Optimization Models for Multiple Resource Planning

Multiple resource planning is a very crucial undertaking for most organizations. Apart from reducing operational complexity, multiple resource planning facilitates efficient allocation of resources, which reduces costs by minimizing the cost of tardiness and the cost for additional capacity. The current research investigates multiple resource loading problems (MRLP). MRLPs are very prevalent in today’s organizational environments and are particularly critical for organizations that handle concurrent, time-intensive, and multiple-resource projects. Using data obtained from the Ministry of Administrative Development, Labor and Social Affairs (ADLSA), a MRLP is proposed. The problem utilizes data regarding staff, time, equipment, and finance to ensure efficient resource allocation among competing projects. In particular, the research proposes a novel model and solution approach for the MRLP. Computational experiments are then performed on the model. The results show that the model performs well, even for higher instances. The positive results attest to the effectiveness of the proposed MRLP problem.

Predicting Composition of Genetic Circuits with Resource Competition: Demand and Sensitivity

The design of genetic circuits typically relies on characterization of constituent modules in isolation to predict the behavior of modules' composition. However, it has been shown that the behavior of a genetic module changes when other modules are in the cell due to competition for shared resources. In order to engineer multi-module circuits that behave as intended, it is thus necessary to predict changes in the behavior of a genetic module when other modules load cellular resources. Here, we introduce two characteristics of circuit modules: the demand for cellular resources and the sensitivity to resource loading. When both are known for every genetic module in a circuit, they can be used to predict any module's behavior upon addition of any other module to the cell. We develop an experimental approach to measure both characteristics for any circuit module using a resource sensor module. Using the measured resource demand and sensitivity for each module in a library, the outputs of the modules can be accurately predicted when they are inserted in the cell in arbitrary combinations. These resource competition characteristics may be used to inform the design of genetic circuits that perform as predicted despite resource competition.

A MATLAB Toolbox for Modeling Genetic Circuits in Cell-Free Systems

We introduce a MATLAB based simulation toolbox, called txtlsim, for an E. coli based Transcription-Translation (TX-TL) system. This toolbox accounts for several cell-free related phenomena, such as resource loading, consumption, and degradation, and in doing so, models the dynamics of TX-TL reactions for the entire duration of solution phase batch-mode experiments. We use a Bayesian parameter inference approach to characterize the reaction rate parameters associated with the core transcription, translation and mRNA degradation mechanics of the toolbox, allowing it to reproduce constitutive mRNA and protein expression trajectories. We demonstrate the use of this characterized toolbox in a circuit behavior prediction case study for an incoherent feed-forward loop.

A simulation-based approach to study the influence of different production flows on manufacturing of customized products

Manufacturing products tailored to the individual requirements of customers is a must if companies want to compete effectively on the market. The production of customized goods poses new challenges for all areas of functioning of production systems. It is necessary to adopt such rules and methods that will allow a flexible response to product design changes and their demand In the organization of production flow (materials and information). The article presents research carried out in the SmartFactory laboratory of the Poznań University of Technology regarding the impact of the structure of products (customization) on the realization of current production orders. The research was carried out using the FlexSim simulation environment. Based on simulation experiments for three forms of organization of production flow with varying degrees of flexibility of production resources, an analysis was made of the time of execution of various sets of production orders and the level of use of available working time. The results of research indicate that in the production of products with low and high planned labor consumption, the use of universal production station is the most advantageous. For such a solution, the degree of utilization of the available working time of production stations is also the highest. It was also found that the principles of scheduling production orders affect the effectiveness of the production system. The best results were obtained for the production schedule, where the sequence of production orders was established from the lowest planned time of resource loading.

An endoribonuclease-based feedforward controller for decoupling resource-limited genetic modules in mammalian cells

Synthetic biology has the potential to bring forth advanced genetic devices for applications in healthcare and biotechnology. However, accurately predicting the behavior of engineered genetic devices remains difficult due to lack of modularity, wherein a device’s output does not depend only on its intended inputs but also on its context. One contributor to lack of modularity is loading of transcriptional and translational resources, which can induce coupling among otherwise independently-regulated genes. Here, we quantify the effects of resource loading in engineered mammalian genetic systems and develop an endoribonuclease-based feedforward controller that can adapt the expression level of a gene of interest to significant resource loading in mammalian cells. Near-perfect adaptation to resource loads is facilitated by high production and catalytic rates of the endoribonuclease. Our design is portable across cell lines and enables predictable tuning of controller function. Ultimately, our controller is a general-purpose device for predictable, robust, and context-independent control of gene expression.

A MATLAB Toolbox for Modeling Genetic Circuits in Cell-Free Systems

We introduce a MATLAB based simulation toolbox, called txtlsim, for an E. coli based Transcription-Translation (TX-TL) system. This toolbox accounts for several cell-free related phenomena, such as resource loading, consumption, and degradation, and in doing so, models the dynamics of TX-TL reactions for the entire duration of batch-mode experiments. We use a Bayesian parameter inference approach to characterize the reaction rate parameters associated with the core transcription, translation and mRNA degradation mechanics of the toolbox, allowing it to reproduce constitutive mRNA and protien expression trajectories. We demonstrate the use of this characterized toolbox in a circuit behavior prediction case study for an incoherent feed-forward loop.