Physical modeling of non-equilibrium processes in biological systems

Funding period 2017-2020

                                                            Public Outreach Article in "Scientia"


IRTG Intro Lecture

Tue, 16/07/2019 - 15:00
Campus SB, Building E2 9 Room 0.07

Prof. Dr. Jochen Hub
Host: Dr. Hendrik Hähl
Theoretical Physics, UdS (SB)

Everything you wanted to know about molecular dynamics simulations*

*But were afraid to ask

First, an introduction to the method of molecular dynamics (MD) simulations is presented, covering the underlying approximations, validation against experimental data, strengths, and limitations.

Ongoing and expected future developments are discussed. Next, a brief overview is given of MD-related projects in our group, covering (i) the simulation-based interpretation of experimental data, (ii) protein/RNA/DNA complexes, and (iii) biological membranes.

SFB Seminar

Tue, 23/07/2019 - 14:30
Campus SB, Building E2 6 Room E.04

Dr. Loisa Reissig
Host: Prof. Dr. Karin Jacobs
Freie Universität Berlin

Differential Photodetectors: From Photonic Devices to their Use as an Analytical Platform

The addition of a thick insulating layer (I) between the semiconductor (S) layer and the metal (M) electrodes in a conventional MSM photodetector induces a differential photoresponse due to capacitive charging/discharging of the insulator layer by the photo-induced polarization of the active semiconductor layer in the MISM device.[1] The magnitude of the photoresponse in such differential photodetectors can be greatly enhanced by using high-k electrolytic insulator layers (I'), such as ionic liquids, through the strong influence of the highly energetic SI' interface on charge separation and stabilization. The move towards liquid insulating systems not only allows direct illumination of the active layer without the need for transparent electrode contacts, but also extends the choice of photoactive materials to include biomolecules, which benefit from a fluid environment.[2] Upon further insertion of a low-k polymer dielectric (I") at the opposite MS contact, yielding a “floating” photoactive layer, the resultant MI'SI"M architecture ensures purely non-Faradaic operation, and allows the responsivity and bandwidth to be mutually improved, thereby breaking the responsivity-bandwidth trade-off that limits the MISM architecture.[3]
In this seminar, I will focus on our recent results in differential photodetection utilizing organic, biological and, more recently, inorganic active layer materials, including viable strategies for their optimization and their applicability for motion detection. Furthermore, using a number of examples, their merits as an analytical tool for the characterization of (novel) (bio)materials will be discussed. Amongst those, I will present our recent results into the use of 3 microbial rhodopsin proteins in such MISM photodetectors - proteins, which are often regarded as the “eyes” of microbes, as they not only resemble the light receptors in our eyes in structure, but also undergo light-induced structural changes that can lead to signaling cascades within microbes to lead them toward favorable territories, or to the production of ATP (the unit of energy in a biological cell). Not only the device performance driven by the activation of such proteins by light, in terms of responsivity, bandwidth and signal stability will be discussed, but also what information we can gain through our studies under a range of conditions (temperature, pH, illumination wavelength), about the biomolecules themselves.
[1] L. Reissig, S. Dalgleish, K. Awaga, AIP Adv. 6, 015306 (2016).
[2] S. Dalgleish, L. Reissig, Y. Sudo et al., Chem. Comm. 51, 16401 (2015).
[3] L. Reissig, S. Dalgleish, K. Awaga, Sci. Rep. 8, 15415 (2018).

SFB Seminar

Tue, 13/08/2019 - 10:00
Campus SB, Building E2 6 Room E.04

Jun.-Prof. Dr. Marcel Lauterbach
Host: Prof. Dr. Christian Wagner
CIPMM, Center for Integrative Physiology and Molecular Medicine, UdS (HOM

Optics for Neuroscience

In this presentation I will demonstrate the benefit of modern optical techniques especially for neuroscience: After an introduction to STED microscopy the first part will present how Fast STED microscopy deciphers neurotransmitter-vesicle motion. Furthermore, it will be shown how integrating phase contrast into a STED microscope provides a second, label-free contrast channel. This allows for easy correlation of morphological structures with high-resolution fluorescence images. It is demonstrated that Spiral Phase Contrast in scanning confocal configuration yields improved optical contrast and allows quantitative phase measurements.

The last part will present microscopy in an unusual model system, turtles. Reptilian cerebral cortex contains 3 layers, similar to hippocampal and piriform cortices of mammals. Turtle cortex offers experimental advantages: it is resistant to anoxia and operates at room temperature. Cortical slabs can be cut in orientations that minimize lesions and keep inter-neuronal connections intact. The entire brain can even be extracted and kept in vitro for several days. Dendritic spines and calcium signaling can be advantageously studied in these preparations.