Literature DB >> 19792475

Trajectory approach to two-state kinetics of single particles on sculpted energy landscapes.

David Wu1, Kingshuk Ghosh, Mandar Inamdar, Heun Jin Lee, Scott Fraser, Ken Dill, Rob Phillips.   

Abstract

We study the trajectories of a single colloidal particle as it hops between two energy wells which are sculpted using optical traps. Whereas the dynamical behaviors of such systems are often treated by master-equation methods that focus on particles as actors, we analyze them instead using a trajectory-based variational method called maximum caliber (MaxCal). We show that the MaxCal strategy accurately predicts the full dynamics that we observe in the experiments: From the observed averages, it predicts second and third moments and covariances, with no free parameters. The covariances are the dynamical equivalents of Maxwell-like equilibrium reciprocal relations and Onsager-like dynamical relations.

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Year:  2009        PMID: 19792475      PMCID: PMC3273425          DOI: 10.1103/PhysRevLett.103.050603

Source DB:  PubMed          Journal:  Phys Rev Lett        ISSN: 0031-9007            Impact factor:   9.161


  13 in total

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2.  Single-molecule kinetics with time-dependent rates: a generating function approach.

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Journal:  Phys Rev Lett       Date:  2003-01-16       Impact factor: 9.161

3.  Reaction mechanism determines NMDA receptor response to repetitive stimulation.

Authors:  Gabriela Popescu; Antoine Robert; James R Howe; Anthony Auerbach
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4.  Pre-unfolding resonant oscillations of single green fluorescent protein molecules.

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Journal:  Science       Date:  2005-08-12       Impact factor: 47.728

5.  Measuring flux distributions for diffusion in the small-numbers limit.

Authors:  Effrosyni Seitaridou; Mandar M Inamdar; Rob Phillips; Kingshuk Ghosh; Ken Dill
Journal:  J Phys Chem B       Date:  2007-02-13       Impact factor: 2.991

6.  Maximum Caliber: a variational approach applied to two-state dynamics.

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Journal:  J Chem Phys       Date:  2008-05-21       Impact factor: 3.488

7.  On/off blinking and switching behaviour of single molecules of green fluorescent protein.

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8.  Teaching the principles of statistical dynamics.

Authors:  Kingshuk Ghosh; Ken A Dill; Mandar M Inamdar; Effrosyni Seitaridou; Rob Phillips
Journal:  Am J Phys       Date:  2006-02-01       Impact factor: 1.022

9.  Measurement of lactose repressor-mediated loop formation and breakdown in single DNA molecules.

Authors:  L Finzi; J Gelles
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10.  Real-time observation of DNA looping dynamics of Type IIE restriction enzymes NaeI and NarI.

Authors:  Bram van den Broek; Francesco Vanzi; Davide Normanno; Francesco S Pavone; Gijs J L Wuite
Journal:  Nucleic Acids Res       Date:  2006-01-10       Impact factor: 16.971

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  5 in total

1.  When Brownian diffusion is not Gaussian.

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Authors:  S Pressé; K Ghosh; K A Dill
Journal:  J Phys Chem B       Date:  2011-04-27       Impact factor: 2.991

3.  Building Predictive Models of Genetic Circuits Using the Principle of Maximum Caliber.

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Journal:  Biophys J       Date:  2017-11-07       Impact factor: 4.033

4.  Inferring potential landscapes from noisy trajectories of particles within an optical feedback trap.

Authors:  J Shepard Bryan; Prithviraj Basak; John Bechhoefer; Steve Pressé
Journal:  iScience       Date:  2022-07-19

5.  Sculpting nanoparticle dynamics for single-bacteria-level screening and direct binding-efficiency measurement.

Authors:  Y Z Shi; S Xiong; Y Zhang; L K Chin; Y -Y Chen; J B Zhang; T H Zhang; W Ser; A Larrson; S H Lim; J H Wu; T N Chen; Z C Yang; Y L Hao; B Liedberg; P H Yap; K Wang; D P Tsai; C-W Qiu; A Q Liu
Journal:  Nat Commun       Date:  2018-02-26       Impact factor: 14.919

  5 in total

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