Spine based shape parameterisation for PDE surfaces

The aim of this paper is to show how the spine of a PDE surface can be generated and how it can be used to efficiently parameterise a PDE surface. For the purpose of the work presented here an approximate analytic solution form for the chosen PDE is utilised. It is shown that the spine of the PDE surface is then computed as a by-product of this analytic solution. Furthermore, it is shown that a parameterisation can be introduced on the spine enabling intuitive manipulation of PDE surfaces

On the spine of a PDE surface

yesThe spine of an object is an entity that can characterise the object¿s topology and describes the object by a lower dimension. It has an intuitive appeal for supporting geometric modelling operations. The aim of this paper is to show how a spine for a PDE surface can be generated. For the purpose of the work presented here an analytic solution form for the chosen PDE is utilised. It is shown that the spine of the PDE surface is then computed as a by-product of this analytic solution. This paper also discusses how the of a PDE surface can be used to manipulate the shape. The solution technique adopted here caters for periodic surfaces with general boundary conditions allowing the possibility of the spine based shape manipulation for a wide variety of free-form PDE surface shapes

Shape morphing of complex geometries using partial differential equations.

An alternative technique for shape morphing using a surface generating method using partial differential equations is outlined throughout this work. The boundaryvalue nature that is inherent to this surface generation technique together with its mathematical properties are hereby exploited for creating intermediate shapes between an initial shape and a final one. Four alternative shape morphing techniques are proposed here. The first one is based on the use of a linear combination of the boundary conditions associated with the initial and final surfaces, the second one consists of varying the Fourier mode for which the PDE is solved whilst the third results from a combination of the first two. The fourth of these alternatives is based on the manipulation of the spine of the surfaces, which is computed as a by-product of the solution. Results of morphing sequences between two topologically nonequivalent surfaces are presented. Thus, it is shown that the PDE based approach for morphing is capable of obtaining smooth intermediate surfaces automatically in most of the methodologies presented in this work and the spine has been revealed as a powerful tool for morphing surfaces arising from the method proposed here

A survey of partial differential equations in geometric design

YesComputer aided geometric design is an area where the improvement of surface generation techniques is an everlasting demand since faster and more accurate geometric models are required. Traditional methods for generating surfaces were initially mainly based upon interpolation algorithms. Recently, partial differential equations (PDE) were introduced as a valuable tool for geometric modelling since they offer a number of features from which these areas can benefit. This work summarises the uses given to PDE surfaces as a surface generation technique togethe

Geometric principles of second messenger dynamics in dendritic spines.

Dendritic spines are small, bulbous protrusions along dendrites in neurons and play a critical role in synaptic transmission. Dendritic spines come in a variety of shapes that depend on their developmental state. Additionally, roughly 14-19% of mature spines have a specialized endoplasmic reticulum called the spine apparatus. How does the shape of a postsynaptic spine and its internal organization affect the spatio-temporal dynamics of short timescale signaling? Answers to this question are central to our understanding the initiation of synaptic transmission, learning, and memory formation. In this work, we investigated the effect of spine and spine apparatus size and shape on the spatio-temporal dynamics of second messengers using mathematical modeling using reaction-diffusion equations in idealized geometries (ellipsoids, spheres, and mushroom-shaped). Our analyses and simulations showed that in the short timescale, spine size and shape coupled with the spine apparatus geometries govern the spatiotemporal dynamics of second messengers. We show that the curvature of the geometries gives rise to pseudo-harmonic functions, which predict the locations of maximum and minimum concentrations along the spine head. Furthermore, we showed that the lifetime of the concentration gradient can be fine-tuned by localization of fluxes on the spine head and varying the relative curvatures and distances between the spine apparatus and the spine head. Thus, we have identified several key geometric determinants of how the spine head and spine apparatus may regulate the short timescale chemical dynamics of small molecules that control synaptic plasticity

