The Waste-to-Biomethane Logistic Problem: A Mathematical Optimization Approach.

In this paper, we propose a new mathematical optimization approach to make decisions on the optimal design of the complex logistic system required to produce biogas from waste. We provide a novel and flexible decision-aid tool that allows decision makers to optimally determine the locations of different types of plants (pretreatment, anaerobic digestion, and biomethane liquefaction plants) and pipelines involved in the logistic process, according to a given budget, as well as the most efficient distribution of the products (from waste to biomethane) along the supply chain. The method is based on a mathematical optimization model that we further analyze and that, after reducing the number of variables and constraints without affecting the solutions, is able to solve real-size instances in reasonable CPU times. The proposed methodology is designed to be versatile and adaptable to different situations that arise in the transformation of waste to biogas. The results of our computational experiments, both in synthetic and in a case study instance, prove the validity of our proposal in practical applications. Synthetic instances with up to 200 farms and potential locations for pretreatment plants and 100 potential locations for anaerobic digestion and biomethane liquefaction plants were solved, exactly, within <20 min, whereas the larger instances with 500 farms were solved within <2 h. The CPU times required to solve the real-world instance range from 2 min to 6 h, being highly affected by the given budget to install the plants and the percent of biomethane that is required to be injected in the existing gas network.

Dynamic Multiplexed Control and Modeling of Optogenetic Systems Using the High-Throughput Optogenetic Platform, Lustro.

The ability to control cellular processes using optogenetics is inducer-limited, with most optogenetic systems responding to blue light. To address this limitation, we leverage an integrated framework combining Lustro, a powerful high-throughput optogenetics platform, and machine learning tools to enable multiplexed control over blue light-sensitive optogenetic systems. Specifically, we identify light induction conditions for sequential activation as well as preferential activation and switching between pairs of light-sensitive split transcription factors in the budding yeast, Saccharomyces cerevisiae. We use the high-throughput data generated from Lustro to build a Bayesian optimization framework that incorporates data-driven learning, uncertainty quantification, and experimental design to enable the prediction of system behavior and the identification of optimal conditions for multiplexed control. This work lays the foundation for designing more advanced synthetic biological circuits incorporating optogenetics, where multiple circuit components can be controlled using designer light induction programs, with broad implications for biotechnology and bioengineering.

Elucidating Molecular-Scale Principles Governing the Anchoring of Liquid Crystal Mixtures on Solid Surfaces.

Computational chemistry calculations are broadly useful for guiding the atom-scale design of hard-soft material interfaces including how molecular interactions of single-component liquid crystals (LCs) at inorganic surfaces lead to preferred orientations of the LC far from the surface. The majority of LCs, however, are not single-component phases but comprise of mixtures, such as a mixture of mesogens, added to provide additional functions such as responsiveness to the presence of targeted organic compounds (for chemical sensing). In such LC mixtures, little is understood about the near-surface composition and organization of molecules and how that organization propagates into the far-field LC orientation. Here, we address this broad question by using a multiscale computational approach that combines density functional theory (DFT)-based calculations and classical molecular dynamics (MD) simulations to predict the interfacial composition and organization of a binary LC mixture of 4'-cyano-4-biphenylcarbolxylic acid (CBCA) and 4'-n-pentyl-4-biphenylcarbonitrile (5CB) supported on anatase (101) titania surfaces. DFT calculations determine the surface composition and atomic-scale organization of CBCA and 5CB at the titania surface, and classical MD simulations build upon the DFT description to describe the evolution of the near-surface order into the bulk LC. A surprising finding is that the 5CB and CBCA molecules adopt orthogonal orientations at the anatase surface and that, above a threshold concentration of CBCA, this mixture of orientations evolves away from the surface to define a uniform far-field homeotropic orientation. These results demonstrate that molecular-level knowledge achieved through a combination of computational techniques permits the design and understanding of functional LC mixtures at interfaces.

Kinetic Modeling and Parameter Estimation of a Prebiotic Peptide Reaction Network.

Although our understanding of how life emerged on Earth from simple organic precursors is speculative, early precursors likely included amino acids. The polymerization of amino acids into peptides and interactions between peptides are of interest because peptides and proteins participate in complex interaction networks in extant biology. However, peptide reaction networks can be challenging to study because of the potential for multiple species and systems-level interactions between species. We developed and employed a computational network model to describe reactions between amino acids to form di-, tri-, and tetra-peptides. Our experiments were initiated with two of the simplest amino acids, glycine and alanine, mediated by trimetaphosphate-activation and drying to promote peptide bond formation. The parameter estimates for bond formation and hydrolysis reactions in the system were found to be poorly constrained due to a network property known as sloppiness. In a sloppy model, the behavior mostly depends on only a subset of parameter combinations, but there is no straightforward way to determine which parameters should be included or excluded. Despite our inability to determine the exact values of specific kinetic parameters, we could make reasonably accurate predictions of model behavior. In short, our modeling has highlighted challenges and opportunities toward understanding the behaviors of complex prebiotic chemical experiments.

