New perspectives from the hydrodynamic modes : fluctuation-dissipation theorem, hydrodynamic boundary condition, and nonlocal correlations in thermal fluctuations

Author(s):  
Xiaohui Deng
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.


Author(s):  
M. Gross ◽  
R. Adhikari ◽  
M. E. Cates ◽  
F. Varnik

Recently, we proposed a theoretical framework to include thermal fluctuations into the Lattice Boltzmann (LB) method for non-ideal fluids. Here, we apply a variant thereof to a certain class of force-based non-ideal fluid LB models. We find that ideal-gas-like noise is an exact result of the fluctuation–dissipation theorem in the hydrodynamic regime. It is shown that satisfactory equilibration of the density and fluid momentum can be obtained in a simulation over a wide range of length scales.


2017 ◽  
Author(s):  
R. Colin ◽  
C. Rosazza ◽  
A. Vaknin ◽  
V. Sourjik

AbstractCellular networks are intrinsically subject to stochastic fluctuations, but analysis of the resulting noise remained largely limited to gene expression. The pathway controlling chemotaxis of Escherichia coli provides one example where posttranslational signaling noise has been deduced from cellular behavior. This noise was proposed to result from stochasticity in chemoreceptor methylation, and it is believed to enhance environment exploration by bacteria. Here we combined single-cell FRET measurements with analysis based on the fluctuation-dissipation theorem (FDT) to characterize origins of activity fluctuations within the chemotaxis pathway. We observed surprisingly large methylation-independent thermal fluctuations of receptor activity, which contribute to noise comparably to the energy-consuming methylation dynamics. Interactions between clustered receptors involved in amplification of chemotactic signals are also necessary to produce the observed large activity fluctuations. Our work thus shows that the high response sensitivity of this cellular pathway also increases its susceptibility to noise, from thermal and out-of-equilibrium processes.


eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Remy Colin ◽  
Christelle Rosazza ◽  
Ady Vaknin ◽  
Victor Sourjik

Cellular networks are intrinsically subject to stochastic fluctuations, but analysis of the resulting noise remained largely limited to gene expression. The pathway controlling chemotaxis of Escherichia coli provides one example where posttranslational signaling noise has been deduced from cellular behavior. This noise was proposed to result from stochasticity in chemoreceptor methylation, and it is believed to enhance environment exploration by bacteria. Here we combined single-cell FRET measurements with analysis based on the fluctuation-dissipation theorem (FDT) to characterize origins of activity fluctuations within the chemotaxis pathway. We observed surprisingly large methylation-independent thermal fluctuations of receptor activity, which contribute to noise comparably to the energy-consuming methylation dynamics. Interactions between clustered receptors involved in amplification of chemotactic signals are also necessary to produce the observed large activity fluctuations. Our work thus shows that the high response sensitivity of this cellular pathway also increases its susceptibility to noise, from thermal and out-of-equilibrium processes.


2009 ◽  
Vol 66 (7) ◽  
pp. 2107-2115 ◽  
Author(s):  
Cegeon J. Chan ◽  
R. Alan Plumb

Abstract In simple GCMs, the time scale associated with the persistence of one particular phase of the model’s leading mode of variability can often be unrealistically large. In a particularly extreme example, the time scale in the Polvani–Kushner model is about an order of magnitude larger than the observed atmosphere. From the fluctuation–dissipation theorem, one implication of these simple models is that responses are exaggerated, since such setups are overly sensitive to any external forcing. Although the model’s equilibrium temperature is set up to represent perpetual Southern Hemisphere winter solstice, it is found that the tropospheric eddy-driven jet has a preference for two distinct regions: the subtropics and midlatitudes. Because of this bimodality, the jet persists in one region for thousands of days before “switching” to another. As a result, the time scale associated with the intrinsic variability is unrealistic. In this paper, the authors systematically vary the model’s tropospheric equilibrium temperature profile, one configuration being identical to that of Polvani and Kushner. Modest changes to the tropospheric state to either side of the parameter space removed the bimodality in the zonal-mean zonal jet’s spatial distribution and significantly reduced the time scale associated with the model’s internal mode. Consequently, the tropospheric response to the same stratospheric forcing is significantly weaker than in the Polvani and Kushner case.


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