Optimization Library Research Articles

Neural Methods for Amortized Inference

Simulation-based methods for statistical inference have evolved dramatically over the past 50 years, keeping pace with technological advancements. The field is undergoing a new revolution as it embraces the representational capacity of neural networks, optimization libraries, and graphics processing units for learning complex mappings between data and inferential targets. The resulting tools are amortized, in the sense that, after an initial setup cost, they allow rapid inference through fast feed-forward operations. In this article we review recent progress in the context of point estimation, approximate Bayesian inference, summary-statistic construction, and likelihood approximation. We also cover software and include a simple illustration to showcase the wide array of tools available for amortized inference and the benefits they offer over Markov chain Monte Carlo methods. The article concludes with an overview of relevant topics and an outlook on future research directions.

Fast and Optimal Extraction for Sparse Equality Graphs

Equality graphs (e-graphs) are used to compactly represent equivalence classes of terms in symbolic reasoning systems. Beyond their original roots in automated theorem proving, e-graphs have been used in a variety of applications. They have become particularly important as the key ingredient in the popular technique of equality saturation, which has notable applications in compiler optimization, program synthesis, program verification, and symbolic execution, among others. In a typical equality saturation workflow, an e-graph is used to store a large number of equalities that are generated by local rewrites during a saturation phase, after which an optimal term is extracted from the e-graph as the output of the technique. However, despite its crucial role in equality saturation, e-graph extraction has received relatively little attention in the literature, which we seek to start addressing in this paper. Extraction is a challenging problem and is notably known to be NP-hard in general, so current equality saturation tools rely either on slow optimal extraction algorithms based on integer linear programming (ILP) or on heuristics that may not always produce the optimal result. In fact, in this paper, we show that e-graph extraction is hard to approximate within any constant ratio. Thus, any such heuristic will produce wildly suboptimal results in the worst case. Fortunately, we show that the problem becomes tractable when the e-graph is sparse, which is the case in many practical applications. We present a novel parameterized algorithm for extracting optimal terms from e-graphs with low treewidth, a measure of how “tree-like” a graph is, and prove its correctness. We also present an efficient Rust implementation of our algorithm and evaluate it against ILP on a number of benchmarks extracted from the Cranelift benchmark suite, a real-world compiler optimization library based on equality saturation. Our algorithm optimally extracts e-graphs with treewidths of up to 10 in a fraction of the time taken by ILP. These results suggest that our algorithm can be a valuable tool for equality saturation users who need to extract optimal terms from sparse e-graphs.

Optimization berth allocation in container terminals: A Pyomo and Google Colab approach

Efficient berth allocation profoundly influences container terminal operations, affecting vessel waiting and turnaround times, and overall performance. This study presents a mixed-integer linear programming (MILP) model addressing the Berth Allocation Problem (BAP) in a Malaysian container port. By incorporating the Pyomo optimization library and CBC (Coin-or Branch and Cut) solver in Google Colab, optimal berth allocations are determined, minimizing vessel turnaround times. Visualized in a Space-Time diagram, the results highlight efficient allocation strategies. Despite limitations, the study optimally resolved three instances, achieving a remarkable 38.54% reduction in overall vessel turnaround time compared to FCFS (First-Come-First-Serve) allocation. By prioritizing port turnaround time, the optimization substantially reduced berthing and departure delays, aligning with UNCTAD's call for enhanced port efficiency and accelerated decarbonization efforts.

MDFit: automated molecular simulations workflow enables high throughput assessment of ligands-protein dynamics.

