Developing Biophysical Tools

A special issue of Processes (ISSN 2227-9717). This special issue belongs to the section "Biological Processes and Systems".

Deadline for manuscript submissions: closed (15 December 2021) | Viewed by 3757

Special Issue Editors


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Guest Editor
Department of Biosystems Science and Engineering, Eidgenössiche Technische Hochschule (ETH) Zürich, Mattenstr. 26, 4058 Basel, Switzerland
Interests: molecular dynamics simulations; multiscaling; method development; biological processes; biomembranes; proteins; post-translational modifications; GPCRs; membrane insertion; protein dimerization; transport
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Guest Editor
Department of Biosystems Science and Engineering, ETH Zürich, Mattenstr. 26, 4058 Basel, Switzerland
Interests: cell mechanics; cell mass; sensing; actuation; bottom–up biology; rheology; statistical mechanics; active matter; finite-elements simulations; transport; viruses; membranes

Special Issue Information

Dear Colleagues,

Developing new biophysical tools opens gateways for us to observe, quantify, model, and manipulate processes in biological systems, ranging from molecules and proteins to cells, organs, multicellular organisms or even the whole ecosystem. To do so, we draw expertise and techniques from a plethora of different disciplines, such as biochmistry, bioinformatics, neuroscience, sensorics or statistical physics. This Special Issue on “Developing Biophysical Tools” will bring the most recent advances of in silico, in vitro, and in vivo methods to a broad audience, with a focus on three main aspects: Firstly, understanding which biological questions might be adressed with novel tools; secondly, new ideas on how to enhance traditional methods or develop entirely new ones; and thirdly, how to combine methods and tools from different disciplines. The latter point is particularly important to gain a holistic insight into the complex world of biological interactions.

Topics include but are not limited to:

  • Developing methods and analyses of molecular dynamics simulations;
  • Spatiotemporal modeling and simulations;
  • Statistical physics applied to experimental phenomena (transport, phase changes etc.);
  • Multicorrelative, experimental approaches (microscopy + AFM, microscopy + microcfluidics, etc.);
  • Novel sensor designs (tension, pH, Voltage);
  • Acquiring dynamic information from static structural information.

Dr. Kristyna Pluhackova
Dr. Gotthold Fläschner
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Processes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2400 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • method development
  • (biological) processes
  • biophysical tools
  • (atomic force) microscopy
  • theoretical models
  • molecular dynamics simulations
  • cryoEM
  • spectroscopy
  • mass spectrometry
  • sensors

Published Papers (1 paper)

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Research

15 pages, 3605 KiB  
Article
Transient Permeabilization of Living Cells: Combining Shear Flow and Acoustofluidic Trapping for the Facilitated Uptake of Molecules
by Andrej Kamenac, Felix L. Schilberth, Ernst Wagner, Achim Wixforth, Ulrich Lächelt and Christoph Westerhausen
Processes 2021, 9(6), 913; https://0-doi-org.brum.beds.ac.uk/10.3390/pr9060913 - 22 May 2021
Cited by 11 | Viewed by 2938
Abstract
Here, we present a novel approach for the transient permeabilization of cells. We combined laminar shear flow in a microchannel with chaotic advection employing surface acoustic waves. First, as a fundamental result on the one hand, and as a kind of reference measurement [...] Read more.
Here, we present a novel approach for the transient permeabilization of cells. We combined laminar shear flow in a microchannel with chaotic advection employing surface acoustic waves. First, as a fundamental result on the one hand, and as a kind of reference measurement for the more complex acoustofluidic approach on the other hand, we studied the permeabilization of cells in pure shear flow in a microchannel with Y-geometry. As a proof of principle, we used fluorescent dyes as model drugs and investigated their internalization into HeLa cells. We found that drug uptake scaled non-linearly with flow rate and thus shear stress. For calcein, we obtained a maximal enhancement factor of about 12 at an optimum flow rate of Q = 500 µL/h in the geometry used here compared to static incubation. This result is discussed in the light of structural phase transitions of lipid membranes accompanied by non-linear effects, as the plasma membrane is the main barrier to overcome. Second, we demonstrated the enhanced permeabilization of acoustically trapped cells in surface acoustic wave induced vortices in a microchannel, with an enhancement factor of about 18 compared to quasi-static incubation. Moreover, we optimized the trapping conditions regarding flow rate, the power level of the surface acoustic wave, and trapping time. Finally, we showed that our method is not limited to small molecules but can also be applied to compounds with higher molecular weight. Full article
(This article belongs to the Special Issue Developing Biophysical Tools)
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