,1742,1762],{"id":1718,"sortIndex":23,"researcher":22,"roles":1719,"affiliations":1720,"properties":1737,"displayName":1739,"givenName":22,"familyName":22},"c4b3daa2-bb4b-4eea-8884-0042fff6eb04",[232],[1721,1729],{"id":1722,"sortIndex":23,"affiliation":1723,"properties":22},"9780d46f-5d46-46ce-9187-52c9b4bd0edd",{"id":1722,"createTime":22,"updateTime":22,"relativeEntities":1724,"slug":22,"properties":1725,"entityType":22,"verifyStatus":22,"verifyTime":22,"verifyNote":22,"languages":22,"translateLanguages":22,"viewCount":22,"url":22,"parentIds":1728,"statistic":22},[],{"title":1726},{"VI":1727},"The Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark",[],{"id":1730,"sortIndex":115,"affiliation":1731,"properties":22},"7ecd79a7-b789-4aa5-8ae8-504cf13b2c27",{"id":1730,"createTime":22,"updateTime":22,"relativeEntities":1732,"slug":22,"properties":1733,"entityType":22,"verifyStatus":22,"verifyTime":22,"verifyNote":22,"languages":22,"translateLanguages":22,"viewCount":22,"url":22,"parentIds":1736,"statistic":22},[],{"title":1734},{"VI":1735},"Department of Chemistry, Harvard University, Cambridge, USA",[],{"title":1738,"gsAuthor":1740},{"VI":1739},"G. 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B15, 385 (2000).",{},{"id":1922,"createTime":1923,"updateTime":1924,"relativeEntities":1925,"slug":1926,"properties":1927,"entityType":223,"verifyStatus":224,"verifyTime":1938,"verifyNote":226,"languages":22,"translateLanguages":22,"viewCount":23,"primaryUrl":1939,"fullTextUrl":22,"authors":1940,"publicationType":258,"publisherRelationship":1973,"citationCount":23,"citationInfo":2033,"publishDate":2036,"publishYear":2034,"citationAnalyzeStatus":21,"lastCitationAnalyze":1924,"indexDatabases":2037,"openAccess":22,"references":22,"isForceReanalyzing":327},"d541fb94-f5d2-4321-8115-3301cef8f1dc","2024-01-13T19:55:31.014+00:00","2026-07-22T13:05:22.916+00:00",[],"Dynamic-Approach-to-DNA-Breathing",{"abstract":1928,"title":1930,"gsPaper":1932,"references":1934,"doi":1936},{"EN":1929},"Even under physiological conditions, the DNA double-helix spontaneously denatures locally, opening up fluctuating, flexible, single-stranded zones called DNA-bubbles. We present a dynamical description of this DNA-bubble breathing in terms of a Fokker-Planck equation for the bubble size, based on the Poland-Scheraga free energy for DNA denaturation. From this description, we can obtain basic quantities such as the lifetime, an important measure for the description of the interaction of a breathing DNA molecule and selectively single-stranded DNA binding proteins. Our approach is consistent with recent single molecule measurements of bubble fluctuation. We also introduce a master equation approach to model DNA breathing, and discuss its differences from the continuous Fokker-Planck description.",{"EN":1931},"Dynamic Approach to DNA Breathing",{"VOID":1933},"[\"7810837834197427379\"]",{"VOID":1935},"Kornberg, A: DNA Synthesis, W.H. Freeman, San Francisco, CA, (1974).\nDelcourt, S.G. and Blake R.D.: Stacking Energies in DNA, J. Biol. Chem. 266 (1991), 15160–15169.\nPoland, D. and Scheraga, H.A.: Theory of Helix-Coil Transitions in Biopolymers, Academic Press, New York, NY, (1970).\nGuéron, M., Kochoyan, M. and Leroy J.-L.: Nature 328 (1987), 89.\nAltan-Bonnet, G., Libchaber, A. and Krichevsky, O.: Phys. Rev. Lett. 90 (2003), 138101.\nde Gennes, P.G., Scaling concepts in polymer physics, Cornell University Press, Ithaca, New York, (1979).\nKittel, C.: Am. J. Phys. 37 (1969), 917.\nZimm, B.H.: J. Chem. Phys. 33 (1960), 1349.\nPoland, D. and Scheraga, H.A.: J. Chem. Phys. 45 (1966), 1456; ibid. 1464.\nFisher, M.E.: J. Chem. Phys. 45 (1966), 1469.\nWartell, R.M. and Benight, A.S.: Phys. Rep. 126 (1983), 67.\nGotoh, O.: Adv. Biophys. 16 (1983), 1.\nRichard, C. and Guttmann, A.J.: J. Stat. Phys. 115 (2004), 925.\nBlake, R.D., Bizzaro, J.W., Blake, J.D., Day, G.R., Delcourt, S.G., Knowles, J., Marx, K.A. and SantaLucia, Jr. J.: Bioinformatics 15 (1999), 370.\nYeramian, E.: Gene 255 (2000), 139; ibid. 151.\nCarlon, E., Malki, M.L. and Blossey, R.: Phys. Rev. Lett. 94 (2005), 178101, E-print (2004), q-bio\u002F0409034.\nHwa, T., Marinari, E., Sneppen K. and Tang, L.-H.: Proc. Natl. Acad. Sci. USA 100 (2003), 4411.\nBlossey, R. and Carlon, E.: Phys. Rev. E 68 (2003), 061911.\nFixman, M. and Freire, J.J.: Biopol. 16 (1977), 2693.\nKafri, Y., Mukamel, D. and Peliti, L.: Phys. Rev. Lett. 85 (2000), 4988; ibid. 90 (2003), 159802.\nHanke, A. and Metzler, R.: Phys. Rev. Lett. 90 (2003), 159801.\nHanke, A and Metzler, R.: Bubble dynamics in DNA, J. Phys. A 36 (2003), L473–L480.