Computation, Volume 11, Issue 12 (December 2023) – 21 articles

In this study, we applied a computer-based protocol to identify novel antioxidant agents that can reduce oxidative stress (OxS), which is one of the main hallmarks of several disorders, including cancer, cardiovascular disease, and neurodegenerative disorders. Accordingly, the identification of novel and safe agents, particularly natural products, could represent a valuable strategy to prevent and slow down the cellular damage caused by OxS. Employing two chemical libraries that were properly prepared and enclosing both natural products and world-approved and investigational drugs, we performed a high-throughput docking campaign to identify potential compounds that were able to target the KEAP1 protein. This protein is the main cellular component, along with NRF2, that is involved in the activation of the antioxidant cellular pathway. Furthermore, several post-search filtering approaches were applied to improve the reliability of the computational protocol, such as the evaluation of ligand binding energies and the assessment of the ADMET profile, to provide a final set of compounds that were evaluated by molecular dynamics studies for their binding stability. By following the screening protocol mentioned above, we identified a few undisclosed natural products and drugs that showed great promise as antioxidant agents. Considering the natural products, isoxanthochymol, gingerenone A, and meranzin hydrate showed the best predicted profile for behaving as antioxidant agents, whereas, among the drugs, nedocromil, zopolrestat, and bempedoic acid could be considered for a repurposing approach to identify possible antioxidant agents. In addition, they showed satisfactory ADMET properties with a safe profile, suggesting possible long-term administration. In conclusion, the identified compounds represent a valuable starting point for the identification of novel, safe, and effective antioxidant agents to be employed in cell-based tests and in vivo studies to properly evaluate their action against OxS and the optimal dosage for exerting antioxidant effects. Full article

Currently, the sampling problem has gained wide popularity in the field of autonomous mobile agent control due to the wide range of practical and fundamental problems described with its framework. This paper considers a combined decentralized control strategy that incorporates both elements of biologically inspired and gradient-based approaches. Its key feature is multitasking, consisting in the possibility of solving several tasks in parallel included in the sampling problem: localization and monitoring of several sources and restoration of the given level line boundaries. Full article

This study introduces a mathematical model for electrolytic chemical reactions, employing an energy variation approach grounded in classical thermodynamics. Our model combines electrostatics and chemical reactions within well-defined energetic and dissipative functionals. Extending the energy variation method to open systems consisting of charge, mass, and energy inputs, this model explores energy transformation from one form to another. Electronic devices and biological channels and transporters are open systems. By applying this generalized approach, we investigate the conversion of an electrical current to a proton flow by cytochrome c oxidase, a vital mitochondrial enzyme contributing to ATP production, the ‘energetic currency of life’. This model shows how the enzyme’s structure directs currents and mass flows governed by energetic and dissipative functionals. The interplay between electron and proton flows, guided by Kirchhoff’s current law within the mitochondrial membrane and the mitochondria itself, determines the function of the systems, where electron flows are converted into proton flows and gradients. This important biological system serves as a practical example of the use of energy variation methods to deal with electrochemical reactions in open systems. We combine chemical reactions and Kirchhoff’s law in a model that is much simpler to implement than a full accounting of all the charges in a chemical system. Full article

In August 2020, the World Health Assembly launched a global initiative to eliminate cervical cancer by 2030, setting three primary targets. One key goal is to achieve a 70% screening coverage rate for cervical cancer, primarily relying on the precise analysis of Papanicolaou (Pap) or digital Pap smears. However, the responsibility of reviewing Pap smear samples to identify potentially cancerous cells primarily falls on pathologists—a task known to be exceptionally challenging and time-consuming. This paper proposes a solution to address the shortage of pathologists for cervical cancer screening. It leverages the OpenAI-GYM API to create a deep reinforcement learning environment utilizing liquid-based Pap smear images. By employing the Proximal Policy Optimization algorithm, autonomous agents navigate Pap smear images, identifying cells with the aid of rewards, penalties, and accumulated experiences. Furthermore, the use of a pre-trained convolutional neuronal network like Res-Net50 enhances the classification of detected cells based on their potential for malignancy. The ultimate goal of this study is to develop a highly efficient, automated Papanicolaou analysis system, ultimately reducing the need for human intervention in regions with limited pathologists. Full article

