BlenderPhotonics - a versatile environment for 3-D complex bio-tissue modeling and light transport simulations based on Blender

Significance: Rapid advances in biophotonics techniques require quantitative, model-based computational approaches to obtain functional and structural information from increasingly complex and multi-scaled anatomies. The lack of efficient tools to accurately model tissue structures and subsequently perform quantitative multi-physics modeling greatly impedes the clinical translation of these modalities. Aim: While the mesh-based Monte Carlo (MMC) method expands our capabilities in simulating complex tissues by using tetrahedral meshes, the generation of such domains often requires specialized meshing tools such as Iso2Mesh. Creating a simplified and intuitive interface for tissue anatomical modeling and optical simulations is essential towards making these advanced modeling techniques broadly accessible to the user community. Approach: We responded to the above challenge by combining the powerful, open-source 3-D modeling software, Blender, with state-of-the-art 3-D mesh generation and MC simulation tools, utilizing the interactive graphical user interface (GUI) in Blender as the front-end to allow users to create complex tissue mesh models, and subsequently launch MMC light simulations. Results: We have developed a Python-based Blender add-on -- BlenderPhotonics -- to interface with Iso2Mesh and MMC, allowing users to create, configure and refine complex simulation domains and run hardware-accelerated 3-D light simulations with only a few clicks. In this tutorial, we provide a comprehensive introduction to this new tool and walk readers through 5 examples, ranging from simple shapes to sophisticated realistic tissue models. Conclusion: BlenderPhotonics is user-friendly and open-source, leveraging the vastly rich ecosystem of Blender. It wraps advanced modeling capabilities within an easy-to-use and interactive interface. The latest software can be downloaded at http://mcx.space/bp.

Airfoil Surface Forming and Conformity Test Using Laser Tracker

In this study, NACA0018 airfoil surface conformity test was conducted using API tracker3 in combination with SpatialAnalyzer (SA) and modeling software SolidWorks. Plaster of Paris is used as a plug making material and a woven-type fiberglass is used as mold and airfoil surface making material. For airfoil surface analysis, three-dimensional model of the airfoil surface was developed in SolidWorks software and imported in IGES file format to SpatialAnalyzer (SA) software. Then, measurements were taken from manufactured airfoil surface using laser tracker through surface scanning method. Surface conformity test was conducted through fitting of measured points to surface model imported from SolidWorks to SpatialAnalyzer (SA) software. The optimized fit summary result shows that the average fit difference is 0.0 having standard deviation from 0.22224 from the average and zero with RMS of 0.2210. The maximum magnitude of the difference including x and y together is 0.5336 and the minimum −0.5077. Thus, with a given range of surface quality specification, laser tracker is an easy and reliable measurement and inspection tool to be considered.

Agents.jl: a performant and feature-full agent-based modeling software of minimal code complexity

Agent-based modeling is a simulation method in which autonomous agents interact with their environment and one another, given a predefined set of rules. It is an integral method for modeling and simulating complex systems, such as socio-economic problems. Since agent-based models are not described by simple and concise mathematical equations, the code that generates them is typically complicated, large, and slow. Here we present Agents.jl, a Julia-based software that provides an ABM analysis platform with minimal code complexity. We compare our software with some of the most popular ABM software in other programming languages. We find that Agents.jl is not only the most performant but also the least complicated software, providing the same (and sometimes more) features as the competitors with less input required from the user. Agents.jl also integrates excellently with the entire Julia ecosystem, including interactive applications, differential equations, parameter optimization, and so on. This removes any “extensions library” requirement from Agents.jl, which is paramount in many other tools.

An Anatomically Placed Tibial Tunnel does not Completely Surround a Simulated PCL Reconstruction Graft in the Proximal Tibia

Introduction It is hypothesized that anatomic tunnel placement will create tunnels with violation of the posterior cortex and subsequently an oblique aperture that is not circumferentially surrounded by bone. In this article, we aimed to characterize posterior cruciate ligament (PCL) tibial tunnel using a three-dimensional (3D) computed tomography (CT) model. Methods Ten normal knee CTs with the patella, femur, and fibula removed were used. Simulated 11 mm PCL tibial tunnels were created at 55, 50, 45, and 40 degrees. The morphology of the posterior proximal tibial exit was examined with 3D modeling software. The length of tunnel not circumferentially covered (cortex violation) was measured to where the tibial tunnel became circumferential. The surface area and volume of the cylinder both in contact with the tibial bone and that not in contact with the tibia were determined. The percentages of the stick-out length surface area and volume not in contact with bone were calculated. Results The mean stick-out length of uncovered graft at 55, 50, 45, and 40 degrees were 26.3, 20.5, 17.3, and 12.7 mm, respectively. The mean volume of exposed graft at 55, 50, 45, and 40 degrees were 840.8, 596.2, 425.6, and 302.9 mm3, respectively. The mean percent of volume of exposed graft at 55, 50, 45, and 40 degrees were 32, 29, 25, and 24%, respectively. The mean surface of exposed graft at 55, 50, 45, and 40 degrees were 372.2, 280.4, 208.8, and 153.3 mm2, respectively. The mean percent of surface area of exposed graft at 55, 50, 45, and 40 degrees were 40, 39, 34, and 34%, respectively. Conclusion Anatomic tibial tunnel creation using standard transtibial PCL reconstruction techniques consistently risks posterior tibial cortex violation and creation of an oblique aperture posteriorly. This risk is decreased with decreasing the angle of the tibial tunnel, though the posterior cortex is still compromised with angles as low as 40 degrees. With posterior cortex violation, a surgeon should be aware that a graft within the tunnel or socket posteriorly may not be fully in contact with bone. This is especially relevant with inlay and socket techniques.

