We report on the state of the art of proteins recognized as potential targets for the development of leishmania treatments through the search of biologically active chemical species, either from experimental in vitro, in vivo, or in silico sources. We classify the gathered information, in several ways: vector taxonomy and geographical distribution, leishmania parasite taxonomic and geographical distribution and enzymatic function (oxidoreductases, transferases, hydrolases, lyases, isomerases, ligases and cytokines). Our aim is to provide a much needed reference layout for research efforts aimed to understand the background of ligand-protein activation/inactivation processes, in this specific case, related with enzymes known to be part of biochemical cascade reactions initiated following a leishmania infectious episode.

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.

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.

In this article, one-dimensional viscous quantum hydrodynamical model of semiconductor devices is numerically investigated. The model treats the propagation of electrons in a semiconductor device as the flow of a charged compressible fluid. It plays an important role in predicting the behavior of electron flow in semiconductor devices. The nonlinear viscous quantum hydrodynamic models contain Euler-type equations for density and current, viscous and quantum correction terms, and a Poisson equation for electrostatic potential. Due to high nonlinearity of model equations, numerical solution techniques are applied to obtain their solutions.. The proposed numerical scheme is a splitting scheme based on the kinetic flux-vector splitting (KFVS) method for the hyperbolic step, and a semi-implicit Runge-Kutta method for the relaxation step. The KFVS method is based on the direct splitting of macroscopic flux functions of the system on the cell interfaces. The second order accuracy of the scheme is achieved by using MUSCL-type initial reconstruction and Runge-Kutta time stepping method. Several case studies are considered. For validation, the results of current scheme are compared with those obtained from the splitting scheme based on the NT central scheme. The effects of various parameters such as device length, viscosities, different doping and voltage are analyzed. The accuracy, efficiency and simplicity of the proposed KFVS scheme validates its generic applicability to the given model equations.

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.

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.

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.

Decades ago, when computational was expensive and limited, the structural design was mostly performed by hand calculations using simple mathematical models. For example, it was a common practice to design a structure as complex as the wing of an aircraft by simple beam analysis. However, ever since the classic paper by Turner et al., due to a rapid increase in computational, more complex mathematical models are being used to simulate the physical behavior of complex structural components. To solve intractable problems unsolvable by hand calculations, numerical techniques like Finite Element Analysis (FEA), Computational Fluid Dynamics (CFD), Finite Difference Method etc. are being employed. In fact, the availability of these methods has led to the development of an entirely new area of research known as Multidisciplinary Design Optimization (MDO) where various disciplines are considered in an optimization problem. The most important question while using a mathematical model to represent practical industrial problems is to what extent these models represent the real-life situation. Computational models are always built on upon assumptions. Simply at looking at the simulation outcomes i.e. the graphical and numerical results, it is often very difficult to ensure if the underlying assumption holds and that the results are reliable. This has led to the development of another field of research known as Verification and Validation (called V&V in short).

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.

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.

Conventional data visualization software have greatly improved the efficiency of the mining and visualization of biomedical data. However, when one applies a grid computing approach the efficiency and complexity of such visualization allows for a hypothetical increase in research opportunities. This paper will present data visualization examples presented in conventional networks, then go into higher details about more complex techniques related to leveraging parallel processing architecture. Part of these complex techniques include the attempt to build a basic general adversarial network (GAN) in order to increase the statistical pool of biomedical data for analysis as well as an introduction to the project utilizing the decentralized-internet SDK. This paper is meant to show you said conventional examples then go into details about the deeper experimentation and self contained results.

Today, computer programming is an essential pillar in the education of individuals. Even though technological evolution has eased the massive need for computer programming, a systematic lit-erature review shows some problems remain with teaching computer programing. To address such issues, in this paper we propose an adapted theory, a method, and a model for teaching some knowledge objects associated with the concepts of variables, expressions, comparisons, loops, and functions in programming fundamentals in computer sciences. The main contribution of this study comprises the extension of the concept of didactic transposition to improve teaching in context; in this paper, the idea is called didactic transposition in extensa sensu. The proposal involves the development of a linguistic corpus based on syllabi, textbooks, reference manuals, and a survey applied to experts in teaching programming fundamentals based on seventy-eight universities worldwide. An adapted theory, a method, and a model for teaching programming fundamentals using computational linguistics are produced. In addition, a template is created for designing teaching practices in this regard. The proposal generates an important alternative for the devel-opment of teaching strategies where the conditions of the context are addressed as a priority; ad-ditionally, several aspects are considered for elaborating teaching strategies using computational linguistic techniques from written documents.

A therapy’s outcome is determined by a tumor’s response to treatment which, in turn, depends on multiple factors such as the severity of the disease and the strength of patient’s immune response. Gold standard cancer therapies are in most cases fragile when sought to break the ties to either tumor kill ratio or patient toxicity. Lately, research has shown that cancer therapy can be at most robust when handling adaptive drug resistance and immune escape patterns developed by evolving tumors. This is due to the stochastic and volatile nature of the interactions, at the tumor environment level, tissue vasculature, and immune landscape, induced by drugs. Herein, we explore the path towards antifragile therapy control, that generates treatment schemes that are not fragile but go beyond robustness. More precisely, we describe a first instantiation of a control-theoretic method to make therapy schemes cope with the systemic variability in the tumor–immune–drug interactions and gain more tumor kill with less patient toxicity. Considering the anti-symmetric interactions within a model of the tumor–immune–drug network, we introduce the antifragile control framework that demonstrates promising results in simulation. We evaluate our control strategy against state-of-the-art therapy schemes on various experiments and discuss the insights we gained on the potential that antifragile control could have in treatment design in clinical settings.

Microfluidic devices or microdevices refer to systems with a characteristic length in the micrometer range. Systems in this size allow handling small quantities of reagents and samples, with reduced residence time, better control of chemical species concentration, high heat and mass transfers, and high surface/volume ratio. These characteristics led to the application of these microdevices in several areas, such as biological systems, energy, liquid-liquid extraction, food, agricultural sectors, pharmaceuticals, flow chemistry, microreactors, and biodiesel synthesis. Microreactors are devices that have interconnected microchannels, in which small amounts of reagents are manipulated and react for a certain period of time. The traditional characteristics of microreactors are less quantities of reagents and samples, high surface area in relation to volume (10000 m² m^-3), reduction of resistance to heat and mass transfer, reduced reaction times, and narrower residence time distributions. In recent years, several studies have been carried out on biodiesel production in microreactors that explore the influence of operating conditions, mixing and reaction yield, numbering, and especially the microdevices design. Despite all the advantages of microreactors, the literature shows that there are only a few applications on an industrial scale. Two main reasons that hinder the adoption of this technology are the scale-up to a large enough volume to deliver the necessary production capacity and the costs related to industrial manufacturing microreactors. It is often stated that large-scale production of microreactors can be easily achieved by numbering-up. However, researches show that an incredibly high number of microdevices would be needed, which results in a technical unfeasibility and a strong impact on the construction costs of the industrial system. The present review aims to show whether microreactors can replace conventional biodiesel production processes and how this replacement technology could be carried out. The current chapter was divided into the following sections: Introduction, Synthesis and Purification of Biodiesel in Microreactors, Fundamentals of CFD, and Fundamentals of Scale-up. Finally, conclusions and future perspectives are exposed.

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.