The paper deals with the exploration of subsequences of polygonal numbers of different sides derived through step-by-step elimination of terms of the original sequences. Eliminations are based on special rules similarly to how the classic sieve of Eratosthenes was developed through the elimination of multiples of primes. These elementary number theory activities, appropriate for technology-enhanced secondary mathematics education courses, are supported by a spreadsheet, Wolfram Alpha, Maple, and the Online Encyclopedia of Integer Sequences. General formulas for subsequences of polygonal numbers referred to in the paper as polygonal number sieves of order k, that include base-two exponential functions of k, have been developed. Different problem-solving approaches to the derivation of such and other sieves based on the technology-immune/technology-enabled framework have been used. The accuracy of computations and mathematical reasoning is confirmed through the technique of computational triangulation enabled by using more than one digital tool. A few relevant excerpts from the history of mathematics are briefly featured. Full article

The laboratory measurements conducted on Vaca Muerta formation samples demonstrate stress-dependent elastic behavior and compaction under representative in situ conditions. The experimental results reveal that the analyzed samples display elastoplastic deformation and shear-enhanced compaction as primary plasticity mechanisms. These experimental findings contradict the expected linear elastic response anticipated before brittle failure, as reported in several studies on the geomechanical characterization of the Vaca Muerta formation. Therefore, we present a comprehensive laboratory analysis of Vaca Muerta formation samples showing their nonlinear elastic behavior and irrecoverable shear-enhanced compaction. Additionally, we calibrate an elastoplastic constitutive model based on these experimental observations. The resulting model accurately reproduces the observed phenomena, playing a pivotal role in geoengineering applications within the energy industry. Full article

This paper proposes a new approach to predicting the distribution of harmful substances in the atmosphere based on the combined use of the parameter estimation technique and machine learning algorithms. The essence of the proposed approach is based on the assumption that the concentration values predicted by machine learning algorithms at observation points can be used to refine the pollutant concentration field when solving a differential equation of the convection-diffusion-reaction type. This approach reduces to minimizing an objective functional on some admissible set by choosing the atmospheric turbulence coefficient. We consider two atmospheric turbulence models and restore its unknown parameters by using the limited-memory Broyden–Fletcher–Goldfarb–Shanno algorithm. Three ensemble machine learning algorithms are analyzed for the prediction of concentration values at observation points, and comparison of the predicted values with the measurement results is presented. The proposed approach has been tested on an example of two cities in the Republic of Kazakhstan. In addition, due to the lack of data on pollution sources and their intensities, an approach for identifying this information is presented. Full article

This study examined the effects of minimal, maximal and conventional running footwear on tibial strains and stress fracture probability using finite element and probabilistic analyses. The current investigation examined fifteen males running in three footwear conditions (minimal, maximal and conventional). Kinematic data were collected during overground running at 4.0 m/s using an eight-camera motion-capture system and ground reaction forces using a force plate. Tibial strains were quantified using finite element modelling and stress fracture probability calculated via probabilistic modelling over 100 days of running. Ninetieth percentile tibial strains were significantly greater in minimal (4681.13 με) (p < 0.001) and conventional (4498.84 με) (p = 0.007) footwear compared to maximal (4069.65 με). Furthermore, tibial stress fracture probability was significantly greater in minimal footwear (0.22) (p = 0.047) compared to maximal (0.15). The observations from this investigation show that compared to minimal footwear, maximal running shoes appear to be effective in attenuating runners’ likelihood of developing a tibial stress fracture. Full article

This paper explores a formal model of autopoiesis as presented by Maturana, Uribe and Varela, and analyzes this model and its implications through the lens of the notions of eigenforms (fixed points) and the intricacies of Goedelian coding. The paper discusses the connection between autopoiesis and eigenforms and a variety of different perspectives and examples. The paper puts forward original philosophical reflections and generalizations about its various conclusions concerning specific examples, with the aim of contributing to a unified way of understanding (formal models of) living systems within the context of natural sciences, and to see the role of such systems and the formation of information from the point of view of analogs of biological construction. To this end, we pay attention to models for fixed points, self-reference and self-replication in formal systems and in the description of biological systems. Full article

