Appropriate estimation of soil settlement is of significant importance since it directly influences the performance of building and infrastructures that are built on soil. In particular, the settlement of fine-grained soils is critical because of low permeability and continuous settlement with time. Coefficient of consolidation (C_c) is a key parameter to estimate settlement of fine-grained soil layers. However, estimation of this parameter is time consuming, needs skilled technicians, and specific equipment. In this study, C_c was estimated using several soil parameters such as liquid limit (LL), plastic limit (PL), and initial void ratio (e₀). Estimating such parameters in laboratory is straight forward and needs substantially less time and cost compared to conventional tests to estimate C_c such as oedometer test. This study presents a novel prediction model for C_c of fine-grained soils using gene-expression programming (GEP). GEP is a biologically inspired technique capable of offering closed-form solution for the optimal solution. A database consisted of 108 different data points was used to develop the model. A closed-form equation solution was derived to estimate C_c based on LL, PL, and e₀. The performance of developed GEP-based model was evaluated through coefficient of determination (R²), root mean squared error (RMSE), and mean average error (MAE). High R² and low error values indicated the descent performance of the model. Furthermore, the model was evaluated using the additional performance measures and met all the suggested criteria. Furthermore, the model had a better performance in terms of R², RMSE, and MAE compared to most of existing models. It is expected that the developed model will decrease the time and cost associate with determining C_c of fine-grained soils.Keywords: evolutionary model, gene-expression programming (GEP), prediction, soil compression index, estimation, soil engineering, soil informatics, civil engineering, machine learning, data science, big data, soft computing, deep learning, forecasting, subject classification codes, construction informatics, computational intelligence (CI), artificial intelligence (AI), estimation

Every biological image contains quantitative data that can be used to test hypotheses about how patterns were formed, what entities are associated with one another, and whether standard mathematical methods inform our understanding of biological phenomena. In particular, spatial point distributions and polygonal tessellations are particularly amendable to analysis with a variety of graph theoretic, computational geometric, and spatial statistical tools such as: Voronoi Polygons; Delaunay Triangulations; Perpendicular Bisectors; Circumcenters; Convex Hulls; Minimal Spanning Trees; Ulam Trees; Pitteway Violations; Circularity; Clark-Evans spatial statistics; Variance to Mean Ratios; Gabriel Graphs; and, Minimal Spanning Trees. Furthermore, biologists have developed a number of empirically related correlations for polygonal tessellations such as: Lewis’s Law (the number of edges of convex polygons are positively correlated with the areas of these polygons): Desch’s Law (the number of edges of convex polygons are positively correlated with the perimeters of these polygons); and Errara’s Law (daughter cell areas should be roughly half that of their parent cells’ areas). We introduce a new Pitteway Law that the number of sides of the convex polygons in a Voronoi tessellation of biological epithelia is proportional to the minimal interior angle of the convex polygons as angles less than 90 degrees result in Pitteway violations of the Delaunay dual of the Voronoi tessellation.

COVID-19 has been extremely difficult to control. The lack of understanding of key aspects of pandemics has affected virus transmission. On the other hand, there is a demand to incorporate Computational Thinking (CT) in the curricula with applications in STEM. However, there are still no exemplars in the curriculum that apply CT to real-world problems such as controlling a pandemic or other similar global crises. In this paper, we fill this gap by proposing exemplars of CT for modeling the pandemic. We designed exemplars following the three pillars of the APEC InMside framework for CT: algorithmic thinking, computational modeling, and machine learning. For each pillar, we designed a progressive sequence of activities that covers from elementary to high school. In an experimental study with elementary and middle school students from 2 schools of high vulnerability, we found that the computational modeling exemplar can be implemented by teachers and correctly understood by students. We conclude that it is feasible to introduce the exemplars at all grade levels, and that this is a powerful example of STEM integration that helps reflect and tackle real-world and challenging public health problems of great impact for students and their families.

Proteins are the main active molecules of Life. While natural proteins play many roles, as enzymes or antibodies for example, there is a need to go beyond the repertoire of natural proteins to produce engineered proteins that precisely meet application requirements, in terms of function, stability, activity or other protein capacities. Computational Protein Design aims at designing new proteins from first principles, using full-atom molecular models. However, the size and complexity of proteins require approximations to make them amenable to energetic optimization queries. These approximations make the design process less reliable and a provable optimal solution may fail. In practice, expensive libraries of solutions are therefore generated and tested. In this paper, we explore the idea of generating libraries of provably diverse low energy solutions by extending Cost Function Network algorithms with dedicated automaton-based diversity constraints on a large set of realistic full protein redesign problems. We observe that it is possible to generate provably diverse libraries in reasonable time and that the produced libraries do enhance the Native Sequence Recovery, a traditional measure of design methods reliability.

The question does P = NP has confounded mathematicians and computer scientists alike for over 50 years and although there is an almost unanimous agreement that it in fact does not, there still is no absolute proof. In this paper, I attempt to prove to that P does not equal NP.

Sex differences are essential factors in disease etiology and manifestation in many diseases such as cardiovascular disease, cancer, and neurodegeneration (1). The biological influence of sex differences (including genomic, epigenetic, hormonal, immunological, and metabolic differences between males and females) and the lack of biomedical studies considering sex differences in their study design has led to several policies. For example, the National Institute of Health’s (NIH) sex as a biological variable (SABV) and Sex and Gender Equity in Research (SAGER)) policies to motivate researchers to consider sex differences (2). However, drug repurposing, a promising alternative to traditional drug discovery by identifying novel uses for FDA-approved drugs, lacks sex-aware methods that can improve the identification of drugs that have sex-specific responses (1,3–5). Sex-aware drug repurposing methods either select drug candidates that are more efficacious in one sex or deprioritize drug candidates based on if they are predicted to cause a sex-bias adverse event (SBAE), unintended therapeutic effects that are more likely to occur in one sex. Computational drug repurposing methods are encouraging approaches to develop for sex-aware drug repurposing because they can prioritize sex-specific drug candidates or SBAEs at lower cost and time than traditional drug discovery. Sex-aware methods currently exist for clinical, genomic, and transcriptomic information (3,6,7). They have not expanded to other data types, such as DNA variation, which has been beneficial in other drug repurposing methods that do not consider sex (8). Additionally, some sex-aware methods suffer from poorer performance because a disproportionate number of male and female samples are available to train computational methods (3). However, there is development potential for several different categories (i.e., data mining, ligand binding predictions, molecular associations, and networks). Low-dimensional representations of molecular association and network approaches are also especially promising candidates for future sex-aware drug repurposing methodologies because they reduce the multiple hypothesis testing burden and capture sex-specific variation better than the other methods (9,10). Here we review how sex influences drug response, the current state of drug repurposing including with respect to sex-bias drug response, and how model organism study design choices influence drug repurposing validation.

A critical challenge underpinning the adoption of Additive Manufacture (AM) as a technology is the postprocessing of manufactured components. For Selective Laser Sintering (SLS) this can involve the removal of powder from the interior of the component, often by vibrating the component to fluidise the powder to encourage drainage. In this paper we develop and validate a computational model of the flow of metal powder suitable for predicting powder removal from such AM components. The model is a continuum Eulerian multiphase model of the powder including models for the granular temperature; the effect of vibration can be included through appropriate wall boundaries for this granular temperature. We validate the individual sub-models appropriate for AM metal powders by comparison with in-house and literature experimental results, and then apply the full model to a more complex geometry typical of an AM Heat Exchanger. The model is shown to provide valuable and accurate results at a fraction of the computational cost of a particle-based model.

Turbulent flow is the first and fundamental physical phenomena to evaluate when optimising cost and reducing emissions from an Anode Baking Furnace (ABF). Gas flow patterns, velocity field, pressure drop, shear stress, and turbulent dissipation rate variables are the main operational parameters to be optimised, considering a specific geometry. Computational Fluid Dynamics (CFD) allows simulating physical phenomena using numerical methods with computer resources. In particular, the finite element method is one of the most used methods to solve the flow equations. This method requires a discretisation of the geometry of the ABF, called mesh. Hence, mesh is the main input to the finite element method. A suitable mesh for applying a discretisation method determines whether the problem can be simulated or not. Generating an appropriate mesh remains a challenge to perform accurate simulations. In this work, a comparison between meshes generated using two mesh generation tools is presented. Results of different study cases are included.

With the increasingly stringent airworthiness standards, the noise generated during the rotorcraft flight is gradually attracting people’s attention. It widely operated helicopters at low altitudes because of their maneuverability. The way to reduce the noise caused by the complex airflow of the helicopter rotor system has progressively become a hot topic for researchers. Using a hybrid acoustic analysis method, this paper investigates the improvement of the noise and thrust of the helicopter’s tail rotor through the tail rotor structural parameters. For the basic model, the turbulence simulation is performed using an incompressible detached eddy simulation (DES) method, and the Lighthill acoustic analog equation is calculated using the finite element method (FEM). We verified the accuracy of the method through wind tunnel tests. We chose a series of structural parameters for sound simulation and fluid simulation calculations. The results indicate that the modified tail rotor noise reduced by 16.5 dBA and the total thrust increased by 19.9% from the prototype model. This work can enhance the duct tail rotor design to improve aerodynamic and aeroacoustic performance.

The Steepest Descent (or Ascent) algorithm is one of the most widely used algorithms in Science, Technology, Engineering, and Mathematics (STEM). However, this powerful mathematical tool is neither taught nor even mentioned in K12 education. We study whether it is feasible for elementary school students to learn this algorithm, while also aligning with the standard school curriculum. We also look at whether it can be used to create enriching activities connected to children’s real-life experiences, thus enhancing the integration of STEM and fostering Computational Thinking. To address these questions, we conducted an empirical study in two phases. In the first phase, we tested the feasibility with teachers. In a face-to-face professional development work-shop with 457 mathematics teachers actively participating using an online platform, we found that after a 10-minute introduction they could successfully apply the algorithm and use it in a couple of models. They were also able to complete two complex and novel tasks: selecting models and adjusting the parameters of a model that uses the steepest descent algorithm. In a second phase, we tested the feasibility with 90 fourth graders from 3 low Socioeconomic Status (SES) schools. Using the same introduction and posing the same questions, we found that they were able to understand the algorithm and successfully complete the tasks on the online platform. Additionally, we found that close to 75% of the students completed the two complex modeling tasks and performed similarly to the teachers.

Appropriate estimation of soil settlement is of significant importance since it directly influences the performance of building and infrastructures that are built on soil. In particular, the settlement of fine-grained soils is critical because of low permeability and continuous settlement with time. Coefficient of consolidation (Cc) is a key parameter to estimate settlement of fine-grained soil layers. However, estimation of this parameter is time consuming, needs skilled technicians, and specific equipment. In this study, Cc was estimated using several soil parameters such as liquid limit (LL), plastic limit (PL), and initial void ratio (e0). Estimating such parameters in laboratory is straight forward and needs substantially less time and cost compared to conventional tests to estimate Cc such as Oedometer test. This study presents a novel prediction model for Cc of fine-grained soils using gene-expression programming (GEP). GEP is a biologically inspired technique capable of offering closed-form solution for the optimal solution. A database consisted of 108 different data points was used to develop the model. A closed-form equation solution was derived to estimate Cc based on LL, PL, and e0. The performance of developed GEP-based model was evaluated through coefficient of determination (R2), root mean squared error (RMSE), and mean average error (MAE). High R2 and low error values indicated the descent performance of the model. Furthermore, the model was evaluated using the additional performance measures and met all the suggested criteria. Furthermore, the model had a better performance in terms of R2, RMSE, and MAE compared to most of existing models. It is expected that the developed model will decrease the time and cost associate with determining Cc of fine-grained soils.

In this paper, we present the extension of the pressure-based solver designed for the simulation of compressible and/or incompressible two-phase flows of viscous fluids. The core of the numerical scheme is based on the hybrid Kurganov— Noele — Petrova/PIMPLE algorithm. The governing equations are discretized in the conservative form and solved for velocity and pressure, with the density evaluated by an equation of state. The acoustic-conservative interface discretization technique helps to prevent the unphysical instabilities on the interface. The solver was validated on various cases in wide range of Mach number, both for single-phase and two-phase flows. The numerical algorithm was implemented on the basis of the well-known open-source Computational Fluid Dynamics library OpenFOAM in the solver called interTwoPhaseCentralFoam. The source code and the pack of test cases are available on GitHub: https://github.com/unicfdlab/hybridCentralSolvers

One of the unfortunate findings from the ongoing COVID-19 crisis is the disproportionate impact the crisis has had on people and communities who were already socioeconomically disadvantaged. It has, however, been difficult to study this issue at scale and in greater detail using social media platforms like Twitter. Several COVID-19 Twitter datasets have been released, but they have very broad scope, both topically and geographically. In this paper, we present a more controlled and compact dataset that can be used to answer a range of potential research questions (especially pertaining to computational social science) without requiring extensive preprocessing or tweet-hydration from the earlier datasets. The proposed dataset comprises tens of thousands of geotagged (and in many cases, reverse-geocoded) tweets originally collected over a 255-day period in 2020 over 10 metropolitan areas in North America. Since there are socioeconomic disparities within these cities (sometimes to an extreme extent, as witnessed in `inner city neighborhoods’ in some of these cities), the dataset can be used to assess such socioeconomic disparities from a social media lens, in addition to comparing and contrasting behavior across cities.