Decoding Optical Responses of Contact-Printed Arrays of Thermotropic Liquid Crystals Using Machine Learning: Detection and Reporting of Aqueous Amphiphiles with Enhanced Sensitivity and Selectivity.

Surfactants and other amphiphilic molecules are used extensively in household products, industrial processes, and biological applications and are also common environmental contaminants; as such, methods that can detect, sense, or quantify them are of great practical relevance. Aqueous emulsions of thermotropic liquid crystals (LCs) can exhibit distinctive optical responses in the presence of surfactants and have thus emerged as sensitive, rapid, and inexpensive sensors or reporters of environmental amphiphiles. However, many existing LC-in-water emulsions require the use of complicated or expensive instrumentation for quantitative characterization owing to variations in optical responses among individual LC droplets. In many cases, the responses of LC droplets are also analyzed by human inspection, which can miss subtle color or topological changes encoded in LC birefringence patterns. Here, we report an LC-based surfactant sensing platform that takes a step toward addressing several of these issues and can reliably predict concentrations and types of surfactants in aqueous solutions. Our approach uses surface-immobilized, microcontact-printed arrays of micrometer-scale droplets of thermotropic LCs and hierarchical convolutional neural networks (CNNs) to automatically extract and decode rich information about topological defects and color patterns available in optical micrographs of LC droplets to classify and quantify adsorbed surfactants. In addition, we report computational capabilities to determine relevant optical features extracted by the CNN from LC micrographs, which can provide insights into surfactant adsorption phenomena at LC-water interfaces. Overall, the combination of microcontact-printed LC arrays and machine learning provides a convenient and robust platform that could prove useful for developing high-throughput sensors for on-site testing of environmentally or biologically relevant amphiphiles.

Integrating a tailored recurrent neural network with Bayesian experimental design to optimize microbial community functions.

Microbiomes interact dynamically with their environment to perform exploitable functions such as production of valuable metabolites and degradation of toxic metabolites for a wide range of applications in human health, agriculture, and environmental cleanup. Developing computational models to predict the key bacterial species and environmental factors to build and optimize such functions are crucial to accelerate microbial community engineering. However, there is an unknown web of interactions that determine the highly complex and dynamic behavior of these systems, which precludes the development of models based on known mechanisms. By contrast, entirely data-driven machine learning models can produce physically unrealistic predictions and often require significant amounts of experimental data to learn system behavior. We develop a physically-constrained recurrent neural network that preserves model flexibility but is constrained to produce physically consistent predictions and show that it can outperform existing machine learning methods in the prediction of certain experimentally measured species abundance and metabolite concentrations. Further, we present a closed-loop, Bayesian experimental design algorithm to guide data collection by selecting experimental conditions that simultaneously maximize information gain and target microbial community functions. Using a bioreactor case study, we demonstrate how the proposed framework can be used to efficiently navigate a large design space to identify optimal operating conditions. The proposed methodology offers a flexible machine learning approach specifically tailored to optimize microbiome target functions through the sequential design of informative experiments that seek to explore and exploit community functions.

Hydroformylation of pyrolysis oils to aldehydes and alcohols from polyolefin waste.

Waste plastics are an abundant feedstock for the production of renewable chemicals. Pyrolysis of waste plastics produces pyrolysis oils with high concentrations of olefins (>50 weight %). The traditional petrochemical industry uses several energy-intensive steps to produce olefins from fossil feedstocks such as naphtha, natural gas, and crude oil. In this work, we demonstrate that pyrolysis oil can be used to produce aldehydes through hydroformylation, taking advantage of the olefin functionality. These aldehydes can then be reduced to mono- and dialcohols, oxidized to mono- and dicarboxylic acids, or aminated to mono- and diamines by using homogeneous and heterogeneous catalysis. This route produces high-value oxygenated chemicals from low-value postconsumer recycled polyethylene. We project that the chemicals produced by this route could lower greenhouse gas emissions ~60% compared with their production through petroleum feedstocks.

Techno-Economic and life cycle assessment of standalone Single-Stream material recovery facilities in the United states.