This research paper presents a deep-learning approach to early detection of skin cancer using image augmentation techniques. We introduce a two-stage image augmentation process utilizing geometric augmentation and a generative adversarial network (GAN) to differentiate skin cancer categories. The public HAM10000 dataset was used to test how well the proposed model worked. Various pre-trained convolutional neural network (CNN) models, including Xception, Inceptionv3, Resnet152v2, EfficientnetB7, InceptionresnetV2, and VGG19, were employed. Our approach demonstrates an accuracy of 96.90%, precision of 97.07%, recall of 96.87%, and F1-score of 96.97%, surpassing the performance of other state-of-the-art methods. The paper also discusses the use of Shapley Additive Explanations (SHAP), an interpretable technique for skin cancer diagnosis, which can help clinicians understand the reasoning behind the diagnosis and improve trust in the system. Overall, the proposed method presents a promising approach to automated skin cancer detection that could improve patient outcomes and reduce healthcare costs. Full article

The significance of robot manipulators in engineering applications and scientific research has increased substantially in recent years. The utilization of robot manipulators to save labor and increase production accuracy is becoming a common practice in industry. Evolutionary computation (EC) techniques are optimization methods that have found their use in diverse engineering fields. This state-of-the-art review focuses on recent developments and progress in their applications for industrial robotics, especially for path planning problems that need to satisfy various constraints that are implied by both the geometry of the robot and its surroundings. We discuss the most-used EC method and the modifications that suit this particular purpose, as well as the different simulation environments that are used for their development. Lastly, we outline the possible research gaps and the expected directions future research in this area will entail. Full article

In recent years, the advancement of micro-aerial vehicles has been rapid, leading to their widespread utilization across various domains due to their adaptability and efficiency. This research paper focuses on the development of a camera-based tracking system specifically designed for low-cost drones. The primary objective of this study is to build up a system capable of detecting objects and locating them on a map in real time. Detection and positioning are achieved solely through the utilization of the drone’s camera and sensors. To accomplish this goal, several deep learning algorithms are assessed and adopted because of their suitability with the system. Object detection is based upon a single-shot detector architecture chosen for maximum computation speed, and the tracking is based upon the combination of deep neural-network-based features combined with an efficient sorting strategy. Subsequently, the developed system is evaluated using diverse metrics to determine its performance for detection and tracking. To further validate the approach, the system is employed in the real world to show its possible deployment. For this, two distinct scenarios were chosen to adjust the algorithms and system setup: a search and rescue scenario with user interaction and precise geolocalization of missing objects, and a livestock control scenario, showing the capability of surveying individual members and keeping track of number and area. The results demonstrate that the system is capable of operating in real time, and the evaluation verifies that the implemented system enables precise and reliable determination of detected object positions. The ablation studies prove that object identification through small variations in phenotypes is feasible with our approach. Full article

Implementing high-performance computing (HPC) to solve problems in energy infrastructure resilience research in a heterogeneous environment based on an in-memory data grid (IMDG) presents a challenge to workflow management systems. Large-scale energy infrastructure research needs multi-variant planning and tools to allocate and dispatch distributed computing resources that pool together to let applications share data, taking into account the subject domain specificity, resource characteristics, and quotas for resource use. To that end, we propose an approach to implement HPC-based resilience analysis using our Orlando Tools (OT) framework. To dynamically scale computing resources, we provide their integration with the relevant software, identifying key application parameters that can have a significant impact on the amount of data processed and the amount of resources required. We automate the startup of the IMDG cluster to execute workflows. To demonstrate the advantage of our solution, we apply it to evaluate the resilience of the existing energy infrastructure model. Compared to similar approaches, our solution allows us to investigate large infrastructures by modeling multiple simultaneous failures of different types of elements down to the number of network elements. In terms of task and resource utilization efficiency, we achieve almost linear speedup as the number of nodes of each resource increases. Full article

A novel approach was developed that combined LP-based row generation with optimization-based sorting to tackle computational challenges posed by budget allocation problems with combinatorial constraints. The proposed approach dynamically generated constraints using row generation and prioritized them using optimization-based sorting to ensure a high-quality solution. Computational experiments and case studies revealed that as the problem size increased, the proposed approach outperformed simplex solutions in terms of solution search time. Specifically, for a problem with 50 projects (N = 50) and 2,251,799,813,685,250 constraints, the proposed approach found a solution in just 1.4 s, while LP failed due to the problem size. The proposed approach demonstrated enhanced computational efficiency and solution quality compared to traditional LP methods. Full article