: Predicting long-term student learning is a critical task for teachers and for educational data mining. However, most of the models do not consider two typical situations in real-life classrooms. The first is that teachers develop their own questions for formative assessment. Therefore, there are a huge number of possible questions, each of which is answered by only a few students. Second, formative assessment often involved open-ended questions that students answer in writing. These types of questions in formative assessment are highly valuable. However, analyzing the responses automatically can be a complex process. In this paper, we address these two challenges. We analyzed 621,575 answers to closed-ended questions and 16,618 answers to open-ended questions by 464 fourth-graders from 24 low-SES schools. We constructed a classifier to detect incoherent responses to open-ended mathematics questions. We then used it in a model to predict scores on an end-of-year national standardized test. We found that despite answering 36.4 times fewer open-ended questions than closed questions, including features of the students’ open responses in our model improved our prediction of their end-of-year test scores. To the best of our knowledge, this is the first time that a predictor of end-of-year test scores has been improved by using automatically detected features of answers to open-ended questions on formative assessments.

Drought is one of the most serious abiotic stressors in the environment, restricting agricultural production by reducing plant growth, development, and productivity. To investigate such a complex and multifaceted stressor and its effects on the plants, a systems biology-based approach is necessitated, entailing the generation of co-expression networks, identification of highly-priority transcription factors (TFs) dynamic mathematical modeling, and computational simulations. Here, we studied a high-resolution drought transcriptome of Arabidopsis. We revealed distinct temporal transcriptional signatures and demonstrated the involvement of specific biological pathways. Generation of a large-scale co-expression network followed by network centrality analyses identified 117 TFs that possess critical properties of hubs, bottlenecks, and high clustering coefficients nodes. Dynamic transcriptional regulatory modeling on integrated TF-target and transcriptome datasets uncovered major transcriptional events during the course of drought stress. Mathematical transcriptional simulations allowed us to ascertain the activation status of major TFs as well as the transcriptional intensity and amplitude of their target genes. Finally, we validated our predictions by providing experimental evidence of gene expression under drought stress for a set of four TFs and their major target genes using qRT-PCR. Taken together, we provided a systems-level perspective on the dynamic transcriptional regulation during drought stress in Arabidopsis and uncovered numerous novel TFs that can potentially be used in future genetic crop engineering programs.

Docked ships are a source of contamination for the city while they keep their engine working. Plumes emissions from large boats can carry a number of pollutants to the nearby cities causing a detrimental effect on the life quality and health of local citizens and ecosystems. A computational fluid dynamics model of the harbour area of Tromsø has been built in order to model the deposition of CO2 gas emitted by docked vessels within the city. The ground level distribution of the emitted gas has been obtained and the influence of the wind speed and direction, vessel chimney height, ambient temperature and exhaust gas temperature has been studied. The deposition range is found to be the largest when the wind speed is low. At high wind speeds, the deposition of pollutants along the wind direction is enhanced and spots of high pollutant concentration can be created. The simulation model is intended for the detailed study of the contamination in cities near the coast or an industrial pollutant source of any type of gas pollutants and can easily be extended for the study of particulate matter.

The present study shows a methodology for analyzing and designing a cylindrical packed-bed reactor considering stationary and dynamic models. The design comprises the reactor's stationary and dynamic governing differential equations for mass and heat transfer under multi-dimensional approaches. The results included simulation of concentration, temperature, and reaction rate profiles via the 1-D and 2-D differential equations solution with FlexPDE software. The analysis was complemented with a scaled 3-D dynamic model implemented in COMSOL Multiphysics. Both FlexPDE and COMSOL Multiphysics relied on the finite element technique to solve the governing differential equations. The simulated concentration and temperature profiles from both FlexPDE and COMSOL models were compared to experimental data gathered from literature (specifically from a Fischer-Tropsch process to produce low-molecular-weight hydrocarbons in a configuration of cylindrical packed-bed reactors). Simulated concentration and temperature profiles from the 2-dimensional dynamic model and the COMSOL model were in good agreement with the trend observed in experimental data. Finally, the predicted reaction rate profiles from the COMSOL model and the 2-dimensional dynamic model followed the temperature trend, thus reflecting the temperature dependence of the reaction.

This dissertation is a rigorous study of ecology and macrocellular biology as a subfield of abstract algebra. We begin with the creation of an axiomatic paradigm, then move onto constructing a universal genetic code of biology. We use this to define increasingly complex algebraic structures (ecosystem, evolving populations, etc.). We prove a variety of theorems regarding to the members of the previous mathematical constructs, notably the following three: 1. There is one unique phenotypic representation of each organism. For example, if you subdivide any piece of genetic code into its phenotypic components, then two identical organisms have identical decomposed DNA 2. There are a finite number of indivisible phenotypic traits. 3. The three sophioid-definitions are equivalent: (a) dynamical evolutionary enlargement of the medial temporal lobe and frontal lobe, (b) reliance upon intelligence, (c) the existence of an intellectually- or socially-hierarchical society. Much has yet to be done on this work, but as a first draft, it stands as a jumping point for future exploits; I am working on an entirely revised second draft.

Drug repurposing, the practice of utilizing existing drugs for novel clinical indications, has tremendous potential for improving human health outcomes and increasing therapeutic development efficiency. The goal of multidisease multitarget drug repurposing, also known as shotgun drug repurposing, is to develop platforms that assess the therapeutic potential of each existing drug for every clinical indication. Our Computational Analysis of Novel Drug Opportunities (CANDO) platform for shotgun multitarget repurposing implements several pipelines via large scale modelling and simulation of interactions between comprehensive libraries of drugs/compounds and protein structures. In these pipelines, each drug is described by an interaction signature that is then compared to all other signatures that are then sorted and ranked based on similarity. Pipelines within the platform are benchmarked based on their ability to recover known drugs for all indications in our library, and predictions are generated based on the hypothesis that (novel) drugs with similar signatures may be repurposed for the same indication(s). The drug-protein interactions in the platform used to create the drug-proteome signatures may be determined by any screening or docking method but the primary approach used thus far has been an in house similarity docking protocol. In this study, we calculated drug-proteome interaction signatures using the publicly available molecular docking method Autodock Vina and created hybrid decision tree pipelines that combined our original bio- and cheminformatic approach with the goal of assessing and benchmarking their drug repurposing capabilities and performance. The hybrid decision tree pipeline outperformed the corresponding two docking-based pipelines it was synthesized from, yielding an average indication accuracy of 13.3% at the top10 cutoff (the most stringent), relative to 10.9% and 7.1% for its constituent pipelines, and a random control accuracy of 2.2%. We demonstrate that docking based virtual screening pipelines have unique performance characteristics and that the CANDO shotgun repurposing paradigm is not dependent on a specific docking method. Our results also provide further evidence that multiple CANDO pipelines can be synthesized to enhance drug repurposing predictive capability relative to their constituent pipelines. Overall, this study indicates that pipelines consisting of varied docking based signature generation methods can capture unique and useful signal for accurate comparison of drug-proteome interaction signatures, leading to improvements in the benchmarking and predictive performance of the CANDO shotgun drug repurposing platform.

Functional Data Analysis (FDA) is a relatively new field of statistics dealing with data expressed in the form of functions. FDA methodologies can be easily extended to the study of imaging data, an application proposed in Wang et al. (2020), where the authors settle the mathematical groundwork and properties of the proposed estimators. This methodology allows for the estimation of mean functions and simultaneous confidence corridors (SCC), also known as simultaneous confidence bands, for imaging data and for the difference between two groups of images. This is especially relevant for the field of medical imaging, as one of the most extended research setups consists on the comparison between two groups of images, a pathological set against a control set. FDA applied to medical imaging presents at least two advantages compared to previous methodologies: it avoids loss of information in complex data structures and avoids the multiple comparison problem arising from traditional pixel-to-pixel comparisons. Nonetheless, computing times for this technique have only been explored in reduced and simulated setups (Arias-López et al., 2021). In the present article, we apply this procedure to a practical case with data extracted from open neuroimaging databases and then measure computing times for the construction of Delaunay triangulations, and for the computation of mean function and SCC for one-group and two-group approaches. The results suggest that previous researcher has been too conservative in its parameter selection and that computing times for this methodology are reasonable, confirming that this method should be further studied and applied to the field of medical imaging.

Background. The treatment of coronary stenosis relies on invasive high risk surgical assessment to generate the fractional flow reserve diagnostics index, a ratio of distal to proximal pressures in respect of coronary atherosclerotic plaque causing stenosis. Non-invasive methods are therefore a need of the times. This study proposes an extensible mathematical description of the coronary vasculature that permits rapid estimation of the coronary fractional flow reserve. Methods. By adapting an existing closed loop model of human coronary blood flow, the effects of large vessel stenosis and microvascular disease on fractional flow reserve were quantified. Several simula-tions generated flow and pressure information which was used to compute fractional flow re-serve under a spectrum of conditions including focal stenosis, diffuse stenosis, and microvascular disease. Sensitivity analysis stratified the influence of model parameters on the index. The model was simulated as coupled non-linear ordinary differential equations and numerically solved us-ing an implicit higher order method. Results. Large vessel stenosis affected fractional flow re-serve. The model predicts that the presence, rather than severity, of microvascular disease affect coronary flow deleteriously. Sensitivity analysis revealed that heart rate may not affect the index. Conclusions. The model provides a computationally inexpensive instrument for future in silico coronary blood flow investigations as well as clinical-imaging decision making. A combination of focal and diffuse stenosis appears to be essential in reducing the index. In addition to pressure measurements in the large epicardial vessels, diagnosis of microvascular disease is essential. The independence of the index with respect to heart rate suggests that computationally inexpensive steady state simulations may provide sufficient information to reliably compute the index.

This paper deals with the characteristics of the cyclone separator from the Lagrangian perspective to design important dependent variables, develops a neural network model for predicting the separation performance parameter, and compares the predictive performance between the traditional surrogate model and the neural network model. In order to design the important parameters of the cyclone separator based on the particle separation theory, the force acting until the particles are separated was calculated using the Lagrangian-based CFD methodology. As a result, it was proved that the centrifugal force and drag acting on the critical diameter having a separation efficiency of 50% were similar, and the particle separation phenomenon in the cyclone occurred from the critical diameter, and it was set as an important dependent variable. For developing a critical diameter prediction model based on machine learning and multiple regression methods, Unsteady-RANS analyzes according to shape dimensions were performed. The input design variables for predicting the critical diameter were selected as four geometry parameters that affect the turbulent flow inside the cyclone. As a result of comparing the model prediction performances, the ML model showed the 32.5 % of improvement rate of R2 compared to the traditional MLR considering the nonlinear relationship between the cyclone design variable and the critical diameter. The proposed techniques have proven to be fast and practical tools for cyclone design.

The number and size of computational models in biology have drastically increased over the past years and continue to grow. Modeled networks are becoming more complex, and reconstructing them from the beginning in an exchangeable and reproducible manner is challenging. Using precisely defined ontologies enables the encoding of field-specific knowledge and the association of disparate data types. In computational modeling, the medium for representing domain knowledge is the set of orthogonal structured controlled vocabularies named Systems Biology Ontology ( SBO). The SBO terms enable modelers to explicitly define and unambiguously describe model entities, including their roles and characteristics. Here, we present the first standalone tool that automatically assigns SBO terms to multiple entities of a given SBML model, named the SBOannotator. The main focus lies on the reactions, as the correct assignment of precise SBO annotations requires their extensive classification. Our implementation does not consider only top-level terms but examines the functionality of the underlying enzymes to allocate precise and highly specific ontology terms to biochemical reactions. Transport reactions are examined separately and are classified based on the mechanism of molecule transport. Pseudo-reactions that serve modeling purposes are given reasonable terms to distinguish between biomass production and the import or export of metabolites. Finally, other model entities, such as metabolites and genes, are annotated with appropriate terms. Including SBO annotations in the models will enhance the reproducibility, usability, and analysis of biochemical networks. Availability: The open-source project SBOannotator is freely available under the terms of LGPL version 3.0 from https://github.com/draeger-lab/SBOannotator/.