Molecular dynamics (MD) simulation is a powerful tool for characterizing ligand-protein conformational dynamics and offers significant advantages over docking and other rigid structure-based computational methods. However, setting up, running, and analyzing MD simulations continues to be a multi-step process making it cumbersome to assess a library of ligands in a protein binding pocket using MD. We present an automated workflow that streamlines setting up, running, and analyzing Desmond MD simulations for protein-ligand complexes using machine learning (ML) models. The workflow takes a library of pre-docked ligands and a prepared protein structure as input, sets up and runs MD with each protein-ligand complex, and generates simulation fingerprints for each ligand. Simulation fingerprints (SimFP) capture protein-ligand compatibility, including stability of different ligand-pocket interactions and other useful metrics that enable easy rank-ordering of the ligand library for pocket optimization. SimFPs from a ligand library are used to build & deploy ML models that predict binding assay outcomes and automatically infer important interactions. Unlike relative free-energy methods that are constrained to assess ligands with high chemical similarity, ML models based on SimFPs can accommodate diverse ligand sets. We present two case studies on how SimFP helps delineate structure-activity relationship (SAR) trends and explain potency differences across matched-molecular pairs of (1) cyclic peptides targeting PD-L1 and (2) small molecule inhibitors targeting CDK9.

Energy optimization algorithms for multi-residential buildings: A model predictive control application

This study presents an optimization algorithm for Model Predictive Control (MPC) of the HVAC systems in multi-family residential buildings assessing the performance of four objective functions. Implemented in C++, using the free OR-Tools optimization library, the model is formulated a Mixed Integer-Linear Programming (MILP) problem. The study analyses the results of tests conducted on a 20-dwelling block in Switzerland across various weather and occupancy conditions, resulting in a parametric study of 64 cases.The models developed for the MPC are Grey-box type for the interconnected energy systems: the building, thermal storage tanks, a heat pump, the ventilation system and PV collectors, highlighting a radiant wall heating system integrated into the building facade. The tanks and the heat pump models were informed with manufacturer data, while for the building a R3C3 thermal-electrical equivalent model was developed, calibrated using TRNSYS simulations with a root mean square error of 1.7%.Findings demonstrate how the algorithm optimizes the operation according to the desired criteria, while ensuring indoor comfort with a 15-minute time resolution. The time execution of the majority of cases is under 3 min in a low-specs computer, affirming its practical viability for real-world implementation.

Machine learning models on a web application to predict short-term postoperative outcomes following anterior cervical discectomy and fusion

BackgroundThe frequency of anterior cervical discectomy and fusion (ACDF) has increased up to 400% since 2011, underscoring the need to preoperatively anticipate adverse postoperative outcomes given the procedure’s expanding use. Our study aims to accomplish two goals: firstly, to develop a suite of explainable machine learning (ML) models capable of predicting adverse postoperative outcomes following ACDF surgery, and secondly, to embed these models in a user-friendly web application, demonstrating their potential utility.MethodsWe utilized data from the National Surgical Quality Improvement Program database to identify patients who underwent ACDF surgery. The outcomes of interest were four short-term postoperative adverse outcomes: prolonged length of stay (LOS), non-home discharges, 30-day readmissions, and major complications. We utilized five ML algorithms - TabPFN, TabNET, XGBoost, LightGBM, and Random Forest - coupled with the Optuna optimization library for hyperparameter tuning. To bolster the interpretability of our models, we employed SHapley Additive exPlanations (SHAP) for evaluating predictor variables’ relative importance and used partial dependence plots to illustrate the impact of individual variables on the predictions generated by our top-performing models. We visualized model performance using receiver operating characteristic (ROC) curves and precision-recall curves (PRC). Quantitative metrics calculated were the area under the ROC curve (AUROC), balanced accuracy, weighted area under the PRC (AUPRC), weighted precision, and weighted recall. Models with the highest AUROC values were selected for inclusion in a web application.ResultsThe analysis included 57,760 patients for prolonged LOS [11.1% with prolonged LOS], 57,780 for non-home discharges [3.3% non-home discharges], 57,790 for 30-day readmissions [2.9% readmitted], and 57,800 for major complications [1.4% with major complications]. The top-performing models, which were the ones built with the Random Forest algorithm, yielded mean AUROCs of 0.776, 0.846, 0.775, and 0.747 for predicting prolonged LOS, non-home discharges, readmissions, and complications, respectively.ConclusionsOur study employs advanced ML methodologies to enhance the prediction of adverse postoperative outcomes following ACDF. We designed an accessible web application to integrate these models into clinical practice. Our findings affirm that ML tools serve as vital supplements in risk stratification, facilitating the prediction of diverse outcomes and enhancing patient counseling for ACDF.