This work addresses the wind farm (WF) optimization layout considering several substations. It is given a set of wind turbines jointly with a set of substations, and the goal is to obtain the optimal design to minimize the infrastructure cost and the cost of electrical energy losses during the wind farm lifetime. The turbine set is partitioned into subsets to assign to each substation. The cable type and the connections to collect wind turbine-produced energy, forwarding to the corresponding substation, are selected in each subset. The technique proposed uses a genetic algorithm (GA) and an integer linear programming (ILP) model simultaneously. The GA creates a partition in the turbine set and assigns each of the obtained subsets to a substation to optimize a fitness function that corresponds to the minimum total cost of the WF layout. The fitness function evaluation requires solving an ILP model for each substation to determine the optimal cable connection layout. This methodology is applied to four onshore WFs. The obtained results show that the solution performance of the proposed approach reaches up to $0.17$% of economic savings when compared to the clustering with ILP approach (an exact approach). Full article

The dynamic behavior of solid Si targets irradiated by nanosecond laser pulses is computationally studied with transient, thermοmechanical three-dimensional finite element method simulations. The dynamic phase changes of the target and the generation and propagation of surface acoustic waves around the laser focal spot are provided by a finite element model of a very fine uniformly structured mesh, able to provide high-resolution results in short and long spatiotemporal scales. The dynamic changes in the Si material properties until the melting regime are considered, and the simulation results provide a detailed description of the irradiated area response, accompanied by the dynamics of the generation and propagation of ultrasonic waves. The new findings indicate that, due to the low thermal expansion coefficient and the high penetration depth of Si, the amplitude of the generated SAW is small, and the time and distance needed for the ultrasound to be generated is higher compared to dense metals. Additionally, in the melting regime, the development of high nonlinear thermal stresses leads to the generation and formation of an irregular ultrasound. Understanding the interaction between nanosecond lasers and Si is pivotal for advancing a wide range of technologies related to material processing and characterization. Full article

In-bed posture classification has attracted considerable research interest and has significant potential to enhance healthcare applications. Recent works generally use approaches based on pressure maps, machine learning algorithms and focused mainly on finding solutions to obtain high accuracy in posture classification. Typically, these solutions use different datasets with varying numbers of sensors and classify the four main postures (supine, prone, left-facing, and right-facing) or, in some cases, include some variants of those main postures. Following this, this article has three main objectives: fine-grained detection of postures of bedridden people, identifying a large number of postures, including small variations—consideration of 28 different postures will help to better identify the actual position of the bedridden person with a higher accuracy. The number of different postures in this approach is considerably higher than the of those used in any other related work; analyze the impact of pressure map resolution on the posture classification accuracy, which has also not been addressed in other studies; and use the PoPu dataset, a dataset that includes pressure maps from 60 participants and 28 different postures. The dataset was analyzed using five distinct ML algorithms (k-nearest neighbors, linear support vector machines, decision tree, random forest, and multi-layer perceptron). This study’s findings show that the used algorithms achieve high accuracy in 4-posture classification (up to 99% in the case of MLP) using the PoPu dataset, with lower accuracies when attempting the finer-grained 28-posture classification approach (up to 68% in the case of random forest). The results indicate that using ML algorithms for finer-grained applications is possible to specify the patient’s exact position to some degree since the parent posture is still accurately classified. Furthermore, reducing the resolution of the pressure maps seems to affect the classifiers only slightly, which suggests that for applications that do not need finer-granularity, a lower resolution might suffice. Full article

This study examines how U.S. senators strategically used hashtags to create political communities on Twitter during the 2022 Midterm Elections. We propose a way to model topic-based implicit interactions among Twitter users and introduce the concept of Building Political Hashtag Communities (BPHC). Using multiplex network analysis, we provide a comprehensive view of elites’ behavior. Through AI-driven topic modeling on real-world data, we observe that, at a general level, Democrats heavily rely on BPHC. Yet, when disaggregating the network across layers, this trend does not uniformly persist. Specifically, while Republicans engage more intensively in BPHC discussions related to immigration, Democrats heavily rely on BPHC in topics related to identity and women. However, only a select group of Democratic actors engage in BPHC for topics on labor and the environment—domains where Republicans scarcely, if at all, participate in BPHC efforts. This research contributes to the understanding of digital political communication, offering new insights into echo chamber dynamics and the role of politicians in polarization. Full article

