One of the central elements in systems biology is the interaction between mathematical modeling and measured quantities. Typically, biological phenomena are represented as dynamical systems, and they are further analyzed and comprehended by identifying model parameters using experimental data. However, all model parameters cannot be found by gradient-based optimization methods by fitting the model to the experimental data due to the non-differentiable character of the problem. Here, we present POPI4SB, a Python-based framework for population-based parameter identification of dynamic models in systems biology. The code is built on top of PySCeS that provides an engine to run dynamic simulations. The idea behind the methodology is to provide a set of derivative-free optimization methods that utilize a population of candidate solutions to find a better solution iteratively. Additionally, we propose two surrogate-assisted population-based methods, namely, a combination of a k-nearest-neigh... [more]

We present the centrifugal microfluidic implementation of a four-plex digital droplet polymerase chain reaction (ddPCR). The platform features 12 identical ddPCR units on a LabDisk cartridge, each capable of generating droplets with a diameter of 82.7 ± 9 µm. By investigating different oil−surfactant concentrations, we identified a robust process for droplet generation and stabilization. We observed high droplet stability during thermocycling and endpoint fluorescence imaging, as is required for ddPCRs. Furthermore, we introduce an automated process for four-color fluorescence imaging using a commercial cell analysis microscope, including a customized software pipeline for ddPCR image evaluation. The applicability of ddPCRs is demonstrated by the quantification of three cancer-associated KRAS point mutations (G12D, G12V and G12A) in a diagnostically relevant wild type DNA background. The four-plex assay showed high sensitivity (3.5−35 mutant DNA copies in 15,000 wild type DNA copies) a... [more]

This study investigated a two-step thermochemical treatment process consisting of carbonization and halogenation for the removal of radionuclides from spent cation-exchange resin (CER). Based on a thermal analysis of cation-exchange resins, we propose a two-step thermochemical treatment process involving the conversion of spent CER into pyrocarbon and then the removal of radioactive elements from the carbonized CER by converting them volatile halides at very high temperatures. The proposed process mainly consists of a carbonization and halogenation reactor, a UHC (unburned hydrocarbon) combustor, and wet scrubber. A step-by-step experimental and numerical optimization study was conducted with the carbonization and halogenation reactor and the UHC combustor. The optimum operating conditions could be established based on the results of a thermal analysis of the CER, a nonisothermal kinetic analysis, a numerical modeling study of a plug flow reactor (PFR)-type combustor, and a thermodynam... [more]

These Aspen Plus v12 simulations are the solution or demonstration files for the book Learn Aspen Plus in 24 Hours, 2nd Edition, by Thomas A. Adams II. They are given as-is with no warranty or guarantee of accuracy or correctness. They are for educational purposes only.

The files list contains a large .zip of all files, or otherwise you can download them independently.

Files correspond to these tutorials:

Tutorial 2 Physical Property Modelling - Selecting physical properties. Understanding the database.
Tutorial 3 Problem Solving Tools - Design Specs and Sensitivity Analyses
Tutorial 4 Heat Exchangers - HEATER, HEATX
Tutorial 5 Equilibrium-based Distillation Models - RadFrac (in equilibrium mode)
Tutorial 6 Advanced Problem Solving Tools - Utilities, GHG Emissions, Optimization
Tutorial 7 Chemical Reactor Models - RSTOIC, REQUIL, RYIELD, RGIBBS, RCSTR, RPFR
Tutorial 8 Rate-based Distillation Models - RadFrac (in rate-based mode)
Tutorial 9 Custom Models and External Con... [more]

The submission includes SimaPro project for LCA of SOFCs with 10-year replacement plan, a text file explaining how to run the SimaPro file, and SOFC inventory tables provided in an Excel file.