Routing and facility location optimization in a dairy products supply chain

Routing and facility location optimization is an important aspect of supply chain management. This is because the problem of determining which facilities within a supply chain echelon should cost-effectively supply products to facilities in the next echelon is usually encountered by supply chain managers and analysts. In this paper, a linear programming model for supply chain routing and facility location optimization has been proposed. The model can be solved using the PuLP optimization library implemented in Python programming language. The model has been applied to a small dairy products supply chain to determine the most cost-effective routes for products in the supply chain. The optimization results proffered the optimal contribution of each factory warehouse to each distribution warehouse in order to satisfy distribution warehouse demand while minimizing costs. The results of the study indicated that the model is efficient in solving the routing and facility location optimization problem usually encountered in supply chain management. Therefore, this study will aid supply chain analysts and managers in determining the most cost-effective route for distributing products between echelons or stages of supply chains under study.

Multi-objective trajectory planning for industrial robots using a hybrid optimization approach

Abstract In this paper, a hybrid approach organized in four phases is proposed to solve the multi-objective trajectory planning problem for industrial robots. In the first phase, a transcription of the original problem into a standard multi-objective parametric optimization problem is achieved by adopting an adequate parametrization scheme for the continuous robot configuration variables. Then, in the second phase, a global search is performed using a population-based search metaheuristic in order to build a first approximation of the Pareto front (PF). In the third phase, a local search is applied in the neighborhood of each solution of the PF approximation using a deterministic algorithm in order to generate new solutions. Finally, in the fourth phase, results of the global and local searches are gathered and postprocessed using a multi-objective direct search method to enhance the quality of compromise solutions and to converge toward the true optimal PF. By combining different optimization techniques, we intend not only to improve the overall search mechanism of the optimization strategy but also the resulting hybrid algorithm should keep the robustness of the population-based algorithm while enjoying the theoretical properties of convergence of the deterministic component. Also, the proposed approach is modular and flexible, and it can be implemented in different ways according to the applied techniques in the different phases. In this paper, we illustrate the efficiency of the hybrid framework by considering different techniques available in various numerical optimization libraries which are combined judiciously and tested on various case studies.

Development of a New Vertical Dynamic Model of a Rail Vehicle for the Analysis of Ride Comfort

The rail vehicle industry wants to produce vehicles with higher speeds, to maintain and increase its market share. However, when the speed of the vehicle increases, it may have an undesirable effect on ride comfort, in terms of ride dynamics. Recent developments towards lighter and faster vehicles make the problem of ride comfort at higher speeds increasingly important. Focusing on the behavior of flexible rather than rigid body behavior should not be neglected when designing long and light car bodies. There are several approaches to incorporate body flexibility in multibody simulations and they have some superiorities and weaknesses. In this study, an efficient and accurate vertical dynamic model for the ride comfort analysis is developed and implemented in a commercial object-oriented modeling (OOM) software Dymola (2015 FD01) which uses the open-source code Modelica. This model includes car body flexibility with the assembling of a rigid body approach. The developed model is compared to a three-dimensional vehicle model in the commercial Vampire software (Pro V5.50) at different velocities. For the vertical ride comfort analysis, the ISO 2631-1 standard was used for both the developed model and the three-dimensional model. The results are presented as acceleration history and awrms—weighted r.m.s (root mean square) of accelerations—as required by the standard. The developed model has shown its feasibility in terms of its efficiency and accuracy for the vertical ride comfort analysis. The accuracy of the model is evidenced by the fact that the car body vibration level at high speeds shows minor differences compared to the results of the Vampire, which is a validated commercial software in the area of rail vehicle dynamics. The approach involving the assembly of rigid bodies is applied for the first time for high-speed trains in dynamical modelling, with flexible car bodies for ride comfort analysis. Furthermore, it can be used for parametrical studies focusing on ride comfort, thereby offering a quite beneficial framework for addressing the challenges of ride comfort analysis in high-speed rail vehicles. Improvements for and analyses of other aspects are also possible, since the optimization and other useful libraries are readily available in Dymola/Modelica.

