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Diffusion and flow in complex liquids

Makuch, Karol and Hołyst, Robert and Kalwarczyk, Tomasz and Garstecki, Piotr and Brady, John F. (2020) Diffusion and flow in complex liquids. Soft Matter, 16 (1). pp. 114-124. ISSN 1744-683X. https://resolver.caltech.edu/CaltechAUTHORS:20191108-080923889

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Abstract

Thermal motion of particles and molecules in liquids underlies many chemical and biological processes. Liquids, especially in biology, are complex due to structure at multiple relevant length scales. While diffusion in homogeneous simple liquids is well understood through the Stokes–Einstein relation, this equation fails completely in describing diffusion in complex media. Modeling, understanding, engineering and controlling processes at the nanoscale, most importantly inside living cells, requires a theoretical framework for the description of viscous response to allow predictions of diffusion rates in complex fluids. Here we use a general framework with the viscosity η(k) described by a function of wave vector in reciprocal space. We introduce a formulation that allows one to relate the rotational and translational diffusion coefficients and determine the viscosity η(k) directly from experiments. We apply our theory to provide a database for rotational diffusion coefficients of proteins/protein complexes in the bacterium E. coli. We also provide a database for the diffusion coefficient of proteins sliding along major grooves of DNA in E. coli. These parameters allow predictions of rate constants for association of proteins. In addition to constituting a theoretical framework for description of diffusion of probes and viscosity in complex fluids, the formulation that we propose should decrease substantially the cost of numerical simulations of transport in complex media by replacing the simulation of individual crowding particles with a continuous medium characterized by a wave-length dependent viscosity η(k).


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1039/c9sm01119fDOIArticle
http://www.rsc.org/suppdata/c9/sm/c9sm01119f/c9sm01119f1.pdfPublisherSupplementary Information
ORCID:
AuthorORCID
Makuch, Karol0000-0002-9769-7646
Hołyst, Robert0000-0002-3211-4286
Kalwarczyk, Tomasz0000-0003-1136-9789
Garstecki, Piotr0000-0001-9101-7163
Brady, John F.0000-0001-5817-9128
Additional Information:© 2019 The Royal Society of Chemistry. This article is licensed under a Creative Commons Attribution 3.0 Unported Licence. The article was received on 04 Jun 2019, accepted on 13 Oct 2019 and first published on 08 Nov 2019. There are no conflicts to declare.
Issue or Number:1
Record Number:CaltechAUTHORS:20191108-080923889
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20191108-080923889
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:99749
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:08 Nov 2019 22:08
Last Modified:18 Dec 2019 19:09

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