Time Fractional Cable Equation And Applications in Neurophysiology

We propose an extension of the cable equation by introducing a Caputo time fractional derivative. The fundamental solutions of the most common boundary problems are derived analitically via Laplace Transform, and result be written in terms of known special functions. This generalization could be useful to describe anomalous diffusion phenomena with leakage as signal conduction in spiny dendrites. The presented solutions are computed in Matlab and plotted.Comment: 10 figures. arXiv admin note: substantial text overlap with arXiv:1702.0532

LeoPARD --- A Generic Platform for the Implementation of Higher-Order Reasoners

LeoPARD supports the implementation of knowledge representation and reasoning tools for higher-order logic(s). It combines a sophisticated data structure layer (polymorphically typed {\lambda}-calculus with nameless spine notation, explicit substitutions, and perfect term sharing) with an ambitious multi-agent blackboard architecture (supporting prover parallelism at the term, clause, and search level). Further features of LeoPARD include a parser for all TPTP dialects, a command line interpreter, and generic means for the integration of external reasoners.Comment: 6 pages, to appear in the proceedings of CICM'2015 conferenc

On Constructor Rewrite Systems and the Lambda Calculus

We prove that orthogonal constructor term rewrite systems and lambda-calculus with weak (i.e., no reduction is allowed under the scope of a lambda-abstraction) call-by-value reduction can simulate each other with a linear overhead. In particular, weak call-by- value beta-reduction can be simulated by an orthogonal constructor term rewrite system in the same number of reduction steps. Conversely, each reduction in a term rewrite system can be simulated by a constant number of beta-reduction steps. This is relevant to implicit computational complexity, because the number of beta steps to normal form is polynomially related to the actual cost (that is, as performed on a Turing machine) of normalization, under weak call-by-value reduction. Orthogonal constructor term rewrite systems and lambda-calculus are thus both polynomially related to Turing machines, taking as notion of cost their natural parameters.Comment: 27 pages. arXiv admin note: substantial text overlap with arXiv:0904.412

3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries

Recent advances in electron microscopy have enabled the imaging of single cells in 3D at nanometer length scale resolutions. An uncharted frontier for in silico biology is the ability to simulate cellular processes using these observed geometries. Enabling such simulations requires watertight meshing of electron micrograph images into 3D volume meshes, which can then form the basis of computer simulations of such processes using numerical techniques such as the Finite Element Method. In this paper, we describe the use of our recently rewritten mesh processing software, GAMer 2, to bridge the gap between poorly conditioned meshes generated from segmented micrographs and boundary marked tetrahedral meshes which are compatible with simulation. We demonstrate the application of a workflow using GAMer 2 to a series of electron micrographs of neuronal dendrite morphology explored at three different length scales and show that the resulting meshes are suitable for finite element simulations. This work is an important step towards making physical simulations of biological processes in realistic geometries routine. Innovations in algorithms to reconstruct and simulate cellular length scale phenomena based on emerging structural data will enable realistic physical models and advance discovery at the interface of geometry and cellular processes. We posit that a new frontier at the intersection of computational technologies and single cell biology is now open.Comment: 39 pages, 14 figures. High resolution figures and supplemental movies available upon reques