An Open Source Mesh Generation Platform for Biophysical Modeling Using Realistic Cellular Geometries

ABSTRACT Advances in imaging methods such as electron microscopy, tomography, and other modalities are enabling high-resolution reconstructions of cellular and organelle geometries. Such advances pave the way for using these geometries for biophysical and mathematical modeling once these data can be represented as a geometric mesh, which, when carefully conditioned, enables the discretization and solution of partial differential equations. In this study, we outline the steps for a naïve user to approach GAMer 2 , a mesh generation code written in C++ designed to convert structural datasets to realistic geometric meshes, while preserving the underlying shapes. We present two example cases, 1) mesh generation at the subcellular scale as informed by electron tomography, and 2) meshing a protein with structure from x-ray crystallography. We further demonstrate that the meshes generated by GAMer are suitable for use with numerical methods. Together, this collection of libraries and tools simplifies the process of constructing realistic geometric meshes from structural biology data. SIGNIFICANCE As biophysical structure determination methods improve, the rate of new structural data is increasing. New methods that allow the interpretation, analysis, and reuse of such structural information will thus take on commensurate importance. In particular, geometric meshes, such as those commonly used in graphics and mathematics, can enable a myriad of mathematical analysis. In this work, we describe GAMer 2 , a mesh generation library designed for biological datasets. Using GAMer 2 and associated tools PyGAMer and BlendGAMer , biologists can robustly generate computer and algorithm friendly geometric mesh representations informed by structural biology data. We expect that GAMer 2 will be a valuable tool to bring realistic geometries to biophysical models

An Open Source Mesh Generation Platform for Biophysical Modeling Using Realistic Cellular Geometries

Advances in imaging methods such as electron microscopy, tomography and other modalities are enabling high-resolution reconstructions of cellular and organelle geometries. Such advances pave the way for using these geometries for biophysical and mathematical modeling once these data can be represented as a geometric mesh, which, when carefully conditioned, enables the discretization and solution of partial differential equations. In this study, we outline the steps for a na\"ive user to approach GAMer 2, a mesh generation code written in C++ designed to convert structural datasets to realistic geometric meshes, while preserving the underlying shapes. We present two example cases, 1) mesh generation at the subcellular scale as informed by electron tomography, and 2) meshing a protein with structure from x-ray crystallography. We further demonstrate that the meshes generated by GAMer are suitable for use with numerical methods. Together, this collection of libraries and tools simplifies the process of constructing realistic geometric meshes from structural biology data.Comment: 6 pages and 4 figures. Supplemental Movie available upon reques

A critical analysis of research potential, challenges and future directives in industrial wireless sensor networks

In recent years, Industrial Wireless Sensor Networks (IWSNs) have emerged as an important research theme with applications spanning a wide range of industries including automation, monitoring, process control, feedback systems and automotive. Wide scope of IWSNs applications ranging from small production units, large oil and gas industries to nuclear fission control, enables a fast-paced research in this field. Though IWSNs offer advantages of low cost, flexibility, scalability, self-healing, easy deployment and reformation, yet they pose certain limitations on available potential and introduce challenges on multiple fronts due to their susceptibility to highly complex and uncertain industrial environments. In this paper a detailed discussion on design objectives, challenges and solutions, for IWSNs, are presented. A careful evaluation of industrial systems, deadlines and possible hazards in industrial atmosphere are discussed. The paper also presents a thorough review of the existing standards and industrial protocols and gives a critical evaluation of potential of these standards and protocols along with a detailed discussion on available hardware platforms, specific industrial energy harvesting techniques and their capabilities. The paper lists main service providers for IWSNs solutions and gives insight of future trends and research gaps in the field of IWSNs

Emergent situations for smart cities: A survey

A smart city is a community that uses communication and information technology to improve sustainability, livability, and feasibility. As any community, there are always unexpected emergencies, which must be treated to preserve the regular order. However, a smart system is needed to be able to respond effectively to these emergent situations. The contribution made in this survey is twofold. Firstly, it provides a comprehensive exhaustive and categorized overview of the existing surveys for smart cities.  The categorization is based on several criteria such as structures, benefits, advantages, applications, challenges, issues, and future directions. Secondly, it aims to analyze several studies with respect to emergent situations and management to smart cities. The analysis is based on several factors such as the challenges and issues discussed, the solutions proposed, and opportunities for future research. The challenges include security, privacy, reliability, performance, scalability, heterogeneity, scheduling, resource management, and latency. Few studies have investigated the emergent situations of smart cities and despite the importance of latency factor for smart city applications, it is rarely discussed

Exploring user experience of digital pen and tablet technology for learning chemistry : applying an activity theory lens

Mobile learning technologies are spreading rapidly in educational institutions throughout the world. Although research findings concerning the efficacy of mobile technologies for improving student outcomes are generally promising, there are still significant gaps in the research literature, particularly data from direct observational studies. This empirical investigation focused on how students made use of tablet devices and digital pens for learning Chemistry in an undergraduate university course. Observational data in the form of videos and static images, as well as, interview responses, were the main sources of data collected for the study. Activity theory was employed as the guiding theoretical framework to analyse and interpret the data. Several themes emerged from the data analyses, including the affordances of digital pen technology for facilitating reflective thinking, flexibility, peer collaboration, emerging learning and focused learning. It was also found that the use of these mobile technologies was contextualized, dependent on individual differences, and had challenges, for example, there was limited synchronicity between the operational design of the mobile devices and natural human movement. One of the main implications of the research is that when higher education institutions consider the potential benefits and challenges associated with mobile technologies they should take account of the interactions that occur between components within a system including, students, technological devices, and emerging learning processes