Many of engineering’s problems are about to optimise equations, functions and process models equations which appear on common or even complex science’s cases. Most applied optimisation methods nowadays can only be used on particular cases, so the main objective of this article is to define a computational method that can optimise or even find target values for specified objective functions and variables, by just using computer effort. Chemical plants involve many differential equations and they can be optimised with more facility now. On this paper, there are shown as example, an optimisation for a chemical reactor, which is found the optimal temperature and volumetric flow rate of feed, for the given objective function being the composition of the desired product. Named Domain’s Sweep, it is an algorithm that evaluate given(s) mathematical function(s) and/or equation(s) by varying your(s) independent variable(s) through loops with a given step size and solving it after closing the degrees of freedom, and finally, with some condition statements, store all the optimum values of given or created objective functions with its respective independent variables. In another words, the user create an objective function and this method find the function’s maximum, minimum or a certain chosen target value, even if it does not have an inflection point in the given search interval of the independent variables.

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.

Introduction: EEGLAB is one of the most famous software for processing, analyzing, and researching experiments that have Electroencephalography (EEG) datasets. Due to the numerous and famous add-ins along with global, widespread communications and online free training, its popularity increased every year. Method: To address this phenomenon from a bibliographic perspective, we found 20,464 citations in Google Scholar for the main EEGLAB reference since 8/27/2023. Then, only the Web of Science (WOS) articles were 12,700 that they were extracted. The results were analyzed with Bibliometrix package from CRAN R software. Results: The time span of these articles is from 2004 to 2023 with 12,700 documents in 1,125 sources (journals, books, etc.), 29,125 authors, 19,062 author’s keywords, 13,707 keywords PLUS, 279,617 references. The annual growth rate is 28.12 %, international Co-authorship is 37.27 % and Co-authors per document is s 4.89 and the average citations per document is 22.51. The most relevant sources are Neuroimage, Frontiers in Human Neurosciences, Scientific Reports, Psychophysiology, and PLOS One with 780, 526, 446,425, and 371 articles, respectively. The most cited countries are the USA, Germany, and the United Kingdom with 93,093, 32,621, and 20,748 total citations, respectively. The ERPLAB, ADJUST, and ICLabel add-ins have the local to global citation ratios equal to 85.4%, 65.1%, and 78.2% respectively. Other bibliometric analyses such as co-occurrence networks and thematic maps of abstracts, titles, and keywords are estimated and presented. Conclusions: EEGLAB is among the most cited MATLAB toolboxes in computational neuroscience. Many developed and developing countries use it in their research publications.

An inducer is one of the most important components of centrifugal pumps, whose presence will result in a significant increase in hydraulic performance and pump efficiency. The primary function of the inducer, however, is to delay the destructive phenomenon of cavitation, which has presented a considerable design challenge. Nevertheless, the amount of improvement and increase in inducer performance in both cavitation and non-cavitation modes depends critically on the radial laxity of the blade tip. As part of this study, the performance of the inducer in the cavitation state has been simulated and compared with the experimental data, which are in good agreement. This paper examines the effect of blade tip lagging on cavitation, and the results indicate that this will improve cavitation ­and delay this destructive phenomenon ­but will negatively affect the non-cavitation performance. With the increase in clearance, the range of the return current will increase at the tip of the inducer blade as well.

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.

In this work we study the following problem, from a computational point of view: If three points are selected in the unit square at random, what is the probability that the triangle obtained is obtuse, acute or right? We provide two convergent strategies: the frst derived from the ideas introduced in [2] and the second built on the combinatorics theory. The combined use of these two methods allows us to address the random triangle theory from a new perspective and, we hope, to work out a general method of dealing with some classes of computational problems.

The microbiome, by virtue of its interactions with the host, is implicated in various host functions including its influence on inflammation, nutrition, and homeostasis. Although driven by a complex combination of intrinsic and extrinsic factors, many chronic diseases such as diabetes, cancer, Inflammatory Bowel Disease among others are characterized by a disruption of microbial communities in at least one biological niche/organ system. Various molecular mechanisms between microbial and host components such as proteins, RNAs, metabolites etc have recently been elucidated, thus filling many gaps in our understanding of how the microbiome modulates host processes. Concurrently, high throughput technologies have enabled the profiling of heterogeneous datasets capturing community level changes in the microbiome as well as the host responses. However, due to pragmatic limitations with respect to parallel sampling and analytical procedures, big gaps still exist in terms of how the microbiome mechanistically influences host functions at a systems and community level. In the past decade, various computational biology and machine learning methodologies and approaches have been developed with an aim to fill these existing gaps. Due to the agnostic nature of the tools, they have been applied in various disease contexts to analyze and infer the interactions between the microbiome and host molecular components, and in the case of a few selected tools, on downstream host processes. Generally, most of the tools are enabled by frameworks to statistically or mechanistically integrate different types of -omic and meta -omic datasets followed by functional/biological interpretation. In this review, we provide an overview of the landscape of computational approaches for investigating mechanistic microbiome-host interactions and their potential benefit for basic and clinical research. These could include but are not limited to the development of activity and mechanism based biomarkers, uncovering mechanisms for therapeutic interventions and generating integrated signatures to stratify patients.

Background: Targeted methods that dominated toxicological research until recently did not allow for screening of all molecular changes involved in toxic response. Therefore, it is difficult to infer if all major mechanisms of toxicity have already been discovered, or if some of them are still overlooked. Objectives: To identify molecular mechanisms sensitive to chemical exposures in an unbiased manner. Methods: We used data on 641,516 unique chemical-gene interactions from the Comparative Toxicogenomic Database. Only data from high-throughput gene expression experiments with human, rat or mouse cells/tissues were extracted. The total number of chemical-gene interactions was calculated for every gene, and used as a measure of gene sensitivity to chemical exposures. These values were further used in enrichment analyses to identify molecular mechanisms sensitive to chemical exposures. Results: Remarkably, use of different input subsets with non-overlapping lists of chemical compounds identified largely the same genes and molecular pathways as most sensitive to chemical exposures, indicative of an unbiased nature of our analysis. One of the most important findings of this study is that almost every known molecular mechanism may be affected by chemical exposures. Predictably, xenobiotic metabolism pathways and mechanisms of cellular response to stress and damage were among the most sensitive. Additionally, our analysis identified a range of highly sensitive molecular pathways, which are not widely recognized by modern toxicology as major targets of toxicants, including lipid metabolism pathways, longevity regulation cascade and cytokine mediated signaling. Discussion: Molecular mechanisms identified as the most sensitive to chemical exposures are relevant for significant public health problems, such as aging, cancer, metabolic and autoimmune disease. Thus, public health system will likely benefit from future research focus on these sensitive molecular mechanisms. Additionally, approach used in this study may guide identification of priority adverse outcome pathways (AOP) for in-vitro and in-silico toxicity testing methods.

History is often thought to be dull and boring – where large numbers of facts are memorized for passing exams. But the past informs the present and future, especially in delineating the context surrounding specific events that, in turn, help provide a deeper understanding of their causes and implications. Scientific progress (whether incremental or breakthroughs) is built upon prior work. Chronological examination of computational chemistry’s evolution reveals the existence of major “epochs” (e.g., transition from semi-empirical methods to first principles calculations), and the centrality of key ideas (e.g., Schrodinger equation and Born Oppenheimer approximation) in potentiating progress in the field. The longstanding question of whether computing power (both capacity and speed) or theoretical insights play a more important role in advancing computational chemistry was examined by taking into account the field’s development holistically. Specifically, availability of large amount of computing power at declining cost, and advent of graphics processing unit (GPU) powered parallel computing are enabling tools for solving hitherto intractable problems. On the other hand, this essay argues (using Born Oppenheimer approximation as an example) that theoretical insights’ role in unlocking problems through simple (but insightful) assumptions is often overlooked. Collectively, the essay should be useful as a primer for appreciating major development periods in computational chemistry, from which counterfactual questions illuminate the relative importance of theoretical insights and advances in computer science in moving the field forward.

