The Fourth Industrial Revolution (Industry 4.0) brings a new chapter at dairy sector. Dairy 4.0 technologies are based on Big Data Analysis, Internet of Things, Robotics and Machine Learning. The usage of smart technologies to processing and analyzing complicated massive data has a significant impact in automation, optimization, functional costs and innovation. Artificial Intelligence tools are applied from dairy farms and production lines – including packaging- to supply chain. The aim of this paper is to demonstrate the most used applications of Machine Learning in dairy production so as to enhance the sustainability and the quality of dairy products. The most significant Machine Learning applications integrate machine vision, smart environmental sensors, activity collars, thermal imaging cameras, and digitized supply chain systems to facilitate inventory management. Challenges like milk adulteration, animal diseases, mastitis, traceability and supply chain losses are also addressed... [more]

Polyhydroxyalkanoates (PHAs) are microbial bioplastics that are fully biodegradable, biocompatible and can be produced by renewable feedstocks through fermentation. These are all desirable attributes for the replacement of current fossil-based plastics. Strong mathematical models describing bioprocesses are invaluable tools that can be used for enhancing bioprocess understanding as well as optimization. In this study, polyhydroxybutyrate (PHB), by Cupriavidus necator DSM 545 was produced using glycerol and ammonium sulphate (AS) as the sole carbon and nitrogen sources, respectively. In addition, a kinetic bioprocess model was developed. The kinetic parameters of the model were calibrated with five fermentation experiments with different initial conditions (e.g. variable glycerol and AS concentrations) in order to properly establish the inhibition regions and provide a generalized model as much as possible. The model was successfully validated by three independent experiments, two with... [more]

This study provides standardized models for the chemical characterization of complex streams, ensuring the necessary adaptations while considering the differences in biomass types and forms. Several datasets are compiled and examined to establish a valid representation of the mixture, according to industry accepted standards and laboratory protocols. For reliable property estimation, correlations of key biomass properties are obtained from both computational models and experimental measurements. Existing data are used to create datasets for the biomass and the biocrude streams. This model builds upon existing knowledge and data technologies with emphasis on hydrothermal liquefaction (HTL). The proposed approach shows potential as a starting point for the design and modelling of more biorefinery-associated technologies. Sludge and pine wood are used as case studies for biomass feedstocks. Two biocrude samples are employed for biocrude characterization. The performance of the developed o... [more]

Soybean is a highly valuable global commodity due to its versatility and numerous derivative products. During harvest, all non-seed materials become “straw”. Currently, this waste is primarily used for low-value purposes such as animal feed, landfilling, and incineration. To address this, the present work proposes a conceptual biorefinery aimed at converting soybean straw into higher-value products. The study began with data collection to identify potential conversion routes. Based on this information, a superstructure was developed, comprising seven conversion routes: four thermochemical routes (pyrolysis, combustion, hydrothermal gasification, and liquefaction), two biological routes (fermentation and anaerobic fermentation), and one chemical route (alkaline extraction). Each process was evaluated based on product yields, conversion times, and associated capital and operating costs. Using this data, an MILP (Mixed-Integer Linear Programming) optimization model was built in Pyomo usin... [more]

The global reliance on fossil-based solvents has driven the search for sustainable alternatives. This study employs the IBSS® CAMD tool to evaluate building blocks derived, directly or indirectly, from agricultural residues - specifically orange and coffee wastes-, to replace toluene in furfural extraction. A three-stage methodology was implemented: (1) identification of potential building blocks from residues, (2) multi-objective optimization using genetic algorithms and group contribution models for properties calculation, and (3) analysis of the resulting candidates based on performance indicators. A total of 13 families were evaluated, generating millions of candidates. Target properties included minimization of Hansen Solubility Parameters (HSP) distance, boiling point above 250°C, melting point below 10°C, flash point above 61°C, and octanol-water partition coefficient (log(kow)) below 3. The most promising candidates were derivatives of glycerol (performance: 0.9986), limonene (... [more]

Renewable energy and energy efficiency are increasingly recognised as crucial for creating new economic opportunities and mitigating environmental impacts. Anaerobic digestion (AD) transforms organic materials into a clean, renewable energy source. Co-digestion of various organic wastes and energy crops addresses the disadvantages of single-substrate digestion, increasing production flexibility yet adding process complexity and sensitivity. This study employs a two-pronged approach to optimise biogas production while considering global warming potential: a nonlinear programming (NLP) model for dynamic system economic optimisation with a model predictive control (MPC) strategy for precise temperature regulation within the digester. The NLP model integrates a combined heat and power (CHP) system to leverage dynamic electricity, heat, and gas prices, accounting for physical and economic parameters such as biomethane potential, chemical oxygen demand, and substrate density. A cardinal temp... [more]

