DOI: 10.5061/dryad.gr5768f
title: Data from: Multi-scale, numerical modeling of spatio-temporal signaling in cone phototransduction

description: Mammals have two types of photoreceptors, rods and cones. While rods are
 exceptionally sensitive and mediate vision at very low illumination
 levels, cones operate in daylight and are responsible for the bulk of
 visual perception in most diurnal animals, including humans. Yet the
 mechanisms of phototransduction in cones is understudied, largely due to
 unavailability of pure cone outer segment (COS) preparations. Here we
 present a novel mathematical model of cone phototransduction that
 explicitly takes into account complex cone geometry and its multiple
 physical scales, faithfully reproduces features of the cone response, and
 is orders of magnitude more efficient than the standard 3D diffusion
 model. This is accomplished through the mathematical techniques of
 homogenization and concentrated capacity. The homogenized model is then
 computationally implemented by finite element method. This homogenized
 model permits one to analyze the effects of COS geometry on visual
 transduction and lends itself to performing large numbers of numerical
 trials, as required for parameter analysis and the stochasticity of rod
 and cone signal transduction. Agreement between the nonhomogenized, (i.e.,
 standard 3D), and homogenized diffusion models is reported along with
 their simulation times and memory costs. Virtual expression of rod
 biochemistry on cone morphology is also presented for understanding some
 of the characteristic differences between rods and cones. These
 simulations evidence that 3D cone morphology and ion channel localization
 contribute to biphasic flash response, i.e undershoot. The 3D
 nonhomogenized and homogenized models are contrasted with more traditional
 and coarser well-stirred and 1D longitudinal diffusion models. The latter
 are single-scale and do not explicitly account for the multi-scale
 geometry of the COS, unlike the 3D homogenized model. We show that simpler
 models exaggerate the magnitude of the current suppression, yield
 accelerated time to peak, and do not predict the local concentration of
 cGMP at the ionic channels.
description: Hom_Single_Photon.tarThis file contains the solution data for the homogenized cone, single photon trials reported by the authors in the manuscript. The files are saved in matlab.Hom_Ten_Photon.tarThis file contains solution data for the homogenized cone, ten photon trials reported by the authors in their manuscript. The files are saved in matlab.NHom.tarThis file contains solution data for the nonhomogenized cone, single and ten photon trials reported by the authors in their manuscript. This includes the current drop as a function of time. However, due to size limitations the cGMP and Ca2+ solution data over the 3D mesh is not included. Those datasets are available upon request to the authors. The Mesh geometry for the NHOM 3D model is included here but not the mass and stiffness matrices owing again to size limitations. Those matrices are also available upon request to the authors. The files are saved in matlab.NHom_sol.tarThis file contains data samples of the numerically predicted concentrations of cGMP and Ca2+ over the nonhomogenized cone mesh.PDE_Inhib.tarThis file contains the data sheets, current totals and current drops for the simulations which increase the beta_dark parameter for comparing to diseases that are caused by incomplete PDE inhibition.Fig_Data.tarFor convenience, the quantities used to generate the figures shown in the main paper -- such as corresponding current drops, HOM and NHOM solution samples -- are collected here in one archive.