Fractionally Predictive Spiking Neurons

Recent experimental work has suggested that the neural firing rate can be interpreted as a fractional derivative, at least when signal variation induces neural adaptation. Here, we show that the actual neural spike-train itself can be considered as the fractional derivative, provided that the neural signal is approximated by a sum of power-law kernels. A simple standard thresholding spiking neuron suffices to carry out such an approximation, given a suitable refractory response. Empirically, we find that the online approximation of signals with a sum of power-law kernels is beneficial for encoding signals with slowly varying components, like long-memory self-similar signals. For such signals, the online power-law kernel approximation typically required less than half the number of spikes for similar SNR as compared to sums of similar but exponentially decaying kernels. As power-law kernels can be accurately approximated using sums or cascades of weighted exponentials, we demonstrate that the corresponding decoding of spike-trains by a receiving neuron allows for natural and transparent temporal signal filtering by tuning the weights of the decoding kernel.Comment: 13 pages, 5 figures, in Advances in Neural Information Processing 201

Geodesic finite elements in spaces of zero curvature

We investigate geodesic finite elements for functions with values in a space of zero curvature, like a torus or the Möbius strip. Unlike in the general case, a closed-form expression for geodesic finite element functions is then available. This simplifies computations, and allows us to prove optimal estimates for the interpolation error in 1d and 2d. We also show the somewhat surprising result that the discretization by Kirchhoff transformation of the Richards equation proposed in Berninger et al. (SIAM J Numer Anal 49(6):2576–2597, 2011) is a discretization by geodesic finite elements in the manifold R with a special metric

The PSurface library

We describe PSurface, a C++ library that allows to store and access piecewise linear maps between simplicial surfaces in R^2 and R^3. Piecewise linear maps can be used, e.g., to construct boundary approximations for finite element grids, and grid intersections for domain decomposition methods. In computer graphics the maps allow to build level-of-detail representations as well as texture- and bump maps. The PSurface library can be used as the basis for the implementation of a wide range of algorithms that use piecewise linear maps between triangulated surfaces. A few simple examples are given in this work. We document the data structures and algorithms and show how PSurface is used in the numerical analysis framework Dune and the visualization software Amira

A fast solver for finite deformation contact problems

We present a new solver for large-scale two-body contact problems in nonlinear elasticity. It is based on an SQP-trust-region approach. This guarantees global convergence to a first-order critical point of the energy functional. The linearized contact conditions are discretized using mortar elements. A special basis transformation known from linear contact problems allows to use a monotone multigrid solver for the inner quadratic programs. They can thus be solved with multigrid complexity. Our algorithm does not contain any regularization or penalization parameters, and can be used for all hyperelastic material models

Interaction of Nucleosides and Related Compounds with Nucleic Acids as Indicated by the Change of Helix-Coil Transition Temperature

A series of compounds has been tested for effectiveness in lowering the melting temperature of poly A and of thymus DNA. The order of increasing activity was found to be: adonitol, methyl riboside (both negligible) < cyclohexanol < phenol, pyrimidine, uridine < cytidine, thymidine < purine, adenosine, inosine, deoxyguanosine < caffeine, coumarin, 2,6-dichloro-7-methylpurine. Urea was ineffective with poly A and only slightly effective with DNA. At a concentration of 0.3 M, purine lowered the Tm of DNA about 9°

Coupling geometrically exact cosserat rods and linear elastic continua

We consider the mechanical coupling of a geometrically exact Cosserat rod to a linear elastic continuum. The coupling conditions are formulated in the nonlinear rod configuration space. We describe a Dirichlet–Neumann algorithm for the coupled system, and use it to simulate the static stresses in a human knee joint, where the Cosserat rods are models for the ligaments

Geodesic finite elements for Cosserat rods

We introduce geodesic finite elements as a new way to discretize the non-linear configuration space of a geometrically exact Cosserat rod. These geodesic finite elements naturally generalize standard one-dimensional finite elements to spaces of functions with values in a Riemannian manifold. For the special orthogonal group, our approach reproduces the interpolation formulas of Crisfield and Jelenić. Geodesic finite elements are conforming and lead to objective and path-independent problem formulations. We introduce geodesic finite elements for general Riemannian manifolds, discuss the relationship between geodesic finite elements and coefficient vectors, and estimate the interpolation error. Then we use them to find static equilibria of hyperelastic Cosserat rods. Using the Riemannian trust-region algorithm of Absil et al. we show numerically that the discretization error depends optimally on the mesh size. Copyright © 2009 John Wiley & Sons, Ltd

Geodesic finite elements on simplicial grids

We introduce geodesic finite elements as a conforming way to discretize partial differential equations for functions $v : \Omega \to M$, where $\Omega$ is an open subset of $\R^d$ and $M$ is a Riemannian manifold. These geodesic finite elements naturally generalize standard first-order finite elements for Euclidean spaces. They also generalize the geodesic finite elements proposed for $d=1$ by the author. Our formulation is equivariant under isometries of $M$, and hence preserves objectivity of continuous problem formulations. We concentrate on partial differential equations that can be formulated as minimization problems. Discretization leads to algebraic minimization problems on product manifolds $M^n$. These can be solved efficiently using a Riemannian trust-region method. We propose a monotone multigrid method to solve the constrained inner problems with linear multigrid speed. As an example we numerically compute harmonic maps from a domain in $\R^3$ to $S^2$

Surface stress of Ni adlayers on W(110): the critical role of the surface atomic structure

Puzzling trends in surface stress were reported experimentally for Ni/W(110) as a function of Ni coverage. In order to explain this behavior, we have performed a density-functional-theory study of the surface stress and atomic structure of the pseudomorphic and of several different possible 1x7 configurations for this system. For the 1x7 phase, we predict a different, more regular atomic structure than previously proposed based on surface x-ray diffraction. At the same time, we reproduce the unexpected experimental change of surface stress between the pseudomorphic and 1x7 configuration along the crystallographic surface direction which does not undergo density changes. We show that the observed behavior in the surface stress is dominated by the effect of a change in Ni adsorption/coordination sites on the W(110) surface.Comment: 14 pages, 3 figures Published in J. Phys.: Condens. Matter 24 (2012) 13500