Anthropogenic pollution of hydrological systems affects diverse communities and ecosystems around the world. Data analytics and modeling tools play a key role in fighting this challenge, as they can help identify key sources as well as trace transport and quantify impact within complex hydrological systems. Several tools exist for simulating and tracing pollutant transport throughout surface waters using detailed physical models; these tools are powerful, but can be computationally intensive, require significant amounts of data to be developed, and require expert knowledge for their use (ultimately limiting application scope). In this work, we present a graph modeling framework - which we call HydroGraphs - for understanding pollutant transport and fate across waterbodies, rivers, and watersheds. This framework uses a simplified representation of hydrological systems that can be constructed based purely on open-source data (National Hydrography Dataset and Watershed Boundary Dataset). The graph representation provides a flexible intuitive approach for capturing connectivity and for identifying upstream pollutant sources and for tracing downstream impacts within small and large hydrological systems. Moreover, the graph representation can facilitate the use of advanced algorithms and tools of graph theory, topology, optimization, and machine learning to aid data analytics and decision-making. We demonstrate the capabilities of our framework by using case studies in the State of Wisconsin; here, we aim to identify upstream nutrient pollutant sources that arise from agricultural practices and trace downstream impacts to waterbodies, rivers, and streams. Our tool ultimately seeks to help stakeholders design effective pollution prevention/mitigation practices and evaluate how surface waters respond to such practices.

Delivery of aerosols to the lung can treat various lung diseases. However, the conducting airways are coated by a protective mucus layer with complex properties that make this form of delivery difficult. Mucus is a non-Newtonian fluid and is cleared from the lungs over time by ciliated cells. Further, its gel-like structure hinders the diffusion of particles through it. Any aerosolized treatment of lung diseases must penetrate the mucosal barrier. Using computational fluid dynamics, a model of the airway mucus and periciliary layer was constructed to simulate the transport of impacted aerosol particles. The model predicts the dosage fraction of particles of a certain size that penetrate the mucus and reach the underlying tissue, as well as the distance downstream of the dosage site where tissue concentration is maximized. Reactions that may occur in the mucus are also considered, with simulated data for the interaction of a model virus and an antibody.

In this work, we discuss the use of surrogate functions and a new optimization framework to create an efficient and robust computational framework for process design. Our model process is the capture chromatography unit operation for monoclonal antibody purification, an important step in biopharmaceutical manufacturing. Simulating this unit operation involves solving a system of non-linear partial differential equations, which can have high computational cost. We implemented surrogate functions to reduce the computational time and make the framework more attractive for industrial applications. This strategy yielded accurate results with a 93% decrease in processing time. Additionally, we developed a new optimization framework to reduce the number of simulations needed to generate a solution to the optimization problem. We demonstrate the performance of our new framework, which uses MATLAB built-in tools, by comparing its performance against individual optimization algorithms for problems with integer, continuous, and mixed-integer variables.

Given that the usual process of developing a new vaccine or drug for COVID-19 demands significant time and funds, drug repositioning has emerged as a promising therapeutic strategy. We propose a method named DRPADC to predict novel drug-disease associations effectively from the original sparse drug-disease association adjacency matrix. Specifically, DRPADC processes the original association matrix with the WKNKN algorithm to reduce its sparsity. Furthermore, multiple types of similarity information are fused by a CKA-MKL algorithm. Finally, a compressed sensing algorithm is used to predict the potential drug-disease (virus) association scores. Experimental results show that DRPADC has superior performance than several competitive methods in terms of AUC values and case studies. DRPADC achieved the AUC value of 0.941, 0.955 and 0.876 in Fdataset, Cdataset and HDVD dataset, respectively. In addition, the conducted case studies of COVID-19 show that DRPADC can predict drug candidates accurately.

Modeling and optimization are essential tasks that arise in the analysis and design of supply chains (SCs). SC models are essential for understanding emergent behavior such as transactions between participants, inherent value of products exchanged, as well as impact of externalities (e.g., policy and climate) and of constraints. Unfortunately, most users of SC models have limited expertise in mathematical optimization, and this hinders the adoption of advanced decision-making tools. In this work, we present ADAM, a web platform that enables the modeling and optimization of SCs. ADAM facilitates modeling by leveraging intuitive and compact graph-based abstractions that allow the user to express dependencies between locations, products, and participants. ADAM model objects serve as repositories of experimental, technology, and socio-economic data; moreover, the graph abstractions facilitate the organization and exchange of models and provides a natural framework for education and outreach. Here, we discuss the graph abstractions and software design principles behind ADAM, its key functional features and workflows, and application examples.