The Rosetta software suite for macromolecular modeling, docking, and design is widely used in pharmaceutical, industrial, academic, non-profit, and government laboratories. Considering its broad modeling capabilities, Rosetta consistently ranks highly when compared to other leading methods created for highly specialized protein modeling and design tasks. Developed for over two decades by a global community of scientists at more than 60 institutions, Rosetta has undergone multiple refactorings, and now comprises over three million lines of code. Here we discuss the methods developed in the last five years, involving the latest protocols for structure prediction, protein–protein and protein–small molecule docking, protein structure and interface design, loop modeling, the incorporation of various types of experimental data, and modeling of peptides, antibodies and other proteins in the immune system, nucleic acids, non-standard amino acids, carbohydrates, and membrane proteins. We briefly discuss improvements to the energy function, user interfaces, and usability of the ­­software. Rosetta is available at www.rosettacommons.org.

I review previous attempts, including recent ones, to introduce technical aspects of digital information and computation into the discussion of ethics. I survey some limitations and advantages of these attempts to produce guiding principles at different scales. In particular, I briefly introduce and discuss questions, approaches, challenges, and limitations based on, or related to, simulation, information theory, integrated information, computer simulation, intractability, algorithmic complexity, and measures of computational organisation and sophistication. I discuss and propose a set of features that ethical frameworks must possess in order to be considered well-grounded, both in theoretical and methodological terms. I will show that while global ethical frameworks that are uncomputable are desirable because they provide non-teleological direction and open-ended meaning, constrained versions should be able to provide guidelines at more local and immediate time scales. In connection to the ethics of artificial intelligence, one point that must be underscored about computational approaches is that (General) AI should only embrace an ethical framework that we humans are willing to adopt. I think that such a framework is possible, taking the form of a general and universal (in the sense of computation) framework built from first computational principles.

The combination of artificial intelligence algorithms and numerical methods has recently become popular in the prediction of macroscopic and microscopic hydrodynamics parameters of bubble column reactors. The multi inputs and outputs machine learning can cover small phase interactions or large fluid behavior in industrial domains. This numerical combination can develop the smart multiphase bubble column reactor with the ability of low-cost computational time. It can also decrease case studies for the optimization process when big data is appropriately used during learning. There are still many model parameters that need to be optimized for a very accurate artificial algorithm, including data processing and initialization, the combination of inputs and outputs, number of inputs and model tuning parameters. For this study, we aim to train four inputs big data during learning process by an adaptive neuro-fuzzy inference system or adaptive-network-based fuzzy inference system (ANFIS) method, and we consider the superficial gas velocity as one of the input variables, while for the first time, one of the computational fluid dynamics (CFD) outputs named gas velocity is used as an output of the artificial algorithm. The results show that the increasing number of input variables improves the intelligence of the ANFIS method up to , and the number of rules during learning process has a significant effect on the accuracy of this type of modeling. The results also show that propper selection of model parameters results in more accuracy in prediction of the flow characteristics in the column structure.

Epidemiological surveillance and phylogenetic studies rely nowadays on processing and analysing huge volumes of data. Processing tasks consist on running and refining a series of intertwined computational tasks. And, despite of existing several web applications for data processing and interactive visualization for phylogenetic studies, integrating many different tools and algorithms, their execution is total or partially on the client side, making them unsuitable for dealing with huge volumes of data. Studies are often also not easy to reproduce. On the other hand, in recent years, data-centric workflow systems have been proposed, allowing to deal better with increasingly larger datasets. The integration of these systems within phylogenetic tools will allow to scale them as required, and will contribute also to promote studies reproducibility. We propose then the FLOWViZ middleware for facilitating the integration of a state of the art data-centric workflow system, Apache Airflow, within web applications for phylogenetic analyses. This framework abstracts contracts and a core API for defining tools and workflows, where tools are assumed to be containerized. FLOWViZ has been tested and evaluated within the PHYLOViZ web application, a tool supporting phylogenetic inference and data visualization.

The aim of this research is to investigate and use a variety of immersive multisensory media techniques in order to create convincing digital models of fossilised tree trunks for use in XR. This is made possible via the use of geospatial data derived from sources such as aerial imaging using UAS, terrestrial material using cameras and also include both the visual and audio element for better immersion, accessible and explorable in 6 Degrees of Freedom (6DoF). Immersiveness is a key factor in order to result in output that is especially engaging to the user. Both conventional and alternative methods are explored and compared, emphasising in the advantages made possible via the help of Machine Learning Computational Photography. Material is collected using both UAS and terrestrial camera devices, including a 3D-360º camera with 6 sensors, using stitched panoramas as sources for photogrammetry processing. Difficulties such as capturing large free standing objects using terrestrial means were overcome using practical solutions involving mounts and remote streaming solutions. Conclusions indicated that superior fidelity can be achieved by the help of Machine Learning Computational Photography processes and higher resolutions and technical specs of equipment not necessarily translating to superior outputs.

The MLL1 gene located on chromosome 11q23, is crucial for histone lysine-specific methylation and is frequently implicated in various leukemia types. Despite prior in silico investigations into non-synonymous single nucleotide polymorphisms (nsSNPs) associated with leukemia in the MLL1 gene, there is a dearth of comprehensive studies evaluating their impact on the protein's structure, function, and post-translational modifications. Addressing this, our study screened 2049 nsSNPs from the dbSNP database, identifying 62 high-risk variants. A thorough domain analysis revealed that these nsSNPs are distributed across seven domains of the MLL1 protein, potentially affecting their functions. Our conservation analysis highlighted 31 nsSNPs as deleterious, suggesting their potential effects on protein stability and function. Furthermore, utilizing the MutPred2 tool, we identified mutations affecting metal-binding, protein loop structures, and post-translational modifications, which could alter the MLL1 protein's native functionality. Interaction network analysis underscored the role of MLL1 in hematopoietic cell development, implying that mutations may influence hematological malignancies. Additionally, a subset of non-coding SNPs was found to possess regulatory capabilities, potentially affecting gene expression and chromatin modification. Most significantly, using CScape and CScape-somatic tools, four nsSNPs were predicted to be oncogenic, with two classified as cancer drivers, underscoring their potential role in leukemia development. The oncogenic nsSNP, D2724G, located between the FY-rich N and FY-rich C domain of the MLL1 protein, has raised significant interest due to its potential impact on proteolytic cleavage. Predictive analyses, such as those by Mutpred2, suggest a loss of cleavage at D2724 caused by this mutation, potentially affecting the formation of essential MLL1 fragments, p320 and p180. These fragments play a crucial role in creating a stable multiprotein complex that localizes to a specific subnuclear region. Therefore, mutations like D2724G can potentially alter gene expression patterns, influencing cellular behavior and possibly fostering a cancer-prone environment. In conclusion, our research provides an in-depth assessment of the effects of nsSNPs in the MLL1 gene on leukemia, offering potential avenues for personalized treatment strategies, early detection, prognosis, and a better understanding of hematological malignancy genesis.

