Heads and Tails: Molecular Imagination and the Lipid Bilayer, 1917–1941

Today, the lipid bilayer structure is nearly ubiquitous, taken for granted in even the most rudimentary introductions to cell biology. Yet the image of the lipid bilayer, built out of lipids with heads and tails, went from having obscure origins deep in colloid chemical theory in 1924 to being “obvious to any competent physical chemist” by 1935. This chapter examines how this schematic, strictly heuristic explanation of the idea of molecular orientation was developed within colloid physical chemistry, and how the image was transformed into a reflection of the reality and agency of lipid molecules in the biological microworld. Whereas in physical and colloid chemistry these images considered secondary to instrumental measurement and mathematical modeling of surface phenomena, in biology the manipulable image of the lipid on paper became an essential tool for the molecularization of the cell

Vesicle computers: Approximating Voronoi diagram on Voronoi automata

Irregular arrangements of vesicles filled with excitable and precipitating chemical systems are imitated by Voronoi automata --- finite-state machines defined on a planar Voronoi diagram. Every Voronoi cell takes four states: resting, excited, refractory and precipitate. A resting cell excites if it has at least one excited neighbour; the cell precipitates if a ratio of excited cells in its neighbourhood to its number of neighbours exceed certain threshold. To approximate a Voronoi diagram on Voronoi automata we project a planar set onto automaton lattice, thus cells corresponding to data-points are excited. Excitation waves propagate across the Voronoi automaton, interact with each other and form precipitate in result of the interaction. Configuration of precipitate represents edges of approximated Voronoi diagram. We discover relation between quality of Voronoi diagram approximation and precipitation threshold, and demonstrate feasibility of our model in approximation Voronoi diagram of arbitrary-shaped objects and a skeleton of a planar shape.Comment: Chaos, Solitons & Fractals (2011), in pres

Dynamic Influence Networks for Rule-based Models

We introduce the Dynamic Influence Network (DIN), a novel visual analytics technique for representing and analyzing rule-based models of protein-protein interaction networks. Rule-based modeling has proved instrumental in developing biological models that are concise, comprehensible, easily extensible, and that mitigate the combinatorial complexity of multi-state and multi-component biological molecules. Our technique visualizes the dynamics of these rules as they evolve over time. Using the data produced by KaSim, an open source stochastic simulator of rule-based models written in the Kappa language, DINs provide a node-link diagram that represents the influence that each rule has on the other rules. That is, rather than representing individual biological components or types, we instead represent the rules about them (as nodes) and the current influence of these rules (as links). Using our interactive DIN-Viz software tool, researchers are able to query this dynamic network to find meaningful patterns about biological processes, and to identify salient aspects of complex rule-based models. To evaluate the effectiveness of our approach, we investigate a simulation of a circadian clock model that illustrates the oscillatory behavior of the KaiC protein phosphorylation cycle.Comment: Accepted to TVCG, in pres

The Performance of Knowledge: Pointing and Knowledge in Powerpoint Presentations

Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG geförderten) Allianz- bzw. Nationallizenz frei zugänglich.This publication is with permission of the rights owner freely accessible due to an Alliance licence and a national licence (funded by the DFG, German Research Foundation) respectively.Powerpoint and similar technologies have contributed to a profound transformation of lecturing and presenting information. In focusing on pointing in powerpoint presentations, the article addresses aspects of this transformation of speech into 'presentations'. As opposed to popular attacks against powerpoint, the analysis of a large number of audio-visually recorded presentations (mainly in German) demonstrates the creativity of these 'performances', based on the interplay of slides (and other aspects of this technology), speech, pointing and body formations. Pointing seems to be a particular feature of this kind of presentation, allowing knowledge to be located in space. Considering powerpoint as one of the typical technologies of so-called 'knowledge societies', this aspect provides some indication as to the social understanding of knowledge. Instead of 'representing' reality, knowledge is defined by the circularity of speaking and showing, thus becoming presented knowledge rather than representing knowledge

The Kinetic Basis of Morphogenesis

It has been shown recently (Shalygo, 2014) that stationary and dynamic patterns can arise in the proposed one-component model of the analog (continuous state) kinetic automaton, or kinon for short, defined as a reflexive dynamical system with active transport. This paper presents extensions of the model, which increase further its complexity and tunability, and shows that the extended kinon model can produce spatio-temporal patterns pertaining not only to pattern formation but also to morphogenesis in real physical and biological systems. The possible applicability of the model to morphogenetic engineering and swarm robotics is also discussed.Comment: 8 pages. Submitted to the 13th European Conference on Artificial Life (ECAL-2015) on March 10, 2015. Accepted on April 28, 201