This article introduces ContCarSim, a benchmark simulator for the development and testing of quality-by-design and quality-by-control strategies in the continuous intensified filtration-drying of paracetamol/ethanol slurries on a novel carousel technology, developed by Alconbury Weston Ltd (United Kingdom). The simulator is based on a detailed mechanistic mathematical modeling framework, and has been validated with filtration and drying experiments on a prototype equipment. A set of design- and control-relevant challenges to be addressed through ContCarSim are proposed. A case study is developed, to demonstrate the features of the simulator and its suitability to design, test and optimize the unit operation. ContCarSim is expected to promote the transition to end-to-end continuous pharmaceutical manufacturing and the adoption of closed-loop quality control by the pharmaceutical industry. The simulator can also be employed as a benchmark for data analytics and process monitoring studies.

After more than a year of online teaching resulting from the COVID-19 pandemic, it is time to take stock of the status quo in teaching practice in all things concerning process systems engineering (PSE), and to derive recommendations for the future to harness what we have experienced to improve the degree to which our students achieve mastery. This contribution presents the experiences and conclusions resulting from the first COVID-19 semester (spring 2020), and how the lessons learned were applied to the process design course taught in the second COVID-19 semester (winter 2020) to a class of 53 students. The paper concludes with general recommendations for fostering active learning by students in all PSE courses, whether taught online or face to face.

Excessive gestational weight gain is a significant public health concern that has been the recent focus of control systems-based interventions. (HMZ) is an intervention study that aims to develop and validate an individually-tailored and "intensively adaptive" intervention to manage weight gain for pregnant women with overweight or obesity using control engineering approaches. This paper presents how Hybrid Model Predictive Control (HMPC) can be used to assign intervention dosages and consequently generate a prescribed intervention with dosages unique to each individuals needs. A Mixed Logical Dynamical (MLD) model enforces the requirements for categorical (discrete-level) doses of intervention components and their sequential assignment into mixed-integer linear constraints. A comprehensive system model that integrates energy balance and behavior change theory, using data from one HMZ participant, is used to illustrate the workings of the HMPC-based control system for the HMZ intervention. Simulations demonstrate the utility of HMPC as a means for enabling optimized complex interventions in behavioral medicine, and the benefits of a HMPC framework in contrast to conventional interventions relying on "IF-THEN" decision rules.

Time-kill experiments can discern the pharmacodynamics of infectious bacteria exposed to antibiotics in vitro, and thus help guide the design of effective therapies for challenging clinical infections. This task is resource-limited, therefore typically bypassed in favor of empirical shortcuts. The resource limitation could be addressed by continuously assessing the size of a bacterial population under antibiotic exposure using optical density measurements. However, such measurements count both live and dead cells and are therefore unsuitable for declining populations of live cells. To fill this void, we develop here a model-based method that infers the count of live cells in a bacterial population exposed to antibiotics from continuous optical-density measurements of both live and dead cells combined. The method makes no assumptions about the underlying mechanisms that confer resistance and is widely applicable. Use of the method is demonstrated by an experimental study on exposed to levofloxacin.

The COVID-19 crisis popularized the importance of mathematical modeling for managing epidemics. A celebrated pertinent model was developed by Kermack and McKendrick about a century ago. A simplified version of that model has long been used and became widely popular recently, even though it has limitations that its originators had clearly articulated and warned against. A basic limitation is that it unrealistically assumes zero time to recovery for most infected individuals, thus underpredicting the peak of infectious individuals in an epidemic by a factor of as much as about 2. One could avoid this limitation by returning to the original comprehensive model, at the cost of higher complexity. To remedy that, we blend Ziegler-Nichols modeling ideas, developed for automatic controller tuning, with Kermack-McKendrick ideas to develop novel model structures that predict infectious peaks accurately yet retain simplicity. We illustrate these model structures with computer simulations on real epidemiological data.

