Glycans are structurally diverse and flexible biomolecules that play key roles in many biological processes. Their conformational variability makes the modeling of their interactions with proteins particularly challenging. This chapter presents a step-by-step protocol for modeling protein-glycan interactions using HADDOCK3, an integrative modeling platform that supports the inclusion of experimental or predicted interaction restraints and allows for flexible refinement of the solutions. The workflow is illustrated using the interaction between a linear homopolymer glycan, 4-beta-glucopyranose, and the catalytic domain of the Humicola grisea Cel12A enzyme, for which an experimental X-ray structure is available as a reference. Detailed instructions are provided for input structure preparation, restraint definition, docking setup, execution, and result analysis. Application of the protocol starting from unbound structures yields models of acceptable to medium quality, with interface-ligand RMSD values below 3 angstroms. Although illustrated on a specific system, the protocol has been optimized and benchmarked on multiple protein-glycan complexes and is broadly applicable to similar sy
Recent advances in combustion science have led to the generation of large volumes of data from high-fidelity simulations, detailed chemical-kinetic calculations and engine-relevant measurements and create new opportunities for data-driven modelling across interacting physical and chemical scales. Among these approaches, artificial intelligence has emerged as a promising framework for constructing surrogate models that reduce computational costs, deliver substantial speed-up and support prediction in complex reacting systems. This review provides a state-of-the-art assessment of AI-powered surrogate modelling for multiscale combustion, spanning chemical kinetics, mechanism reduction, turbulent flames, combustors, engines, and emissions prediction. Supervised, unsupervised, and hybrid or physics-guided learning approaches are examined and compared in terms of predictive accuracy, physical consistency, computational efficiency, and generalizability across conditions and scales. The review further discusses key challenges, including limited transferability across fuels and operating regimes, extrapolation errors, inconsistency in datasets and benchmarks, and the difficulty of building
Frequently in socio-environmental sciences, models are used as tools to represent, understand, project and predict the behaviour of these complex systems. Along the modelling chain, Good Modelling Practices have been evolving that ensure - amongst others - that models are transparent and their results replicable. Whenever such models are represented in software, Good Modelling meet Good Software Practices, such as a tractable development workflow, good code, collaborative development and governance, continuous integration and deployment; and they meet Good Scientific Practices, such as attribution of copyrights and acknowledgement of intellectual property, publication of a software paper and archiving. Too often in existing socio-environmental model software, these practices have been regarded as an add-on to be considered at a later stage only; modellers have shied away from publishing their model as open source out of fear that having to add good practices is too demanding. We here argue for making a habit of following a list of simple and not so simple practices early on in the implementation of the model life cycle. We contextualise cherry-picked and hands-on practices for supp
Computer-assisted modelling is an essential approach to design new devices. It speeds up the process from the initial idea to an actual device and saves resources by reducing the number of built prototypes. This is also a significant practical motivator behind scientific research in contemporary high-temperature superconductor (HTS) AC loss modelling. However, in the scientific literature in this field, consistent practices about modelling terminology have not been established. Then, it is up to the reader to decide, what is the true intent and meaning of the authors. Consequently, the interpretation of such literature might be very much reader-dependent. Moreover, an inseparable part of the whole modelling process is the development of modelling approaches and numerical methods and comparing the predictions obtained via modelling to experimentally achieved results: It is commonplace to discuss the accuracy of modelling results or the validation of a model. In this paper, we discuss the terminology related to theories, models and experiments in the context of HTS AC loss modelling. We discuss the recursive nature of theories and models in this context, discuss the compatibility of
Modelling the progression of Degenerative Diseases (DD) is essential for detection, prevention, and treatment, yet it remains challenging due to the heterogeneity in disease trajectories among individuals. Factors such as demographics, genetic conditions, and lifestyle contribute to diverse phenotypical manifestations, necessitating patient stratification based on these variations. Recent methods like Subtype and Stage Inference (SuStaIn) have advanced unsupervised stratification of disease trajectories, but they face potential limitations in robustness, interpretability, and temporal granularity. To address these challenges, we introduce Disease Progression Modelling and Stratification (DP-MoSt), a novel probabilistic method that optimises clusters of continuous trajectories over a long-term disease time-axis while estimating the confidence of trajectory sub-types for each biomarker. We validate DP-MoSt using both synthetic and real-world data from the Parkinson's Progression Markers Initiative (PPMI). Our results demonstrate that DP-MoSt effectively identifies both sub-trajectories and subpopulations, and is a promising alternative to current state-of-the-art models.