Industrial pig farming is associated with negative technological pressure on the bodies of pigs. Leg weakness and lameness are the sources of significant economic loss in raising pigs. Therefore, it is important to identify predictors of limb condition. This work presents assessments of the state of limbs using indicators of growth and meat characteristics of pigs based on machine learning algorithms. We have evaluated and compared the accuracy of prediction for several ML classification algorithms (Random Forest, K-Nearest Neighbors, Artificial Neural Networks, C50Tree, Support Vector Machines, Naive Bayes, Generalized Linear Models, Boost, and Linear Discriminant Analysis) and have identified the Random Forest and K-Nearest Neighbors as the best performing algorithms for predicting pig leg weakness using a small set of simple measurements that can be taken at an early stage of animal development. Muscle Thickness, Back Fat amount, and Average Daily Gain serve as significant predictors of conformation of pig limbs. Our work demonstrates the utility and relative ease of using machine learning algorithms to assess the state of limbs in pigs based on growth rate and meat characteristics.

The pulsatile flow rate (PFR) in the cerebral artery system and shunt ratios in bifurcated arteries are two patient-specific parameters which may affect the hemodynamic characteristics on the pathobiology of cerebral aneurysms (CAs). Accordingly, a systematic study was employed to investigate the effects of the two parameters on hemodynamic characteristics in two internal carotid artery sidewall aneurysms (i.e., ICASA-1 and ICASA-2) models. Numerical results indicate larger PFRs can cause higher WSS in some local regions of the aneurysmal dome that may increase the probability of small/secondary aneurysms generation than under smaller PFRs. The low WSS and relatively high oscillatory shear index (OSI) could appear under a smaller PFR, which has the potential to cause aneurysmal sac growth and rupture. However, the variances in PFRs and bifurcated shunt ratios have rare impacts on the time-average pressure distributions on the aneurysmal sac, although a higher PFR can contribute more to the pressure increase in ICASA-1 dome due to the relatively stronger impingement by the redirected blood stream than in ICASA-2. Simulation results also present the variances of shunt ratios have rare impacts on the hemodynamic characteristics in sacs, mainly because the bifurcated location is not close enough to the sac in present models. Furthermore, it has been found that the vortex location plays a major role in the temporal and spatial distribution of the WSS on the luminal wall, varying significantly with the cardiac period.

Deformation behavior of MXene based polymer composites with bioinspired brick and mortar structures is analyzed. MXene/Polymer nanocomposites are modeled at microscale using bioinspired configurations of nacre-mimetic brick-and-mortar assembly structure. MXenes (brick) with polymer matrix (mortar) are modeled using classical analytical methods and numerical methods based on Finite Elements (FE). The analytical methods provide less accurate estimation of elastic properties compared to numerical one. MXene nanocomposite models analyzed with FE method provide estimates of elastic constants in the same order of magnitude as literature reported experimental results with good consistency. Bioinspired design of MXene nanocomposites results in the effective Young’s modulus of the nanocomposite increase by 25.1 % and the strength (maximum stress capacity within elastic limits) increase by 42.3 %. The brick and mortar structure of the nanocomposites leads to interlocking mechanism between MXene fillers in polymer matrix, resulting in effective load transfer, good strength, and damage resistance. This is demonstrated in this paper by numerical analysis of MXene nanocomposites subjected to quasi-static loads.

In this paper an integrated methodology for the coupling between 1D- and 3D-CFD simulation codes is presented, which has been developed to support the design and calibration of new diesel engines. The aim of the proposed methodology is to couple 1D engine models, which may be available in the early-stage engine development phases, with 3D predictive combustion simulations, in order to obtain reliable estimates of engine performance and emissions for newly designed automotive diesel engines. The coupling procedure features simulations performed in 1D-CFD by means of GT-SUITE and in 3D-CFD by means of Converge, executed within a specifically designed calculation methodology. An assessment of the coupling procedure has been performed by comparing its results with experimental data acquired on an automotive Diesel engine, considering different working points including both part load and full load conditions. Different multiple injection schedules have been evaluated for part-load operation, including pre and post injections. The proposed methodology, featuring detailed 3D chemistry modeling, was proven to be capable to properly assess pollutant formation, specifically to estimate NOx concentrations. Soot formation trend was also well-matched for most of the explored working points. The proposed procedure can therefore be considered as a suitable methodology to support the design and calibration of new Diesel engines, thanks to its ability to provide reliable engine performance and emissions estimations from the early-stage of a new engine development.

This study aims to determine the optimal configuration (position and operation duration) for wall mounted mechanical mixers based on the comparison of three-dimensional computational fluid dynamics (CFD) modelling results and physical data collected from the treatment plant. A three-dimensional model of anoxic zone 1, 2 and 3 of Northern Wastewater Treatment Plant (WWTP) located at Cairns Regional Council, Cairns, Queensland, Australia was developed and validated. The model was used to simulate the flow pattern of the WWTP and the simulation results are in good agreement with the physical data varying between 0% to 15% in key locations. The anoxic zones were subject to velocities less than the desired 0.3 metres per second however results for suspended solids concentration indicate that good mixing is being achieved. Results for suspended solids concentrations suggest that the anoxic zones are towards the upper limits recommended by literature for specific power dissipation. The duration for operation of mechanical mixers was investigated and identified that the duration could be reduced from 900 seconds down to 150 seconds. Alternative mixer positioning was also investigated and identified positioning which would increase the average flow velocity with decreased duration (150 seconds). The study identified that Council may achieve savings of $24,000 per year through optimisation of the mechanical mixers.

Filament wound composite pipes are frequently used in the field were transmission of high pressured chemical fluids, disposal of industrial wastes, oil and natural gas transmission takes place. In oil and gas industry, the pipelines transporting heavy crude oil are subjected to variable pressure waves causing fluctuating stress levels in the pipes. Computational Fluid Dynamics Analysis was performed using Ansys 15.0 Fluent software to study the effects of these pressure waves on some specified joints in the pipes. Depending on the type of heavy crude oil being used, the flow behavior indicated a considerable degree of stress levels in certain connecting joints, causing the joints to become weak over a prolonged period of use. In this research comparison of various pipe joints was done by using different material and the output result of the stress levels of the pipe joints were checked so that the life of the pipe joints can be optimized by the change of material.

In this study, the external magnetic field emitted by a wireless power transfer (WPT) system and the internal electric field induced into human body models during recharging operations of a compact electric vehicle (EV) are evaluated. To this aim an ad-hoc formulation for the source modeling is coupled with a commercial software that performs numerical dosimetry. Specifically, two realistic anatomical models both in a driving position and in a standing posture are considered, and the chassis of the EV is modeled either as a currently employed aluminum alloys and as a futuristic carbon fiber composite panel. Aligned and misaligned coil configurations of the WPT system are considered as well. The analysis of the obtained results shows that the ICNIRP reference levels are exceeded in the driving position, especially for the carbon fiber chassis, whereas no exceedance is observed in terms of basic restrictions, at least for the considered scenarios.

Objective: Cerebrovascular accidents are the second leading cause of death and the third leading cause of disability worldwide. We hypothesized that cerebellar transcranial direct current stimulation (ctDCS) of the dentate nuclei and the lower-limb representations in the cerebellum can improve standing balance functional reach in chronic (> 6 months’ post-stroke) stroke survivors. Materials and Methods: Magnetic resonance imaging(MRI) based subject-specific electric field was computed across 10 stroke survivors and one healthy MRI template to find an optimal bipolar bilateral ctDCS montage to target dentate nuclei and lower-limb representations (lobules VII-IX). Then, in a repeated-measure crossover study on 5 stroke survivors, we compared 15minutes of 2mA ctDCS based on the effects on successful functional reach(%) during standing balance task. Three-way ANOVA investigated the factors of interest– brain regions, montages, stroke participants, and their interactions.Results: “One-size-fits-all” ctDCS montage for the clinical study was found to be bipolar PO9h – PO10h for dentate nuclei and bipolar Exx7–Exx8 for lobules VII-IX with contalesional anode. Bipolar PO9h–PO10h ctDCS performed significantly (alpha=0.05) better in facilitating successful functional reach (%) when compared to bipolar Exx7–Exx8 ctDCS. Furthermore, a linear relationship between successful functional reach (%) and electric field strength was found where bipolar PO9h–PO10h montage resulted in a significantly (alpha=0.05) higher electric field strength when compared to bipolar Exx7–Exx8 montage for the same 2mA current. Conclusion: We presented a rational neuroimaging based approach to optimize deep ctDCS of the dentate nuclei and lower limb representations in the cerebellum for post-stroke balance rehabilitation.

The accurate prediction of molecular properties such as lipophilicity and aqueous solubility are of great importance and pose challenges in several stages of the drug discovery pipeline. Machine learning methods like graph-based neural networks (GNNs) have shown exceptionally good performance in predicting these properties. In this work, we introduce a novel GNN architecture, called directed edge graph isomorphism network (D-GIN). It is composed of two distinct sub-architectures (D-MPNN, GIN) and achieves an improvement in accuracy over its sub-architectures employing various learning, and featurization strategies. We argue that combining models with different key aspects help make graph neural networks deeper and simultaneously increase their predictive power. Furthermore, we address current limitations in assessment of deep-learning models, namely, comparison of single training run performance metrics, and offer a more robust solution.

With the increase in life expectancy and consequent aging of the world’s population, the prevalence of many neurodegenerative diseases is increasing, without concomitant improvement in diagnostics and therapeutics. These diseases share neuropathological hallmarks, including mitochondrial dysfunction. In fact, as mitochondrial alterations appear prior to neuronal cell death at an early phase of the disease onset, the study and modulation of mitochondrial alterations rise as promising strategies to predict and prevent neurotoxicity and neuronal cell death before the onset of cell viability alterations. In this work, differentiated SH-SY5Y cells were treated with the mitochondrial-targeted neurotoxicants 6-hydroxydopamine and rotenone. These compounds were used at different concentrations and for different time points to understand the similarities and differences in their mechanisms of action. To accomplishing this, data on mitochondrial parameters was acquired and analyzed using unsupervised (hierarchical clustering) and supervised (decision tree) machine learning methods. Both biochemical and computational analyses resulted in an evident distinction between the neurotoxic effects of 6-hydroxydopamine and rotenone, specifically for the highest concentrations of both compounds.

Experimental test facilities are generally characterised using linear transfer functions to relate the wavemaker forcing amplitude to wave elevation at a probe located in the wavetank. Second and third order correction methods are becoming available but are limited to certain ranges of waves in their applicability. Artificial intelligence has been shown to be a suitable tool to find even highly nonlinear functional relationships. This paper reports on a numerical wavetank implemented using the OpenFOAM software package which is characterised using artificial intelligence. The aim of the research is to train neural networks to represent non-linear transfer functions mapping a desired surface-elevation time-trace at a probe to the wavemaker input required to create it. These first results already demonstrate the viability of the approach and the suitability of a single setup to find solutions over a wide range of sea states and wave characteristics.

The knowledge of what separates us genetically from our less-evolved relatives is crucial for gaining new biomedical insights about the human-chimpanzee relatedness for the use of appropriate stand-in towards the development of new treatments and diagnostic aids for various ailments. Although the genomes of humans and chimpanzees share 99% similarity, significant differences exist between the two species in their non-coding intronic regions. However, no work has been carried out in the aspects of target prediction concerning the ‘predicted homology’ in their microRNA sequences. Non-coding miRNAs which are post-transcriptional regulators of development, differentiation, growth, and metabolism, harboring the intronic regions may be crucial for expanding the horizons of our understanding. In this study, we proposed to perform the target prediction for the human-chimp miRNA homologs in the PHEX gene of the human X chromosome using various computational tools and databases. We identified a total of 1296 human miRNAs, 46, 957 gene targets, and 30, 563 targets of human and homologous chimp miRNAs respectively. Furthermore, we analysed gene interacting networks to identify the top interacting targets in both the species. Finally, we interpreted the biological importance of top-interacting miRNAs and their targets. The results demonstrated varying levels of multiplicity and cooperativity between the predicted miRNAs and target genes in the two genera. Such miRNAs may be responsible for the dysregulation of gene expression in several signaling pathways.

This study aimed to rank cancers by the strength of relationship between comprehensive mRNA expression of the most harmful or protective genes and patient survival. Using TCGA dataset including RNA-SEQ and clinical data, we investigated not only gene specific prognostic availability, but also comprehensive prognostic availability of prognostic genes filtered by cox coefficient, and ranked cancers by specially designed prognostic indicator. Through Kaplan-Meier plots, we checked that cancers vary in the strength of influence of prognostic genes, and they follow as the rank. Developing treatment with method to reduce or increase expression of biomarkers for specific cancer which ranked bottom, it would be not efficient in high probability. The results of this study can be a scientific evidence for that.

Multiphase systems are important in minerals processing, and usually include solid-solid and solid-fluid systems. Examples of operations in multiphase systems include flotation, dewatering, and magnetic separation, among several other unit operations. In this paper, the current trends in the process system engineering tasks of modeling, design, and optimization, in multiphase systems, are analyzed. Different scales of size and time are included, and therefore the analysis includes modeling at the molecular level and unit operation level, and the application of optimization for the design of a plant. New strategies for the modeling and optimization of multiphase systems are also included, with a strong focus on the application of artificial intelligence (AI) and the combination of experimentation and modeling with response surface methodology (RSM). The paper finishes with tools to study the uncertainty, both epistemic and stochastic, which is present in all mineral processing operations. It is shown that all these areas are very active and can help to understand, operate, design, and optimize mineral processing that involves multiphase systems.