With an ever increasing amount of research data available, it becomes constantly more important to possess data literacy skills to benefit from this valuable resource. An integrative course was developed to teach students the fundamentals of data literacy through an engaging genome sequencing project. Each cohort of students performed planning of the experiment, DNA extraction, nanopore sequencing, genome sequence assembly, prediction of genes in the assembled sequence, and assignment of functional annotation terms to predicted genes. Students learned how to communicate science through writing a protocol in the form of a scientific paper, providing comments during a peer-review process, and presenting their findings as part of an international symposium. Many students enjoyed the opportunity to own a project and to work towards a meaningful objective.

The aim of this research is to investigate and use a variety of immersive multisensory media techniques in order to create convincing digital models of fossilised tree trunks for use in XR. This is made possible via the use of geospatial data derived from sources such as aerial imaging using UAS, terrestrial material using cameras and also include both the visual and audio element for better immersion, accessible and explorable in 6 Degrees of Freedom (6DoF). Immersiveness is a key factor in order to result in output that is especially engaging to the user. Both conventional and alternative methods are explored and compared, emphasising in the advantages made possible via the help of Machine Learning Computational Photography. Material is collected using both UAS and terrestrial camera devices, including a 3D-360º camera with 6 sensors, using stitched panoramas as sources for photogrammetry processing. Difficulties such as capturing large free standing objects using terrestrial means were overcome using practical solutions involving mounts and remote streaming solutions. Conclusions indicated that superior fidelity can be achieved by the help of Machine Learning Computational Photography processes and higher resolutions and technical specs of equipment not necessarily translating to superior outputs.

In this paper, we study the black hole solution of self-similar gravitational collapse in the Einstein-axion-dilaton system for the elliptic class in four dimensions. The solution is invariant under space-time dilation, which is combined with internal SL(2,R) transformations. Due to the complex and highly nonlinear pattern of the equations of motion in the physics of black holes, researchers typically have to use various numerical techniques to make the equations tractable to estimate the parameters and the critical solutions. To this end, they have to ignore the numerical measurement errors in estimating the parameters. To our knowledge, for the first time in the literature on axion-dilation systems, we propose to estimate the critical collapse functions in a Bayesian framework. We develop a novel methodology to translate the modelling of the complexity of the elliptic black hole to a sampling problem using Hamiltonian Monte Carlo with stacked neural networks. Unlike methods in the literature, this probabilistic approach enables us not only to recover the available deterministic solution but also to explore possibly all physically distinguishable self-similar solutions that may occur due to numerical measurement errors.

Healthy brain functioning depends on balancing stable integration between brain areas for effective coordinated functioning, with bursts of desynchronisation to allow subsystems to reconfigure and express functional specialisation. Metastability, a concept originated in statistical physics and dynamical systems theory, has been proposed as a key signature that characterises this balance. Building on this principle, the neuroscience literature has employed markers of metastability to investigate various aspects of brain function including cognitive performance, healthy ageing, meditation, sleep, responses to pharmacological challenges, and to characterise psychiatric conditions or disorders of consciousness. However, this body of work often uses the notion of metastability heuristically, and sometimes inaccurately, making it hard for the uninitiated to navigate the vast literature, interpret findings, and foster further development of theoretical and experimental methodologies. In this paper we provide a comprehensive review of metastability and its applications in neuroscience, covering its scientific and historical foundations and the practical estimators used to estimate it in empirical data. We also provide a critical analysis of recent theoretical developments, clarifying common misconceptions and paving the road for future developments.

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.

Since the discovery of graphene, due to its excellent optical, thermal, mechanical and electrical properties, it has a broad application prospect in energy, materials, biomedicine, electromagnetism and other fields. A great quantity of researches on the physical mechanism of graphene has been applied to engineering in electromagnetism and optics. To study the properties of graphene, different kinds of numerical methods have been developed for simulating the electromagnetic field effects of graphene, and equivalent boundary conditions have been employed to replace graphene in the computational domain. In this work, the numerical methods with equivalent boundary conditions are reviewed, and some examples are provided to illustrate their applicability.

The main objective of this study is to demonstrate proof of principle that computational fluid dynamics (CFD) modeling is a tool for studying the contribution of covert and overt vascular architecture to the risk of cerebrovascular disease in in sickle cell disease (SCD) as well as uncover one or more mechanism of response to therapy such as chronic red blood cell (cRBC) transfusion. We analyzed baseline (screening), pre-randomization and study exit magnetic resonance angiogram (MRA) images from 10 (5 each from the transfusion and observation arms) pediatric sickle SCD participants in the silent cerebral infarct transfusion (SIT) trial, using CFD modeling. We reconstructed the intracranial portion of the internal carotid artery and branches and extracted the geometry using 3D Slicer. We cut specific potions of the large intracranial artery to include segments of the internal carotid, middle, anterior, and posterior cerebral artery such that the vessel segment analyzed extended from the intracranial beginning of the internal carotid artery up to immediately after (~0.25 inches) the middle cerebral artery branching point. Cut models were imported into Ansys 2021R2/2022R1 and laminar and time-dependent flow simulation was performed. Change in time averaged mean velocity, wall shear stress, and vessel tortuosity were compared between the observation and cRBC arm. We did not observe a correlation between time averaged mean velocity (TAMV) and mean transcranial doppler (TCD) velocity at study entry. There was also no difference in change in time average mean velocity, wall shear stress (WSS), and vessel tortuosity between the observation and cRBC transfusion arms. WSS and TAMV were abnormal for 2 (developed TIA) out of the 3 participants (one participant had SCI) that developed neurovascular outcomes. CFD approaches allows for the evaluation of vascular topology and hemodynamics in SCD using MRA images. In this proof of principle study, we show that CFD could be a useful tool and we intend to carry out future studies with a larger sample to enable more robust conclusions.

: 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.

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.

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.

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.

In a thin-volume photobioreactor where a concentrated suspension of microalgae is circulated throughout the established spatial irradiance gradient, microalgal cells experience a time-variable irradiance. Deploying this feature is the most convenient way of obtaining the so-called “flashing light” effect, improving biomass production in high irradiance. This work investigates the light flashing features of sloping wavy photobioreactors, a recently proposed type, by introducing and validating a Computational Fluid Dynamics model. Two characteristic flow zones (straight top-bottom stream and local recirculation stream), both effective toward light flashing, have been found and characterised: a recirculation-induced frequency of 3.7 Hz and straight flow-induced frequency of 5.6 Hz were estimated. If the channel slope is increased, the recirculation area becomes less stable while the recirculation frequency is nearly constant with flow rate. The validated CFD model is a mighty tool that could be reliably used to further increase the flashing frequency by optimising the design, the dimensions, the installation and the operational parameters of the sloping wavy photobioreactor.

Because only two variables are needed to characterize a simple thermodynamic system in equilibrium, any such system is constrained on a 2D manifold. Of particular interest are the exact 1-forms on the cotangent space of that manifold, since the integral of exact 1-forms is path-independent, a crucial property satisfied by state variables such as internal energy dE and entropy dS. Our prior work [1] shows that given an appropriate language of vector calculus, a machine can re-discover the Maxwell equations and the incompressible Navier-Stokes equations from data. In this paper, We enhance this language by including differential forms and show that machines can re-discover the equation for entropy dS given data. Since entropy appears in various fields of science in different guises, a potential extension of this work is to use the machinery developed in this paper to let machines discover the expressions for entropy from data in fields other than classical thermodynamics.

