scholarly journals Superstatistical modelling of protein diffusion dynamics in bacteria

2021 ◽  
Vol 18 (176) ◽  
Author(s):  
Yuichi Itto ◽  
Christian Beck
Keyword(s):  
Anomalous Diffusion ◽  
Recent Experiment ◽  
Diffusion Processes ◽  
Diffusion Constant ◽  
Protein Diffusion ◽  
Gaussian Form ◽  
Diffusion Constants ◽  
Diffusion Dynamics ◽  
Associated Proteins ◽  
Good Agreement

A recent experiment (Sadoon AA, Wang Y. 2018 Phys. Rev. E 98 , 042411. ( doi:10.1103/PhysRevE.98.042411 )) has revealed that nucleoid-associated proteins (i.e. DNA-binding proteins) exhibit highly heterogeneous diffusion processes in bacteria where not only the diffusion constant but also the anomalous diffusion exponent fluctuates for the various proteins. The distribution of displacements of such proteins is observed to take a q -Gaussian form, which decays as a power law. Here, a statistical model is developed for the diffusive motion of the proteins within the bacterium, based on a superstatistics with two variables. This model hierarchically takes into account the joint fluctuations of both the anomalous diffusion exponents and the diffusion constants. A fractional Brownian motion is discussed as a possible local model. Good agreement with the experimental data is obtained.

scholarly journals A rapid method for determining diffusion constants in solution

1948 ◽  
Vol 192 (1030) ◽  
pp. 382-402 ◽  
Keyword(s):  
Monochromatic Light ◽  
Diffusion Constant ◽  
Initial Boundary ◽  
Optic Axis ◽  
Theory And Practice ◽  
Dilute Solution ◽  
Sharp Boundary ◽  
Diffusion Constants ◽  
A Cell ◽  
Molecular Substances

A method has been rediscovered, and developed in theory and practice, for optical observation of the earliest stages of diffusion across an initially sharp boundary between a dilute solution and a solvent. It enables the diffusion constant of a monodisperse solute to be measured about fifty times as quickly as by other methods, at lower concentration and possibly with greater accuracy; it should therefore be particularly valuable for the study of high molecular substances. The method is based on the interference pattern which is formed when monochromatic light from a horizontal slit is focused after passing through a cell where diffusion is occurring. The pattern, a set of horizontal bands, contracts towards the optic axis as diffusion proceeds, at a rate from which the diffusion constant can be calculated. By counting the bands in the pattern the refractive increment of the solute can be determined. The sharp initial boundary is obtained by flowing the solution and solvent out through a common narrow horizontal slit. The construction, calibration, and use of the apparatus are described.

DIFFUSION OF Tl+ IONS THROUGH THE INTERFACE OF SOLID NaCl, KCl OR RbCl AND LIQUID TlCl

2002 ◽  
Vol 16 (01n02) ◽  
pp. 108-113
Author(s):  
W. YU ◽  
A. FUJII
Keyword(s):  
Sodium Chloride ◽  
Single Crystals ◽  
Optical Method ◽  
Diffusion Constant ◽  
Liquid Interface ◽  
Diffusion Constants ◽  
Diffusion Phenomena ◽  
Diffusion Source ◽  
Solid Liquid Interface ◽  
Solid Liquid

The diffusion phenomena of thallous ions ( Tl + ions) through solid-liquid interface of liquid Tl + ions diffusion source and sodium chloride (NaCl) , potassium chloride (KCl) or rubidium chloride (RbCl) single crystals are studied by optical method. The characterisic absorption peaks of Tl + center in NaCl, KCl or RbCl single crystals were used as the tracer for measurements and the diffusion constants are evaluated at various temperatures. The results show that the diffusion constant of solid-liquid interface is about 103 times larger than that of solid-solid interface of KCl and TlCl .

SCALING LAWS IN STOCHASTIC SYSTEMS WITH ANOMALOUS DIFFUSION

2002 ◽  
Vol 02 (04) ◽  
pp. L273-L278 ◽  
Author(s):  
DMITRII KHARCHENKO
Keyword(s):  
Phase Space ◽  
Anomalous Diffusion ◽  
Stochastic System ◽  
Hurst Exponent ◽  
Special Class ◽  
Scaling Laws ◽  
Stochastic Systems ◽  
Diffusion Processes ◽  
Anomalous Behaviour ◽  
Proposed Model

We consider the stochastic system with an anomalous diffusion. According to the obtained relations between characteristics of diffusion processes the special class of models which exhibit the anomalous behaviour is considered. It was shown that indexes of super- and subdiffusion are related to the Hürst exponent which defines the properties of the phase space inherent to the proposed model of stochastic system.