In this paper we propose a computational framework that merges mechanistic modeling with deep neural networks obeying the Systems Biology Markup Language (SBML) standard. Over the last 20 years, the systems biology community has developed a large number of mechanistic models in SBML that are currently stored in public databases. With the proposed framework, existing SBML mechanistic models may be upgraded to hybrid systems through the incorporation of deep neural networks into the model core, using a freely available python tool. The so-formed hybrid mechanistic/neural network models are trained with a deep learning algorithm based on the adaptive moment estimation method (ADAM), stochastic regularization and semidirect sensitivity equations. The trained hybrid models are encoded in SBML and stored back in model databases, where they can be further analyzed as regular SBML models. The application of this approach is illustrated with three well-known case studies: the threonine synthesis model in Escherichia coli, the P58IPK signal transduction model, and the Yeast glycolytic oscillations model. The proposed framework is expected to greatly facilitate the widespread use of hybrid modeling techniques for systems biology applications.

Tapping panel dryness (TPD) syndrome is a complex disease of Rubber tree (Hevea brasiliensis L.) which causes cessation of latex drainage upon tapping of rubber tree. Rubber tree virus (RTV1) was identified as a novel pathogen associated with rubber tree and a potential causal agent of TPD. RTV1 is a monopartite RNA virus that is linear, non-enveloped and has a single-stranded (ss) positive RNA genome of approximately 6081 nucleotides and is composed of two major open reading frames (ORFs), ORF1 (polyprotein), and ORF2 (movement protein. This study aimed to investigate the possibility of rubber genome encoded tree microRNAs (miRNAs) as novel therapeutic targets against RTV1 using in silico algorithms. Mature rubber tree miRNAs are retrieved from the miRBase database and are used for hybridization of RTV1 using five different five different computational algorithms including miRanda, RNA22, RNAhybrid and psRNATarget. A total of eleven common rubber tree miRNAs were identified based on consensus genomic positions. The consensus of four algorithms predicted the hybridization sites of hbr-miR396a and hbr-miR398 at common locus positions 6676, 1840 respectively. To validate the prediction, secondary structures of the consensual rubber tree miRNAs and free energy of duplex binding were calculated using the RNAfold and RNAcofold algorithms respectively. We created a plot between rubber tree miRNAs and RTV1 ORFs by using Circos algorithm. In this study, we predicted eleven consensual rubber tree miRNAs. Among these miRNAs, hbr-miR398 was identified as the most effectual miRNA that may target the ORF1 gene of the RTV1 genome. The predicted data will be important in the development of rubber trees resistant to RTV1.

Herein, we present a combination of experimental and computational study on the mitochondrial F0F1-ATPase nanotoxicity inhibition induced by single-walled carbon nanotubes (SWCNT-pristine, SWCNT-COOH). To this end, the in vitro inhibition responses in submitochondrial particles (SMP) as F0F1-ATPase enzyme were strongly dependent on the concentration assay (from 3 to 5 µg/ml) for both types of carbon nanotubes. Besides, both SWCNTs show an interaction inhibition pattern like the oligomycin A (the specific mitochondria F0F1-ATPase inhibitor). Furthermore, the best crystallography binding pose obtained for the docking complexes based on the free energy of binding (FEB), fit well with the previous in vitro evidences from the thermodynamics point of view. Following an affinity order as: FEB (oligomycin A/F0-ATPase complex) = -9.8 kcal/mol > FEB (SWCNT-COOH/F0-ATPase complex) = - 6.8 kcal/mol ~ FEB (SWCNT-pristine complex) = -5.9 kcal/mol. With predominance of van der Waals hydrophobic nanointeractions with key F0-ATPase binding site residues (Phe 55 and Phe 64). By the other hand, results on elastic network models, and fractal-surface analysis suggest that SWCNTs induce significant perturbations by triggering abnormal allosteric responses and signals propagation in the inter-residue network which could affect the substrate recognition ligand geometrical specificity of the F0F1-ATPase enzyme in order (SWCNT-pristine > SWCNT-COOH). Besides, the performed Nano-QSTR models for both SWCNTs show that this method may be used for the prediction of the nanotoxicity induced by SWCNT. Overall, the obtained results may open new avenues toward to the better understanding and prediction of new nanotoxicity mechanisms, rational drug-design based nanotechnology, and potential biomedical application in precision nanomedicine.

Intelligent algorithms are recently used in the optimization process in chemical engineering and application of multiphase flows such as bubbling flow. This overview of modeling can be a great replacement with complex numerical methods or very time-consuming and disruptive measurement experimental process. In this study, we develop the adaptive network-based fuzzy inference system (ANFIS) method for mapping inputs and outputs together and understand the behavior of the fluid flow from other output parameters of the bubble column reactor. Neural cells can fully learn the process in their memory and after the training stage, the fuzzy structure predicts the multiphase flow data. Four inputs such as x coordinate, y coordinate, z coordinate, and air superficial velocity and one output such as pressure gradient are considered in the learning process of the ANFIS method. During the learning process, the different number of the membership function, type of membership functions and the number of inputs are examined to achieve the intelligent algorithm with high accuracy. The results show that as the number of inputs increases the accuracy of the ANFIS method rises up to almost for all cases, while the increment in the number of rules has a effect on the intelligence of artificial algorithm. This finding shows that the density of neural objects or higher input parameters enables the moded for better understanding. We also proposed a new evaluation of data in the bubble column reactor by mapping inputs and outputs and shuffle all parameters together to understand the behaviour of the multiphase flow as a function of either inputs or outputs. This new process of mapping inputs and outputs data provides a framework to fully understand the flow in the fluid domain in a short time of fuzzy structure calculation.

Distributed Systems architectures are becoming the standard computational model for processing and transportation of information, especially for Cloud Computing environments. The increase in demand for application processing and data management from enterprise and end-user workloads continues to move from a single-node client-server architecture to a distributed multitier design where data processing and transmission are segregated. Software development must considerer the orchestration required to provision its core components in order to deploy the services efficiently in many independent, loosely coupled - physically and virtually interconnected - data centers spread geographically, across the globe. This network routing challenge can be modeled as a variation of the Travelling Salesman Problem (TSP). This paper proposes a new optimization algorithm for optimum route selection using Algorithmic Information Theory. The Kelly criterion for a Shannon-Bernoulli process is used to generate a reliable quantitative algorithm to find a near optimal solution tour. The algorithm is then verified by comparing the results with heuristic solutions in 3 test cases. A statistical analysis is designed to measure the significance of the results between the algorithms and the entropy function can be derived from the distribution. The tested results shown an improvement in the solution quality by producing routes with smaller length and time requirements. The quality of the results proves the flexibility of the proposed algorithm for problems with different complexities without relying in nature-inspired models such as Genetic Algorithms and Simulated Annealing. This algorithm can be used by orchestration applications to deploy services across large cluster of nodes by making better decision in the route design.

In the power plant industry, the turbine inlet temperature (TIT) plays a key role in the efficiency of the gas turbine and, therefore, the overall—in most cases combined—thermal power cycle efficiency. Gas turbine efficiency increases by increasing TIT. However, an increase of TIT would increase the turbine component temperature which can be critical (e.g., hot gas attack). Thermal barrier coatings (TBCs)—porous media coatings—can avoid this case and protect the surface of the turbine blade. This combination of TBC and film cooling produces a better cooling performance than conventional cooling processes. The effective thermal conductivity of this composite is highly important in design and other thermal/structural assessments. In this article, the effective thermal conductivity of a simplified model of TBC is evaluated. This work details a numerical study on the steady-state thermal response of two-phase porous media in two dimensions using personal finite element analysis (FEA) code. Specifically, the system response quantity (SRQ) under investigation is the dimensionless effective thermal conductivity of the domain. A thermally conductive matrix domain is modeled with a thermally conductive circular pore arranged in a uniform packing configuration. Both the pore size and the pore thermal conductivity are varied over a range of values to investigate the relative effects on the SRQ. In this investigation, an emphasis is placed on using code and solution verification techniques to evaluate the obtained results. The method of manufactured solutions (MMS) was used to perform code verification for the study, showing the FEA code to be second-order accurate. Solution verification was performed using the grid convergence index (GCI) approach with the global deviation uncertainty estimator on a series of five systematically refined meshes for each porosity and thermal conductivity model configuration. A comparison of the SRQs across all domain configurations is made, including uncertainty derived through the GCI analysis.

Production of electricity using hydro-kinetic tidal turbines has many challenges that must to be overcome to ensure reliable, economic and practical solutions. Energy from flowing water is converted by a system comprising: the turbine rotor blades, a gearbox, an electrical generator, control systems, power electronics, export cables, and a connection to the electricity grid. To date these have often been modelled using simulations of independent systems, lacking bi-directional, real-time, coupling. This approach leads to critical effects being missed. Turbulence in the flow, results in large velocity fluctuations around the blades, causing rapid variation in the shaft torque and generator speed, and consequently in the voltage seen by the power electronics and consequently the export power quality. The resulting poor quality power may be unacceptable to the grid. Conversely, grid frequency and voltage changes can also cause the generator speed to change, resulting in changes to the shaft speed and torque and consequently changes to the lift and drag forces acting on the blades. Clearly, fully integrated, bi-directional, models are needed. Here we present two fully coupled models which use different approaches to model the hydrodynamics of rotor blades. The first model uses Blade Element Momentum Theory (BEMT), resulting in an efficient tool for turbine designers. The second model also uses BEMT combines this with an actuator line model of the blades coupled to an unsteady computational fluid dynamics (CFD) simulation. This simulation, implemented in OpenFOAM, uses an energy balance to compute the shaft speed. Both the BEMT and CFD models are coupled to an Open Modellica model of the electro-mechanical system. Both models have been used to simulate the performance of a 1.2m diameter, scale model, of a three bladed horizontal axis tidal turbine tested in the University of Edinburgh FloWave Ocean Energy Research Facility. The turbulent flow around the blades and the mechanical-electrical variables during the stable period of operation are analysed. Time series and tabulated average values of mechanical thrust, power, torque, and rotational speed as well as electrical variables of generator power, electromagnetic torque, voltage and current are presented for the coupled system simulation. The relationship between the mechanical and electrical variables and the results from both tidal turbine approaches are discussed. Our comparison shows that while the BEMT model provides an effective design tool (leading to slightly more conservative designs), the CFD/BEMT simulations provide more accurate predictions of the blade loads which can be especially important in assessing fatigue on the blades (though at an increased computational cost).

This work presents the results of a computational study of the chemical reactivity and bioactivity properties of the members of the Theopapuamides A-D family of marine peptides by making use of our own proposed methodology named Computational Peptidology (CP) that has been successfully considered in previous studies of this kind of molecular systems. CP allowed for the determination of the global and local descriptors that come from Conceptual Density Functional Theory (CDFT) that can give an idea of the chemical reactivity properties of the marine natural products under study which are already known to be related to their bioactivity. At the same time, the validity of the procedure based on the adoption of the KID (Koopmans in DFT) technique as well as the MN12SX/Def2TZVP/H2O model chemistry has been successfully verified. Together with several Chemoinformatic tools that can be used for the improvement of process of Virtual Screening, some additional properties of these marine peptides were identified related to their ability to behave as useful drugs. With the further object of analyzing their bioactivity some parameters of usefulness for future QSAR studies, their predicted biological targets and the the ADMET (Absorption, Distribution, Metabolism, Excretion and Toxicity) parameters related to the Theopapuamides A-D pharmacokinetics are also reported.

Molecular motors play a vital role in the transport of material within the cell. A family of motors of growing interest are burnt bridge ratchets (BBRs). BBRs rectify spatial fluctuations into directed motion by creating and destroying motor-substrate bonds. It has been shown that the motility of a BBR can be optimized as a function of the system parameters. However, the amount of energy input required to generate such motion and the resulting efficiency has been less well characterized. Here, using a deterministic model, we calculate the efficiency of a particular type of BBR, namely a polyvalent hub interacting with a surface of substrate. We find that there is an optimal burn rate and substrate concentration that leads to optimal efficiency. Additionally, the substrate turnover rate has important implications on motor efficiency. We also consider the effects of force-dependent unbinding on the efficiency and find that under certain conditions the motor works more efficiently when bond breaking is included. Our results provide guidance for how to optimize the efficiency of BBRs.