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

Conceptual distance refers to the degree of proximity between two concepts within a conceptualization. It is closely linked with semantic similarity and relationship, but its computation relies entirely on the context of the given concepts. The DIS-C algorithm, which requires using search algorithms such as Breadth First Search, represents an advance in computing the semantic similarity/relation regardless of the type of knowledge structure and semantic relationships. The shortest path algorithm facilitates the determination of the semantic closeness between two indirectly connected concepts in an ontology by propagating local distances. This process is implemented for each concept pair to establish the most effective and efficient paths to connect these concepts. The algorithm identifies the shortest path between the concepts, allowing for the inference of the most relevant relationships between them. This approach contributes to developing a comprehensive understanding of the ontology and enhances the accuracy and precision of the semantic representation of the concepts. However, one of the critical issues is associated with the computational complexity due to the nature of the algorithm, which is errorn3. This paper studies alternatives to accelerate the DIS-C based on approximation and optimized algorithms, focusing on Dijkstra, pruned Dijkstra, and Sketched-based algorithms to compute conceptual distance. Based on the experiments, we discovered that the bottleneck can be avoided using the proposed 2-hop coverages, bringing DIS-C almost linearity.

This research, which focuses on wave energy generating technology, suggests a brand-new oscillating float-type wave energy conversion system that is appropriate for the offshore wave environment. To accurately model the device, a three-dimensional viscous numerical pool is created based on STAR-CCM+. The array-type power generation device is numerically simulated using theoretical analysis and numerical simulation, and the wave energy power generation device is arranged as double floats in the front and rear rows, representing triangular array type and rectangular array type, respectively. The triangular array type is a superior layout and can make greater use of marine resources, according to this paper's analysis of the hydrodynamic and power generation impacts of the three array types. The findings are meant to serve as a guide for engineering practice.

Regulation at the level of translation plays an essential role in modulating gene expression. Given the importance of knowledge about translationally active mRNAs as an indicator of translation efficiency, it is crucial for researchers to have at their disposal organised sources of functional information on translation - plant translatomic maps similar to transcription maps. The development of a general experimental and computational methodology for constructing translatome maps is essential to address this challenge. In this manuscript, we discuss what researchers can do to design plant translatome maps, namely, we review: (i) experimental methods to obtain translationally active mRNA fractions, considering their advantages and limitations; (ii) additional methodological approaches to obtain complete pools of translationally active mRNAs; (iii) sequencing methods to qualitatively and quantitatively assess different mRNA fractions; and (iv) multivariate analyses of sequencing results by bioinformatics methods, including metrics for assessing mRNA translational activity.

An axial wind turbine's performance is analyzed numerically using geometrical and operational parameters. The performance of an axial wind turbine is simulated using three-dimensional computational fluid dynamics (CFD) and compared with experimental data, which confirms the validity of the assumptions and method used. A study of the effects of air in clean and sand particlesy conditions is then conducted. A study was also conducted on mechanical power and the impact of the blade tip on the extension of the vortex. It has been found that different sand particle sizes have a significant impact on wind performance numerically from 0.1 to 0.9, and the results indicate that mechanical power and thrust increase as wind velocity increases, but larger sand particle sizes reduce power, thrust, and torque as wind velocity increases. The turbulence intensity causes the pressure distribution on the walls to be irregular, thereby increasing mechanical power and propulsion force. Moreover, as the wind velocity increases, the tip speed ratio increases and the vortexes are subsequently extended.

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.

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.

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.

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.

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.

Differential equation models to understand interaction between plant and nutrient solution are presented. The root cells selectively emit H+ ions with active transport consuming ATPs to establish electrical gradient along the cell membrane. It establishes electrical field with Nernst potential to make positively charged ions outside the cell membrane flow into the root cell. Anion influx is also modulated by H+ ion concentration because plant root cell absorbs negatively charged particles with symport. If an anion collides with H+ cell to make net charge as neutral, at symport channel, it can flow through. In this paper, mathematical models for cation and anion absorption are introduced. Cation absorption model was induced from Ohm's law combined with Goldman's equation. Anion absorption model is similar to chemical reaction rate model. Both models have physiological terms influenced by gene expression pattern, species or phenotypes. Cation model also includes terms for ion's kinetic and electrical properties, growth of plant and interaction between the root and the surroundings. Simulation for 20 different sets of coefficients showed that the physiology-related coefficient has important role on nutrition absorption tendencies of plants.

A lensless camera is an ultra-thin computational-imaging system. Existing lensless cameras are based on the axial arrangement of an image sensor and a coding mask, and therefore, the back side of the image sensor cannot be captured. In this paper, we propose a lensless camera with a novel design that can capture the front and back sides simultaneously. The proposed camera is composed of multiple coded image sensors, which are complementary-metal-oxide-semiconductor~(CMOS) image sensors in which air holes are randomly made at some pixels by drilling processing. When the sensors are placed facing each other, the object-side sensor works as a coding mask and the other works as a sparsified image sensor. The captured image is a sparse coded image, which can be decoded computationally by using compressive-sensing-based image reconstruction. We verified the feasibility of the proposed lensless camera by simulations and experiments. The proposed thin lensless camera realizes super field-of-view imaging without lenses or coding masks, and therefore can be used for rich information sensing in confined spaces. This work also suggests a new direction in the design of CMOS image sensors in the era of computational imaging.

Due to poor ventilation conditions in the tunnel, if gas pipeline leaks, the consequence of the accident will be more serious. Therefore, before the emergency repair, gas in the tunnel needs to be excharged so as not to explode during the repair process. Therefore, it is necessary to study the ventilation of gas in the tunnel. Based on the computational fluid dynamics (CFD) theory and taking the Yanyingshan tunnel section of China-Myanmar pipeline as an example, this paper uses Fluent software to establish the leakage model of the gas pipeline and fan model in the tunnel and analyzes the influence of different fan locations and number of fans on gas concentration. It can be concluded that: (1) the use of press-in method makes it more efficient to discharge gas out of the tunnel. (2) In order to make ventilation efficient, the fan should be arranged in a higher position and needs to be at a distance from the top of the tunnel. (3) Parallel use of two fans has better ventilation effect than single fan.

Smoothed particle hydrodynamics (SPH) is regarded as a pure Lagrangian approach, which can solve fluid dynamics problems without the creation of mesh. In this paper, a paralleled SPH solver is developed to solve particle-based computational acoustics (PCA). The aim of this paper is to study the feasibility of using SPH to solve acoustic problems and to improve the efficiency of solving processes by paralleling some procedures on GPU during calculating. A stand SPH code running serially in a CPU is proposed to solve wave equation. This is a wave propagating in a two-dimensional domain. After finishing the computation, the results are compared with the theoretical solutions and they agree well. So its feasibility is verified. There are two main methods for searching neighbor particles: all-pair search method and linked-list search method. Both methods are used in different codes to simulate an identical problem and their runtimes are compared to investigate their searching efficiencies. The runtime results show that linked-list search method has a higher efficiency, which can save a lot of searching time when simulating problems with huge amounts of particles. Furthermore, the percentages of different procedures’ runtimes in a simulation are also discussed to find the most consuming one. Then, some codes are modified to run in different GPUs and their runtimes are compared with those of serial ones on a CPU. Runtime results show that the paralleled algorithm can be more than 80 times faster than the serial one. The result shows that GPU paralleled SPH computing can achieve desirable accuracy and speed in solving acoustic problems.

