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In situ dynamics and fluidics of biological matter

English title In situ dynamics and fluidics of biological matter
Applicant Pfohl Thomas
Number 130171
Funding scheme Project funding
Research institution Physikalische Chemie Departement Chemie Universität Basel
Institution of higher education University of Basel - BS
Main discipline Physical Chemistry
Start/End 01.04.2010 - 31.03.2012
Approved amount 147'242.00
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All Disciplines (2)

Discipline
Physical Chemistry
Biophysics

Keywords (14)

microfluidics; DNA condensation/decondensation; Actin networks; Fibrin networks; Self-assembly; Small angle X-ray scattering; in situ dynamics; in-homogenous networks; X-ray photon correlation spectroscopy; in situ analysis; network formation; actin; extracellular proteins; hydrodynamics of polymers

Lay Summary (English)

Lead
Lay summary
LeadBy combining optical and spectroscopic microscopy and X-ray techniques with state of the art microfluidic technologies, we will be able to characterize transient reaction pathways of self-assembly, bundling, and network formation of fibrous proteins and the complex flow behavior of soft matter on a mesoscopic as well as molecular scale. HintergrundThe hierarchical self-organization of biological matter in cells, tissues, and organisms is one of the most fascinating phenomena in life science. As many biological processes consist of a series of transient steps in the reaction pathway, which are undetectable in bulk measurements, microfluidic-based experiments have the advantage of measuring kinetic and structural changes in assembly processes and association reactions. Thus, detection in microfluidics can reveal transient steps far from equilibrium, even if they exist only briefly, revealing fundamental information about reaction mechanisms. Das ZielThe experiments on cytoskeletal and extracellular matrix proteins follow a bottom-up approach to understand the fundamental mechanisms of bundling and network formation with increasing hierarchy and complexity. Using microfluidics we have a tool at hand not only to study the evolution of filament growth, bundling, and cross-linking within protein networks but also to probe the influence of external stimuli and hydrodynamic stress on these networks. BedeutungThe proposed research aims at a deeper fundamental understanding of the self-assembly, bundling and network formation of filamentous proteins and their complex response on external stimuli and hydrodynamic flow on a mesoscopic as well as molecular scale. The innovative nature of the proposed experimental approaches will allow the monitoring of dynamic processes far from equilibrium, giving access to the detection of intermediate reaction states. Currently, these research approaches are starting to receive significant interest by the scientific community worldwide because of their potential use for studies of a wide range of soft materials and of their impact on the development of new functional materials.
Direct link to Lay Summary Last update: 21.02.2013

Responsible applicant and co-applicants

Employees

Name Institute

Publications

Publication
Droplet based microfluidics
Seemann R, Brinkmann M, Pfohl T, Herminghaus S (2012), Droplet based microfluidics, in REPORTS ON PROGRESS IN PHYSICS, 75(1), 016601--.
Gold Nanoparticles Stabilized by Thioether Dendrimers
Hermes JP, Sander F, Peterle T, Urbani R, Pfohl T, Thompson D, Mayor M (2011), Gold Nanoparticles Stabilized by Thioether Dendrimers, in CHEMISTRY-A EUROPEAN JOURNAL, 17(48), 13473-13481.
Dynamics of intermediate filament assembly followed in micro-flow by small angle X-ray scattering.
Brennich Martha Elisabeth, Nolting Jens-Friedrich, Dammann Christian, Nöding Bernd, Bauch Susanne, Herrmann Harald, Pfohl Thomas, Köster Sarah (2011), Dynamics of intermediate filament assembly followed in micro-flow by small angle X-ray scattering., in Lab on a chip, 11(4), 708-16.
Biophysical Chemistry
Haussinger D, Pfohl T (2010), Biophysical Chemistry, in CHIMIA, 64(12), 874-876.

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
Dynamics Days Europe 2011 12.09.2011 Oldenburg, Deutschland
8th EBSA European Biophysics Congress 23.08.2011 Budapest, Ungarn
4th International SAXS Workshop 08.09.2010 Leoben, Österreich
Third International NanoBio Conference 2010 24.08.2010 Zürich
Swiss Soft Days 2 23.06.2010 Lausanne


Associated projects

Number Title Start Funding scheme
139133 Structure, dynamics and interactions of paramagnetic centers characterised by Electrn Paramagnetic Resonance 01.12.2011 R'EQUIP
141270 In situ dynamics and fluidics of biological matter 01.04.2012 Project funding
128747 Dynamics of hierarchical self-assembly processes characterized by small angle X-ray scattering 01.12.2009 R'EQUIP

Abstract

The hierarchical self-organization of biological matter in cells, tissues, and organisms is one of the most fascinating phenomena in life science. Therefore, great efforts are devoted to elucidate the dynamics of the self-organization processes as well as to mimic these biological systems. As many biological processes consist of a series of transient steps in their reaction pathways that are undetectable in bulk measurements, microfluidic-based experiments provide an opportunity to study the complexity of hierarchical dynamic and structural assembly and to generate models, which reproduce biological processes in vitro. Thus, detection in microfluidics can reveal transient steps far from equilibrium, even if they exist only briefly, revealing fundamental information about reaction mechanisms. By combining optical and spectroscopic microscopy, scanning small angle X-ray scattering and X-ray photon correlation spectroscopy with state of the art microfluidic technologies, we are able to characterize the self-assembly of chromatin-like materials, the bundling and network formation of filamentous proteins and their complex response on external stimuli and hydrodynamic flow on a mesoscopic as well as molecular scaleOur in situ studies of the condensation, disintegration, and transcription of DNA have an enormous relevance towards understanding the physical and chemical phenomena that are important in chromatin organization. We expect to illuminate to what extent the hierarchical organization of chromatin arises due to energy consuming processes, how far it is dominated by pure electrostatic interactions between opposite charges and how different charge distributions on cationic particles affect this organization. Furthermore, exploring the evolution of transcription processes with microfluidic-based techniques envisages developing a greater understanding of the interactions between transcription factors and condensed chromatin.The experiments on cytoskeletal and extracellular matrix proteins follow a bottom-up approach to understand the fundamental mechanisms of bundling and network formation with increasing hierarchy and complexity. Using microfluidics we have a tool at hand not only to study the evolution of filament growth, bundling, and cross-linking within protein networks but also to probe the influence of external stimuli and hydrodynamic stress on these networks. Apart from their fundamental relevance, the unique phenomena of soft biological objects under microflow conditions, such as cross-streamline migration and tumbling, may have a great impact in biotechnical applications, such as analyzing and sorting individual molecules or organisms based on of their mechanical properties.
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