Mathematical Models for the Single-Channel and Multi-Channel PMU Allocation Problem and Their Solution Algorithms

Phasor measurement units (PMUs) are deployed at power grid nodes around the transmission grid, determining precise power system monitoring conditions. In real life, it is not realistic to place a PMU at every power grid node; thus, the lowest PMU number is optimally selected for the full observation of the entire network. In this study, the PMU placement model is reconsidered, taking into account single- and multi-capacity placement models rather than the well-studied PMU placement model with an unrestricted number of channels. A restricted number of channels per monitoring device is used, instead of supposing that a PMU is able to observe all incident buses through the transmission connectivity lines. The optimization models are declared closely to the power dominating set and minimum edge cover problem in graph theory. These discrete optimization problems are directly related with the minimum set covering problem. Initially, the allocation model is declared as a constrained mixed-integer linear program implemented by mathematical and stochastic algorithms. Then, the 0/1 integer linear problem is reformulated into a non-convex constraint program to find optimality. The mathematical models are solved either in binary form or in the continuous domain using specialized optimization libraries, and are all implemented in YALMIP software in conjunction with MATLAB. Mixed-integer linear solvers, nonlinear programming solvers, and heuristic algorithms are utilized in the aforementioned software packages to locate the global solution for each instance solved in this application, which considers the transformation of the existing power grids to smart grids.

HVAC energy cost minimization in smart grids: A cloud-based demand side management approach with game theory optimization and deep learning

In this paper, we present a novel cloud-based demand side management (DSM) optimization approach for the cost reduction of energy usage in heating, ventilation and air conditioning (HVAC) systems in residential homes at the district level. The proposed approach achieves optimization through scheduling of HVAC energy usage within permissible bounds set by house users. House smart home energy management (SHEM) devices are connected to the utility/aggregator via a dedicated communication network that is used to enable DSM. Each house SHEM can predict its own HVAC energy usage for the next 24 h using minimalistic deep learning (DL) prediction models. These predictions are communicated to the aggregator, which will then do day ahead optimizations using the proposed game theory (GT) algorithm. The GT model captures the interaction between aggregator and customers and identifies a solution to the GT problem that translates into HVAC energy peak shifting and peak reduction achieved by rescheduling HVAC energy usage. The found solution is communicated by the aggregator to houses SHEM devices in the form of offers via DSM signals. If customers’ SHEM devices accept the offer, then energy cost reduction will be achieved. To validate the proposed algorithm, we conduct extensive simulations with a custom simulation tool based on GridLab-D tool, which is integrated with DL prediction models and optimization libraries. Results show that HVAC energy cost can be reduced by up to 36% while indirectly also reducing the peak-to-average (PAR) and the aggregated net load by up to 9.97%.

