Michaelis-Menten dynamics in protein subnetworks

To understand the behaviour of complex systems it is often necessary to use models that describe the dynamics of subnetworks. It has previously been established using projection methods that such subnetwork dynamics generically involves memory of the past, and that the memory functions can be calculated explicitly for biochemical reaction networks made up of unary and binary reactions. However, many established network models involve also Michaelis-Menten kinetics, to describe e.g. enzymatic reactions. We show that the projection approach to subnetwork dynamics can be extended to such networks, thus significantly broadening its range of applicability. To derive the extension we construct a larger network that represents enzymes and enzyme complexes explicitly, obtain the projected equations, and finally take the limit of fast enzyme reactions that gives back Michaelis-Menten kinetics. The crucial point is that this limit can be taken in closed form. The outcome is a simple procedure that allows one to obtain a description of subnetwork dynamics, including memory functions, starting directly from any given network of unary, binary and Michaelis-Menten reactions. Numerical tests show that this closed form enzyme elimination gives a much more accurate description of the subnetwork dynamics than the simpler method that represents enzymes explicitly, and is also more efficient computationally

Toward an ecological aesthetics: music as emergence

In this article we intend to suggest some ecological based principles to support the possibility of develop an ecological aesthetics. We consider that an ecological aesthetics is founded in concepts as “direct perception”, “acquisition of affordances and invariants”, “embodied embedded perception” and so on. Here we will purpose that can be possible explain especially soundscape music perception in terms of direct perception, working with perception of first hand (in a Gibsonian sense). We will present notions as embedded sound, detection of sonic affordances and invariants, and at the end we purpose an experience with perception/action paradigm to make soundscape music as emergence of a self-organized system

Dynamics of gene expression and the regulatory inference problem

From the response to external stimuli to cell division and death, the dynamics of living cells is based on the expression of specific genes at specific times. The decision when to express a gene is implemented by the binding and unbinding of transcription factor molecules to regulatory DNA. Here, we construct stochastic models of gene expression dynamics and test them on experimental time-series data of messenger-RNA concentrations. The models are used to infer biophysical parameters of gene transcription, including the statistics of transcription factor-DNA binding and the target genes controlled by a given transcription factor.Comment: revised version to appear in Europhys. Lett., new titl

FLASHlight MRI in real time - a step towards Star Trek medicine

This work describes a dynamic magnetic resonance imaging (MRI) technique for local scanning of the human body with use of a handheld receive coil or coil array. Real-time MRI is based on highly undersampled radial gradient-echo sequences with joint reconstructions of serial images and coil sensitivity maps by regularized nonlinear inversion (NLINV). For this proof-of-concept study, a fixed slice position and field-of-view (FOV) were predefined from the operating console, while a local receive coil (array) is moved across the body—for the sake of simplicity by the subject itself. Experimental realizations with a conventional 3 T magnet comprise dynamic anatomic imaging of the head, thorax and abdomen of healthy volunteers. Typically, the image resolution was 0.75 to 1.5 mm with 3 to 6 mm section thickness and acquisition times of 33 to 100 ms per frame. However, spatiotemporal resolutions and contrasts are highly variable and may be adjusted to clinical needs. In summary, the proposed FLASHlight MRI method provides a robust acquisition and reconstruction basis for future diagnostic strategies that mimic the usage of ultrasound. Necessary extensions for this vision require remote control of all sequence parameters by a person at the scanner as well as the design of more flexible gradients and magnets

Scale-Free topologies and Activatory-Inhibitory interactions

A simple model of activatory-inhibitory interactions controlling the activity of agents (substrates) through a "saturated response" dynamical rule in a scale-free network is thoroughly studied. After discussing the most remarkable dynamical features of the model, namely fragmentation and multistability, we present a characterization of the temporal (periodic and chaotic) fluctuations of the quasi-stasis asymptotic states of network activity. The double (both structural and dynamical) source of entangled complexity of the system temporal fluctuations, as an important partial aspect of the Correlation Structure-Function problem, is further discussed to the light of the numerical results, with a view on potential applications of these general results.Comment: Revtex style, 12 pages and 12 figures. Enlarged manuscript with major revision and new results incorporated. To appear in Chaos (2006

Lie bialgebras of generalized Witt type

In a paper by Michaelis a class of infinite-dimensional Lie bialgebras containing the Virasoro algebra was presented. This type of Lie bialgebras was classified by Ng and Taft. In this paper, all Lie bialgebra structures on the Lie algebras of generalized Witt type are classified. It is proved that, for any Lie algebra $W$ of generalized Witt type, all Lie bialgebras on $W$ are coboundary triangular Lie bialgebras. As a by-product, it is also proved that the first cohomology group $H^1(W,W \otimes W)$ is trivial.Comment: 14 page

Hamiltonian type Lie bialgebras

We first prove that, for any generalized Hamiltonian type Lie algebra $L$, the first cohomology group $H^1(L,L \otimes L)$ is trivial. We then show that all Lie bialgebra structures on $L$ are triangular.Comment: LaTeX, 16 page

Patterns and localized structures in bistable semiconductor resonators

We report experiments on spatial switching dynamics and steady state structures of passive nonlinear semiconductor resonators of large Fresnel number. Extended patterns and switching front dynamics are observed and investigated. Evidence of localization of structures is given.Comment: 5 pages with 9 figure

Ongoing outbreaks of hepatitis A among men who have sex with men (MSM), Berlin, November 2016 to January 2017 – linked to other German cities and European countries

Since 14 November 2016, 38 cases of hepatitis A have been notified in Berlin; of these, 37 were male and 30 reported to have sex with men (MSM). Median age of MSM cases is 31 years (range: 24–52 years). Phylogenetic analysis revealed three distinct sequences, linking cases in Berlin to those in other German cities and to clusters recognised in other European countries in 2016