Embryonic development proceeds through a series of differentiation events. The mosaic version of this process (binary cell divisions) can be analyzed by comparing early development of Ciona intestinalis and Caenorhabditis elegans. To do this, we reorganize lineage trees into differentiation trees using the graph theory ordering of relative cell volume. Lineage and differentiation trees provide us with means to classify each cell using binary codes. Extracting data characterizing lineage tree position, cell volume, and nucleus position for each cell during early embryogenesis, we conduct several statistical analyses, both within and between taxa. We compare both cell volume distributions and cell volume across developmental time within and between single species and assess differences between lineage tree and differentiation tree orderings. This enhances our understanding of the differentiation events in a model of pure mosaic embryogenesis and its relationship to evolutionary conservation. We also contribute several new techniques for assessing both differences between lineage trees and differentiation trees, and differences between differentiation trees of different species. The results suggest that at the level of differentiation trees, there are broad similarities between distantly related mosaic embryos that might be essential to understanding evolutionary change and phylogeny reconstruction. Differentiation trees may therefore provide a basis for an Evo-Devo Postmodern Synthesis.

The usage of Quantum Similarity through the equation Z = {∀θ ∈ Z → ∃s ∈ S ∧ ∃t ∈ T : θ = (s, t)}, represents a way to analyze the way communication works in our DNA. Being able to create the object set reference for z being (s, t) in our DNA strands, we are able to set logical tags and representations of our DNA in a completely computational form. This will allow us to have a better understanding of the sequences that happen in our DNA. With this approach, we can also utilize mathematical formulas such as the Euler–Mascheroni constant, regression analysis, and computational proofs to answer important questions on Quantum biology, Quantum similarity, and Theoretical Physics.

In recent years, applying deep learning to solve physics problems has attracted much attention. Data-driven deep learning methods produce operators that can learn solutions to the whole system of partial differential equations. However, the existing methods are only evaluated on simple flow equations (e.g., Burger's equation), and only consider the generalization ability on different initial conditions. In this paper, we construct CFDBench, a benchmark with four classic problems in computational fluid dynamics (CFD): lid-driven cavity flow, laminar boundary layer flow in circular tubes, dam flows through the steps, and periodic Karman vortex street. Each flow problem includes data with various boundary conditions, fluid physical properties, and domain geometries. Compared to existing datasets, the advantages of CFDBench are (1) comprehensive. It contains common physical parameters such as velocity, pressure, and cavity fraction. (2) realistic. It is very suitable for deep learning solutions of fluid mechanics equations. (3) challenging. It has a certain learning difficulty, prompting to find models with strong learning ability. (4) standardized. CFDBench facilitates a comprehensive and fair comparison of different deep learning methods for CFD. We make appropriate modifications to popular deep neural networks to apply them to CFDBench and enable the accommodation of more changing inputs. The evaluation on CFDBench reveals some new shortcomings of existing works and we propose possible directions for solving such problems.

Computational Fluid Dynamics (CFD)-based simulation has been the traditional way to model complex industrial systems and processes. One very large and complex industrial system that has benefited from CFD-based simulations is the steel blast furnace. The problem with the CFD-based simulation approach is that it tends to be very slow to generate data. The CFD-only approach may not be fast enough for use in real-time decision-making. To address this issue, in this work, the authors propose the use of machine learning techniques to train and test models based on data generated via CFD simulation. Regression models based on neural networks are compared to tree boosting models. In particular, several areas (tuyere, raceway, and shaft) of the blast furnace are modeled using these approaches. The results of the model training and testing are presented and discussed. The obtained R2 metrics are, in general, very high. The results look promising and may help to improve the efficiency of operator and process engineer decision-making when running a blast furnace.

Backgroumd: The feeling of nasal obstruction is one of the most complaints of the Ear Nose and Throats (ENT) patients. The reason of this complaint is variable, such as Nasal Septal Deviation (NSD). NSD is a significant obstacle to normal respiration and the volume of air entering the lungs. Understanding how the deviation causes the obstruction is so important, because it leads to better management of this disease. Rhinomanometry and acoustic rhinometry are methods that are used for objective evaluation of upper airway, but they are semi invasive and the accuracy are not guaranteed. With development of Computed Tomography (CT scan) and Computational Fluid Dynamics (CFD), numerical studies on airflow in different parts of the nasal cavity have been performed. Objectives: The purpose of this study was to compare nasal airflow patterns between patient with NSD and healthy nasal cavity using a computational fluid dynamics (CFD) Methods: A patient with NSD and a healthy human were selected. Using CFD, the maximal airflow velocity, nasal resistance, maximal Wall Shear Stress (WSS), and pressure drop in bilateral nostrils of both cases were assessed. Results: Pressure and velocity profiles are evaluated at a mass flow rate of 17.4 Liters Per Minute (LPM). The velocity profile shows an abnormal flow profile in the septal deviated nasal cavity and the peak velocity is observed at the middle nasal region, whereas this point is at the nasal valve level in a healthy nasal cavity. Wall shear stress (WSS) caused by NSD is lower than in normal nasal cavities. The pressure drop in a nasal cavity with deviated septum is higher than in a healthy nasal cavity. Based on the results of this investigation nasal resistance in NSD was higher than in normal, healthy nasal cavity. Conclusions: NSD plays an important role in nasal airflow regime and it results in the feeling of obstruction comparing to normal nasal cavity. Also there is a promising future for CFD to become a useful tool in understanding airflow physiology and pathology.

Aim: Streptococcus pneumoniae and influenza H1N1 virus are common organisms associated with human infections. These infections could play a significant role in immune regulation. The study was performed to analyse the genome sequences of these organisms with human genome and study its functional significance. Methods: The study was performed to analyse the overlapping of genome sequences in Streptococcus pneumoniae and Influenza (H1N1) virus against human genome sequences by BLASTn sequence analysis. The alignments are studied against the corresponding genes for their functional significance with DAVID and NDEx software.Results: Several hits or overlapping nucleotide segments were identified. Between streptococcus and homo sapiens 287 overlaps were identified, and among influenza and homo sapiens 124 hits were identified. A wide range of functional significance of these genes were identified, and the results are presented in this study. The results show insights into functional pathways and biological activities associated with the respective vaccinations or infections by these microorganisms. Conclusion: The common organisms like Streptococcus pneumoniae and Influenza H1N1 virus actively interact with the immune system and result in a wide range of immune regulations.

Cross flow heat exchangers are commonly used in the thermal industry to transfer heat from hot tubes to cooling fluid. To protect the heat exchanger tubes from corrosion and dust accumulation, microscale coatings are often applied. In this study, we present machine-learning models for predicting heat transfer from hot tubes with different micro-sized coatings to cooling fluid in a turbulent flow using computational fluid dynamics simulations. A dataset of approximately 1000 cases was generated by varying the coating coverage thickness of each tube, the inlet Reynolds number, fluid flow inlet temperature, and wall temperature of tubes. The machine-learning models were generated to predict the overall heat flow rate in the heat exchanger, and it was found that combining the features based on their importance preserved the accuracy of the models while maintaining all the relevant information. The simulation results demonstrate that the proposed method increases the coefficient of determination (R2) for the models. The R2 values for unseen data for Random Forest, K-Nearest Neighbors, and Support Vector Regression were 0.9810, 0.9037, and 0.9754, respectively, indicating the usefulness of the proposed model for predicting heat transfer in various types of heat exchangers.

