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Parallel simulation and optimization framework of supplies production processes for unconventional emergencies.

ABSTRACT: The outbreak of unconventional emergencies leads to a surge in demand for emergency supplies. How to effectively arrange emergency production processes and improve production efficiency is significant. The emergency manufacturing systems are typically complex systems, which are difficult to be analyzed by using physical experiments. Based on the theory of Random Service System (RSS) and Parallel Emergency Management System (PeMS), a parallel simulation and optimization framework of production processes for surging demand of emergency supplies is constructed. Under this novel framework, an artificial system model paralleling with the real scenarios is established and optimized by the parallel implementation processes. Furthermore, a concrete example of mask shortage, which occurred at Huoshenshan Hospital in the COVID-19 pandemic, verifies the feasibility of this method.

SUBMITTER: Zhu D

PROVIDER: S-EPMC8758009 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

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Parallel simulation and optimization framework of supplies production processes for unconventional emergencies.

Zhu Dan D Wei Yaoyao Y Huang Hainan H Xie Tian T

PloS one 20220113 1

The outbreak of unconventional emergencies leads to a surge in demand for emergency supplies. How to effectively arrange emergency production processes and improve production efficiency is significant. The emergency manufacturing systems are typically complex systems, which are difficult to be analyzed by using physical experiments. Based on the theory of Random Service System (RSS) and Parallel Emergency Management System (PeMS), a parallel simulation and optimization framework of production pr ...[more]

PMID: 35025918

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Project description:BackgroundExperiments in silico using stochastic reaction-diffusion models have emerged as an important tool in molecular systems biology. Designing computational software for such applications poses several challenges. Firstly, realistic lattice-based modeling for biological applications requires a consistent way of handling complex geometries, including curved inner- and outer boundaries. Secondly, spatiotemporal stochastic simulations are computationally expensive due to the fast time scales of individual reaction- and diffusion events when compared to the biological phenomena of actual interest. We therefore argue that simulation software needs to be both computationally efficient, employing sophisticated algorithms, yet in the same time flexible in order to meet present and future needs of increasingly complex biological modeling.ResultsWe have developed URDME, a flexible software framework for general stochastic reaction-transport modeling and simulation. URDME uses Unstructured triangular and tetrahedral meshes to resolve general geometries, and relies on the Reaction-Diffusion Master Equation formalism to model the processes under study. An interface to a mature geometry and mesh handling external software (Comsol Multiphysics) provides for a stable and interactive environment for model construction. The core simulation routines are logically separated from the model building interface and written in a low-level language for computational efficiency. The connection to the geometry handling software is realized via a Matlab interface which facilitates script computing, data management, and post-processing. For practitioners, the software therefore behaves much as an interactive Matlab toolbox. At the same time, it is possible to modify and extend URDME with newly developed simulation routines. Since the overall design effectively hides the complexity of managing the geometry and meshes, this means that newly developed methods may be tested in a realistic setting already at an early stage of development.ConclusionsIn this paper we demonstrate, in a series of examples with high relevance to the molecular systems biology community, that the proposed software framework is a useful tool for both practitioners and developers of spatial stochastic simulation algorithms. Through the combined efforts of algorithm development and improved modeling accuracy, increasingly complex biological models become feasible to study through computational methods. URDME is freely available at http://www.urdme.org.

Project description:Quantitative estimation of the radionuclide activity concentration in positron emission tomography (PET) requires precise modeling of PET physics. The authors are focused on designing unconventional PET geometries for specific applications. This work reports the creation of a generalized reconstruction framework, capable of reconstructing tomographic PET data for systems that use right cuboidal detector elements positioned at arbitrary geometry using a regular Cartesian grid of image voxels.The authors report on a variety of design choices and optimization for the creation of the generalized framework. The image reconstruction algorithm is maximum likelihood-expectation-maximization. System geometry can be specified using a simple script. Given the geometry, a symmetry seeking algorithm finds existing symmetry in the geometry with respect to the image grid to improve the memory usage/speed. Normalization is approached from a geometry independent perspective. The system matrix is computed using the Siddon's algorithm and subcrystal approach. The program is parallelized through open multiprocessing and message passing interface libraries. A wide variety of systems can be modeled using the framework. This is made possible by modeling the underlying physics and data correction, while generalizing the geometry dependent features.Application of the framework for three novel PET systems, each designed for a specific application, is presented to demonstrate the robustness of the framework in modeling PET systems of unconventional geometry. Three PET systems of unconventional geometry are studied. (1) Virtual-pinhole half-ring insert integrated into Biograph-40: although the insert device improves image quality over conventional whole-body scanner, the image quality varies depending on the position of the insert and the object. (2) Virtual-pinhole flat-panel insert integrated into Biograph-40: preliminary results from an investigation into a modular flat-panel insert are presented. (3) Plant PET system: a reconfigurable PET system for imaging plants, with resolution of greater than 3.3 mm, is shown. Using the automated symmetry seeking algorithm, the authors achieved a compression ratio of the storage and memory requirement by a factor of approximately 50 for the half-ring and flat-panel systems. For plant PET system, the compression ratio is approximately five. The ratio depends on the level of symmetry that exists in different geometries.This work brings the field closer to arbitrary geometry reconstruction. A generalized reconstruction framework can be used to validate multiple hypotheses and the effort required to investigate each system is reduced. Memory usage/speed can be improved with certain optimizations.

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Parallel simulation and optimization framework of supplies production processes for unconventional emergencies.

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Parallel simulation and optimization framework of supplies production processes for unconventional emergencies.

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