A finite difference method for Piecewise Deterministic Processes with memory

In this paper the numerical approximation of solutions of Liouville-Master Equations for time-dependent distribution functions of Piecewise Deterministic Processes with memory is considered. These equations are linear hyperbolic PDEs with non-constant coefficients, and boundary conditions that depend on integrals over the interior of the integration domain. We construct a finite difference method of the first order, by a combination of the upwind method, for PDEs, and by a direct quadrature, for the boundary condition. We analyse convergence of the numerical solution for distribution functions evolving towards an equilibrium. Numerical results for two problems, whose analytical solutions are known in closed form, illustrate the theoretical finding.Comment: 20 pages, 7 figure

Fractals in the Nervous System: conceptual Implications for Theoretical Neuroscience

This essay is presented with two principal objectives in mind: first, to document the prevalence of fractals at all levels of the nervous system, giving credence to the notion of their functional relevance; and second, to draw attention to the as yet still unresolved issues of the detailed relationships among power law scaling, self-similarity, and self-organized criticality. As regards criticality, I will document that it has become a pivotal reference point in Neurodynamics. Furthermore, I will emphasize the not yet fully appreciated significance of allometric control processes. For dynamic fractals, I will assemble reasons for attributing to them the capacity to adapt task execution to contextual changes across a range of scales. The final Section consists of general reflections on the implications of the reviewed data, and identifies what appear to be issues of fundamental importance for future research in the rapidly evolving topic of this review

Precision of readout at the hunchback gene: analyzing short transcription time traces in living fly embryos

The simultaneous expression of the hunchback gene in the numerous nuclei of the developing fly embryo gives us a unique opportunity to study how transcription is regulated in living organisms. A recently developed MS2-MCP technique for imaging nascent messenger RNA in living Drosophila embryos allows us to quantify the dynamics of the developmental transcription process. The initial measurement of the morphogens by the hunchback promoter takes place during very short cell cycles, not only giving each nucleus little time for a precise readout, but also resulting in short time traces of transcription. Additionally, the relationship between the measured signal and the promoter state depends on the molecular design of the reporting probe. We develop an analysis approach based on tailor made autocorrelation functions that overcomes the short trace problems and quantifies the dynamics of transcription initiation. Based on live imaging data, we identify signatures of bursty transcription initiation from the hunchback promoter. We show that the precision of the expression of the hunchback gene to measure its position along the anterior-posterior axis is low both at the boundary and in the anterior even at cycle 13, suggesting additional post-transcriptional averaging mechanisms to provide the precision observed in fixed embryos

The iEBE-VISHNU code package for relativistic heavy-ion collisions

The iEBE-VISHNU code package performs event-by-event simulations for relativistic heavy-ion collisions using a hybrid approach based on (2+1)-dimensional viscous hydrodynamics coupled to a hadronic cascade model. We present the detailed model implementation, accompanied by some numerical code tests for the package. iEBE-VISHNU forms the core of a general theoretical framework for model-data comparisons through large scale Monte-Carlo simulations. A numerical interface between the hydrodynamically evolving medium and thermal photon radiation is also discussed. This interface is more generally designed for calculations of all kinds of rare probes that are coupled to the temperature and flow velocity evolution of the bulk medium, such as jet energy loss and heavy quark diffusion.Comment: 47 pages, 21 figures. Manuscript was accepted by Computer Physics Communication