The coordination of interconnected elements across the different layers of the supply chain is essential for all industrial processes and the key to optimal decision-making. Yet, the modeling and optimization of such interdependent systems are still burdensome. In this paper, we address the simultaneous modeling and optimization of medium-term planning and short-term scheduling problems under demand uncertainty using mixed-integer bi-level multi-follower programming and data-driven optimization. Bi-level multi-follower programs model the natural hierarchy between different layers of supply chain management holistically, while scenario analysis and data-driven optimization allow us to retrieve the guaranteed feasible solutions of the integrated formulation under various demand considerations. We address the data-driven optimization of this challenging class of problems using the DOMINO framework, which was initially developed to solve single-leader single-follower bi-level optimization problems to guaranteed feasibility. This framework is extended to solve single-leader multi-follower stochastic formulations and its performance is characterized by well-known single and multi-product process scheduling case studies. Through our data-driven algorithmic approach, we present guaranteed feasible solutions to linear and nonlinear mixed-integer bi-level formulations of simultaneous planning and scheduling problems and further characterize the effects of the scheduling level complexity on the solution performance, which spans over several hundred continuous and binary variables, and thousands of constraints.

Combination therapy for treatment of multi-drug resistant bacterial infections is becoming common. In vitro testing of drug combinations under realistic pharmacokinetic conditions is needed before a corresponding combination is eventually put into clinical use. The current standard for design of such in vitro simulations for drugs with different half-lives is heuristic and limited to two drugs. To address that void, we develop a rigorous design method suitable for an arbitrary number of drugs with different half-lives. The method developed offers substantial flexibility and produces novel designs even for two drugs. Explicit design equations are rigorously developed and are suitable for immediate use by experimenters. These equations were used in experimental verification using a combination of three antibiotics with distinctly different half-lives. In addition to antibiotics, the method is applicable to any anti-infective or anti-cancer drugs with distinct elimination pharmacokinetics.

Process design and optimization continue to provide computational challenges as the chemical engineering and process optimization communities seek to address more complex and larger scale applications. Software tools for digital design and flowsheet simulation are readily available for traditional chemical processing applications such as in commodity chemicals and hydrocarbon processing; however, tools for pharmaceutical manufacturing are much less well developed. This paper introduces, PharmaPy, a Python-based modelling platform for pharmaceutical manufacturing systems design and optimization. The versatility of the platform is demonstrated in simulation and optimization of both continuous and batch processes. The structure and features of a Python-based modeling platform, PharmaPy are presented. Illustrative examples are shown to highlight key features of the platform and framework.

Discovered well over two centuries ago and little used for long, the Lambert function has emerged in an increasing number of science and engineering applications in the last couple of decades. Here we present case studies relevant to the diverse interests of chemical engineers. We show how the Lambert function can be used for both analysis and computation. While some of these studies expound on prior literature results, the rest are new. We conjecture that if this tool becomes more widely known, many more instances of application will appear. Therefore, given its simplicity and usefulness, we would reasonably argue that the Lambert function should be included in the standard mathematical toolbox of chemical engineers.

Montmorillonite clays could be promising sorbents to mitigate toxic compound exposures. Bisphenols A (BPA) and S (BPS) as well as phthalates, dibutyl phthalate (DBP) and di-2-ethylhexyl phthalate (DEHP), are ubiquitous environmental contaminants linked to adverse health effects. Here, we combined computational and experimental methods to investigate the ability of montmorillonite clays to sorb these compounds. Molecular dynamics simulations predicted that parent, unamended, clay has higher binding propensity for BPA and BPS than for DBP and DEHP; carnitine-amended clay improved BPA and BPS binding, through carnitine simultaneously anchoring to the clay through its quaternary ammonium cation and forming hydrogen bonds with BPA and BPS. Experimental isothermal analysis confirmed that carnitine-amended clay has enhanced BPA binding capacity, affinity and enthalpy. Our studies demonstrate how computational and experimental methods, combined, can characterize clay binding and sorption of toxic compounds, paving the way for future investigation of clays to reduce BPA and BPS exposure.

The different stages of Covid-19 pandemic can be described by two key-variables: ICU patients and deaths in hospitals. We propose simple models that can be used by medical doctors and decision makers to predict the trends on both short-term and long-term horizons. Daily updates of the models with real data allow forecasting some key indicators for decision-making (an Excel file in the Supplemental material allows computing them). These are beds allocation, residence time, doubling time, rate of renewal, maximum daily rate of change (positive/negative), halfway points, maximum plateaus, asymptotic conditions, and dates and time intervals when some key thresholds are overtaken. Doubling time of ICU beds for Covid-19 emergency can be as low as 2-3 days at the outbreak of the pandemic. The models allow identifying the possible departure of the phenomenon from the predicted trend and thus can play the role of early warning systems and describe further outbreaks.

