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Volumn 66, Issue 1, 2002, Pages

Dynamics and configurational fluctuations of single DNA molecules in linear mixed flows

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

EID: 33748705728     PISSN: 1063651X     EISSN: None     Source Type: Journal    
DOI: 10.1103/PhysRevE.66.011915     Document Type: Article
Times cited : (78)

References (46)
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    • R.B. Bird, C.F. Curtiss, R.C. Armstrong, and O. Hassager, Dynamics of Polymeric Liquids: Vol. 2 Kinetic Theory (Wiley, New York, 1987)
    • R.B. Bird, C.F. Curtiss, R.C. Armstrong, and O. Hassager, Dynamics of Polymeric Liquids: Vol. 2 Kinetic Theory (Wiley, New York, 1987).
  • 3
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    • R.G. Larson, The Structure and Rheology of Complex Fluids (Oxford University Press, Oxford, 1999)
    • R.G. Larson, The Structure and Rheology of Complex Fluids (Oxford University Press, Oxford, 1999).
  • 14
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    • (1998) , vol.281 , pp. 5381
    • Smith, D.E.1    Chu, S.2
  • 23
    • 85036308153 scopus 로고    scopus 로고
    • J. Chem. Phys.U.S. Agarwal3, 397 (2000
    • (2000) , vol.3 , pp. 397
    • Agarwal, U.S.1
  • 26
    • 0034508074 scopus 로고    scopus 로고
    • J. Chem. Phys.A. Dua and B.J. Cherayil, 113, 10776 (2000);
    • (2000) , vol.113 , pp. 10776
    • Dua, A.1    Cherayil, B.J.2
  • 32
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    • C. W. Gardiner, Handbook of Stochastic Methods (Springer, Berlin, 1985)
    • C. W. Gardiner, Handbook of Stochastic Methods (Springer, Berlin, 1985).
  • 33
    • 85036421636 scopus 로고    scopus 로고
    • F. Reif, Fundamentals of Statistical and Thermal Physics (McGraw Hill, New York, 1965)
    • F. Reif, Fundamentals of Statistical and Thermal Physics (McGraw Hill, New York, 1965).
  • 34
    • 85036260870 scopus 로고    scopus 로고
    • (Formula presented) is defined as (Formula presented) where l is the Kuhn length, (Formula presented) is a dimensionless strain/shear rate, D is the diffusivity and thus (Formula presented) is a ratio of diffusion time scale and characteristic convective time scale
    • (Formula presented) is defined as (Formula presented) where l is the Kuhn length, (Formula presented) is a dimensionless strain/shear rate, D is the diffusivity and thus (Formula presented) is a ratio of diffusion time scale and characteristic convective time scale.
  • 35
    • 85036211491 scopus 로고    scopus 로고
    • (Formula presented) was determined by fitting the remaining 30% of the average molecular extension (Formula presented)] of 400–2000 initially stretched chains to a single exponential function (Formula presented). The longest relaxation time calculated in this manner is in quantitative agreement with those calculated from either normal stress or birefrigence decay
    • (Formula presented) was determined by fitting the remaining 30% of the average molecular extension (Formula presented)] of 400–2000 initially stretched chains to a single exponential function (Formula presented). The longest relaxation time calculated in this manner is in quantitative agreement with those calculated from either normal stress or birefrigence decay.
  • 36
    • 85036272433 scopus 로고    scopus 로고
    • For the Kramers’ chain simulation, we use 150 bead chains and for the worm-like and Rouse chain simulation we use 15 spring chains. The chains were equilibriated for 20 times each longest relaxation time (Formula presented) before they were put in flow. The steady simulaions were run upto (Formula presented) time steps using a single chain and the transient runs were averaged over 500-800 chains at each time step
    • For the Kramers’ chain simulation, we use 150 bead chains and for the worm-like and Rouse chain simulation we use 15 spring chains. The chains were equilibriated for 20 times each longest relaxation time (Formula presented) before they were put in flow. The steady simulaions were run upto (Formula presented) time steps using a single chain and the transient runs were averaged over 500-800 chains at each time step.
  • 39
    • 85036144481 scopus 로고    scopus 로고
    • (Formula presented) stands for 50.05% straining and 49.95% vorticity. For shear flow, there’s equal contribution from straining and vorticity. The angle between the principal axes can be defined as (Formula presented) for flows that have larger contribution from straining than vorticity and is only (Formula presented) and (Formula presented) for the (Formula presented) (Formula presented) flows respectively
    • (Formula presented) stands for 50.05% straining and 49.95% vorticity. For shear flow, there’s equal contribution from straining and vorticity. The angle between the principal axes can be defined as (Formula presented) for flows that have larger contribution from straining than vorticity and is only (Formula presented) and (Formula presented) for the (Formula presented) (Formula presented) flows respectively.
  • 43
    • 85036341789 scopus 로고    scopus 로고
    • H.P. Babcock et al. (unpublished)
    • H.P. Babcock et al. (unpublished).
  • 44
    • 85036295508 scopus 로고    scopus 로고
    • A similar overlap of birefringence data of a polymer solution at various (Formula presented) was reported by Fuller et al. 9. We have also calculated the steady birefringence of (Formula presented)-DNA molecules using Kramers’ chains and have found a universal curve for various (Formula presented) over a range of (Formula presented) suggesting that birefringence reflects the sharp coil-stretch transition of the molecule
    • A similar overlap of birefringence data of a polymer solution at various (Formula presented) was reported by Fuller et al. 9. We have also calculated the steady birefringence of (Formula presented)-DNA molecules using Kramers’ chains and have found a universal curve for various (Formula presented) over a range of (Formula presented) suggesting that birefringence reflects the sharp coil-stretch transition of the molecule.
  • 45
    • 85036405206 scopus 로고    scopus 로고
    • J.S. Hur, Ph.D. thesis, Stanford University, 2001
    • J.S. Hur, Ph.D. thesis, Stanford University, 2001.


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.