Material Recovery Facilities (MRFs) are crucial players in achieving a circular economy. MRFs receive complex waste streams and separate valuable recyclables from these mixtures. This study conducts techno-economic analysis (TEA) to estimate the net present value (NPV) and life cycle assessment (LCA) to estimate different environmental impacts of a commercial scale standalone, single-stream MRF to assess the economic feasibility and environmental impacts of recovering valuable recyclables from an MRF processing 120,000 tonnes per year (t/y). The TEA employs a discounted cash flow rate of return (DCFROR) analysis over a 20-year facility lifetime, along with a sensitivity analysis on the impact of different operating and economic parameters. Results show that the total fixed cost of building the MRF facility is $23 MM, and the operating cost is $45.48/tonne. The NPV of the MRF can vary from $3.57 MM to $60 MM, while 100-year global warming potential can range from 5.98 to 8.53 kg carbon dioxide equivalents (CO2-eq) per tonne of MSW. We have also found that MSW composition (arising from regional effects) significantly impacts costs, 100-year global warming potential, and other impact categories such as acidification potential, eutrophication potential, ecotoxicity, ozone depletion, photochemical oxidation, carcinogenic effects, and non-carcinogenic effects. Sensitivity and uncertainty analysis indicate that waste composition and market prices significantly impact the profitability of the MRF, and the waste composition mostly impacts global warming potential. Our analysis also indicates that facility capacity, fixed capital cost, and waste tipping fees are vital parameters that affect the economic viability of MRF operations.

Multi-site, multi-pollutant atmospheric data analysis using Riemannian geometry.

We demonstrate the benefits of using Riemannian geometry in the analysis of multi-site, multi-pollutant atmospheric monitoring data. Our approach uses covariance matrices to encode spatio-temporal variability and correlations of multiple pollutants at different sites and times. A key property of covariance matrices is that they lie on a Riemannian manifold and one can exploit this property to facilitate dimensionality reduction, outlier detection, and spatial interpolation. Specifically, the transformation of data using Reimannian geometry provides a better data surface for interpolation and assessment of outliers compared to traditional data analysis tools that assume Euclidean geometry. We demonstrate the utility of using Riemannian geometry by analyzing a full year of atmospheric monitoring data collected from 34 monitoring stations in Beijing, China.

Topological Analysis of Molecular Dynamics Simulations using the Euler Characteristic.

Molecular dynamics (MD) simulations are used in diverse scientific and engineering fields such as drug discovery, materials design, separations, biological systems, and reaction engineering. These simulations generate highly complex data sets that capture the 3D spatial positions, dynamics, and interactions of thousands of molecules. Analyzing MD data sets is key for understanding and predicting emergent phenomena and in identifying key drivers and tuning design knobs of such phenomena. In this work, we show that the Euler characteristic (EC) provides an effective topological descriptor that facilitates MD analysis. The EC is a versatile, low-dimensional, and easy-to-interpret descriptor that can be used to reduce, analyze, and quantify complex data objects that are represented as graphs/networks, manifolds/functions, and point clouds. Specifically, we show that the EC is an informative descriptor that can be used for machine learning and data analysis tasks such as classification, visualization, and regression. We demonstrate the benefits of the proposed approach through case studies that aim to understand and predict the hydrophobicity of self-assembled monolayers and the reactivity of complex solvent environments.

A graph-based modeling framework for tracing hydrological pollutant transport in surface waters.

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.

Dynamic Multiplexed Control and Modeling of Optogenetic Systems Using the High-Throughput Optogenetic Platform, Lustro.

The ability to control cellular processes using optogenetics is inducer-limited, with most optogenetic systems responding to blue light. To address this limitation we leverage an integrated framework combining Lustro, a powerful high-throughput optogenetics platform, and machine learning tools to enable multiplexed control over blue light-sensitive optogenetic systems. Specifically, we identify light induction conditions for sequential activation as well as preferential activation and switching between pairs of light-sensitive spit transcription factors in the budding yeast, Saccharomyces cerevisiae . We use the high-throughput data generated from Lustro to build a Bayesian optimization framework that incorporates data-driven learning, uncertainty quantification, and experimental design to enable the prediction of system behavior and the identification of optimal conditions for multiplexed control. This work lays the foundation for designing more advanced synthetic biological circuits incorporating optogenetics, where multiple circuit components can be controlled using designer light induction programs, with broad implications for biotechnology and bioengineering.

ADAM: A web platform for graph-based modeling and optimization of supply chains.

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.

Ordering Transitions of Liquid Crystals Triggered by Metal Oxide-catalyzed Reactions of Sulfur Oxide Species.

