Understanding the role of thermal fluctuations in DNA looping

Author(s):  
David P. Wilson ◽  
Todd Lillian ◽  
Sachin Goyal ◽  
Alexei V. Tkachenko ◽  
Noel C. Perkins ◽  
...  
2005 ◽  
Author(s):  
Seth Blumberg ◽  
Arivalagan Gajraj ◽  
Matthew Pennington ◽  
Alexei Tkachenko ◽  
Jens-Christian Meiners

2021 ◽  
Vol 103 (3) ◽  
Author(s):  
Moupriya Das ◽  
Holger Kantz
Keyword(s):  

2016 ◽  
Vol 7 ◽  
pp. 328-350 ◽  
Author(s):  
Igor Goychuk

The main physical features and operating principles of isothermal nanomachines in the microworld, common to both classical and quantum machines, are reviewed. Special attention is paid to the dual, constructive role of dissipation and thermal fluctuations, the fluctuation–dissipation theorem, heat losses and free energy transduction, thermodynamic efficiency, and thermodynamic efficiency at maximum power. Several basic models are considered and discussed to highlight generic physical features. This work examines some common fallacies that continue to plague the literature. In particular, the erroneous beliefs that one should minimize friction and lower the temperature for high performance of Brownian machines, and that the thermodynamic efficiency at maximum power cannot exceed one-half are discussed. The emerging topic of anomalous molecular motors operating subdiffusively but very efficiently in the viscoelastic environment of living cells is also discussed.


2009 ◽  
Vol 96 (3) ◽  
pp. 20a
Author(s):  
David P. Wilson ◽  
J.C. Meiners ◽  
Todd Lillian ◽  
Alexei Tkachenko ◽  
Noel C. Perkins

2011 ◽  
Vol 100 (3) ◽  
pp. 71a
Author(s):  
Luke Czapla ◽  
David Swigon ◽  
Wilma K. Olson

2015 ◽  
Vol 785 ◽  
pp. 189-218 ◽  
Author(s):  
N. J. Hoh ◽  
R. N. Zia

Hydrodynamic diffusion in the absence of Brownian motion is studied via active microrheology in the ‘pure-hydrodynamic’ limit, with a view towards elucidating the transition from colloidal microrheology to the non-colloidal limit, falling-ball rheometry. The phenomenon of non-Brownian force-induced diffusion in falling-ball rheometry is strictly hydrodynamic in nature; in contrast, analogous force-induced diffusion in colloids is deeply connected to the presence of a diffusive boundary layer even when Brownian motion is very weak compared with the external force driving the ‘probe’ particle. To connect these two limits, we derive an expression for the force-induced diffusion in active microrheology of hydrodynamically interacting particles via the Smoluchowski equation, where thermal fluctuations play no role. While it is well known that the microstructure is spherically symmetric about the probe in this limit, fluctuations in the microstructure need not be – and indeed lead to a diffusive spread of the probe trajectory. The force-induced diffusion is anisotropic, with components along and transverse to the line of external force. The latter is identically zero owing to the fore–aft symmetry of pair trajectories in Stokes flow. In a naïve first approach, the vanishing relative hydrodynamic mobility at contact between the probe and an interacting bath particle was assumed to eliminate all physical contribution from interparticle forces, whereby advection alone drove structural evolution in pair density and microstructural fluctuations. With such an approach, longitudinal force-induced diffusion vanishes in the absence of Brownian motion, a result that contradicts well-known experimental measurements of such diffusion in falling-ball rheometry. To resolve this contradiction, the probe–bath-particle interaction at contact was carefully modelled via an excluded annulus. We find that interparticle forces play a crucial role in encounters between particles in the hydrodynamic limit – as they must, to balance the advective flux. Accounting for this force results in a longitudinal force-induced diffusion $D_{\Vert }=1.26aU_{S}{\it\phi}$, where $a$ is the probe size, $U_{S}$ is the Stokes velocity and ${\it\phi}$ is the volume fraction of bath particles, in excellent qualitative and quantitative agreement with experimental measurements in, and theoretical predictions for, macroscopic falling-ball rheometry. This new model thus provides a continuous connection between micro- and macroscale rheology, as well as providing important insight into the role of interparticle forces for diffusion and rheology even in the limit of pure hydrodynamics: interparticle forces give rise to non-Newtonian rheology in strongly forced suspensions. A connection is made between the flow-induced diffusivity and the intrinsic hydrodynamic microviscosity which recovers a precise balance between fluctuation and dissipation in far from equilibrium suspensions; that is, diffusion and drag arise from a common microstructural origin even far from equilibrium.


1982 ◽  
Vol 25 (4) ◽  
pp. 517-521 ◽  
Author(s):  
S K Samaddar ◽  
D Sperber ◽  
M Zielinska-Pfabé ◽  
M I Sobel

2018 ◽  
Vol 115 (46) ◽  
pp. 11784-11789 ◽  
Author(s):  
Diana M. Cook ◽  
Maggie Bennett ◽  
Brandon Friedman ◽  
Josh Lawrimore ◽  
Elaine Yeh ◽  
...  

De novo kinetochore assembly, but not template-directed assembly, is dependent on COMA, the kinetochore complex engaged in cohesin recruitment. The slowing of replication fork progression by treatment with phleomycin (PHL), hydroxyurea, or deletion of the replication fork protection protein Csm3 can activate de novo kinetochore assembly in COMA mutants. Centromere DNA looping at the site of de novo kinetochore assembly can be detected shortly after exposure to PHL. Using simulations to explore the thermodynamics of DNA loops, we propose that loop formation is disfavored during bidirectional replication fork migration. One function of replication fork stalling upon encounters with DNA damage or other blockades may be to allow time for thermal fluctuations of the DNA chain to explore numerous configurations. Biasing thermodynamics provides a mechanism to facilitate macromolecular assembly, DNA repair, and other nucleic acid transactions at the replication fork. These loop configurations are essential for sister centromere separation and kinetochore assembly in the absence of the COMA complex.


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