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

Shape manipulation using physically based wire deformations

This paper develops an efficient, physically based shape manipulation technique. It defines a 3D model with profile curves, and uses spine curves generated from the profile curves to control the motion and global shape of 3D models. Profile and spine curves are changed into profile and spine wires by specifying proper material and geometric properties together with external forces. The underlying physics is introduced to deform profile and spine wires through the closed form solution to ordinary differential equations for axial and bending deformations. With the proposed approach, global shape changes are achieved through manipulating spine wires, and local surface details are created by deforming profile wires. A number of examples are presented to demonstrate the applications of our proposed approach in shape manipulation

Cyclic animation using Partial differential Equations

YesThis work presents an efficient and fast method for achieving cyclic animation using Partial Differential Equations (PDEs). The boundary-value nature associ- ated with elliptic PDEs offers a fast analytic solution technique for setting up a framework for this type of animation. The surface of a given character is thus cre- ated from a set of pre-determined curves, which are used as boundary conditions so that a number of PDEs can be solved. Two different approaches to cyclic ani- mation are presented here. The first consists of using attaching the set of curves to a skeletal system hold- ing the animation for cyclic motions linked to a set mathematical expressions, the second one exploits the spine associated with the analytic solution of the PDE as a driving mechanism to achieve cyclic animation, which is also manipulated mathematically. The first of these approaches is implemented within a framework related to cyclic motions inherent to human-like char- acters, whereas the spine-based approach is focused on modelling the undulatory movement observed in fish when swimming. The proposed method is fast and ac- curate. Additionally, the animation can be either used in the PDE-based surface representation of the model or transferred to the original mesh model by means of a point to point map. Thus, the user is offered with the choice of using either of these two animation repre- sentations of the same object, the selection depends on the computing resources such as storage and memory capacity associated with each particular application

Parametric Representations of Facial Expressions on PDE-Based Surfaces

NoParameterisation of facial expressions on PDE surface representations of human faces are presented in this work. Taking advantage of the boundary-value approach inherent to Bloor-Wilson PDE method, facial expressions are achieved by manipulating the original boundary curves. Such curves are responsible for generating a surface representation of a human face in its neutral configuration, so that regions on these curves represent a given facial expression in a fast and realistic manner. Additionally, the parameterisation proposed here is carried out by applying different mathematical transformations to the affected curves according to the corresponding facial expression. Full analytic expressions parameterising some of the most common facial expressions such as smiling and eyebrow raising are in this work. Some graphical examples of these facial expressions are used to illustrate the results obtained using Bloor-Wilson PDE method as the foundations of the parameterisation scheme proposed here. Thus, it is shown that an efficient, intuitive and realistic parameterisation of facial expressions is attainable using Bloor-Wilson PDE method in along with a suitable mathematical expression

Synchrotron radiation of self-collimating relativistic MHD jets

The goal of this paper is to derive signatures of synchrotron radiation from state-of-the-art simulation models of collimating relativistic magnetohydrodynamic (MHD) jets featuring a large-scale helical magnetic field. We perform axisymmetric special relativistic MHD simulations of the jet acceleration region using the PLUTO code. The computational domain extends from the slow magnetosonic launching surface of the disk up to 6000^2 Schwarzschild radii allowing to reach highly relativistic Lorentz factors. The Poynting dominated disk wind develops into a jet with Lorentz factors of 8 and is collimated to 1 degree. In addition to the disk jet, we evolve a thermally driven spine jet, emanating from a hypothetical black hole corona. Solving the linearly polarized synchrotron radiation transport within the jet, we derive VLBI radio and (sub-) mm diagnostics such as core shift, polarization structure, intensity maps, spectra and Faraday rotation measure (RM), directly from the Stokes parameters. We also investigate depolarization and the detectability of a lambda^2-law RM depending on beam resolution and observing frequency. We find non-monotonic intrinsic RM profiles which could be detected at a resolution of 100 Schwarzschild radii. In our collimating jet geometry, the strict bi-modality in polarization direction (as predicted by Pariev et al.) can be circumvented. Due to relativistic aberration, asymmetries in the polarization vectors across the jet can hint to the spin direction of the central engine.Comment: Submitted to Ap