With the explosion of applications of Data Science, the field is has come loose from its foundations. This article argues for a new program of applied research in areas familiar to researchers in Bayesian methods in AI that are needed to ground the practice of Data Science by borrowing from AI techniques for model formulation that we term ``Decision Modelling.'' This article briefly reviews the formulation process as building a causal graphical model, then discusses the process in terms of six principles that comprise \emph{Decision Quality}, a framework from the popular business literature. We claim that any successful applied ML modelling effort must include these six principles. We explain how Decision Modelling combines a conventional machine learning model with an explicit value model. To give a specific example we show how this is done by integrating a model's ROC curve with a utility model.
Nanoparticle (NP)-based applications are becoming increasingly important in the biomedical field. However, understanding the interactions of NPs with biofluids and cells is a major issue in order to develop novel approaches aimed at boosting their internalization and, therefore, their translation into the clinic. To this end, we put forward a transport mathematical model to describe the spatio-temporal dynamics of iron oxide NPs and their interaction with cells under moderate centrifugation. Our numerical simulations allowed us to quantify the relevance of the flux density as one of the unavoidable key features driving NPs interaction with the media as well as for cell internalization processes. These findings will help to increase the efficiency of cell labelling for biomedical applications.
Mitral valve regurgitation is the most common valvular disease, affecting 10% of the population over 75 years old. Left untreated, patients with mitral valve regurgitation can suffer declining cardiac health until cardiac failure and death. Mitral valve repair is generally preferred over valve replacement. However, there is a direct correlation between the volume of cases performed and surgical outcomes, therefore there is a demand for the ability of surgeons to practice repairs on patient specific models in advance of surgery. This work demonstrates a semi-automated segmentation method to enable fast and accurate modelling of the mitral valve that captures patient-specific valve geometry. This modelling approach utilizes 3D active contours in a user-in-the-loop system which segments first the atrial blood pool, then the mitral leaflets. In a group of 15 mitral valve repair patients, valve segmentation and modelling attains an overall accuracy (mean absolute surface distance) of 1.40+-0.26 mm, and an accuracy of 1.01+-0.13 mm when only comparing the extracted leaflet surface proximal to the ultrasound probe. Thus this image-based segmentation tool has the potential to improve the w
Repeat asymptomatic testing in order to identify and quarantine infectious individuals has become a widely-used intervention to control SARS-CoV-2 transmission. In some workplaces, and in particular health and social care settings with vulnerable patients, regular asymptomatic testing has been deployed to staff to reduce the likelihood of workplace outbreaks. We have developed a model based on data available in the literature to predict the potential impact of repeat asymptomatic testing on SARS-CoV-2 transmission. The results highlight features that are important to consider when modelling testing interventions, including population heterogeneity of infectiousness and correlation with test-positive probability, as well as adherence behaviours in response to policy. Furthermore, the model based on the reduction in transmission potential presented here can be used to parameterise existing epidemiological models without them having to explicitly simulate the testing process. Overall, we find that even with different model paramterisations, in theory, regular asymptomatic testing is likely to be a highly effective measure to reduce transmission in workplaces, subject to adherence.
The nature of Systems of Systems (SoSs), large complex systems composed of independent, geographically distributed and continuously evolving constituent systems, means that faults are unavoidable. Previous work on defining contractual specifications of the constituent systems of SoSs does not provide any explicit consideration for faults. In this paper we address that gap by extending an existing pattern for modelling contracts with fault modelling concepts. The proposed extensions are introduced with respect to an Audio Visual SoS case study from Bang and Olufsen, before discussing how they relate to previous work on modelling faults in SoSs.