757 Machine Learning-Driven Web Application for Enhanced Clinical Decision Support in Thoracolumbar Spinal Cord Injuries

INTRODUCTION: Thoracolumbar spinal cord injuries (tlSCI) can result in negative short-term in-hospital outcomes, underscoring the importance of precise prediction tools. METHODS: This retrospective cohort study included 147,826 patients from the American College of Surgeons Trauma Quality Program database. XGBoost, LightGBM, CatBoost, and Random Forest algorithms were utilized in combination with the Optuna optimization library for hyperparameter tuning. Models were evaluated graphically with receiver operating characteristic (ROC) curves, precision-recall curves, and numerically with precision, recall, F1 score, accuracy, area under ROC (AUROC), and area under PRC. The best-performing models were integrated into an open-access web application for individualized predictions. RESULTS: The best-performing models for each outcome were as follows: for predicting mortality, Random Forest achieved the highest AUROC (0.865, 95% CI 0.848-0.879); in predicting non-home discharges, LightGBM had the highest AUROC (0.801, 95% CI 0.794-0.804); and for predicting major complications, Random Forest performed best with an AUROC of 0.733 (95% CI 0.642-0.808). Algorithms' receiver operator curves for the outcomes: (A) mortality, (B) non-home discharges, and (C) major complications. CONCLUSIONS: This study successfully developed ML models to predict critical in-hospital outcomes for patients with tlSCI. By incorporating the top-performing algorithms into a user-friendly web application, these models have the potential to improve clinical decision-making and management strategies for tlSCI patients, ultimately enhancing patient care and outcomes.

Phosphonium-Catalyzed Monoreduction of Bisphosphine Dioxides: Origin of Selectivity and Synthetic Applications.

Controlling product selectivity in successive reactions of the same type is challenging owing to the comparable thermodynamic and kinetic properties of the reactions involved. Here, the synergistic interaction of the two phosphoryl groups in bisphosphine dioxides (BPDOs) with a bromo-phosphonium cation was studied experimentally to provide a practical tool for substrate-catalyst recognition. As the eventual result, we have developed a phosphonium-catalyzed monoreduction of chiral BPDOs to access an array of synthetically useful bisphosphine monoxides (BPMOs) with axial, spiro, and planar chirality, which are otherwise challenging to synthesize before. The reaction features excellent selectivity and impressive reactivity. It proceeds under mild conditions, avoiding the use of superstoichiometric amounts of additives and metal catalysts to simplify the synthetic procedure. The accessibility and scalability of the reaction allowed for the rapid construction of a ligand library for optimization of asymmetric Heck-type cyclization, laying the foundation for a broad range of applications of chiral BPMOs in catalysis.

Machine Learning–Driven Prognostication in Traumatic Subdural Hematoma: Development of a Predictive Web Application

BACKGROUND AND OBJECTIVES: Our focus was on creating an array of machine learning (ML) models to predict unfavorable in-hospital outcomes after acute traumatic subdural hematoma (atSDH). Our subsequent aim was to deploy these models in an accessible web application, showcasing their practical value. METHODS: Data from the American College of Surgeons Trauma Quality Program database were used to identify patients with atSDH. In-hospital mortality was the primary outcome of interest. Secondary outcomes were (1) nonhome discharges, (2) prolonged length of stay (LOS), (3) prolonged length of stay in the intensive care unit (ICU-LOS), and (4) major complications. Feature selection was performed with least absolute shrinkage and selection operator algorithm. Five ML algorithms, including TabPFN, TabNET, XGBoost, LightGBM, and Random Forest, were used along with the Optuna optimization library for hyperparameter tuning. RESULTS: There were 104 055 patients included in the analysis for the outcome mortality, 82 988 for the outcome nonhome discharges, 104 207 for the outcome prolonged LOS, 62 543 for the outcome prolonged ICU-LOS, and 100 241 for the outcome major complications. The models with the highest area under receiver operating characteristic curve (AUROC) values included TabPFN for mortality and major complications, and LightGBM for nonhome discharges, prolonged LOS, and ICU-LOS. The TabPFN model for the primary outcome of our study, in-hospital mortality, showed an AUROC of 0.934. The models with the highest AUROC values were integrated into an application to predict the outcomes of interest. CONCLUSION: Our findings show that ML tools aid in predicting various outcomes for patients with atSDH. We developed a web application that has the potential to integrate the developed models into clinical practice.