Liquid crystals (LCs), when supported on reactive surfaces, undergo changes in ordering that can propagate over distances of micrometers, thus providing a general and facile mechanism to amplify atomic-scale transformations on surfaces into the optical scale. While reactions on organic and metal substrates have been coupled to LC-ordering transitions, metal oxide substrates, which offer unique catalytic activities for reactions involving atmospherically important chemical species such as oxidized sulfur species, have not been explored. Here, we investigate this opportunity by designing LCs that contain 4'-cyanobiphenyl-4-carboxylic acid (CBCA) and respond to surface reactions triggered by parts-per-billion concentrations of SO2 gas on anatase (101) substrates. We used electronic structure calculations to predict that the carboxylic acid group of CBCA binds strongly to anatase (101) in a perpendicular orientation, a prediction that we validated in experiments in which CBCA (0.005 mol %) was doped into an LC (4'-n-pentyl-4-biphenylcarbonitrile). Both experiment and computational modeling further demonstrated that SO3-like species, produced by a surface-catalyzed reaction of SO2 with H2O on anatase (101), displace CBCA from the anatase surface, resulting in an orientational transition of the LC. Experiments also reveal the LC response to be highly selective to SO2 over other atmospheric chemical species (including H2O, NH3, H2S, and NO2), in agreement with our computational predictions for anatase (101) surfaces. Overall, we establish that the catalytic activities of metal oxide surfaces offer the basis of a new class of substrates that trigger LCs to undergo ordering transitions in response to chemical species of relevance to atmospheric chemistry.

Sensing Gas Mixtures by Analyzing the Spatiotemporal Optical Responses of Liquid Crystals Using 3D Convolutional Neural Networks.

We report how analysis of the spatial and temporal optical responses of liquid crystal (LC) films to targeted gases, when performed using a machine learning methodology, can advance the sensing of gas mixtures and provide important insights into the physical processes that underlie the sensor response. We develop the methodology using O3 and Cl2 mixtures (representative of an important class of analytes) and LCs supported on metal perchlorate-decorated surfaces as a model system. Although O3 and Cl2 both diffuse through LC films and undergo redox reactions with the supporting metal perchlorate surfaces to generate similar initial and final optical states of the LCs, we show that a three-dimensional convolutional neural network can extract feature information that is encoded in the spatiotemporal color patterns of the LCs to detect the presence of both O3 and Cl2 species in mixtures and to quantify their concentrations. Our analysis reveals that O3 detection is driven by the transition time over which the brightness of the LC changes, while Cl2 detection is driven by color fluctuations that develop late in the optical response of the LC. We also show that we can detect the presence of Cl2 even when the concentration of O3 is orders of magnitude greater than the Cl2 concentration. The proposed methodology is generalizable to a wide range of analytes, reactive surfaces, and LCs and has the potential to advance the design of portable LC monitoring devices (e.g., wearable devices) for analyzing gas mixtures using spatiotemporal color fluctuations.

Comparative Analysis of the Chloroplast Genomes of Quercus × morehus and the Presumptive Parents Q. wislizeni and Q. kelloggii (Fagaceae) from California.

Here, we present the complete chloroplast genomes of Quercus × morehus, Q. wislizeni, and Q. kelloggii from California. The genomes are 161,119 to 161,130 bp and encode 132 genes. Quercus × morehus and Q. wislizeni are identical in sequence but differ from Q. kelloggii by three indels and eight SNPs.

Natural Rubber Blend Optimization via Data-Driven Modeling: The Implementation for Reverse Engineering.

Natural rubber formulation methodologies implemented within industry primarily implicate a high dependence on the formulator's experience as it involves an educated guess-and-check process. The formulator must leverage their experience to ensure that the number of iterations to the final blend composition is minimized. The study presented in this paper includes the implementation of blend formulation methodology that targets material properties relevant to the application in which the product will be used by incorporating predictive models, including linear regression, response surface method (RSM), artificial neural networks (ANNs), and Gaussian process regression (GPR). Training of such models requires data, which is equal to financial resources in industry. To ensure minimum experimental effort, the dataset is kept small, and the model complexity is kept simple, and as a proof of concept, the predictive models are used to reverse engineer a current material used in the footwear industry based on target viscoelastic properties (relaxation behavior, tanδ, and hardness), which all depend on the amount of crosslinker, plasticizer, and the quantity of voids used to create the lightweight high-performance material. RSM, ANN, and GPR result in prediction accuracy of 90%, 97%, and 100%, respectively. It is evident that the testing accuracy increases with algorithm complexity; therefore, these methodologies provide a wide range of tools capable of predicting compound formulation based on specified target properties, and with a wide range of complexity.