In this paper, a linear mathematical model for a quad copter unmanned aerial vehicle (UAV) is derived. The three degrees of freedom (3DOF) and six degrees of freedom (6DOF) quad copter state-space models are developed starting from basic Newtonian equations. These state space models are very important to control the quad copter system which is inherently dynamically unstable.
In this work we describe a set of Coarse-grained (CG) tools that allow to simulate the uptake of the nanoparticles (NPs) coated with proteins by a lipid bilayer. We describe a CG model to calculate the adsorption energies and the most favorable adsorption orientations of proteins onto a hydrophobic NP. The proposed method is then used to calculate the adsorption energies of two common proteins in human blood onto neutral and negative charged NPs. We also report the effect of the NP radius on the adsorption energies and validate the proposed methodology against full atomistic simulations. We also describe a methodology in which full atomistic simulations of a lipid bilayer and various lipid-cholesterol mixtures are used for the extraction of CG pair potentials. We also compare and validate the predictions of simulations at molecular and CG level. Finally, we present a CG simulation of the interaction a bare NP and of a NP-protein complex with a lipid bilayer.
Mixed-species growth models are needed as a synthesis of ecological knowledge and for guiding forest management. Individual-tree models have been commonly used, but the difficulties of reliably scaling from the individual to the stand level are often underestimated. Emergent properties and statistical issues limit their effectiveness. A more holistic modelling of aggregates at the whole stand level is a potentially attractive alternative. This work explores methodology for developing biologically consistent dynamic mixture models where the state is described by aggregate stand-level variables for species or age/size cohorts. The methods are demonstrated and tested with a two-cohort model for spruce-aspen mixtures named SAM. The models combine single-species submodels and submodels for resource partitioning among the cohorts. The partitioning allows for differences in competitive strength among species and size classes, and for complementarity effects. Height growth reduction in suppressed cohorts is also modelled. SAM fits well the available data, and exhibits behaviors consistent with current ecological knowledge. The general framework can be applied to any number of cohorts, and
Large language models (LLMs) can now synthesize non-trivial executable code from textual descriptions, raising an important question: can LLMs reliably implement agent-based models from standardized specifications in a way that supports replication, verification, and validation? We address this question by evaluating 17 contemporary LLMs on a controlled ODD-to-code translation task, using the PPHPC predator-prey model as a fully specified reference. Generated Python implementations are assessed through staged executability checks, model-independent statistical comparison against a validated NetLogo baseline, and quantitative measures of runtime efficiency and maintainability. Results show that behaviorally faithful implementations are achievable but not guaranteed, and that executability alone is insufficient for scientific use. GPT-4.1 consistently produces statistically valid and efficient implementations, with Claude 3.7 Sonnet performing well but less reliably. Overall, the findings clarify both the promise and current limitations of LLMs as model engineering tools, with implications for reproducible agent-based and ecological modeling.
Herbivorous wild species constantly strive to optimize the trade-off between energy and nutrient intake and predation risk during foraging. This has led to the selection of several evolutionary traits -- such as diet, habitat selection, and behavior -- which are simultaneously shaped by the spatio-temporal variability of the habitat. Among camelid species, polygyny is a prevalent behavioral strategy that encompasses both mating and foraging activities. This group-level behavior has multiple interacting dimensions, contributing to an interesting ecological and evolutionary complexity. We developed an individual-based stochastic model in which camelid females transition between different familial groups in response to their environmental conditions, aiming to maximize individual fitness. Our results indicate that the behavioral strategy of individual females can shape, by itself, emergent population-level properties, including group size and fitness distribution. Furthermore, these properties are modulated, in a non-additive manner, by other factors such as population density, sex ratio and system heterogeneity.