Road vehicles are a large contributor to Nitrogen Oxides (NOx) pollution. The routine road-side monitoring stations, however, may underrepresent the severity of personal exposure in urban areas, because long-term average readings cannot capture the effects of momentary, high peaks of air pollution. While numerical modelling tools historically have been used to propose an improved distribution of monitoring stations, ultra-high resolution Computational Fluid Dynamics models can further assist the relevant stakeholders in understanding the important details of pollutant dispersion and exposure at local level. This study deploys a 10 cm-resolution CFD model to evaluate actual high peaks of personal exposure to NOx from traffic, by tracking the gases emitted from the tailpipe of moving vehicles being dispersed towards the roadside. The investigation shows that a set of four Euro 5-rated diesel vehicles travelling at constant speed may generate momentary road-side concentrations of NOx as high as 1.25 mg/m3, with 25% expected increase for doubling the number of vehicles and approximately 50% reduction when considering Euro 6-rated vehicles. The paper demonstrates how the numerical tool can be used to identify the impact of measures to reduce personal exposure, such as protective urban furniture, as traffic patterns and environmental conditions change.

Three finger toxins (3FTX) are a group of peptides that affect multiple receptor types. One group of proteins affected by 3FTX are nicotinic acetylcholine receptors (nAChR). Structural information on how neurotoxins interact with nAChR is limited and are confined to a small group of neurotoxins. Therefore, in silico methods are valuable in understanding the interactions between 3FTX and different nAChR subtypes, but there are no established protocols to model 3FTX – nAChR interactions. We developed a homology modeling and protein docking protocol to address this issue and tested its success on three different systems. First, neurotoxin peptides co-crystallized with acetylcholine binding protein (AChBP) were re-docked to assess whether Rosetta protein – protein docking can reproduce the native poses. Second, experimental data on peptide binding to AChBP was used to test whether the docking protocol can qualitatively distinguish AChBP-binders from non-binders. Finally, we docked eight peptides with known α7 and muscle-type nAChR binding properties to test whether the protocol can explain the differential activities of the peptides at the two receptor subtypes. Overall, our docking protocol succeeded in predicting both qualitative and specific aspects of 3FTX binding to nAChR and shed light on some unknown aspects of 3FTX binding to different receptor subtypes.

Drug repurposing is a valuable tool for combating the slowing rates of novel therapeutic discovery. The Computational Analysis of Novel Drug Opportunities (CANDO) platform performs shotgun repurposing of 2030 indications/diseases using 3733 drugs/compounds to predict interactions with 46,784 proteins and relating them via proteomic interaction signatures. An accuracy is calculated by comparing interaction similarities of drugs approved for the same indications. We performed a unique subset analysis by breaking down the full protein library into smaller subsets and then recombining the best performing subsets into larger supersets. Up to 14% improvement in accuracy is seen upon benchmarking the supersets, representing a 100–1000 fold reduction in the number of proteins considered relative to the full library. Further analysis revealed that libraries comprised of proteins with more equitably diverse ligand interactions are important for describing compound behavior. Using one of these libraries to generate putative drug candidates against malaria results in more drugs that could be validated in the biomedical literature than the list suggested by the full protein library. Our work elucidates the role of particular protein subsets and corresponding ligand interactions that play a role in drug repurposing, with implications for drug design and machine learning approaches to improve the CANDO platform.

The present study explores the effect of using two porous deflectors on the performance of the Savonius wind turbine compared to only one porous deflector. The numerical simulation is performed to solve the unsteady Navier-Stokes equations using the SST k-

Orthogonal operators can successfully be used to calculate eigenvalues and eigenvector compositions in complex spectra. Orthogonality ensures least correlation between the operators and thereby more stability in the fit, even for small interactions. The resulting eigenvectors are used to transform the pure transition matrix into realistic intermediate coupling transition probabilities. Calculated transition probabilities for close lying levels illustrate the power of the complete orthogonal operator approach.

This study presents an extensive collection of data on the aerodynamic behavior at a low Reynolds number and geometric coefficients for 2900 airfoils obtained through the class shape transformation (CST) method. By employing a verified OpenFOAM-based CFD simulation framework, lift and drag coefficients were determined at a Reynolds number of 10^5. Considering the limited availability of data on low Reynolds number airfoils, this dataset is invaluable for a wide range of applications, including unmanned aerial vehicles (UAVs) and wind turbines. Additionally, the study offers a method for automating CFD simulations that could be applied to obtain aerodynamic coefficients at higher Reynolds numbers. The breadth of this dataset also supports the enhancement and creation of machine learning (ML) models, further advancing research into the aerodynamics of airfoils and lifting surfaces.

Liquid manipulation by photoisomerization attracts recent attentions as a new active droplet control method for micro-chemical analysis. Such a non-inverse manipulation can be realized by a use of solution liquid of surfactant that exhibits the \emph{cis}-\emph{trans} isomerization triggered by light irradiation with a specific wavelength such as ultraviolet light. Since the isomerization is accompanied by changes in fluid properties, a light irradiation on one of liquid-air interfaces of a liquid column in a tube would generate differences in the wettability accompanied between the both sides of the finite liquid column. Although this technique has been demonstrated experimentally by Muto et al. (\emph{Euro.~Phys.~J.~Special Topics}, {\bf 226}, 2016, 1199--1205), its dynamics and developments of each isomer distribution are not understood. In order to reveal the liquid-column migration phenomenon, we have performed numerical simulations of air-liquid two-phase flows and its scalar transport of the isomer, using the Volume-of-Fluid method in conjunction with the Continuum-Surface-Force model and Continuous-Species-Transfer method. We validated present results by comparison with experimental result in terms of the migration distance of the liquid column. We confirmed a termination of the liquid-column migration occurs when the \emph{cis} isomer distribution reaches the non-irradiated region. The migration speed was less dependent on the liquid-column length and was proportional to the tube diameter.

This paper proposes the use of non-uniform extended surfaces installed externally to the tubes of the radiation section of fired heaters, in order to obtain a better heat flux distribution to the coils. To this end, the heat transfer mechanisms present in such equipment were studied through computational fluid dynamics (CFD), using simplified geometries that represent typical sizes of fired heaters. Also, a simplified model for the combustion was considered. Although this model oversimplifies the physics of the problem, it was able to give satisfactory results for the parameters being optimized, considering the main objective of this paper, that is to minimize the non-uniformity of heat flux in the tubes of the radiant section of fired heaters. It was possible to obtain optimized geometric parameters for different types of extended surfaces evaluated, coupling the results of these models with the Particle Swarm optimization method through the use of a response surface technique,. The results indicate a significant improvement in the uniformity of the heat flux distribution to the tubes through the use of the proposed extended surfaces. Thus, this solution reveals to be an interesting alternative to reduce the risks of fluid degradation and coking formation. Future studies must investigate the non-uniformity of the heat flux due to the presence of the flame and consider the interaction between the reactive flow and the participating medium. Nevertheless, this paper presents some results that justify the optimization of such extended surfaces taking into consideration thermal radiation.

Covid-19 is an airborne disease, with the vast majority of infections occurring indoors. By comparison, little transmission occurs outdoors. Here, we investigate the airborne transmission pathways that differentiate the indoors from outdoors, and conclude that profound differences exist, which help to explain why SARS-CoV-2 transmission is much more prevalent indoors. Near and far-field transmission pathways are discussed along with factors that affect infection risk, with aerosol concentration, air entrainment, thermal plumes, and occupancy duration all identified as being influential. In particular, we present the fundamental equations that underpin the Wells-Riley model, and show the mathematical relationship between inhaled virus particles and quanta of infection. A simple model is also presented for assessing infection risk in spaces with incomplete air mixing. Transmission risk is assessed in terms of aerosol concentration using simple 1D equations, followed by a description of thermal plume-ceiling interactions. With respect to this, we present new experimental results using Schlieren-visualisation and Computational Fluid Dynamics (CFD) based on the Eulerian-Lagrangian approach. Pathways of airborne infection are discussed, with the key differences identified between indoors and outdoors. In particular, the contribution of thermal and exhalation plumes is evaluated, and the presence of near-field/far-field feedback loop postulated, which is absent outdoors.

This paper looks at key elements of global culture that are driving a new paradigm shift in museums causing them to question their raison d'être, their design and physical space, recognizing the need to accommodate visitor interaction and participation, and to reprioritize institutional outcomes and goals reexamining their priorities. As heritage sharing in online spaces reaches across national, political, and social boundaries on platforms and networks, this has been driven by museum engagement with Internet life during the pandemic. Museum relationships and interactions with communities both local and global, continue to challenge core values and precepts, leading to radical changes in how museums define their roles and responsibilities. In this new cultural landscape, museums are responding to human digital identity in a tidal wave of human interactions on the Internet, from social media to online sharing of images and videos. This is revealing shared perspectives on cultural conflict as being tied to freedom of expression of one’s heritage embedded in digital identity.

Several problems of radiative transfer are yet unsolved because of the difficulties of the calculations involved in them, especially if the intervening shapes are geometrically complex. The main goal of our investigation in this domain is to convert the formulas that were previously derived, into a graphical interface based on the projected solid-angle principle. Such procedure is now feasible by virtue of several widely diffused programs for Algorithms Aided Design (AAD). Accuracy and reliability of the process is controlled by means of the analytical software DianaX developed at an earlier stage by the authors. With this new approach the often cumbersome procedure of lighting and thermal exchange calculations can be simplified and made available for the neophyte, with the undeniable advantage of reduced computer time.

In this article, author performs computational analysis for the generalized zeta functions by using computational software Mathematica. To achieve the purpose recently obtained difference equations are used. These difference equations have a computational power to compute these functions accurately while they can not be computed by using their known integral represenations. Several authors investigated such functions and their analytic properties, but no work has been reported to study the graphical representations and zeors of these functions. Author performs numerical computations to evaluate these functions for different values of the involved parameters. Taylor series expansions are also presented in this research.

Chemistry has been viewed as one of the most fruitful near-term applications to science of quantum computing. Recent work in transitioning classical algorithms to a quantum computer has led to great strides in improving quantum algorithms and illustrating their quantum advantage. Much less effort has been placed on how one finishes these calculations by using the results from the quantum computer (on the active region of the molecule) and embeds them back into the remainder of the molecule in order to determine the properties of the entire molecule. Such strategies are critical if one wants to expand the focus to biochemical molecules that contain active regions that cannot be properly explained with classical algorithms on classical computers. While we do not solve this problem here, we provide an overview of where the field is going to enable such problems to be tackled in the future.

The term Concept has been a prominent part of investigations in psychology and neurobiology where, mostly, it is mathematically or theoretically represented. The Concepts are also studied computationally through their symbolic, distributed and hybrid representations. The majority of these approaches focused on addressing concrete concepts notion, but the view of the abstract concept is rarely explored. Moreover, most computational approaches have a predefined structure or configurations. The proposed method, Regulated Activation Network (RAN), has an evolving topology and learns representations of Abstract Concepts by exploiting the geometrical view of Concepts, without supervision. In the article, the IRIS data was used to demonstrate: the RAN's modeling; flexibility in concept identifier choice; and deep hierarchy generation. Data from IoT's Human Activity Recognition problem is used to show automatic identification of alike classes as abstract concepts. The evaluation of RAN with 8 UCI benchmarks and the comparisons with 5 Machine Learning models establishes the RANs credibility as a classifier. The classification operation also proved the RAN's hypothesis of abstract concept representation. The experiments demonstrate the RANs ability to simulate psychological processes (like concept creation and learning) and carry out effective classification irrespective of training data size.

Radiation Fireballs are singular phenomena which involve severe thermal radiation and consequently, they need to be duly assessed and prevented. Although the radiative heat transfer produced by a sphere is relatively well known, the shadowing measures implemented to control the fireball’s devastating effects have frequently posed a difficult analytical instance, mainly due to its specific configuration. In this article, since the usual solving equations for the said cases are impractical, the authors propose a novel graphic-algorithm method that sorts the problem efficiently for different kinds of obstructions and relative positions of the fireball and the defenses. Adequate application of this method may improve the safety of a significant number of facilities exposed to such risks.

We present a novel approach for adapting text written in standard Finnish to different dialects. We experiment with character level NMT models both by using a multi-dialectal and transfer learning approaches. The models are tested with over 20 different dialects. The results seem to favor transfer learning, although not strongly over the multi-dialectal approach. We study the influence dialectal adaptation has on perceived creativity of computer generated poetry. Our results suggest that the more the dialect deviates from the standard Finnish, the lower scores people tend to give on an existing evaluation metric. However, on a word association test, people associate creativity and originality more with dialect and fluency more with standard Finnish.