Analysis of incentive policies for phosphorus recovery at livestock facilities in the Great Lakes area.

Livestock operations have been highly intensified over the last decades, resulting in the advent of large concentrated animal feeding operations (CAFOs). Intensification decreases production costs but also leads to substantial environmental impacts. Specifically, nutrient runoff from livestock waste results in eutrophication, harmful algal blooms, and hypoxia. The implementation of nutrient recovery systems in CAFOs can abate nutrient releases and negative ecosystem responses, although they might negatively affect the economic performance of CAFOs. We design and analyze potential incentive policies for the deployment of phosphorus recovery technologies at CAFOs considering the geospatial vulnerability to nutrient pollution. The case study demonstration consists of 2217 CAFOs in the U.S. Great Lakes area. The results reveal that phosphorus recovery is more economically viable in the largest CAFOs due to economies of scale, although they also represent the largest eutrophication threats. For small and medium-scale CAFOs, phosphorus credits progressively improve the profitability of nutrient management systems. The integration of biogas production does not improve the economic performance of phosphorus recovery systems at most of CAFOs, as they lack enough size to be cost-effective. Phosphorus recovery proves to be economically beneficial by comparing the net costs of nutrient management systems with the negative economic impact derived from phosphorus releases. The incentives necessary for avoiding up to 20.7×103 ton/year phosphorus releases and achieve economic neutrality in the Great Lakes area are estimated at $223 million/year. Additionally, the fair distribution of limited incentives is studied using a Nash allocation scheme, determining the break-even point for allocating monetary resources.

Predicting Critical Micelle Concentrations for Surfactants Using Graph Convolutional Neural Networks.

Surfactants are amphiphilic molecules that are widely used in consumer products, industrial processes, and biological applications. A critical property of a surfactant is the critical micelle concentration (CMC), which is the concentration at which surfactant molecules undergo cooperative self-assembly in solution. Notably, the primary method to obtain CMCs experimentally-tensiometry-is laborious and expensive. In this study, we show that graph convolutional neural networks (GCNs) can predict CMCs directly from the surfactant molecular structure. In particular, we developed a GCN architecture that encodes the surfactant structure in the form of a molecular graph and trained it using experimental CMC data. We found that the GCN can predict CMCs with higher accuracy on a more inclusive data set than previously proposed methods and that it can generalize to anionic, cationic, zwitterionic, and nonionic surfactants using a single model. Molecular saliency maps revealed how atom types and surfactant molecular substructures contribute to CMCs and found this behavior to be in agreement with physical rules that correlate constitutional and topological information to CMCs. Following such rules, we proposed a small set of new surfactants for which experimental CMCs are not available; for these molecules, CMCs predicted with our GCN exhibited similar trends to those obtained from molecular simulations. These results provide evidence that GCNs can enable high-throughput screening of surfactants with desired self-assembly characteristics.

Reducing Antisolvent Use in the STRAP Process by Enabling a Temperature-Controlled Polymer Dissolution and Precipitation for the Recycling of Multilayer Plastic Films.

The recently reported processing strategy called solvent-targeted recovery and precipitation (STRAP) enables deconstruction of multilayer plastic packaging films into their constituent resins by selective dissolution. It uses a series of solvent washes that are guided by thermodynamic calculations of polymer solubility. In this work, the use of antisolvents in the STRAP process was reduced and solvent mixtures were considered to enable the temperature-controlled dissolution and precipitation of the target polymers in multilayer films. This was considered as a means to further improve the STRAP process and its estimated costs. Two STRAP approaches were compared based on different polymer precipitation techniques: precipitation by the addition of an antisolvent (STRAP-A) and precipitation by decreasing the solvent temperature (STRAP-B). Both approaches were able to separate the constituent polymers in a post-industrial film composed primarily of polyethylene (PE), ethylene vinyl alcohol (EVOH), and polyethylene terephthalate (PET) with near 100 % material efficiency. Technoeconomic analysis indicates that the minimum selling price (MSP) of the recycled resins with STRAP-B is 21.0 % lower than that achieved with STRAP-A. This provides evidence that thermally driven polymer precipitation is an option to reduce the use of antisolvents, making the STRAP process more economically and environmentally attractive. A third process, STRAP-C, was demonstrated with another post-industrial multilayer film of a different composition. The results demonstrate that this process can also recover polymers at similar costs to those of virgin resins, indicating that the STRAP technology is flexible and can remain economically competitive as the plastic feed complexity is increased.