Predictive power of non-identifiable models.

Resolving practical non-identifiability of computational models typically requires either additional data or non-algorithmic model reduction, which frequently results in models containing parameters lacking direct interpretation. Here, instead of reducing models, we explore an alternative, Bayesian approach, and quantify the predictive power of non-identifiable models. We considered an example biochemical signalling cascade model as well as its mechanical analogue.

The MAPK/ERK channel capacity exceeds 6 bit/hour.

Living cells utilize signaling pathways to sense, transduce, and process information. As the extracellular stimulation often has rich temporal characteristics which may govern dynamic cellular responses, it is important to quantify the rate of information flow through the signaling pathways. In this study, we used an epithelial cell line expressing a light-activatable FGF receptor and an ERK activity reporter to assess the ability of the MAPK/ERK pathway to transduce signal encoded in a sequence of pulses.

From Light-Powered Motors, to Micro-Grippers, to Crawling Caterpillars, Snails and Beyond-Light-Responsive Oriented Polymers in Action.

"How would you build a robot, the size of a bacteria, powered by light, that would swim towards the light source, escape from it, or could be controlled by means of different light colors, intensities or polarizations?" This was the question that Professor Diederik Wiersma asked PW on a sunny spring day in 2012, when they first met at LENS-the European Laboratory of Nonlinear Spectroscopy-in Sesto Fiorentino, just outside Florence in northern Italy. It was not just a vague question, as Prof. Wiersma, then the LENS director and leader of one of its research groups, already had an idea (and an ERC grant) about how to actually make such micro-robots, using a class of light-responsive oriented polymers, liquid crystal elastomers (LCEs), combined with the most advanced fabrication technique-two-photon 3D laser photolithography.

Optical Pliers: Micrometer-Scale, Light-Driven Tools Grown on Optical Fibers.

The ability to grip and handle small objects, from sub-millimeter electronic components to single-micrometer living cells, is vital for numerous ever-shrinking technologies. Mechanical grippers, powered by electric, pneumatic, hydraulic or piezoelectric servos, are well suited for the job at larger scales, but their complexity and need for force transmission prevent their miniaturization and remote control in tight spaces. Using liquid crystal elastomer microstructures that can change shape quickly and reversibly in response to light, a light-powered gripping tool-optical pliers-is built by growing two bending jaws on the tips of optical fibers.

Mean-Potential Law in Evolutionary Games.

The Letter presents a novel way to connect random walks, stochastic differential equations, and evolutionary game theory. We introduce a new concept of a potential function for discrete-space stochastic systems. It is based on a correspondence between one-dimensional stochastic differential equations and random walks, which may be exact not only in the continuous limit but also in finite-state spaces.

Importins promote high-frequency NF-κB oscillations increasing information channel capacity.

Background: Importins and exportins influence gene expression by enabling nucleocytoplasmic shuttling of transcription factors. A key transcription factor of innate immunity, NF-κB, is sequestered in the cytoplasm by its inhibitor, IκBα, which masks nuclear localization sequence of NF-κB. In response to TNFα or LPS, IκBα is degraded, which allows importins to bind NF-κB and shepherd it across nuclear pores.

Effective reaction rates for diffusion-limited reaction cycles.

Biological signals in cells are transmitted with the use of reaction cycles, such as the phosphorylation-dephosphorylation cycle, in which substrate is modified by antagonistic enzymes. An appreciable share of such reactions takes place in crowded environments of two-dimensional structures, such as plasma membrane or intracellular membranes, and is expected to be diffusion-controlled. In this work, starting from the microscopic bimolecular reaction rate constants and using estimates of the mean first-passage time for an enzyme-substrate encounter, we derive diffusion-dependent effective macroscopic reaction rate coefficients (EMRRC) for a generic reaction cycle.