Optimizing the effect of charging electric vehicles on distribution transformer using demand side management

This paper mainly aims to present the demand side management (DSM) of electric vehicles (EVs) by considering distribution transformer capacity at a residential area. The objective functions are formulated to obtain charging schedule for individual owner by i) minimizing the load variance and ii) price indicated charging mechanism. Both the objective functions profit the owner in the following ways: i) fulfilling their needs, ii) minimizing overall charging cost, iii) lessening the peak load, and iv) avoiding the overloading of distribution transformer. The proposed objective functions were worked on a residential area with 8 houses each house with an EV connected to a 20 kVA distribution transformer. The formulations were tested in LINGO platform optimization modeling software for linear, nonlinear, and integer programming. The results obtained were compared which gives good insight of EV load scheduling without actual price prediction.

Modeling SARS-CoV-2 RNA Degradation in Small and Large Sewersheds

Wastewater-based epidemiology has played a significant role in monitoring the COVID-19 pandemic, yet little is known about degradation of SARS-CoV-2 in sewer networks. Here, we used advanced sewershed modeling software...

Computational Fluid Dynamic Analysis of Conceptual 3D Car Model

From past decades, people are giving more attention to conservation of the fuels. The increasing number of passenger cars have increased the amount of traffic which directly impacts pollution and traffic congestion. Manufacturers are indulged into making lightweight and performance efficient automobiles. Implementation of different designs and materials has been in practice since ages. We need smaller vehicle designs for personal transport and electric vehicles to tackle the raising problems. In future designs, vehicles will be efficient enough to save more fuel and also the traffic problems may be solved. But for the design optimizations and experiments we need different analyses to be performed, one of which is aerodynamic analysis. In this paper a CFD analysis is done to check the aerodynamic performance of a proposed car design. The car has been designed using Onshape modeling software and analyzed in Simscale software. The car is subjected to different vehicle speeds and the results of drag coefficients and pressure plots are shown. Keywords: Design and analysis of a vehicle, CFD analysis, Aerodynamic analysis, 3D modelling, Drag coefficient, Pressure plot, Concept car, Performance Optimization.

The Effect of Different Implant-Abutment Mis-Matches on Stress Distribution: A 3-Dimensional Finite Element Study

Platform-switching reduces peri-implant marginal bone loss (MBL), and the aim of this study was to compare the effect of platform-switching on stress within crestal bone using different implant-abutment mis-matches (0.65 and 1mm) under two different vertical loads (30 N vs 200 N) for implants placed in posterior jaw sites. 3-D modeling software was used for an implant of 4.5mm diameter and 13mm length. Molars were modeled using CT images of bone density in human maxilla (D3 bone) and mandible (D2 bone). Collected data were analyzed using CATIA software. In posterior mandible, stress of 30 N force with platform mis-matches of 0.65 or 1mm were 2.920 and 2.440 MPa respectively. Using 200 N force, values increased to 19.44 and 16.30 MPa. In posterior maxilla and 30 N force, stresses with mis-matches of 0.65 and 1mm were 3.77 and 3.18 MPa respectively increasing to 25.14 & 20.17 with 200 N force. The effect can be predicted to be greatest as the mis-match increases with implants placed into lower quality bone (posterior maxilla with D3 quality).

Integrated and Control-Oriented Simulation Tool for Optimizing Urban Drainage System Operation

With the management and operation of urban drainage systems (UDS) becoming more complicated and difficult, integrated models aiming to control and manage the entire drainage system are under enormous demand. Ideally, integrated models, as a potential tool for meeting the increasing demands, should combine both conceptual and mechanistic models that merge all UDS components and balance simulation accuracy with time constraints. Within this context, our study introduces an innovative modeling software, Simuwater, which couples multiple principles, simulates multiple components, and combines optimized control functions, playing a role in the integrated simulation and overflow control application of UDS. The software has been utilized in a real-time case-control study in one city of China, and it obtained significant optimized operation results to reduce combined sewer overflow (CSO) by making full use of the storage facilities and actuators. As the Simuwater model continues to improve in depth and breadth, it will play an increasingly important role in more application scenarios of UDS.