The world of science is drowned in a wealth of information. How to make sense of this wealth of published articles, blog posts and abstracts has become an important challenge given the importance of science to different aspects of societal function. At the crux of the issue lies the increasing trend where scientific discovery informs decision making at the societal level. One example, is the elucidation of the ozone hole to the promulgation of the Montreal Protocol in 1987, and documenting increasing atmospheric carbon dioxide concentration led to climate action and signing of the Paris Agreement in 2015. Hence, understanding a research field becomes an important need for many decision makers across different sectors of society. But, the scientific literature is cryptic and esoteric, and presents a significant barrier to comprehension. One approach to ameliorate the problem is statistical machine reading, which provides the critical capability of identifying key concepts that underpins a research field. Such important concepts help provide an incision point to gain further understanding of the field and initiating further conversation about the field. This work sought to validate the concept of whether applying statistical machine reading to a body of literature comprising short blog posts and abstracts of published articles help in understanding the field of metabolic engineering. One important angle pursued in this research is whether the tabulated list of terms and phrases identified by statistical machine reading could be creatively analyzed to gain a deeper understanding of the research field. For example, the most frequently occurring terms and phrases could describe key concepts of the research field. Moving down in frequency occurrence would be terms and phrases that describe methodologies and approaches of the field. Finally, less frequently occurring terms and phrases may be tools and resources used in the research field. Results validated the utility of statistical machine reading in identifying important terms and phrases associated with the research field. But the small dataset of blog posts and abstracts used in this study severely hampered the identification of most of the key concepts of metabolic engineering, which is a fairly broad field of research. Overall, statistical machine reading shows utility in identifying terms and phrases that could describe a field. However, the level of understanding is closely tied in to the breadth and depth of reading material available, which meant that the methodology is data intensive in nature. Future use of supercomputing or quantum computing could help alleviate constraints of computational capacity, and help tackle the exponential rise in computational complexity as the size of the reading material for machine reading expands.

Working memory refers to the capability of the nervous system to selectively retain short-term memories in an active state. The long-standing viewpoint is that neurons play an indispensable role and working memory is encoded by synaptic plasticity. Furthermore, some recent studies have shown that calcium signaling assists the memory processes and the working memory might be affected by the astrocyte density. Over the last few decades, growing evidence has also revealed that astrocytes exhibit diverse coverage of synapses which are considered to participate in neuronal activities. However, very little effort has yet been made to attempt to shed light on the potential correlations between these observations. Hence, in this article we will leverage a computational neuron-astrocyte model to study the short-term memory performance subject to various astrocytic coverage and we will demonstrate that the short-term memory is susceptible to this factor. Our model may also provide plausible hypotheses for the various sizes of calcium events as they are reckoned to be correlated with the astrocytic coverage.

The Kwee van Woerden (KvW) method for the determination of eclipse minimum times has been a staple in eclipsing binary research for decades, due its simplicity and independence of external input parameters. However, its estimates of the timing error have been known to be of low reliability. During the analysis of very precise photometry of CM Draconis eclipses from TESS space mission data, KvW’s original equation for the timing error estimate produced numerical errors, which evidenced a fundamental problem in this equation. This contribution introduces an improved way to calculate the timing error with the KvW method. A code that implements this improved method, together with several further updates over the original method is presented as well. An example application on the CM Draconis light curves from TESS is given, where we show that its timing error estimates of about 1 second are in excellent agreement with error estimates obtained by other means.

This paper presents a numerical two-scale framework for the simulation of fiber reinforced concrete under impact loading. The numerical homogenization framework considers the full balance of linear momentum at the microscale. This allows for the study of microscopic inertia effects affecting the macroscale. After describing the ideas of the dynamic framework and the material models applied at the microscale, the experimental behavior of the fiber and the fiber-matrix bond under varying loading rates are discussed. To capture the most important features, a simplified matrix cracking and a strain rate sensitive fiber pullout model are utilized at the microscale. A split Hopkinson bar tension test is used as an example to present the capabilities of the framework to analyze different sources of dynamic behavior measured at the macroscale. The induced loading wave is studied and the influence of structural inertia on the measured signals within the simulation are verified. Further parameter studies allow the analysis of the macroscopic response resulting from the rate dependent fiber pullout as well as the direct study of the microscale inertia. Even though the material models and the microscale discretization used within this study are still simplified, the value of the numerical two-scale framework to study material behavior under impact loading is shown.

Using only a limited number of computationally expensive functions, we show a way how to construct accurate and computationally efficient approximations of the Colebrook equation for flow friction. The presented approximations are based on the asymptotic series expansion of the Wright ω-function and symbolic regression. The results are verified with 8 million of Quasi-Monte Carlo points covering the domain of interest for engineers. In comparison with the built-in “wrightOmega” feature of Matlab R2016a, the herein introduced related approximations of the Wright ω-function significantly accelerate the computation. With only two logarithms and several basic arithmetic operations used, the presented approximations are not only computationally efficient but also extremely accurate. The maximal relative error of the most promising approximation which is given in the form suitable for engineers’ use is limited to 0.0012%, while for a little bit more complex variant is limited to 0.000024%.

The Oxford English Dictionary includes 17 definitions for the word “model” as a noun and other 11 as a verb. Therefore, context is necessary to understand the meaning of the word model. For in-stance, “model railways” refer to replicas of railways and trains at a smaller scale and a “model student” refers to an exemplar individual. In some cases, a specific context, like cancer research, may not be sufficient to provide one specific meaning of a model. Even if the context is narrowed, specifically to the research related to the tumour microenvironment, a “model” can be understood in a wide variety of ways, from an animal model, to a mathematical expression. This paper presents a review of the different “models” of the tumour microenvironment grouped by the different def-initions of the word into four categories: model organisms, in vitro models, mathematical models, and computational models. Then, the frequency of different meanings of the word “model” related to the tumour microenvironment is measured from the number of entries in the MEDLINE database of the United States National Library of Medicine at the National Institutes of Health. The frequency of the main components of the microenvironment and the organ-related cancers modelled are also assessed quantitatively with specific keywords. Whilst animal models, in particular xenografts and mouse models are the most common used “models”, the number of entries have been slowly de-creasing. Mathematical models, prognostic and risk models follow in frequency and these have been growing in use.

Coded aperture 3D imaging techniques have been rapidly evolving in the recent years. The two main directions of evolution are in aperture engineering to generate the optimal optical field and in development of computational reconstruction to reconstruct the object’s image from the intensity distribution with a minimal noise. The goal is to find the ideal aperture-reconstruction method pair and if not, to optimize one to match the other for designing an imaging system with required 3D imaging characteristics. Lucy-Richardson-Rosen algorithm (LR²A), a recently developed computational reconstruction method was found to perform better than its predecessors such as matched filter, Weiner filter, phase-only filter, Lucy-Richardson algorithm and non-linear reconstruction (NLR) for certain apertures when the point spread function (PSF) is a real and symmetric function. For other cases of PSF, NLR performed better than the rest of the methods. In this tutorial, LR²A has been presented as a generalized approach for any optical field along with MATLAB codes for reconstruction of any image when the PSF is known. The common problems and pitfalls in using LR²A has been discussed. Simulation and experimental studies for common optical fields such as spherical, Bessel, vortex beams and exotic optical fields such as Airy, scattered and self-rotating beams have been presented. From this study, it can be seen that it is possible to transfer the 3D imaging characteristics from non-imaging type exotic fields to indirect imaging systems faithfully using LR²A. The application of LR²A to medical images such as colonoscopy images and cone beam computed tomography images with synthetic PSF has been demonstrated. We believe that the tutorial will provide a deeper understanding of computational reconstruction using LR²A.

This paper analyzes the collection of George Viau (1855-1939) from a computational perspective. Indeed, this dental surgeon, close to the Impressionists, collected several hundred works of art in the first half of the 20th century: the auctions of his collection, in 1907, 1930 and after his death, in 1942, 1943 and 1948, accounted for 642 artworks and, during the Occupation, the 1942 sale produced a total of more than 46 million francs. Thanks to statistics, econometrics, network analysis and cartography, it is possible to understand the salient features of the collection and its place in the world of Parisian auctions.

Nowadays, many political campaigns are using social influence (SI) in order to convince voters to support/oppose a specific candidate/party. In election control via SI problem, an attacker tries to find a set of limited influencers to start disseminating a political message in a social network of voters. A voter will change his opinion when he receives and accepts the message. In constructive case, the goal is to maximize the number of votes/winners of a target candidate/party, while in destructive case, the attacker tries to minimize them. Recent works considered the problem in different models and presented some hardness and approximation results. In this work, we consider multi-winner election control through SI on different graph structures and diffusion models, and our goal is to maximize/minimize the number of winners in our target party. We show that the problem is hard to approximate when voters' connections form a graph, and the diffusion model is the linear threshold model. We also prove the same result considering an arborescence under independent cascade model. Moreover, we present a dynamic programming algorithm for the cases that the voting system is a variation of straight-party voting, and voters form a tree.

An adaptive deep neural network is used in an inverse system identification setting to approximate the inverse of a nonlinear plant with the aim of constituting the plant controller by copying to the latter the weights and architecture of the converging deep neural network. This deep learning (DL) approach to the adaptive inverse control (AIC) problem is shown to outperform adaptive filtering techniques and algorithms normally used in adaptive control, especially when the plant is nonlinear. The deeper the controller the better the inverse function approximation, provided that the nonlinear plant have an inverse and that this inverse can be approximated. Simulation results prove the feasibility of this DL-based adaptive inverse control scheme. The DL-based AIC system is robust to parameter change of the nonlinear plant in that, under such change, the plant output reassumes the value of the reference signal considerably faster than with the adaptive filter counterpart of the deep neural network. Settling times and rise times of the step response are shown to improve in the DL-based AIC system.

This paper focuses on the combination of the method of moments and the wire-grid approximation as an effective computational technique for modeling symmetrical antennas with low computational cost and quite accurate results. The criteria and conditions for the use of wire-grid surface approximation from various sources are presented together with new recommendations for modeling symmetrical antenna structures using the wire-grid approximation. These recommendations are used to calculate the characteristics of biconical and horn antennas at different frequencies. The results obtained using different grid and mesh settings are compared to those obtained analytically. Moreover, the results are compared to those obtained using the finite difference time domain numerical method, as well as the measured ones. All results are shown to be in a good agreement. The used recommendations for building a symmetrical wire-grid of those symmetrical antenna elements provided the most advantageous parameters of the grid and mesh settings and the wire radius, which are able to give a quite accurate results with low computational cost. Additionally, the known equal area rule was modified for a rectangular grid form. The obtained radiation patterns of a conductive plate using both the original rule and the modified one are compared with the electrodynamic analysis results. It is shown that the use of the modified rule is more accurate when using a rectangle grid form.

We present a general process for the halting problem, valid regardless of the time and space computational complexity of the decision problem. It can be interpreted as the maximization of entropy for the utility function of a given Shannon-Kolmogorov-Bernoulli process. Applications to non-polynomials problems are given. The new interpretation of information rate proposed in this work is a method that models the solution space boundaries of any decision problem (and non polynomial problems in general) as a communication channel by means of Information Theory. We described a sort method that order objects using the intrinsic information content distribution for the elements of a constrained solution space - modeled as messages transmitted through any communication systems. The limits of the search space are defined by the Kolmogorov-Chaitin complexity of the sequences encoded as Shannon-Bernoulli strings. We conclude with a discussion about the implications for general decision problems in Turing machines.

Predicting long-term student achievement is a critical task for teachers and for educational data mining. However, most of the models do not consider two typical situations in real-life classrooms. The first is that teachers develop their own questions for online formative assessment. Therefore, there are a huge number of possible questions, each of which is answered by only a few students. Second, online formative assessment often involves open-ended questions that students answer in writing. These types of questions in online formative assessment are highly valuable. However, analyzing the responses automatically can be a complex process. In this paper, we address these two challenges. We analyzed 621,575 answers to closed-ended questions and 16,618 answers to open-ended questions by 464 fourth-graders from 24 low-SES schools. Using linguistic features of the answers and an automatic incoherent response classifier, we built a linear model that predicts the score on and end-of-year national standardized test. We found that despite answering 36.4 times fewer open-ended questions than closed questions, including features of the students’ open responses in our model improved our prediction of their end-of-year test scores. To the best of our knowledge, this is the first time that a predictor of end-of-year test scores has been improved by using automatically detected features of answers to open-ended questions on online formative assessments.

In the realm of modern drug discovery, the integration of chemoinformatics and quantitative structure-activity relationship (QSAR) modeling has emerged as a formidable alliance, enabling researchers to harness the vast potential of machine learning (ML) techniques for predictive molecular design and analysis. This review delves into the fundamental aspects of chemoinformatics, elucidating the intricate nature of chemical data and the crucial role of molecular descriptors in unveiling the underlying molecular properties. Molecular descriptors, including 2D fingerprints and topological indices, in conjunction with the structural-activity relationships (SARs), play a pivotal role in unlocking the pathway to small-molecule drug discovery. Technical intricacies of developing robust ML-QSAR models, including feature selection, model validation, and performance evaluation, are discussed herewith. Various ML algorithms, such as regression analysis and support vector machines, are showcased in the text for their ability to predict and comprehend the relationships between molecular structures and biological activities. This review serves as a comprehensive guide for researchers, providing an understanding of the synergy between chemoinformatics, QSAR, and ML. By embracing these cutting-edge technologies, predictive molecular analysis holds promise for expediting the discovery of novel therapeutic agents in the pharmaceutical sciences.