The Mixing Length Derived from Kármán’s Similarity Hypothesis

1973 ◽  
Vol 24 (1) ◽  
pp. 71-76 ◽  
Author(s):  
Michio Nishioka ◽  
Shūsuke Iida
Keyword(s):  
Boundary Layer ◽  
Shear Stress ◽  
Reasonable Agreement ◽  
Diffusion Constant ◽  
Turbulent Shear ◽  
Appreciable Effect ◽  
Mixing Length ◽  
Similarity Hypothesis ◽  
Turbulent Shear Stress ◽  
Good Agreement

SummaryFrom Kármán’s similarity hypothesis, we derive the equation which describes the mixing length in terms of the turbulent shear stress. For a boundary layer with linear stress distribution, the equation is in reasonable agreement with Bradshaw’s measurements. For a boundary layer with injection, it is shown that injection has an appreciable effect upon the mixing length when (vw/2) /(τ/ρ)1/2becomes comparable to the Kármán constant. Close similarity is also pointed out between the hypotheses due to Kármán and Townsend. Moreover, the diffusion constant in Townsend’s hypothesis is determined to be 0.25, which is in good agreement with the value 0.2 obtained by Townsend from one experiment.

scholarly journals The (UP)Scaling of Renewable Energy Technologies: Experiences from The Austrian Biomass District Heating Niche

2014 ◽  
Vol 22 (2) ◽  
pp. 44-54 ◽  
Author(s):  
Markus Seiwald
Keyword(s):  
Diffusion Processes ◽  
Linear Trend ◽  
District Heating ◽  
Small Scale ◽  
Structured Interviews ◽  
Renewable Energy Technologies ◽  
Sustainable Technologies ◽  
Energy Technologies ◽  
Diffusion Dynamics ◽  
Dominant Designs

Abstract The successful diffusion of sustainable technologies is termed “upscaling” in the transition studies literature. This paper maintains that upscaling is an ambiguous notion that suggests that technology diffusion processes follow a linear trend from small-scale pilot plants to industrial-scale facilities. On the ground, however, socio-technical configurations are implemented at a variety of scales, simultaneously. These issues are demonstrated in this paper by analysing the historical development of the Austrian biomass district heating niche. Drawing on secondary statistical data and primary qualitative semi-structured interviews, it is possible to identify four generic socio-technical configurations or dominant designs that, in conjunction, shape the diffusion dynamics of this technology in Austria

scholarly journals Area and perimeter covered by anomalous diffusion processes

2013 ◽  
Vol 15 (6) ◽  
pp. 063034 ◽  
Author(s):  
Mirko Luković ◽  
Theo Geisel ◽  
Stephan Eule
Keyword(s):  
Anomalous Diffusion ◽  
Diffusion Processes ◽  
Area And Perimeter

scholarly journals The accidental ally: Nucleosomal barriers can accelerate cohesin mediated loop formation in chromatin

2019 ◽  
Author(s):  
Ajoy Maji ◽  
Ranjith Padinhateeri ◽  
Mithun K. Mitra
Keyword(s):  
Effective Diffusion ◽  
Diffusion Constant ◽  
Loop Formation ◽  
Base Pairs ◽  
Diffusion Constants ◽  
Dna Backbone ◽  
The Mean ◽  
The Times ◽  
Lower Loop ◽  
Kinetics Of

AbstractAn important question in the context of the 3D organization of chromosomes is the mechanism of formation of large loops between distant base pairs. Recent experiments suggest that the formation of loops might be mediated by Loop Extrusion Factor proteins like cohesin. Experiments on cohesin have shown that cohesins walk diffusively on the DNA, and that nucleosomes act as obstacles to the diffusion, lowering the permeability and hence reducing the effective diffusion constant. An estimation of the times required to form the loops of typical sizes seen in Hi-C experiments using these low effective diffusion constants leads to times that are unphysically large. The puzzle then is the following, how does a cohesin molecule diffusing on the DNA backbone achieve speeds necessary to form the large loops seen in experiments? We propose a simple answer to this puzzle, and show that while at low densities, nucleosomes act as barriers to cohesin diffusion, beyond a certain concentration, they can reduce loop formation times due to a subtle interplay between the nucleosome size and the mean linker length. This effect is further enhanced on considering stochastic binding kinetics of nucleosomes on the DNA backbone, and leads to predictions of lower loop formation times than might be expected from a naive obstacle picture of nucleosomes.

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