Modern computational biology makes widespread use of mathematical models of biological systems, in particular systems of ordinary differential equations, as well as models of dynamic systems described in other formalisms, such as agent-based models. Parameters are numerical values of quantities reflecting certain properties of a modeled system and affecting model solu-tions. At the same time, depending on parameter values, different dynamic regimes - stationary, oscillatory, established as a result of transient modes of various types - can be implemented in the system. Predicting changes in the solution dynamics type depending on changes of model parameters is an important scientific task. Nevertheless, this problem does not have an analytical solution for all formalisms in a general case. The routinely used method of performing a series of computa-tional experiments, i.e. solving a series of direct problems with various sets of parameters fol-lowed by expert analysis of solution plots is labor-intensive with a large number of parameters and a decreasing step of the parametric grid. In this regard, the development of methods allow-ing to obtain and analyze information on a set of computational experiments in an aggregate form is relevant. This work is devoted to developing a method for visualization and classification of various dy-namic regimes of a model using a composition of the dynamic time warping (DTW-algorithm) and principal coordinates analysis (PCoA) methods. This method allows to obtain a qualitative visualisation of the results of the set of solutions of a mathematical model and to carry out the correspondence between the values of the model parameters and the type of dynamic regimes of its solutions. This method has been tested on the Lotka-Volterra model and artificial sets of var-ious dynamics

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.

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.

The chemical graph theory is a subfield of mathematical chemistry which applies classic graph theory to chemical entities and phenomena. Chemical graphs are main data structures to represent chemical structures in cheminformatics. Computable properties of graphs lay the foundation for (quantitative) structure activity and structure property predictions - a core discipline of cheminformatics. It has a historic relevance for natural sciences, such as chemistry, biochemistry and biology, and is in the heart of modern disciplines, such as cheminformatics and bioinformatics. This review first covers the history of chemical graph theory, then provides an overview of its various techniques and applications for CASE, and finally summarises modern tools using chemical graph theory for CASE.

Dynamical system tools offer a complementary approach to detailed biophysical seizure modeling, with a high potential for clinical applications. This review describes the theoretical framework that provides a basis for theorizing certain properties of seizures and for their classification according to their dynamical properties at onset and offset. We describe various modeling approaches spanning different scales, from single neurons to large-scale networks. This narrative review provides an accessible overview of this field, including non-exhaustive examples of key recent works.

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.

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.

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.

Background: The antimalarial drug chloroquine and antimicrobial drug azithromycin have received significant attention during the current COVID-19 pandemic. Both drugs can alter cardiac electrophysiology and have been associated with drug-induced arrhythmias. Meanwhile, sympathetic activation is commonly observed during systemic inflammation and oxidative stress (e.g., in SARS-CoV-2 infection), and may influence the electrophysiological effects of chloroquine and azithromycin. Here, we investigated the effect of beta-adrenergic stimulation on proarrhythmic properties of chloroquine and azithromycin using a detailed in silico model of ventricular electrophysiology. Methods: Concentration-dependent chloroquine and azithromycin-induced alterations in ion-channel function were incorporated into the Heijman canine ventricular cardiomyocyte model. Single and combined drug effects on action-potential (AP) properties were analyzed using a population of 592 models accommodating inter-individual variability. Sympathetic stimulation was simulated by an increase in pacing rate and experimentally validated isoproterenol-induced changes in ion-channel function. Results: At 1 Hz pacing, therapeutic doses of chloroquine and azithromycin (5 and 20 µM, respectively) individually prolonged AP duration (APD) by 33% and 13%. Their combination produced synergistic APD prolongation (+161%) with incidence of proarrhythmic early afterdepolarizations in 53.5% of models. Increasing the pacing frequency to 2 Hz shortened APD and together with 1 µM isoproterenol corrected the drug-induced APD prolongation. No afterdepolarizations occurred following increased rate and simulated application of 0.1-1 µM isoproterenol. Conclusion: Sympathetic stimulation limits chloroquine- and azithromycin-induced proarrhythmia by reducing their APD-prolonging effect, suggesting the importance of heart rate and autonomic status monitoring in particular conditions (e.g., COVID-19).

Causal molecular interactions represent key building blocks used in computational modeling, where they facilitate the assembly of regulatory networks. These regulatory networks can then be used to predict biological and cellular behavior by system perturbations and in silico simulations. Today, broad sets of these interactions are being made available in a variety of biological knowledge resources. Moreover, different visions, based on distinct biological interests, have led to the development of multiple ways to describe and annotate causal molecular interactions. Therefore, data users can find it challenging to efficiently explore resources of causal interaction and to be aware of recorded contextual information that ensures valid use of the data. This manuscript presents a review of public resources collecting causal interactions and the different views they convey, together with a thorough description of the export formats established to store and retrieve these interactions. Our goal is to raise awareness amongst the targeted audience, i.e., logical modelers, but also any scientist interested in molecular causal interactions, about existing data resources and how to get familiar with them.

The growth and dynamics of multicellular tissues involve tightly regulated and coordinated morphogenetic cell behaviours, such as shape changes, movement, and division, which are governed by subcellular machinery and involve coupling through short- and long-range signals. A key challenge in the fields of developmental biology, tissue engineering and regeneration is to understand how relationships between scales produce emergent tissue-scale behaviours. Recent advances in molecular biology, live-imaging and ex vivo techniques have revolutionised our ability to study these processes experimentally. To fully leverage these techniques and obtain a more comprehensive understanding of the causal relationships underlying tissue dynamics, computational modelling approaches are increasingly spanning multiple spatial and temporal scales, and are coupling cell shape, growth, mechanics and signalling. Yet such models remain technically challenging: modelling at each scale requires different areas of technical skills, while integration across scales necessitates the solution to novel mathematical and computational problems. This review aims to summarise recent progress in multiscale modelling of multicellular tissues and to highlight ongoing challenges associated with the construction, implementation, interrogation and validation of such models.

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.

Integrated information theory (IIT) proposes a measure of integrated information (Φ) to capture the level of consciousness for a physical system in a given state. Unfortunately, calculating Φ itself is currently only possible for very small model systems, and far from computable for the kinds of systems typically associated with consciousness (brains). Here, we consider several proposed measures and computational approximations, some of which can be applied to larger systems, and test if they correlate well with Φ. While these measures and approximations capture intuitions underlying IIT and some have had success in practical applications, it has not been shown that they actually quantify the type of integrated information specified by the latest version of IIT. In this study, we evaluated these approximations and heuristic measures, based not on practical or clinical considerations, but rather based on how well they estimate the Φ values of model systems. To do this, we simulated networks consisting of 3–6 binary linear threshold nodes randomly connected with excitatory and inhibitory connections. For each system, we then constructed the system’s state transition probability matrix (TPM), as well as its state transition matrix (STM) over time for all possible initial states. From these matrices, we calculated, approximations to Φ, and measures based on state differentiation, state entropy, state uniqueness, and integrated information. All measures were correlated with Φ in a state dependent and state independent manner. Our findings suggest that Φ can be approximated closely in small binary systems by using one or more of the readily available approximations (r > 0.95), but without major reductions in computational demands. Furthermore, Φ correlated strongly with measures of signal complexity (LZ, r_s = 0.722), decoder based integrated information (Φ*, r_s = 0.816), and state differentiation (D1, r_s = 0.827), on the system level (state independent). These measures could allow for efficient estimation of Φ on a group level, or as accurate predictors of low, but not high, Φ systems. While it’s uncertain whether the results extend to larger systems or systems with other dynamics, we stress the importance that measures aimed at being practical alternatives to Φ are at a minimum rigorously tested in an environment where the ground truth can be established.

