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

Numerical simulation of three-phase flow in an external gear pump using immersed boundary approach

This paper presents a three-phase fully compressible model applied along with an immersed boundary model for predicting cavitation occurring in a two dimensional gear pump in the presence of non-condensable gas (NCG). Combination of these models is capable of overcoming numerical challenges such as modelling the contact between the gears and simulating the effect of NCG in cavitation. The model accounting for the effect of NCG also has broader applicability, since gas dissolved in liquids can come out of the solution when exposed to low pressures; this plays a significant role in the pump performance and cavitation erosion. Here the simulation results are presented for the gear pump at different operating conditions including the contact between gear, gear RPM and % of NCG; their effects on performance and cavitation is demonstrated. The results suggest that modelling the contact between the gears play a role in the cavitation prediction inside the gear pump. An increase in cavitation is observed when the contact is modelled even for the small pressure difference considered between the inlet and outlet. An increase in the RPM of the gears also results in increased cavitation within the pump, whereas an increase in the percentage of NCG content by a small amount can reduce the cavitation to a greater extent. This reduction is due to the expansion of the gas at a lower pressure which recovers the pressure and prevents or delays the phase-change process of the working fluid. The fluctuations in the outflow rate is also found to increase when the gears are in contact and also with increasing gas content

The 1999 Center for Simulation of Dynamic Response in Materials Annual Technical Report

Introduction: This annual report describes research accomplishments for FY 99 of the Center for Simulation of Dynamic Response of Materials. The Center is constructing a virtual shock physics facility in which the full three dimensional response of a variety of target materials can be computed for a wide range of compressive, ten- sional, and shear loadings, including those produced by detonation of energetic materials. The goals are to facilitate computation of a variety of experiments in which strong shock and detonation waves are made to impinge on targets consisting of various combinations of materials, compute the subsequent dy- namic response of the target materials, and validate these computations against experimental data

Designing of a new seismic base isolation system

The design of a new base isolation system is proposed in this research with the objective that the system does not transmit any force to the structure under horizontal loading. The structure must remain operational and steady. Before investigating the dynamics problem of the base isolation system, the isolator components of the model can be solved analytically using different approaches. In order to calculate the deformation of any element of the isolator due to a compressive vertical load, the analysis focuses on the primary instability region to determine all deformations parameters which can lead to frictions coefficients. This region is located at the interaction contact point between the elements. The design is based on the contact point developed by different approaches. In the present study, the mathematical analysis methods by using formulations can calculate the different dimensions and deformations of the elements of the system and which are verified using ANSYS finite element analysis.  After ensuring the adequate dimensions of the different parts of the isolator system from the analysis, the system can be applied on the structure. This technique can reduce significantly the displacements and accelerations at the underground level with a new seismic isolation system, which it is an uncoupled system between the structure and the underground

On the Calculation of Solid-Fluid Contact Angles from Molecular Dynamics

A methodology for the determination of the solid-fluid contact angle, to be employed within molecular dynamics (MD) simulations, is developed and systematically applied. The calculation of the contact angle of a fluid drop on a given surface, averaged over an equilibrated MD trajectory, is divided in three main steps: (i) the determination of the fluid molecules that constitute the interface, (ii) the treatment of the interfacial molecules as a point cloud data set to define a geometric surface, using surface meshing techniques to compute the surface normals from the mesh, (iii) the collection and averaging of the interface normals collected from the post-processing of the MD trajectory. The average vector thus found is used to calculate the Cassie contact angle (i.e., the arccosine of the averaged normal z-component). As an example we explore the effect of the size of a drop of water on the observed solid-fluid contact angle. A single coarse-grained bead representing two water molecules and parameterized using the SAFT-γ Mie equation of state (EoS) is employed, meanwhile the solid surfaces are mimicked using integrated potentials. The contact angle is seen to be a strong function of the system size for small nano-droplets. The thermodynamic limit, corresponding to the infinite size (macroscopic) drop is only truly recovered when using an excess of half a million water coarse-grained beads and/or a drop radius of over 26 nm