Moving from the exact result that drainage network configurations minimizing total energy dissipation are stationary solutions of the general equation describing landscape evolution, I shall review the static properties and the dynamic origins of the scale-invariant structure of optimal river patterns. Optimal channel networks (OCNs) are feasible optimal configurations of a spanning network...
Interactions between biological molecules are challenging to elucidate with current techniques. An orthogonal approach is to probe for 'response signatures' that identify specific circuit motifs. For example, bistability, hysteresis, or irreversibility are used to detect positive feedback loops. For adapting systems, such signatures are not known. Two circuit motifs generate adaptation:...
To explain spontaneous polarization of motile cells, we have recently proposed a novel model of self-organizing cell activity, where local cell-edge dynamics depends on the distance from the cell center, but not on the orientation with respect to the front–back axis as assumed in previous models (Raynaud et al., Nat. Physics 12, 367-373, 2016). Here we show that traction-forces exerted by...
The surface of biomolecules is composed of nano-domains characterized by varying hydrophobicity. The textbook understanding is that these domains contribute additively to interfacial properties. Yet, recent observations show limitations of this model.
Here, we use a combined experimental and simulation study to propose a generalized equation which includes terms that consider domain...
We present a novel concept of magnetoplasmonic biosensor with ultranarrow resonances and high sensitivity. Our approach is based on the combination of a specially designed one-dimensional photonic crystal and a ferromagnetic layer to realize ultralong-range propagating magnetoplasmons and to detect alteration of the environment refractive index via observation of the modifications in the...
The protein self-assembly related neurodegenerative disorders such as Alzheimer’s diseases have not been fully understood.
To obtain a better understanding on the mechanism of protein fibrillization, we mapped time-lapse images of insulin aggregates as a model of multi-stranded fibril by resolution Atomic Force Microscopy(AFM). With statistical analysis of their periodically fluctuated...
We analyze maximum entropy approaches to infer the functional design of elastic materials exhibiting allostery, i.e. the property of highly specific responses to ligand binding at a distant active site.
We consider the functional designs of in silico evolved allosteric architectures which propagate efficiently energy (including shear, hinge, twist) or strain (resulting in a less-constrained...
Biological membranes represent the selective barrier of every cell, where they shape organelles, steer vesicles trafficking and modulate interactions with integral and peripheral proteins. Thus, capturing their complexity in terms of lipids composition, concentration and chemical features is crucial to accurately describe protein-membrane interactions. Molecular modelling and multiscale...
Pattern formation and growth of developing tissues involve the graded distribution of morphogens. Scaling of the morphogen gradient ensures proportioned morphological patterning of tissues with different sizes. On the other hand, we showed that growth of the drosophila wing disc is mediated by a mechanism in which cells compute the relative time derivative of the concentration of a morphogen:...
Exciton dynamics in DNA oligomers plays a crucial role in photoprotection. Using ultrafast broadband deep-UV transient absorption spectroscopy on Deoxyadenosine monophosphate oligomers of various lengths, we observe the effect of π-π stacking. The latter adds new relaxation channels, which are not seen in the monomer. Furthermore, these channels also differ for strand lengths between 2 to 20...
Circular dichroism (CD) spectroscopy is a well-established tool in analytical biochemistry. In the deep-UV range (< 300 nm), it is sensitive to the spatial arrangement of transition dipoles on amino acid residues, nucleotides and peptides. Time-resolved CD spectroscopy is thus a promising experimental technique that is sensitive to changes in biomolecular configuration as a function of time,...
The SAFIR collaboration is developing a PET insert for a pre-clinical MRI system, aiming at excellent temporal resolution, of ~5s time frames. Image reconstruction is performed using the Software for Tomographic Image Reconstruction (STIR). An accurate model of the scanner geometry is important for the precise reconstruction of quantitative PET data. Within STIR, a simplified model of the...
The aim of the SAFIR collaboration is the construction of a positron emission tomography (PET) insert for a preclinical magnetic resonance imaging device. The device will be able to handle high source activities and the data acquisition time for one PET image acquisition will be 5s or less.
The presented prototype consists of the same components as the full system. It fulfils all mechanical...