The use of metabolic networks is extremely valuable for design and optimisation of bioprocesses as they provide great insight into cellular metabolism. Within bioprocess optimisation, they have enabled better (economic) objective performance through more accurate network-based models. However, one of the drawbacks of using metabolic networks is their underdeterminacy, leading to non-unique flux distributions. Flux Balance Analysis (FBA) reduces this issue by making assumptions on the behaviour of the cell. However, for metabolic networks of higher complexity, can still struggle with underdeterminacy. Metabolic network reduction can remove or greatly reduce this effect but can be difficult, especially when data is limited. Structural analysis of the metabolic network through Elementary Flux Modes (EFM) or Extreme Pathways (EP) can help locate the relevant information within the network. This work presents a metabolic network reduction approach based on the EPs that best explain a small... [more]

Global biomanufacturing is projected to expand rapidly in the coming decade due to advancements in DNA sequencing and manipulation. However, the complexity of cellular behaviour introduces difficulty in modelling and optimizing biomanufacturing processes. Phenomenological models that represent the physics of the system in empirical equations suffer from poor robustness, while their machine learning (ML) counterparts suffer from poor extrapolative capability. On the other hand, hybrid models allow us to leverage both physical constraints and the flexibility of ML. This work describes a new approach for hybrid modeling that integrates the time-variant parameter estimation and ML model training into a singular step. We implement this approach on a proposed scheme for the cell-mediated conversion of a lignin derivative into a bioplastic precursor and show that our integrated hybrid model outperforms the traditional two-step hybrid, phenomenological, and ML model counterparts. Lastly, we de... [more]

Most industrial fermentations in food and drink use a single, high purity sugar as a substrate. These pure substrates are more expensive and less sustainable than mixed substrates, that can be derived from agricultural byproducts such as straw. However, use of mixed substrates in fermentation leads to challenging modelling and parameter estimation problems, particularly when much academic research, intended to inform industrial applications, uses batch fermentations, while large-scale fermentation is usually continuous, thanks to its cost and productivity advantages. Our findings highlight key challenges in using batch-derived experimental data to inform models of the continuous fermentation processes used at industrial scale. Extrapolating from data obtained in batch to continuous fermentation is risky, as models with near-equivalent data-fit and predictions in a batch context give very different predictions for continuous culture. For continuous fermentations to switch to mixed subst... [more]

Miniaturised stirred bioreactors are crucial in high-throughput bioprocesses for their simplicity and cost-effectiveness. To accelerate process optimisation in chemical and bioprocess industries, models that integrate CFD-predicted flow fields with (bio)reaction kinetics are needed. However, conventional two-step coupling methods, which freeze flow fields after solving hydrodynamics and then address (bio)reaction transport, face numerical challenges in miniaturised systems due to unsteady radial flows, recirculation zones, and secondary vortices. These flow fluctuations prevent steady-state hydrodynamic convergence. This study addresses these challenges by time-averaging the RANS solutions of the transitional SST model to achieve statistical hydrodynamic convergence. This method is particularly effective for internal flow problems at low to midrange Reynolds numbers (100 W/m²) due to light limitation. This model provides a framework for optimising stirring speeds and refining operation... [more]

Precision modeling and forecasting of soil moisture are essential for implementing smart irrigation systems and mitigating agricultural drought. Most agro-hydrological models are based on the standard Richards equation, a highly nonlinear, degenerate elliptic-parabolic partial differential equation (PDE) with first order time derivative. However, research has shown that standard Richards equation is unable to model preferential flow in soil with fractal structure. In such a scenario, the soil exhibits anomalous non-Boltzmann scaling behavior. Incorporating the anomalous non-Boltzmann scaling behavior into the Richards equation leads to a generalized, time-fractional Richards equation based on fractional time derivatives. As expected, solving the time-fractional Richards equation for accurate modeling of water flow dynamics in soil faces extensive computational challenges. To target these challenges, we propose a novel numerical method that integrates finite volume method (FVM), adaptiv... [more]

Effective prediction of nutrient demands is crucial for optimising microalgae growth, maximising productivity and minimising the waste of resources. With the increasing amount of data related to microalgae cultivation systems, data mining and machine learning models to extract additional knowledge have gained popularity. In the development of such models, a data preprocessing stage is necessary due to the poor data quality. At this stage, cleaning and outlier removal techniques are employed to eliminate missing data and outliers, respectively. Afterwards, data splitting and cross-validation strategies are employed to ensure that the models are trained and evaluated with representative subsets of the data. Principal component analysis is also applied to simplify complex environmental datasets by reducing the number of features while retaining as much information as possible. To further improve prediction capabilities, ensemble methods are incorporated, leveraging multiple models to achi... [more]