Large language model (LLM) is a representation of a major advancement in AI, and has been used in multiple natural language processing tasks. Nevertheless, in different business scenarios, LLM requires fine-tuning by engineers to achieve satisfactory performance, and the cost of achieving target performance and fine-tuning may not match. Based on the Baidu STI dataset, we study the upper bound of the performance that classical information retrieval methods can achieve under a specific business, and compare it with the cost and performance of the participating team based on LLM. This paper gives an insight into the potential of classical computational linguistics algorithms, and which can help decision-makers make reasonable choices for LLM and low-cost methods in business R&D.

Fluid flow and chemokine gradients play a large part in not only regulating homeostatic processes in the brain, but also in pathologic conditions by directing cell migration. Tumor cells in particular are superior at invading into the brain resulting in tumor recurrence. One mechanism that governs cellular invasion is autologous chemotaxis, whereby pericellular chemokine gradients form due to interstitial fluid flow (IFF) leading cells to migrate up the gradient. Glioma cells have been shown to specifically use CXCL12 to increase their invasion under heightened interstitial flow. Computational modeling of this gradient offers better insight into the extent of its development around single cells, yet very few conditions have been modelled. In this paper, a computational model is developed to investigate how a CXCL12 gradient may form around a tumor cell and what conditions are necessary to affect its formation. Through finite element analysis using COMSOL and coupled convection-diffusion/mass transport equations, we show that velocity (IFF magnitude) has the largest parametric effect on gradient formation, multidirectional fluid flow causes gradient formation in the direction of the resultant which is governed by IFF magnitude, common treatments and flow patterns have a spatiotemporal effect on pericellular gradients, exogenous background concentrations can abrogate the autologous effect depending on how close the cell is to the source, that there is a minimal distance away from the tumor border required for a single cell to establish an autologous gradient, and finally that the development of a gradient formation is highly dependent on specific cell morphology.

This research presents a comprehensive bibliometric and sentiment analysis of nanocomposite literature from 1990 to 2024. Employing cutting-edge computational methods, the study delves deep into the progression of microstructural characterization, electrical properties, and mechanical behaviors of nanocomposites. The analysis utilizes advanced Boolean search strategies from the Scopus database, ensuring a thorough extraction of thematic content. The results explore various themes and insights, shedding light on trends evident in the Scopus database, particularly the prominence of research on nanocomposite microstructure, electrical attributes, and mechanical performance. The paper also offers textual analytics and bibliometric data, showcasing critical collaborative efforts and influential studies. Significant discoveries encompass the evolution of research language, shifts in thematic focus, and global contributions, providing a comprehensive perspective on the current landscape of nanocomposite research and its dynamic evolution. Moving forward, the "State-of-the-Art and Gaps Extracted from Results and Discussions" section of the paper delves into the most recent advancements in nanocomposite research. It delves into various types of nanocomposites, with a particular emphasis on their microstructural characteristics, electrical properties, mechanical dynamics, and the application of nanocomposite films. This section identifies key research themes, traces historical progress, and highlights emerging trends while underscoring the significance of collaboration and the influence of pivotal studies that have shaped the field. Lastly, in the "Literature Review Guided by Artificial Intelligence" section, the paper introduces a revised approach for researching nanocomposites through AI-guided techniques. This approach prioritizes articles published in 2023 based on citation frequency. Here, the focus is on exploring the relationship between nanocomposites and their electrical properties, emphasizing their fundamental interactions and impact on electrical characteristics. Various nanocomposite systems are covered, highlighting their composition, structure, and functionality. Findings from recent studies are integrated to provide a comprehensive overview of the current state of knowledge in this area. Notably, the sentiment analysis, anchored by an average sentiment score of 0.638771, underscores a positive trajectory in academic discourse, emphasizing the growing recognition of the potential of nanocomposites. The bibliometric exploration maps the intellectual domain, emphasizing pivotal research themes and the influence of crosslinking time on nanocomposite attributes. While this study is thorough, it acknowledges its limitations and advocates for broader database inclusion in future research endeavors. This work elucidates the prevailing trends in nanocomposite research, emphasizing the indispensable role of computational tools in comprehending this vast wealth of information.

Computer simulation relies on well-defined experimental supported theories, models, and numerical methods. Computer simulation is an alternative to fill the gaps where the experiment is pricy or limited in engineering. Computer simulation is a high-fidelity computational technique that can work as an engineering innovation tool to try imaginative ideas beyond the available technologies. The accuracy of current computer simulation results is reliable enough to accelerate innovation for new materials and mechanical technologies without experimental validation. So, we may need to urge relying on computer simulation results without any experimental validation to accelerate engineering innovations. In addition, using high-fidelity computer simulation for engineering innovation acceleration without validation will be promoted if it is credited as a new classification. This subject and a related justification's classification in engineering have been discussed.

As cancer remains resistant to several modes of treatment, novel therapeutics are still under active investigation to overcome treatment inefficacy in cancer. Given the high attrition rate of de novo drug discovery, drug screening, and drug repurposing have offered time- and cost-effective alternative strategies for the identification of potentially effective therapeutics. In contrast to large-scale drug screens, computational approaches for drug repurposing leverage the increasing amounts of biomedical data to predict candidate therapeutic agents prior to testing in biological models. Current studies in drug repurposing for cancer therapy prediction have increasingly focused on the prediction of combination therapies, as combination therapies have numerous advantages over monotherapies. These include increased effect from synergistic interactions, reduced toxicity from lowered drug doses, and a reduced risk of resistance due to multiple non-overlapping mechanisms of action. This review provides a summary of several classes of computational methods used for drug combination therapy prediction in cancer research, including networks, regression-based machine learning, classifier machine learning models, and deep learning approaches, with the goal of presenting current progress in the field, particularly to non-computational cancer biologists. We conclude by discussing the need for further advancements in technologies that incorporate disease mechanisms, drug characteristics, multi-omics data, and clinical considerations to generate effective patient-specific drug combinations, as holistic data integration will inevitably result in optimal targeted therapeutics for cancer.

The current study presents a computational fluid dynamics model designed to simulate the isolation of 2D graphene components from their dispersion using a microfiltration hollow fiber membrane unit. The model utilizes Navier-Stokes and mass conservation equations to predict the flow and concentration behaviors in the system, and it employs the resistance-in-series approach to couple the fouling of the non-exfoliated graphites in the dispersion to the model. Specifically, the model accounts for the effects of the concentration polarization and cake formation of the fouling component, resulting in the increment of the transmembrane pressure (TMP) of the system. Additionally, we assumed the wettability of polymeric membrane’s inner wall enhances upon fouling by the flat layered structure material, leading to the reduction of the transmemrabe pressure. This approach demosntrates accurate reproduction of the exceptional experimental TMP behavior corresponding to the fouling of the graphite.

This study presents the computational model to determine the wear behaviour of polymer gears. Using PrePoMax finite element numerical calculation software, a proposed computational model was built to predict wear behaviour based on Archard's wear model. This allows the calculation of the wear depth in each loading cycle with constant mesh updating. The developed computational model has been evaluated on the spur gear pair, where the pinion made of POM has meshed with a support gear made of steel. The computational results that were obtained were compared with the analytical results according to the VDI 2736 guidelines. Based on this comparison, it was concluded that the proposed computational model could be used to simulate the wear behaviour of contacting mechanical elements like gears, bearings, etc. The main advantage of the model, if compared to the standardised procedure according to the VDI 2736 guidelines, is the geometry updating after a chosen number of loading cycles, which enables a more accurate prediction of wear behaviour under rolling/sliding loading conditions.

In recent years, Neural networks are increasingly deployed in various fields to learn complex patterns and make accurate predictions. However, designing an effective neural network model is a challenging task that requires careful consideration of various factors, including architecture, optimization method, and regularization technique. This paper aims to comprehensively overview the state-of-the-art artificial neural network (ANN) generation and highlight key challenges and opportunities in machine learning applications. It provides a critical analysis of current neural network model design methodologies, focusing on the strengths and weaknesses of different approaches. Also, it explores the use of different learning approaches, including convolutional neural networks (CNN), deep neural networks (DNN), and recurrent neural networks (RNN) in image recognition, natural language processing, and time series analysis. Besides, it discusses the benefits of choosing the ideal values for the different components of ANN, such as the number of Input/output layers, hidden layers number, activation function type, epochs number, and model type selection, which help improve the model performance and generalization. Furthermore, it identifies some common pitfalls and limitations of existing design methodologies, such as overfitting, lack of interpretability, and computational complexity. Finally, it proposes some directions for future research, such as developing more efficient and interpretable neural network architectures, improving the scalability of training algorithms, and exploring the potential of new paradigms, such as Spiking Neural Networks, quantum neural networks, and neuromorphic computing.

Interdisciplinary conferences play a vital role in advancing explainable Artificial Intelligence (AI) within increasingly intersecting healthcare and computational biology arenas. Challenges result-ing from algorithmic bias and the necessity for domain-specific Explainable AI (XAI) techniques underscore the increasing significance of transparent and interpretable AI systems used in patient care. Collaborative efforts between clinicians, data scientists, and various stakeholders are nec-essary to innovate solutions tailored to healthcare needs. Specialized conferences may foster these interdisciplinary interactions, providing platforms for knowledge exchange, networking, and collaborative partnerships. The legal, ethical, and societal dimensions of medical AI advocate for an integrative approach that aligns technological advancements with patient-centered care val-ues. The role of specialized conferences is therefore essential for shaping future directions in ex-plainable AI and computational biology that contribute to improved patient outcomes and healthcare innovations.

Liver is structurally organized into zonation where LSECs endothelial cells play a crucial role during chronic liver injury and early stages of fibrosis. Fibrosis can be reversed if diagnosed early at molecular level in zonation before progressing to advanced stages like bridging fibrosis. This study identified zonation marker genes using scRNA-seq and spatial transcriptomics molecular profiling technologies in normal and diseased fibrotic human liver. DEG analysis is performed over LSECs and identified the top 20 expressed genes in periportal, perivenous, and intermediate acinar zones. Multi-omics and scRNA-seq analysis over Visium images and ECs liver cells figured out OIT3, DNASE1L3, CLEC4G, LYVE1, FCN2, CRHBP as commonly expressed mid-lobular zonation-specific genes. Also, this study detected STAB2, F8, AQP1, TEK, TIMP3, TIE1, CTSL genes as expressed in DILI and NASH ECs populations. The connection between LSECs marker genes in zone 2 and liver fibrosis holds significant promise for advancing our understanding in developing new therapeutic strategies for fibrosis reversal and designing computational molecular biomarkers in NASH and DILI fibrotic liver diseases.

Why do neurons communicate through spikes? By definition, spikes are all-or-none neural events which occur at continuous times. In other words, spikes are on one side binary, existing or not without further details, and on the other can occur at any asynchronous time, without the need for a centralized clock. This stands in stark contrast to the analog representation of values and the discretized timing classically used in digital processing and at the base of modern-day neural networks. As neural systems almost systematically use this so-called event-based representation in the living world, a better understanding of this phenomenon remains a fundamental challenge in neurobiology in order to better interpret the profusion of recorded data. With the growing need for intelligent embedded systems, it also emerges as a new computing paradigm to enable the efficient operation of a new class of sensors and event-based computers, called neuromorphic, which could enable significant gains in computation time and energy consumption — a major societal issue in the era of the digital economy and global warming. In this review paper, we provide evidence from biology, theory and engineering that the precise timing of spikes plays a crucial role in our understanding of the efficiency of neural networks.

The basis for computation in the brain is the quantum threshold of the ‘soliton’ accompanying the ion changes of the action potential and the refractory membrane at convergences. We provide a logical explanation from the action potential to a neuronal model of the coding and computation of the retina and have explained how the visual cortex operates by quantum phase processing. In the small world network parallel frequencies collide into definable patterns of distinct objects. Elsewhere we have shown how many sensory cells are mean sampled to a single neuron and that convergences of neurons are common. We have also demonstrated, using the threshold and refractory period of a quantum phase pulse, that action potentials diffract across a neural network due to the annulment of parallel collisions in phase ternary computation (PTC). Thus, PTC applied to neuron convergences results in collective mean sampled frequency and is the only mathematical solution within the constraints of brain neural networks (BNN). In the retina and other sensory areas, we discuss how this information is coded and then understood in terms of network abstracts within the lateral geniculate nucleus (LGN) and visual cortex. First by defined neural patterning within a neural network, and then in terms of contextual networks, we demonstrate that the output of frequencies from the visual cortex contain information amounting to abstract representations of objects in increasing detail. We show that nerve tracts from the LGN provide time synchronisation to the neocortex (defined as the location of the combination of connections of the visual cortex, motor cortex, auditory cortex, etc). The full image is therefore combined in the neocortex with other sensory modalities so that it receives information about the object from the eye, and all abstracts that make up the object. Spatial patterns in the visual cortex are formed from individual patterns illuminating the retina and memory is encoded by reverberatory loops of computational actions potentials (CAPs). We demonstrate that a similar process of PTC may take place in the cochlea and associated ganglia, as well as ascending information from the spinal cord, and that this function should be considered universal where convergences of neurons occur.