\nChuang, J., Kantor, Y. and Kardar, M.: Phys. Rev. E 65 (2002), 011802.\nAmbjörnsson, T. and Metzler, R.: Phys. Rev. E 72 (2005), 030901 (R), E-print q-bio.BM\u002F0411053.\nvan Kampen, N.G.: Stochastic Processes in Physics and Chemistry, North-Holland, Amsterdam, (1981).\nPant, K., Karpel, R.L. and Williams, M.C.: J. Mol. Biol. 327 (2003), 571.\nAmbjörnsson, T. and Metzler, R.: Dynamics of bubble breathing in heterogeneous DNA, unpublished.",{"VOID":1937},"10.1007\u002Fs10867-005-2410-y","2024-06-24T01:39:36.737+00:00","https:\u002F\u002Flink.springer.com\u002Farticle\u002F10.1007\u002Fs10867-005-2410-y",[1941,1958],{"id":1942,"sortIndex":23,"researcher":22,"roles":1943,"affiliations":1944,"properties":1953,"displayName":1955,"givenName":22,"familyName":22},"072e0cc2-394f-4318-8501-104ad0fd8e17",[232],[1945],{"id":1946,"sortIndex":23,"affiliation":1947,"properties":22},"ab0cb0ea-cdef-4996-8913-ee0bc276fe4a",{"id":1946,"createTime":22,"updateTime":22,"relativeEntities":1948,"slug":22,"properties":1949,"entityType":22,"verifyStatus":22,"verifyTime":22,"verifyNote":22,"languages":22,"translateLanguages":22,"viewCount":22,"url":22,"parentIds":1952,"statistic":22},[],{"title":1950},{"VI":1951},"NORDITA – Nordic Institute for Theoretical Physics, Copenhagen Ø, 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kinds of experiments have been designed in attempting to observe theparity violation of electroweak force at the phase transition of singlecrystals of D- and L-alanine and valine.(1) An obvious λ phasetransition at 270 ± 1 K was shown in the specific heat measurement ofalanine and valine enantiomers by differential scanning calorimetry. Thebiologically dominant L-enantiomer was found to have lower energy. (2)Magnetization of single crystals of D- and L-alanine and D-valine weremeasured as a function of temperature using the SQUID magnetometer. Thedifference of the mass susceptibility χρ ∼ T curve between theD-alanine and L-alanine is attributable to the variation of intramoleculargeometry of chirality density, which is related to the parity violationenergy shift of a chiral molecule and is a consequence of the short rangeof the weak interaction between the nuclei and electrons. (3) Laser Ramanspectra of D- and L-alanine at different low temperatures (100 K, 250 K,260 K, 270 K, 280 K and 290 K) showed that the second order Cα–Hdeformation modes at 2606 cm-1, 2724 cm-1 of D-alanine vanishedat 270 K but reappeared at 100 K. In the same method, L-alanine has nosuch phenomenon. An obvious decrease in the scattering intensity of themethyne group Cα–H stretching mode at 2964 cm-1 in D-alanineoccurs at the λ transition temperature. We present our experimentsinvolving the possible relevance of Z0 force with Salam's putativephase transition in the origin of homochirality.",{"EN":2048},"Parity Violation of Electroweak Force in Phase Transitions of Single Crystals of D- and L-Alanine and Valine",{"VOID":2050},"[\"16184109651469688414\"]",{"VOID":2052},"Bouchiat, M.A. and Pottier, L.: An atomic preference between left and right, Scientific American (1984), 76–86.\nSalam, A.: The origin of chirality, the role of phase transitions and their induction in amino acids, In: Cyril Ponnamperuma and Julian Chela-Flores (eds.), Chemical Evolution: Origin of Life, Hampton, Virginia, U.S.A., A Deepak Publishing (1993), 101–117.\nSimpson, H.J. and Marsh, R.E.: The crystal structure of L-alanine, Acta Cryst. 20 (1966), 550.\nWang, W.Q. and Sheng, X.R., et al.: Susceptibility behaviour and specific heat anomaly in single crystals of alanine and valine, J. Biol. Phys. 22 (1996), 65–71.\nGrunenberg, A., Bougeard, D. and Schrader, B.: DSC-investigations of 22 crystalline neutral aliphatic amino acids in the temperature range 233 to 423 K, Thermochimica Acta 77 (1984), 59–66.\nMason, S.F. and Tranter, G.E.: The parity-violating energy difference between enantiomeric molecules, Molec. Phys. 53 (1984), 1091–1111.\nHegstrom, Roger A. and Kondepudi, Dilip K.: The handedness of the universe, Scientific American, January 1990, 98–105.\nHegstrom, Roger A.: Electron Chirality, J. of Molecular Structure (Theochem) 232 (1974), 69–73.\nVonsovskii, S.V.: Magnetism, Vol. 1, Wiley, New York (1974), 69–73.\nShimanouch, T.: tables of molecular vibrational frequencies, Consolidated Vol. 1 NSRDS-NBS 39, U.S. Govt. Printing Office, Washington, 1972.\nSimons, L. and Bergstrom, G., et al.: Comment. Phys. Math. 42 (1972), 125.\nHarris, M.J., Loving, C.E. and Sandars, P.G.H.: Atomic shielding and DNC optical rotation in bismuth, J. Phys. Chem. 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