Stochastic circuits are used in applications that require low area and power consumption. The computing performed using these circuits is referred to as Stochastic computing (SC). The arithmetic operations in this computing can be realized using minimum logic circuits. The SC system allows a tradeoff of computational accuracy and area; thereby, the challenge in SC is improving the accuracy. The accuracy depends on the SC system’s stochastic number generator (SNG) part. SNGs provide the appropriate stochastic input required for stochastic computation. Hence we explore the accuracy in SC for various arithmetic operations performed using stochastic computing with the help of logic circuits. The contributions in this paper are; first, we have performed stochastic computing for arithmetic components using two different SNGs. The SNGs considered are Linear Feed-back Shift Register (LFSR) -based traditional stochastic number generators and S-box-based stochastic number generators. Second, the arithmetic components are implemented in a combinational circuit for algebraic expression in the stochastic domain using two different SNGs. Third, computational analysis for stochastic arithmetic components and the stochastic algebraic equation has been conducted. Finally, accuracy analysis and measurement are performed between LFSR-based computation and S-box-based computation. The novel aspect of this work is the use of S-box-based SNG in the development of stochastic computing in arithmetic components. Also, the implementation of stochastic computing in the combinational circuit using the developed basic arithmetic components, and exploration of accuracy with respect to stochastic number generators used is presented. Full article

The baking process in tunnel ovens can be influenced by many parameters. Among these, the most important can be considered as: the baking time, the volume of dough pieces, the texture and humidity of the dough, the distribution of temperature inside the oven, as well as the flow of air currents applied in the baking chamber. In order to obtain a constant quality of bakery or pastry products, and for the efficient operation of the oven, it is necessary that the solution made by the designers be subjected to modelling, simulation and analysis processes, before their manufacture, and in this sense it can be applied to the Computational Fluid Dynamics (CFD) numerical simulation tool. In this study, we made an analysis of the air flow inside the baking chamber of an oven. The analyzed oven was used very frequently on the pastry lines. After performing the modelling and simulation, the temperature distribution inside the oven was obtained in the longitudinal and transverse planes. For the experimental validation of the temperatures obtained in the computer-assisted simulation, the temperatures inside the analyzed electric oven were measured. The measured temperatures validated the simulation results with a maximum error of 7.6%. Full article

SO₂ (sulfur dioxide) is a toxic substance emitted into the environment due to burning sulfur-containing fossil fuels in cars, factories, power plants, and homes. This issue is of grave concern because of its negative effects on the environment and human health. Therefore, the search for a material capable of interacting to detect SO₂ and the research on developing effective materials for gas detection holds significant importance in the realm of environmental and health applications. It is well known that one of the effective methods for predicting the structure and electronic properties of systems capable of interacting with a molecule is a method based on quantum mechanical approaches. In this work, the DFT (Density Functional Theory) program DMol³ in Materials Studio was used to study the interactions between the SO₂ molecule and four systems. The adsorption energy, bond lengths, bond angle, charge transfer, and density of states of SO₂ molecule on pristine graphene, N-doped graphene, Ga-doped graphene, and -Ga-N- co-doped graphene were investigated using DFT calculations. The obtained data indicate that the bonding between the SO₂ molecule and pristine graphene is relatively weak, with a binding energy of −0.32 eV and a bond length of 3.06 Å, indicating physical adsorption. Next, the adsorption of the molecule on an N-doped graphene system was considered. The adsorption of SO₂ molecules on N-doped graphene is negligible; generally, the interaction of SO₂ molecules with this system does not significantly change the electronic properties. However, the adsorption energy of the gas molecule on Ga-doped graphene relative to pristine graphene increased significantly. The evidence of chemisorption is increased adsorption energy and decreased adsorption distance between SO₂ and Ga-doped graphene. In addition, our results show that introducing -Ga-N- co-dopants of an “ortho” configuration into pristine graphene significantly affects the adsorption between the gas molecule and graphene. Thus, this approach is significantly practical in the adsorption of SO₂ molecules. Full article