The human gastrointestinal (GI) tract is colonized by a highly diverse and complex microbial community (i.e., microbiota). The microbiota plays an important role in the development of the immune system, specifically mediating inflammatory responses, however the exact mechanisms are poorly understood. We have developed a mathematical model describing the effect of indole on host inflammatory signaling in HCT-8 human intestinal epithelial cells. In this model, indole modulates transcription factor nuclear factor κ B (NF-κB) and produces the chemokine interleukin-8 (IL-8) through the activation of the aryl hydrocarbon receptor (AhR). Phosphorylated NF-κB exhibits dose and time-dependent responses to indole concentrations and IL-8 production shows a significant down-regulation for 0.1 ng/mL TNF-α stimulation. The model shows agreeable simulation results with the experimental data for IL-8 secretion and normalized NF-κB values. Our results suggest that microbial metabolites such as indole can modulate inflammatory signaling in HTC-8 cells through receptor-mediated processes.

A simulator for testing automatic control algorithms for nonlinear systems with time-varying parameters, variable time delays, and uncertainties is developed. It is based on simulation of virtual patients with Type 1 diabetes (T1D). Nonlinear models are developed to describe glucose concentration (GC) variations based on user-defined scenarios for meal consumption, insulin administration, and physical activity. They compute GC values and physiological variables, such as heart rate, skin temperature, accelerometer, and energy expenditure, that are indicative of physical activities affecting GC dynamics. This is the first simulator designed for assessment of multivariable controllers that consider supplemental physiological variables in addition to GC measurements to improve glycemic control. Virtual patients are generated from distributions of identified model parameters using clinical data. The simulator will enable testing and evaluation of new control algorithms proposed for automated insulin delivery as well as various control algorithms for nonlinear systems with uncertainties, time-varying parameters and delays.

We propose a coordination framework for managing urban and rural organic waste in a scalable manner by orchestrating waste exchange, transportation, and transformation into value-added products. The framework is inspired by coordinated management systems that are currently used to operate power grids across the world and that have been instrumental in achieving high levels of efficiency and technological innovation. In the proposed framework, suppliers and consumers of waste and derived products as well as transportation and technology providers bid into a coordination system that is operated by an independent system operator. Allocations and prices for waste and derived products are obtained by the operator by solving a dispatch problem that maximizes the social welfare and that balances supply and demand across a given geographical region. Coordination enables handling of complex constraints and interdependencies that arise from transportation and bio-physico-chemical transformations of waste into products. We prove that the coordination system delivers prices and product allocations that satisfy economic and efficiency properties of a competitive market. The framework is scalable in that it can provide open access that fosters transactions between small and large players in urban and rural areas and over wide geographical regions. Moreover, the framework provides a systematic approach to enable coordinated responses to externalities such as droughts and extreme weather events, to monetize environmental impacts and remediation, to achieve complex social goals such as geographical nutrient balancing, and to justify technology investment and development efforts. Furthermore, the framework can facilitate coordination with electrical, natural gas, water, and transportation, and food distribution infrastructures.

The Quality-by-Design (QbD) guidance issued by the US Food and Drug Administration (FDA) has catalyzed the modernization of pharmaceutical manufacturing practices including the adoption of continuous manufacturing. Active process control was highlighted recently as a means to improve the QbD implementation. This advance has since been evolving into the concept of Quality-by-Control (QbC). In this study, the concept of QbC is discussed, including a definition of QbC, a review of the recent developments towards the QbC, and a perspective on the challenges of QbC implementation in continuous manufacturing. The QbC concept is demonstrated using a rotary tablet press, integrated into a pilot scale continuous direct compaction process. The results conclusively showed that active process control, based on product and process knowledge and advanced model-based techniques, including data reconciliation, model predictive control (MPC), and risk analysis, is indispensable to comprehensive QbC implementation, and ensures robustness and efficiency.

The renin angiotensin system is a major regulator of blood pressure and a target for many anti-hypertensive therapies; yet the efficacy of these treatments varies between the sexes. We use published data for systemic RAS hormones to build separate models for four groups of rats: male normotensive, male hypertensive, female normotensive, and female hypertensive rats. We found that plasma renin activity, angiotensinogen production rate, angiotensin converting enzyme activity, and neutral endopeptidase activity differ significantly among the four groups of rats. Model results indicate that angiotensin converting enzyme inhibitors and angiotensin receptor blockers induce similar decreases in angiotensin I and II between groups, but substantially different decreases. We further propose that a major difference between the male and female RAS may be the strength of the feedback mechanism, by which receptor bound angiotensin II impacts the production of renin.