The forthcoming energy transition calls for a new generation of thermal power generation systems with low- or zero-emission and highly flexible operation. Dynamic modelling and simulation is a key enabling factor in this field, as controlling such plants is a difficult task for which there is no previous experience and very short design times are expected. The steady-state initialization of those dynamic models is an essential step in the design process, but is unfortunately a difficult task which involves the numerical solution of large systems of nonlinear equations with iterative Newton methods, which is often prone to numerical failures. In this work, several strategies and methodologies are discussed to successfully achieve steady-state initialization of first-principles equation-based, object-oriented models of advanced thermal power generation systems. These are presented in the context of the Modelica modelling language, but could be applied to other equation-based, object-oriented modelling and simulation environments. Finally, the successful application of such strategies and methodologies to the SOS-CO2 advanced power generation system is presented.
Accurate and rapid prediction of wildfire trends is crucial for effective management and mitigation. However, the stochastic nature of fire propagation poses significant challenges in developing reliable simulators. In this paper, we introduce PyTorchFire, an open-access, PyTorch-based software that leverages GPU acceleration. With our redesigned differentiable wildfire Cellular Automata (CA) model, we achieve millisecond-level computational efficiency, significantly outperforming traditional CPU-based wildfire simulators on real-world-scale fires at high resolution. Real-time parameter calibration is made possible through gradient descent on our model, aligning simulations closely with observed wildfire behavior both temporally and spatially, thereby enhancing the realism of the simulations. Our PyTorchFire simulator, combined with real-world environmental data, demonstrates superior generalizability compared to supervised learning surrogate models. Its ability to predict and calibrate wildfire behavior in real-time ensures accuracy, stability, and efficiency. PyTorchFire has the potential to revolutionize wildfire simulation, serving as a powerful tool for wildfire prediction and
Transient grating spectroscopy (TGS) is a material characterization technique based on laser-induced thermoelastic excitation of thermal and acoustic gratings. On opaque samples, these gratings are dynamic surface displacements that reflect the sample's elastic and thermal properties, enabling both types of parameters to be determined from a single experiment. Here, we develop a detailed finite element model (FEM) of the TGS experiment that fully captures the coupling between the thermal and mechanical fields, as well as the optical detection of surface displacement using a heterodyning approach. Using custom-designed two-dimensional elements, the model is particularly suitable for analyzing TGS measurements on anisotropic media, for which analytical theory is insufficient. The simulation captures not only the anisotropic relaxation of the thermoelastic field but also several acoustic features that arise at very short (ultra-transient) timescales and provide additional information about the elastic properties of the examined material. The model offers new opportunities for the in silico testing of various modifications of TGS experiments and their applications to a broad class of m
In this paper the accuracy and robustness of quality measures for the assessment of machine learning models are investigated. The prediction quality of a machine learning model is evaluated model-independent based on a cross-validation approach, where the approximation error is estimated for unknown data. The presented measures quantify the amount of explained variation in the model prediction. The reliability of these measures is assessed by means of several numerical examples, where an additional data set for the verification of the estimated prediction error is available. Furthermore, the confidence bounds of the presented quality measures are estimated and local quality measures are derived from the prediction residuals obtained by the cross-validation approach.
In software applications, user models can be used to specify the profile of the typical users of the application, including personality traits, preferences, skills, etc. In theory, this would enable an adaptive application behavior that could lead to a better user experience. Nevertheless, user models do not seem to be part of standard modeling languages nor common in current model-driven engineering (MDE) approaches. In this paper, we conduct a systematic literature review to analyze existing proposals for user modeling in MDE and identify their limitations. The results showcase that there is a lack of a unified and complete user modeling perspective. Instead, we observe a lot of fragmented and partial proposals considering only simple user dimensions and with lack of proper tool support. This limits the implementation of richer user interfaces able to better support the user-specific needs. Therefore, we hope this analysis triggers a discussion on the importance of user models and their inclusion in MDE pipelines. Especially in a context where, thanks to the rise of AI techniques, personalization, based on a rich number of user dimensions, is becoming more and more of a possibili