Understanding the complexity of human digestion is critical for designing models that serve as valuable research tools for process simulation and prediction. Due to the high cost of medical intervention & recent advancements in in vitro digestion protocols, increased demand for inexpensive in silico solutions emerges. This study aims to develop a mathematical model that simulates the in vitro dynamic Food Digestion SIMulator (FooDSIM) functionalities via a digital twin approach. Ordinary Differential Equations (ODEs) simulate the system as a series of Continuously Stirred Tank Reactors (CSTRs) and describe different regions of human organs (stomach, duodenum, ileum, colon) of the human Gastrointestinal Tract (GIT). Various time horizons were used to investigate the effect of periodic feeding on the dynamic stabilisation of the inherently simulated processes (hydraulics, pH, biochemical interactions between enzymes & substrates, and nutrient absorption). A Polynomial Chaos Expansion (P... [more]

Predicting water quality is essential for effective environmental management and pollution control. Dissolved oxygen (DO), one of key water quality parameters, plays a vital role in biological wastewater treatment [1]. This study aims to forecast DO levels in activated sludge tanks of an oil refinery’s wastewater treatment plant (WWTP). Proper oxygen concentration is critical for microbial activity, as inadequate levels can disrupt the biological breakdown of pollutants. The objective is to develop predictive models to identify operational risks early, enhancing treatment efficiency and optimizing resources like chemicals, bacterial cultures, and aeration systems. Additionally, the study aims to provide early warnings to operators, minimizing reliance on laboratory tests and ensuring optimal conditions for bacteria, leading to better operational performance, cost reduction, and improved water quality ultimately promoting sustainable wastewater treatment. Various deep learning models, i... [more]

Water lily (Eichhornia crassipes) has been identified as an invasive exotic plant with high proliferation in Mexico, affecting aquatic bodies, such as lakes. After extraction, the water hyacinth biomass can be used as raw material for the production of bioproducts and bioenergy, however, the majority of them not covered the region's needs, and their economic profitability decreases significantly. Also, few reports present its use as raw material inside a biorefinery scheme. In this work, we propose a local biorefinery scheme to produce power and bioproducts from water lilies, using Aspen Plus V.10.0, per the needs of the Patzcuaro Lake community in Michoacán, Mexico. The scheme has been designed to process the harvested and sun-dried water lily from 197.6 kg/h of total wet harvested biomass, according to the extraction region schedule. The biomass is separated: root (RT) and stems-leaves (SL). The processing scheme involves the RT combustion to produce electric power, and two process... [more]

Optimizing greenhouse operations in arid regions is essential for sustainable agriculture due to limited water resources and high energy demands for climate control. This paper proposes a multi-objective optimization framework aimed at minimizing both the operational costs and environmental emissions of a climate-controlled greenhouse. The framework determines optimal allocation of growing area among three crops (tomato, cucumber, and bell pepper) throughout the year. These crops were selected for their varying growth conditions, which induce variability in energy and water inputs, providing a comprehensive assessment of the optimization model. The model integrates factors such as temperature, humidity, light intensity, and irrigation requirements specific to each crop. It is solved using a genetic algorithm combined with Pareto front analysis to address the multi-objective nature effectively. This approach facilitates the identification of optimal trade-offs between cost, emissions, a... [more]

The extraction of lycopene from tomato waste has been largely evaluated at an experimental level, leading to the creation of polynomial models or response surfaces that allow the representation of the extraction behavior. However, these studies are based on laboratory level and an extraction process has not yet been scaled up. This study evaluates the design and optimization of the lycopene extraction process from tomato waste. The proposed model is solved through a link between Python and Aspen Plus, performing the optimization a genetic algorithm (GA) in Pymoo. The minimum value of TAC is 211,692.2 USD/yr, corresponding to a production of 2.29 g/h of lycopene, starting from 1000 kg/h of tomato waste. This work represents a first approach to the design of a commercial-scale lycopene production process.

Due to the importance of unsaturated fatty acids for human health and the increasing global demand in the food and food crop area, oleaginous yeasts are promising alternative microorganisms for commercial lipid production due to the high volumetric productivity, with Metchnikowia pulcherrima being an underexplored oleaginous yeast with potential as a lipid producer. Critical to achieving high productivity lipid production are nutrient factors. A sensitivity test identified carbon and nitrogen sources as important factors in nitrogen limited broth (NLB) for lipid production in M. pulcherrima i.e. glucose, yeast extract and Ammonium sulphate. Response Surface Methodology (RSM) involving sets of 15 experimental runs of three-factor three-level Box-Behnken Design (BBD) was implemented for exploring the design of the carbon and nitrogen source in the growth media composition. Quadratic surfaces were least-square fitted and used to identify regions of optimal lipid yield. Multiple sets of ru... [more]

Incorporating process knowledge from various sources often presents challenges in process development, optimization, and control. To utilize available knowledge, linking existing process mo-dels is a viable approach. This work introduces a methodology using latent variable models, specifically sequential and orthogonalized partial least squares (SO-PLS), to capture and quantify the contribution of first-principles knowledge in process models. Applied to a continuously stirred tank reactor (CSTR) case study, the methodology demonstrates how available knowledge can be quantified and how structural and parametric errors in first-principles are addressed using measured data. The methodology is discussed in relation to root cause analysis in bioprocesses.

