scholarly journals Single molecule optical-probes measured power law distribution of polymer dynamics

2016 ◽  
Vol 65 (21) ◽  
pp. 218201
Author(s):  
Li Bin ◽  
Zhang Guo-Feng ◽  
Jing Ming-Yong ◽  
Chen Rui-Yun ◽  
Qin Cheng-Bing ◽  
...  
Keyword(s):  
Single Molecule ◽  
Power Law ◽  
Polymer Dynamics ◽  
Power Law Distribution ◽  
Optical Probes ◽  
Measured Power

scholarly journals Power-law behavior of transcription factor dynamics at the single-molecule level implies a continuum affinity model

2021 ◽  
Author(s):  
David A Garcia ◽  
Gregory Fettweis ◽  
Diego M Presman ◽  
Ville Paakinaho ◽  
Christopher Jarzynski ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Single Molecule ◽  
Power Law ◽  
Dwell Time ◽  
Specific Binding ◽  
Power Law Distribution ◽  
Single Molecule Level ◽  
Binding Behavior ◽  
Chromatin Template ◽  
Nuclear Domains

Abstract Single-molecule tracking (SMT) allows the study of transcription factor (TF) dynamics in the nucleus, giving important information regarding the diffusion and binding behavior of these proteins in the nuclear environment. Dwell time distributions obtained by SMT for most TFs appear to follow bi-exponential behavior. This has been ascribed to two discrete populations of TFs—one non-specifically bound to chromatin and another specifically bound to target sites, as implied by decades of biochemical studies. However, emerging studies suggest alternate models for dwell-time distributions, indicating the existence of more than two populations of TFs (multi-exponential distribution), or even the absence of discrete states altogether (power-law distribution). Here, we present an analytical pipeline to evaluate which model best explains SMT data. We find that a broad spectrum of TFs (including glucocorticoid receptor, oestrogen receptor, FOXA1, CTCF) follow a power-law distribution of dwell-times, blurring the temporal line between non-specific and specific binding, suggesting that productive binding may involve longer binding events than previously believed. From these observations, we propose a continuum of affinities model to explain TF dynamics, that is consistent with complex interactions of TFs with multiple nuclear domains as well as binding and searching on the chromatin template.

scholarly journals Power-law behaviour of transcription factor dynamics at the single-molecule level implies a continuum affinity model

2019 ◽  
Author(s):  
David A. Garcia ◽  
Gregory Fettweis ◽  
Diego M. Presman ◽  
Ville Paakinaho ◽  
Christopher Jarzynski ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Single Molecule ◽  
Power Law ◽  
Specific Binding ◽  
Power Law Distribution ◽  
Single Molecule Level ◽  
Complex Interactions ◽  
Chromatin Template ◽  
Nuclear Domains

ABSTRACTSingle-molecule tracking (SMT) allows the study of transcription factor (TF) dynamics in the nucleus, giving important information regarding the search and binding behaviour of these proteins in the nuclear environment. Dwell time distributions for most TFs have been described by SMT to follow bi-exponential behaviour. This is consistent with the existence of two discrete populations bound to chromatin in vivo, one non-specifically bound to chromatin (i.e. searching mode) and another specifically bound to target sites, as originally defined by decades of biochemical studies. However, alternative models have started to emerge, from multiple exponential components to power-law distributions. Here, we present an analytical pipeline with an unbiased model selection approach based on different statistical metrics to determine the model that best explains SMT data. We found that a broad spectrum of TFs (including glucocorticoid receptor, oestrogen receptor, FOXA1, CTCF) follow a power-law distribution, blurring the temporal line between non-specific and specific binding, and suggesting that productive binding may involve longer binding events than previously thought. We propose a continuum of affinities model to explain the experimental data, consistent with the movement of TFs through complex interactions with multiple nuclear domains as well as binding and searching on the chromatin template.

scholarly journals The structure of co-publications multilayer network

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Ghislain Romaric Meleu ◽  
Paulin Yonta Melatagia
Keyword(s):  
Power Law ◽  
Degree Distribution ◽  
Preferential Attachment ◽  
Small World ◽  
Generation Model ◽  
Small World Network ◽  
Power Law Distribution ◽  
Multilayer Networks ◽  
Multilayer Network ◽  
Scientific Papers

AbstractUsing the headers of scientific papers, we have built multilayer networks of entities involved in research namely: authors, laboratories, and institutions. We have analyzed some properties of such networks built from data extracted from the HAL archives and found that the network at each layer is a small-world network with power law distribution. In order to simulate such co-publication network, we propose a multilayer network generation model based on the formation of cliques at each layer and the affiliation of each new node to the higher layers. The clique is built from new and existing nodes selected using preferential attachment. We also show that, the degree distribution of generated layers follows a power law. From the simulations of our model, we show that the generated multilayer networks reproduce the studied properties of co-publication networks.

The Single-Molecule Conductance and Electrochemical Electron-Transfer Rate Are Related by a Power Law

ACS Nano ◽  
2013 ◽  
Vol 7 (6) ◽  
pp. 5391-5401 ◽  
Author(s):  
Emil Wierzbinski ◽  
Ravindra Venkatramani ◽  
Kathryn L. Davis ◽  
Silvia Bezer ◽  
Jing Kong ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Single Molecule ◽  
Power Law ◽  
Transfer Rate ◽  
Electron Transfer Rate

scholarly journals Explaining the power-law distribution of human mobility through transportationmodality decomposition

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Kai Zhao ◽  
Mirco Musolesi ◽  
Pan Hui ◽  
Weixiong Rao ◽  
Sasu Tarkoma
Keyword(s):  
Power Law ◽  
Human Mobility ◽  
Power Law Distribution

MASS FUNCTION OF HALOS: A NEW ANALYTICAL APPROACH

2004 ◽  
Vol 13 (07) ◽  
pp. 1345-1349 ◽  
Author(s):  
JOSÉ A. S. LIMA ◽  
LUCIO MARASSI
Keyword(s):  
Power Law ◽  
Free Parameter ◽  
Analytical Approach ◽  
Mass Function ◽  
New Method ◽  
Power Law Distribution ◽  
The Press ◽  
The Universe ◽  
Special Case

A generalization of the Press–Schechter (PS) formalism yielding the mass function of bound structures in the Universe is given. The extended formula is based on a power law distribution which encompasses the Gaussian PS formula as a special case. The new method keeps the original analytical simplicity of the PS approach and also solves naturally its main difficult (the missing factor 2) for a given value of the free parameter.

scholarly journals Assessing the power law distribution of TGFs

2011 ◽  
Vol 116 (A10) ◽  
pp. n/a-n/a ◽  
Author(s):  
Andrew B. Collier ◽  
Thomas Gjesteland ◽  
Nikolai Østgaard
Keyword(s):  
Power Law ◽  
Power Law Distribution
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