Development and internal validation of machine learning models for personalized survival predictions in spinal cord glioma patients

BACKGROUND CONTEXTNumerous factors have been associated with the survival outcomes in patients with spinal cord gliomas (SCG). Recognizing these specific determinants is crucial, yet it is also vital to establish a reliable and precise prognostic model for estimating individual survival outcomes. OBJECTIVEThe objectives of this study are twofold: first, to create an array of interpretable machine learning (ML) models developed for predicting survival outcomes among SCG patients; and second, to integrate these models into an easily navigable online calculator to showcase their prospective clinical applicability. STUDY DESIGNThis was a retrospective, population-based cohort study aiming to predict the outcomes of interest, which were binary categorical variables, in SCG patients with ML models. PATIENT SAMPLEThe National Cancer Database (NCDB) was utilized to identify adults aged 18 years or older who were diagnosed with histologically confirmed SCGs between 2010 and 2019. OUTCOME MEASURESThe outcomes of interest were survival outcomes at three specific time points postdiagnosis: 1, 3, and 5 years. These outcomes were formed by combining the “Vital Status” and “Last Contact or Death (Months from Diagnosis)” variables. Model performance was evaluated visually and numerically. The visual evaluation utilized receiver operating characteristic (ROC) curves, precision-recall curves (PRCs), and calibration curves. The numerical evaluation involved metrics such as sensitivity, specificity, accuracy, area under the PRC (AUPRC), area under the ROC curve (AUROC), and Brier Score. METHODSWe employed five ML algorithms—TabPFN, CatBoost, XGBoost, LightGBM, and Random Forest—along with the Optuna library for hyperparameter optimization. The models that yielded the highest AUROC values were chosen for integration into the online calculator. To enhance the explicability of our models, we utilized SHapley Additive exPlanations (SHAP) for assessing the relative significance of predictor variables and incorporated partial dependence plots (PDPs) to delineate the influence of singular variables on the predictions made by the top performing models. RESULTSFor the 1-year survival analysis, 4,913 patients [5.6% with 1-year mortality]; for the 3-year survival analysis, 4,027 patients (11.5% with 3-year mortality]; and for the 5-year survival analysis, 2,854 patients (20.4% with 5-year mortality) were included. The top models achieved AUROCs of 0.938 for 1-year mortality (TabPFN), 0.907 for 3-year mortality (LightGBM), and 0.902 for 5-year mortality (Random Forest). Global SHAP analyses across survival outcomes at different time points identified histology, tumor grade, age, surgery, radiotherapy, and tumor size as the most significant predictor variables for the top-performing models. CONCLUSIONSThis study demonstrates ML techniques can develop highly accurate prognostic models for SCG patients with excellent discriminatory ability. The interactive online calculator provides a tool for assessment by physicians (https://huggingface.co/spaces/MSHS-Neurosurgery-Research/NCDB-SCG). Local interpretability informs prediction influences for a given individual. External validation across diverse datasets could further substantiate potential utility and generalizability. This robust, interpretable methodology aligns with the goals of precision medicine, establishing a foundation for continued research leveraging ML's predictive power to enhance patient counseling.

SuPyMode: an open-source library for design and optimization of fiber optic components,

Recent advancements in photonic lantern design have stirred interest in computational tools to develop fiber-based components. Addressing the complex design challenges, we introduce SuPyMode, a Python package that enables comprehensive fiber component design analysis. This study details its mathematical framework and verifies its accuracy and reliability through simulation results. We demonstrate its practicality using a design study on modally-specific photonic lanterns, underlining the tool’s versatility and efficacy. SuPyMode is instrumental for researchers and engineers in the design and optimization of fiber components, thereby advancing photonics technology.

