On the Role of Physics in the Growth and Pattern Formation of Multi-Cellular Systems: What can we Learn from Individual-Cell Based Models?

We demonstrate that many collective phenomena in multi-cellular systems can be explained by models in which cells, despite their complexity, are represented as simple particles which are parameterized mainly by their physical properties. We mainly focus on two examples that nevertheless span a wide range of biological sub-disciplines: Unstructured cell populations growing in cell culture and growing cell layers in early animal development. While cultured unstructured cell populations would apriori been classified as particularly suited for a biophysical approach since the degree to which they are committed to a genetic program is expected to be modest, early animal development would be expected to mark the other extreme—here the degree of determinism according to a genetic program would be expected to be very high. We consider a number of phenomena such as the growth kinetics and spatial structure formation of monolayers and multicellular spheroids, the effect of the presence of another cell type surrounding the growing cell population, the effect of mutations and the critical surface dynamics of monolayers. Different from unstructured cell populations, cells in early development and at tissue interfaces usually form highly organized structures. An example are tissue layers. Under certain circumstances such layers are observed to fold. We show that folding pattern again can largely be explained by physical mechanisms either by a buckling instability or active cell shape changes. The paper combines new and published material and aims at an overview of a wide range of physical aspects in unstructured populations and growing tissue layers.     

Automated phase correction via maximization of the real signal

Due to improved quantification capabilities and enhanced signal-to-noise ratio (SNR), phase-corrected real reconstruction in magnetic resonance imaging is superior to the common magnitude reconstruction, especially at low SNR. This requires the development of an automated phase-correction algorithm. Existing methods are not well suited for multiple unconnected regions of very low SNR. For this situation, a method based on the real-signal maximization is implemented, in which the experimental image phase is approximated by a three-dimensional polynomial of up to third order. The presented implementation was successfully applied to data originating from different samples and pulse sequences.     

Sub-200 fs microjoule pulses from a monolithic linear fiber CPA system

An all-fiber-integrated linear chirped-pulse amplifier system generating microjoule pulse energies is reported. It is seeded by an all-fiber dissipative-soliton laser and incorporates a newly developed fiber stretcher, whose dispersive properties match that of the grating compressor. Pulse durations of 189 fs with energies of 2.2 μJ were achieved after compression. The average power was 9.8 W at the repetition rate of 4.5 MHz.     

Carbonates,thiocarbonates, and the corresponding monoalkyl derivatives: III. The 13C chemical shift tensors in potassium carbonate,bicarbonate and related monomethyl derivatives

The principal values of the 13C chemical shift tensors in potassium carbonate (K2CO3), trithiocarbonate (K2CS3), bicarbonate (KHCO3), methylcarbonate (KO2COCH3), S-methyl-monothiocarbonate (KO2CSCH3), O-methyl-monothiocarbonate (KOSCOCH3), S-methyl-dithiocarbonate (KOSCSCH3), and O-methyl-dithiocarbonate (KS2COCH3), were measured in solid-state nuclear magnetic resonance experiments. Chemical shift tensor calculations on the corresponding isolated anions were used to assign the chemical shift tensor orientations in the molecular frames of all anions. The correlation between experimental and calculated principal values improves significantly when the calculations are performed on isolated anions with proton-optimized X-ray geometries rather than on isolated anions with fully optimized geometries. Further considerable improvement in the correlation is achieved by utilizing the embedded ion method, which was recently developed to include electrostatic crystal potentials in chemical shift tensor calculations on ionic compounds. Similarities and differences in the chemical shift tensor orientations and principal values of the trigonal sp2 carbon atoms in the carbonate and thiocarbonate anions are compared with those known for condensed polyaromatic hydrocarbons.     

Artifact Reduction Based on Sinogram Interpolation for the 3D Reconstruction of Nanoparticles Using Electron Tomography

Electron tomography is a well‐known technique providing a 3D characterization of the morphology and chemical composition of nanoparticles. However, several reasons hamper the acquisition of tilt series with a large number of projection images, which deteriorate the quality of the 3D reconstruction. Here, an inpainting method that is based on sinogram interpolation is proposed, which enables one to reduce artifacts in the reconstruction related to a limited tilt series of projection images. The advantages of the approach will be demonstrated for the 3D characterization of nanoparticles using phantoms and several case studies.     

Estimating the spatial distribution of artificial groundwater recharge using multiple tracers

Stable isotopes of water, organic micropollutants and hydrochemistry data are powerful tools for identifying different water types in areas where knowledge of the spatial distribution of different groundwater is critical for water resource management. An important question is how the assessments change if only one or a subset of these tracers is used. In this study, we estimate spatial artificial infiltration along an infiltration system with stage–discharge relationships and classify different water types based on the mentioned hydrochemistry data for a drinking water production area in Switzerland. Managed aquifer recharge via surface water that feeds into the aquifer creates a hydraulic barrier between contaminated groundwater and drinking water wells. We systematically compare the information from the aforementioned tracers and illustrate differences in distribution and mixing ratios. Despite uncertainties in the mixing ratios, we found that the overall spatial distribution of artificial infiltration is very similar for all the tracers. The highest infiltration occurred in the eastern part of the infiltration system, whereas infiltration in the western part was the lowest. More balanced infiltration within the infiltration system could cause the elevated groundwater mound to be distributed more evenly, preventing the natural inflow of contaminated groundwater.

Dedicated to Professor Peter Fritz on the occasion of his 80th birthday     

Reversible photomechanical switching of individual engineered molecules at a metallic surface

We have observed reversible light-induced mechanical switching for individual organic molecules bound to a metal surface. Scanning tunneling microscopy (STM) was used to image the features of individual azobenzene molecules on Au(111) before and after reversibly cycling their mechanical structure between trans and cis states using light. Azobenzene molecules were engineered to increase their surface photomechanical activity by attaching varying numbers of tert-butyl (TB) ligands ("legs") to the azobenzene phenyl rings. STM images show that increasing the number of TB legs "lifts" the azobenzene molecules from the substrate, thereby increasing molecular photomechanical activity by decreasing molecule-surface coupling.