Pharmacokinetic and pharmacodynamic (PK/PD) models are used to predict drug transport in the body and to assess treatment efficacy and optimal dosage. The kinetic parameters embedded in the models, which define transport across body compartments or drug efficacy, can be linked to patient-specific characteristics; understanding the parameter space-model output relationship is critical towards linking patient population heterogeneity to the therapeutic outcome variability. Global Sensitivity Analysis (GSA) is a well-established tool used to examine parameter-to-parameter interactions, shedding light on underlying interactions towards enhanced system understanding. Despite its potential and usefulness, GSA performance is dependent to the model complexity; large-scale and nonlinear PK/PD models, which often have large sets of parameters, can render GSA challenging to perform, requiring excessive computational effort. Proposed approaches to reduce GSA complexity, such as segmentation in par... [more]

In recent years, burgeoning interest in products derived from microbial production across various sectors has significantly propelled the evolution of the field of metabolic engineering. As a Gram-negative bacterium, Vibrio natriegens is characterized by its fast growth, robust metabolic capabilities, and a broad substrate spectrum, making it a promising candidate as a standard biological host for the industrial bioproduction of metabolites. Genome-scale metabolic models (GSMMs) are mathematical representations constructed based on genome annotations and gene-protein-reaction (GPR) associations within a cell. These models enable the computational simulation of intracellular reaction flux distributions. In this study, we developed a hybrid method based on metaheuristic algorithms and the GSMM to optimize metabolism for the production of ethanol and 1,3-propanediol (1,3-PDO) as target products in Vibrio natriegens. The modified GSMM used in this study contains 1195 reactions, 1094 metabo... [more]

The European Union is transitioning towards a circular and low-carbon economy, emphasizing renewable biological resources. This study explores the production of high-value compounds like chitosan from fungal biomass and presents a potential design for a sustainable biorefinery process, contributing to the diversification and optimisation of biomass feedstock utilisation. The process simulation includes dedicated sub-models for each unit operation, based on laboratory data and integrated into a comprehensive process flow sheet using COCO-COFE. The productivity of the simulated plant results in 2 500 tons of triglyceride oils and 1 800 tons of chitosan that can be produced from 15 000 tons of Aspergillus niger. On-site acetic acid production meets 45% of the total plant's demand, significantly reducing the amount of additional acetic acid to be purchased as raw material. Additionally, large-scale enzyme consumption and the substantial heat demand for biomass processing are key economic a... [more]

Machine learning algorithms have led to the development of numerous vector embeddings for biological entities such as metabolites, proteins, genes, and enzymes. However, these embeddings often lack contextual information due to their specialized focus on individual omics. Disease progression and biosynthesis pathways are increasingly understood through complex, multi-layered networks that integrate diverse omics data and intricate signaling and reaction sequences. Capturing these relationships in a meaningful way requires embeddings that account for both functional and multi-modal dependencies. We propose an embedding approach that unifies these different biological modalities by treating them as directions in a shared space rather than as isolated data types. Similar to how word embeddings in natural language processing reveal meaningful relationships (e.g., Tokyo – Japan + UK = London, indicating a directional representation of capitals), we can model genes and proteins in a way that... [more]

To match the growing demand for biomethane production, anaerobic digestors need an optimal and time-varying adaptation of the input diet. Dynamic co-digestion constitutes a hard challenge for the limited instrumentation and control equipment typically installed aboard full-scale plants. The development of prediction models is foreseen to support process (optimal) design and control. In this work, a rigorous framework was applied to take full-scale applicability into account while dealing with the design and training of both high-fidelity and control-oriented first-principle/grey-box models, to be used for real-time optimization and process control respectively.

Microalgae cultivation on liquid digestate from the anaerobic co-digestion of agricultural feedstocks is an interesting option for digestate nutrient removal and resource recovery coupled to value-added biomass production. In this paper, a first-principle plant-wide modelling of the process is described. Two well-established models for anaerobic digestion (IWA – ADM1) and algae-based bioremediation processes (ALBA) were considered and modified with necessary equations and extensions to develop a coherent interface between the state variables of the two models. The resulting system is composed by highly non-linear and non-smooth DAEs. Open-loop scenario analysis for different upstream co-digester design and operating conditions was carried out to assess the impacts on the downstream microalgae outputs. It highlighted the importance of a proper biorefinery design and yet a noteworthy robustness of the system performance. The exploitation of the model can facilitate: a more realistic asse... [more]