Applications to Life Science

Understanding the fundamentals

Understanding the fundamental principles underlying biological processes and finding ways to compute and simulate these realistically brings our research in numerics, scientific and high performance computing to applications in life sciences. Our main focus is to address neuroscientific problems by including all three space dimensions, time and detailed morphology that serves as the computational domain.

(Simulation by M. Breit)

Major topics include

Detailed calcium dynamics in neurons

Electrodiffusion effects in post-synaptic spines

Cadherin-Calcium interactions at the synaptic cleft

Transcranial Magnetic Stimulation at the cellular level

Vesicle dynamics in boutons of the Drosophila Neuromuscular Junction

Calcium signaling in nuclei

Coupled neural network and cellular dynamics 

Some of our research projects in this area

Calcium signaling at spines and dendrites

Intracellular calcium dynamics are regulated by a complex cellular infrastructure. Calcium interacts with mobile buffers, is transported across the plasma membrane by voltage-dependent calcium channels, or is sequestered in internal calcium stores, like the endoplasmic reticulum or mitochondra. Bi-directional exchange across the endoplasmic membrane is controlled by SERCA pumps, ryanodine receptors, and Inositol-3-phosphate receptors. The architecture and positioning of intracellular organelles and the three-dimensional distribution and density of calcium exchangers plays a crucial role when trying to understand the propagation of calcium signals along dendrites towards the cell nucleus. Using advanced three-dimensional simulations of electrical and biochemical signals enables us to systematically investigate the broad range of cellular players involved in calcium signaling from synapse to nucleus.
(Simulation by M. Ke├čler)

Ultrastructural spine simulations

Understanding the fundamentals of cell signaling sometimes requires a close look at the ultrastructural cellular composition. The Poisson-Nernst-Planck equations (so called electro-diffusion) is a model for describing ion movement in an electrically charged domain at the micro-level. Using ultra-structural image reconstruction data of synaptic spines, the actin filament network and intracellular organelles allows us to simulate and study ion dynamics in this complex surrounding in an attempt to understand the functional role of spine protrusions at dendrites.
(Image by M. Breit)

Cellular morphology controls electrical and biochemical signals

Using reconstruction methods such as NeuRA and AnaMorph we study the electrical and biochemical behavior of healthy and diseased (morphologically altered) cells. One-dimensional cell reconstructions for electrical simulations can then be coupled to an equivalent three-dimensional cell study of biochemical signaling, using multi-scale techniques developed by our group (e.g. Grein et al.)
(Simulation by M. Breit)

Molecular dynamics of cadherins in transcellular coupling

Trans-cellular coupling involves the cadherin molecule that forms cis- and trans-connections between two neurons at chemical synapses. Molecular dynamics studies show that the rigidity of cadherin molecules depend on calcium ions. This might be due to dehydration effects of hydrogen bonds, a topic currently studied by our group.
(Simulation by S. Grein) 

Transcranial Magnetic Stimulation at the cellular level

Transcranial Magnetic Stimulation (TMS) is a non-invasive clinical technique to stimulate certain parts of the brain, for diagnostic and therapeutic purposes. While TMS is used in various clinical settings, the underlying functions are not fully understood. Especially at the cellular level, where long-term changes could be induced by TMS it remains unclear what the optimal positioning and stimulation protocol for a specific treatment should look like. We are currently focussing research at TMS function at the cellular and biochemical level to better understand long-term effects. This knowledge could be used to optimize TMS for treatment protocols.

Nuclear calcium dynamics

Nuclear calcium regulates many downstream processes towards gene transcription. Understanding which players are involved in shaping nuclear calcium signals is therefore an interesting topic. In one of our studies we were able to show that the nuclear morphology, which can be very versatile in hippocampal neurons, controls nuclear calcium signals and can be employed by the cell as a signal frequency detector.
(Movie by G. Queisser)