Improving Computation Time for Optimization Runs of Modelica-Based Energy Systems

Mathematical optimization is a widespread method in order to improve, for instance, the efficiency of energy systems. A simulation approach based on partial differential equations can typically not be formulated as an optimization problem, thus requiring interfacing to an external optimization environment. This is, among others, also true for the programming language Modelica. Because of high computation time, such coupled approaches are often limited to small-scale optimization problems. Since simulation models tend to get more complex, simulation time and, in turn, associated optimization time rise significantly. To enable proper sampling of the search space, individual optimization runs need to be solved in acceptable times. This paper addresses the search for a proper optimization approach and tool to couple with Modelica/Dymola. The optimization is carried out on an exemplary power plant model from the ClaRa-Library using an evolutionary algorithm (SPEA2-based) with Ansys optiSlang. To verify and evaluate the results, a comparison with the standard Dymola optimization library is performed. Both parallelization and indirect optimization with surrogate models achieved a significant runtime reduction by a factor of up to 5.4. The use of meta models is particularly advantageous for repetitive optimization runs of the same optimization problem but may lead to deviations due to the calculated approximations.

Modeling and Rapid Prototyping of Integrated Transmission-Distribution OPF Formulations With PowerModelsITD.jl

Conventional electric power systems are composed of different unidirectional power flow stages of generation, transmission, and distribution, managed independently by transmission system and distribution system operators. However, as distribution systems increase in complexity due to the integration of distributed energy resources, coordination between transmission and distribution networks will be imperative for the optimal operation of the power grid. However, coupling models and formulations between transmission and distribution is non-trivial, in particular due to the common practice of modeling transmission systems as single-phase, and distribution systems as multi-conductor phase-unbalanced. To enable the rapid prototyping of power flow formulations, in particular in the modeling of the boundary conditions between these two seemingly incompatible data models, we introduce PowerModelsITD.jl, a free, open-source toolkit written in Julia for integrated transmission-distribution (ITD) optimization that leverages mature optimization libraries from the InfrastructureModels.jl-ecosystem. The primary objective of the proposed framework is to provide baseline implementations of steady-state ITD optimization problems, while providing a common platform for the evaluation of emerging formulations and optimization problems. In this work, we introduce the nonlinear formulations currently supported in PowerModelsITD.jl, which include AC-polar, AC-rectangular, current-voltage, and a linear network transportation model. Results are validated using combinations of IEEE transmission and distribution networks.

Setup and Applications of Modular Protein Expression Toolboxes (MoPET) for Mammalian Systems.

The design and generation of an optimal protein expression construct is the first and essential step in the characterization of any protein of interest. However, the exchange and modification of the coding and/or noncoding elements to analyze their effect on protein function or generating the optimal result can be a tedious and time-consuming process using standard molecular biology cloning methods. To streamline the process to generate defined expression constructs or libraries of otherwise difficult to express proteins, the Modular Protein Expression Toolbox (MoPET) has been developed (Weber E, PloS One 12(5):e0176314, 2017). The system applies Golden Gate cloning as an assembly method and follows the standardized modular cloning (MoClo) principle (Weber E, PloS One 6(2):e16765, 2011). This cloning platform allows highly efficient DNA assembly of pre-defined, standardized functional DNA modules effecting protein expression with a focus on minimizing the cloning burden in coding regions. The original MoPET system consists of 53 defined DNA modules divided into eight functional main classes and can be flexibly expanded dependent on the need of the experimenter and expression host. However, already with a limited set of only 53 modules, 792,000 different constructs can be rationally designed or used to generate combinatorial expression optimization libraries. We provide here a detailed protocol for the (1) design and generation of level 0 basic parts, (2) generation of defined expressions constructs, and (3) generation of combinatorial expression libraries.

Preparation of geomechanical rock properties library for reservoir optimization of hydraulic fracturing design at the sites of JSC Samotlorneftegaz

Preparation of geomechanical rock properties library for reservoir optimization of hydraulic fracturing design at the sites of JSC Samotlorneftegaz