Advanced state-of-the-art technologies, mainly computational intelligence including Machine/Deep Learning and Fuzzy Computing, through applied research, can provide added value to modern science and, in general, to entrepreneurship and the economy. Artificial intelligence is the field of computer science that attempts to model concepts such as learning, adaptability and perception to synthesize intelligent behavior in solving complex problems, utilizing elements of adaptation to the environment and philosophical reasoning. About the science of civil engineering and, in general, the construction industry, which is one of the most important in economic entrepreneurship, both in terms of the size of the workforce employed and the amount of capital invested, the penetration of artificial intelligence is possible to change industry business models, eliminate costly mistakes, reduce Jobsite injuries and generally make large-scale engineering projects more efficient. The purpose of the paper is to present the recent research on artificial intelligence methods (machine-deep learning, computer vision, natural language processing, fuzzy systems, robotics, etc.) and the corresponding related technologies related to it (extensive data analysis, blockchain, cloud computing, internet of things, augmented reality), in the fields of application of civil engineering science, including structural engineering, geotechnical engineering, hydraulics and water resources management, marine and coastal technology, transport and transportation infrastructure, planning and technical project management, critical infrastructure security and disaster mitigation..

This paper presents a novel theoretical and computational methodology for the generation of an onset turbulent field with prescribed properties in the numerical simulation of an arbitrary viscous flow. The methodology is based on the definition of a suitable distribution of volume force terms in the right–hand side of the Navier–Stokes equations. The distribution is represented by harmonic functions that are randomly variable in time and space. The intensity of the distribution is controlled by a simple PID strategy in order to obtain that the generated turbulent flow matches a prescribed turbulence intensity. A further condition is that a homogeneous isotropic flow is es- tablished downstream of the region where volume force terms are imposed. Although it is general, the proposed methodology is primarily intended for the computational modelling of hydrokinetic turbines in turbulent flows representative of tidal or riverine installations. A first numerical applica- tion is presented by considering the injection of homogeneous and isotropic turbulence with 16% intensity into a uniform unbounded flow. The analysis of statistical properties as auto-correlation, power spectral density, probability density functions, demonstrates that the generated flow tends to achieve satisfactory levels of stationarity and isotropy, whereas the simple control strategy used determines overestimated turbulent intensity levels.

In music, the role of the interpreter is to play her/his part manipulating the performance parameters in order to offer a sonic rendition of the piece capable of conveying specific expressive intentions. Since the 1980s there has been a growing interest in computational expressive music performance (EMP). This research field has two fundamental objectives: the understanding of the phenomenon of human musical interpretation and the automatic generation of expressive performances. Rule based, statistical, machine and deep learning approaches have been proposed, most of them devoted to the classical repertoire, in particular to piano pieces. On the contrary, we present an introduction to the role of expressive performance within popular music and to the contemporary ecology of pop music production, based on the use of Digital Audio Workstations (DAWs) and virtual instruments. After an analysis of the tools related to expressiveness commonly available to modern producers we propose a detailed survey of research into the computational EMP field, highlighting the potential and limits of what is present in literature with respect to the context of popular music, which by its nature cannot be completely superimposed on the classical one. In the concluding discussion we suggest possible lines of future research in the field of computational expressiveness applied to pop music.

Mutations in epidermal growth factor receptor (EGFR) occur in about 48% of Asian and 19% of Western patients with lung adenocarcinoma (LUAD), leading to its constitutive activation and subsequent uncontrolled cell proliferation. To counteract this, tyrosine kinase inhibitors (TKIs) have been developed, targeting EGFR activity. However, the emergence of metastases and resistance mutations often undermines the durability of the treatment response. Knowledge-based mechanistic models that replicate existing clinical trial outcomes, tailored to specific population characteristics, provide invaluable assistance in designing future clinical trials. These models are particularly effective in identifying optimal responders to specific treatments, thereby enhancing therapeutic efficacy. We have developed physiologically based pharmacokinetic (PBPK) models for gefitinib and osimertinib, representing two distinct generations of EGFR TKIs, to accurately simulate the drugs’ distribution within the primary tumor and metastatic sites following oral administration. These models were integrated with a pathophysiological mechanistic model of EGFR-mutant LUAD, enabling the representation of the effects of both gefitinib and osimertinib on EGFR activation-induced signaling pathways. This comprehensive model outputs detailed evolutions of the primary tumor and each metastatic site, facilitating the evaluation of patient progression in alignment with RECIST guidelines (version 1.1). Notably, the model encapsulates the heterogeneity within the tumor, through the representation of various subclones, each characterized by unique mutation profiles, thereby reflecting differential responses to treatment. Calibration of the model was achieved using publicly available data from the NEJ002 and FLAURA clinical trials. Rigorous visual predictive checks and statistical tests were employed to ensure the proper behavior of the model. The model adeptly replicated the time to progression observed in real clinical trials in EGFR-mutant LUAD patients receiving gefitinib or osimertinib as first-line therapy. In addition, the model was able to reproduce the results from a retrospective study comparing gefitinib and osimertinib, a study that was not used to inform the model. With a consistent virtual population as a reference, the combined model facilitated a comparative analysis of the efficacy of both treatments, thereby underscoring its utility in evaluating therapeutic strategies. The faithful replication of real-world data significantly enhances the credibility of our model, rendering it a vital investigational tool for deriving pertinent insights and informing treatment strategies, particularly in identifying optimal responders to various generations of EGFR TKIs. Following its consecutive prospective validations in the FLAURA2 and MARIPOSA trials, the model is poised to facilitate the generation of synthetic control arms in future clinical trials. This advancement promises a more nuanced analysis of covariate relationships, especially when comparing investigational treatments to established standards of care. Additionally, it potentially reduces the required patient cohort size in such trials, optimizing resource utilization.

We extend a previously developed model for the Stark resonances of the water molecule. The method employs a partial-wave expansion of the single-particle orbitals using spherical harmonics. To find the resonance positions and decay rates, we use the exterior complex scaling approach which involves the analytic continuation of the radial variable into the complex plane and yields a non-hermitian Hamiltonian matrix. The real part of the eigenvalues provides the resonance positions (and thus the Stark shifts), while the imaginary parts $-\Gamma/2$ are related to the decay rates $\Gamma$, i.e., the full-widths at half-maximum of the Breit-Wigner resonances. We focus on the three outermost (valence) orbitals, as they are dominating the ionization process. We find that for forces directed along the three Cartesian co-ordinates, the fastest ionizing orbital always displays a non-monotonic Stark shift. For the case of fields along the molecular axis we show results as a function of the number of spherical harmonics included ($\ell_{\max}=3,4$). Comparison is made with total molecule resonance parameters from the literature obtained with Hartree-Fock and coupled cluster methods.

Small peptides are an important component of the vertebrate immune system. They are important molecules for distinguishing proteins that originate in the host from proteins derived of a pathogenic organism, such as a virus or bacterium. Consequently, these peptides are central for the vertebrate host response to intracellular and extracellular pathogens. Computational models for prediction of these peptides have been based on a narrow sample of data with an emphasis on the position and chemical properties of the amino acids. In past literature, this approach has resulted in higher predictability than models that rely on the geometrical arrangement of atoms. However, protein structure data from experiment and theory are a source for building models at scale, and, therefore, knowledge on the role of small peptides and their immunogenicity in the vertebrate immune system. The following sections introduce procedures that contribute to theoretical prediction of peptides and role in immunogenicity. Lastly, deep learning is discussed as it applies to immunogenetics and the acceleration of knowledge by a capability for modeling the complexity of natural phenomena.

Detailed flow distributions in vascular systems are the key to identifying hemodynamic risk factors for the development and progression of vascular diseases. Although computational fluid dynamics (CFD) has been widely used in bioengineering research on hemodynamics predictions, not only are high-fidelity CFD simulations time-consuming and computing-expensive, but also not friendly to clinical applications due to the difficulty of comprehensive numerical calculations. Machine learning (ML) algorithums to estimate the flow field in vascular systems based on the angiographic images of the blood flow using existed diagnostic tools are emerging as a new pathway to facilitate the mapping of hemodynamics. In present work, the dye injection in a water flow was simulated as an analogy of the contrast perfusion in blood flow using CFD. In the simulation, the light passes through the flow field and generates projective images, as an analogy of X-ray imaging. The simulations provide both the ground truth velocity field and the projective images of the flow with dye patterns. A rough velocity field was estimated using the optical flow method (OFM) based on projective images. ML algorithums are then trained using the ground truth CFD data and the OFM velocity estimation as the input. Finally, the interpretable (logistic regression) and deep (neural networks, convolutional neural networks, long short term memory) machine learning models are validated by using parallel in vitro experiments on the same flow setup. The validation results showed that the employed ML model significantly reduced the error rate from 53.5% to 2.5% in average for the v-velocity estimation.

Cyber-Physical Systems (CPS) are integrations of computation and physical processes. Physical processes are monitored and controlled by embedded computers and networks, which frequently have feedback loops where physical processes affect computations and vice versa. To ease the analysis of a system, the costly physical plants can be replaced by high-fidelity virtual models that provide a framework for Digital-Twins (DT). This paper aims to briefly review the state-of-the-art and recent developments in DT and CPS. Three main components in CPS, including communication, control, and computation, are reviewed. Besides, the main tools and methodologies required for implementing practical DT are discussed by following the main applications of DT in the fourth industrial revolution through aspects of smart manufacturing, sixth wireless generation (6G), health, production, energy, and so on. Finally, the main limitations and ideas for future remarks are talked about followed by a short guideline for real-world application of DT towards CPS.

Tissue engineered heart valves can grow, repair, and remodel after implantation, presenting a more favorable long-term solution compared to mechanical and porcine valves. Achieving functional engineered valve tissue requires the maturation of human cells seeded onto valve scaffolds under favorable growth conditions in bioreactors. The mechanical stress and strain on developing valve tissue caused by different pressure and flow conditions in bioreactors are currently unknown. The aim of this study is to quantify the wall shear stress (WSS) magnitude in heart valve prostheses under different valve geometries and bioreactor flow rates. To achieve this, the study used fluid-structure interaction simulations to obtain the valve's opening geometries during the systolic phase. These geometries were then used in computational fluid dynamics simulations with refined near-wall mesh elements and ranges of prescribed inlet flow rates. The data obtained included histograms and regression curves that characterized the distribution, peak, and median WSS for various flow rates and opening configurations. The study also found that the upper region of the valve near the commissures experienced higher WSS magnitudes than the rest of the valve.

Recently, more wind turbine systems are being installed in deep waters far from the coast. Several concepts of floating wind turbine systems (FWTSs) are developed, among which the semisubmersible platform, due to its applicability in different water depths, good hydrodynamic performance, and facility in the installation process, constitutes the most explored technology compared to the others. However, a significant obstacle to the industrialization of this technology is a design of a cost-effective FWTS, which can be achieved by optimizing the geometry, size and weight of the floating platform, along with the mooring system. This is only possible by selecting a method capable of accurately analyzing the FWTS coupled hydro-aero-structural dynamics at each design stage. Accordingly, this paper aims at providing a detailed overview of the most common coupled numerical and physical methods, including their basic assumptions, formulations, limitations, and costs, used for analyzing the dynamics of FWTSs, mainly those supported by a semisubmersible, to assist the choice of the most suitable method at each design phase of FWTSs. Finally, the article discusses possible future research to address challenges in modeling FWTSs dynamics that persist to date.

Direct imaging systems that create an image of an object directly on the sensor in a single step are prone to many constraints as a perfect image is required to be recorded within this step. In designing high resolution direct imaging systems with a diffractive lens, the outermost zone width either reaches the lithography limit or the diffraction limit itself imposing challenges in fabrication. However, if the imaging mode is switched to an indirect one consisting of multiple steps to complete imaging, then different possibilities open up. One such methods is the widely used indirect imaging method with Golay configuration telescopes. In this study, a Golay-like configuration has been adapted to realize a large area diffractive lens with three sub-aperture diffractive lenses. The sub-aperture diffractive lenses are not required to collect light and focus them to a single point as in a direct imaging system but to focus independently on different points within the sensor area. This approach of Large Area Diffractive lens with Integrated Sub-Apertures (LADISA) relaxes the fabrication constraints and allows the sub-aperture diffractive elements to have a larger outermost zone width and smaller area. The diffractive sub-apertures were manufactured using photolithography. The fabricated diffractive element has been implemented in indirect imaging mode using non-linear reconstruction and Lucy-Richardson-Rosen algorithm with synthesized point spread functions. The computational optical experiments revealed an improved optical and computational imaging resolutions compared to previous studies.

The present paper is aimed at presenting an updated review of prediction methods for the aerodynamic noise of ducted rotor-stator stages. Indeed, ducted rotating-blade technologies are in continuous evolution and increasingly used, for both aeronautical propulsion units, power generation and air conditioning systems. Different needs are faced, from the early design stage to the final definition of a machine. Fast-running, approximate analytical approaches and high-fidelity numerical simulations are considered as the best suited tools for each, respectively. Recent advances are discussed, with emphasis on their pros and cons.