Topological Data Analysis (TDA) refers to a collection of methods that find the structure of shapes in data. Although recently, TDA methods have been used in many areas of data mining, it has not been widely applied to text mining tasks. In most text processing algorithms, the order in which different entities appear or co-appear is being lost. Assuming these lost orders are informative features of the data, TDA may play a significant role in the resulted gap on text processing state of the art. Once provided, the topology of different entities through a textural document may reveal some additive information regarding the document that is not reflected in any other features from traditional text processing methods. In this paper, we introduce a novel approach that hires TDA in text processing in order to capture and use the topology of different same-type entities in textural documents. First, we will show how to extract some topological signatures in the text using persistent homology-i.e., a TDA tool that captures topological signature of data cloud. Then we will show how to utilize these signatures for text classification.

Three-dimensional (3D) imaging has attracted more and more interests because of its widespread applications, especially in information and life science. These techniques can be broadly divided into two types: ray-based and wavefront-based 3D imaging. Issues such as imaging quality and system complexity of these techniques limit the applications significantly, and therefore many investigations have focused on 3D imaging from depth measurements. This paper presents an overview of 3D imaging from depth measurements, and provides a summary of the connection between these the ray-based and wavefront-based 3D imaging techniques.

The concept of smart morphing blades, which can control themselves to reduce or eliminate the need for active control systems, is a highly attractive solution in blade technology. In this paper an innovative passive control system based on Shape Memory Alloys (SMAs) is proposed. On the basis of previous thermal and shape characterization of a single morphing blade for a heavy-duty automotive cooling axial fan, this study deals with the numerical analysis of the aerodynamic loads acting on the fan. By coupling CFD and FEM approaches it is possible to analyze the actual blade shape resulting from both the aerodynamic and centrifugal loads. The numerical results indicate that the polymeric blade structure ensures proper resistance and enables shape variation due to the action of the SMA strips.

Brain is the most complex organ in the human body and it is divided into two hemispheres - left and right hemispheres. Left hemisphere is responsible for control of right side of our body whereas right hemisphere is responsible for control of left side of our body. Brain image segmentation from different neuroimaging modalities is one of the important parts in clinical diagnostic tools. Neuroimaging based digital imagery generally contain noise, inhomogeneity, aliasing artifacts, and orientational deviations. Therefore, accurate segmentation of brain images is a very difficult task. However, the development of accurate segmentation of brain images is very important and crucial for a correct diagnosis of any brain related diseases. One of the fundamental segmentation tasks is to identify and segment inter-hemispheric fissure/mid-sagittal plane, which separate the two hemispheres of the brain. Moreover, the symmetric/asymmetric analyses of left and right hemispheres of brain structures are important for radiologists to analyze diseases such as Alzheimer's, Autism, Schizophrenia, Lesions and Epilepsy. Therefore, in this paper we have analyzed the existing computational techniques used to find brain symmetric/asymmetric analysis in various neuroimaging techniques (MRI/CT/PET/SPECT), which are utilized for detecting various brain related disorders.

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.

Potentilla nepalensis belongs to the Rosaceae family, and has numerous therapeutic applications as potent plant-based medicine. Forty phytoconstituents (PCs) from the root and stem through n-hexane (NR and NS) and methanolic (MR and MS) extracts were identified in our earlier studies. However, the PCs affecting human genes and their roles in the body are not disclosed till now. In this study, we employed network pharmacology, molecular docking, molecular dynamics simulations (MDS), and MMGBSA methodologies. SMILES format of PCs from the PubChem used as input to DIGEP-Pred, 764 identified as the inducing genes. Their enrichment studies have shown inducing genes gene ontology descriptions, involved pathways, associated diseases, and drugs. PPI networks constructed in String DB and network topological analysing parameters done in Cytoscape v3.10 revealed three biomarkers, TP53 from MS, NR, and NS induced genes; HSPCB and Nf-kB1 from MR induced genes. From 40 PCs, two PCs 1b (MR) and 2a (MS), showed better binding scores (kcal/mol) with p53 protein of -8.6, and -8.0; three PCs 3a, (NR) 4a and 4c (NS) with HSP protein of -9.6, -8.7, and -8.2. MDS and MMGBSA revealed these complexes are stable without higher deviations with better free energy values. Biomarkers identified in this study, have a prominent role in numerous cancers. Thus, further investigations such as in-vivo and in-vitro should be done to find the molecular functions and interlaying mechanism of the identified biomarkers on numerous cancer cell lines in considering the PCs of P.nepalensis.

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.

Traditional numerical techniques such as sliding mesh, dynamic grid mesh, and others, have many limitations in dealing with flow simulation with large-scale movement of solid boundaries; which is the case for complex-shaped hydraulic turbomachinery such as propellers, pumps and turbines. The immersed boundary (IB) method provides a new approach to solve the above limitations. Therefore, this study proposes an sharp-interface IB method based on the level-set function that is suitable for simulating the flow through turbomachinery with complex geometries. This method is applied to actual three-dimensional numerical simulations of high-Reynolds number propellers using an in-house computational fluid dynamics solver. The results show that the proposed method can provide comparatively accurate predictions of unsteady load coefficients within the propeller flow passage, and capture the correct propeller wake characteristics as well as the interaction between the propeller wake and free surface. This study aims at providing a theoretical basis and engineering reference for the application of the IB method in engineering numerical simulations.

Drag-dominant tidal turbine energy holds tremendous clean energy potential but faces significant hurdles as unsuitability of Disk Actuator theory due to the varying swept blockage area, unaccounted bypass flow downstream interaction and rotor parasitic drag whereas Blade Element Momentum theory is computably effective for majorly 3-blade lift-dominated aerofoil. This study proposes a novel method to find the optimal TSR of any turbine with a cost-effective and user-friendly Moment Balancing algorithm to support robust tidal energy development. Performance analysis CFD study of Pinwheel and Savonius tidal turbines was carried out. Dynamic TSR matrix was developed with varying rotational speeds and fluid velocities for reliability, unlike previous works simulated at a fixed fluid velocity. Novel parameters such as thrust and idle moment are introduced as functions of only inlet fluid velocity and rotational speed respectively. These relationships are verified through regression analysis, and the turbines' net moment equations are established based on these parameters. Rotational speed was a reliable predictor for Pinwheel's idle moment, while inlet velocity was a reliable predictor for thrust moment in both models. The optimal (Cp, TSR) values for Pinwheel and Savonius turbines were (2.37, 0.223) and (0.63, 0.16) respectively, within an acceptable error range for experimental validation.

Unsmooth reversing is one of the most common faults in the four-way reversing valve of air conditioning system, and the airflow in the valve chamber and the shape of the slider of the reversing valve are the main factors in unsmooth reversing. In order to study the influence of the airflow in the chamber and the slider shape on the reversing process, the fluid flow in the valve chamber of a four-way reversing valve is obtained using computational fluid dynamics (CFD) simulations, and the influence of slider structure on slider thrust and resistance of the four-way reversing valve is analyzed. Four-way reversing valves with no-cutting, straight-cutting and arc-cutting sliders are employed to evaluate the reversing characteristics. A pressure measuring device for a four-way reversing valve chamber is designed, which is performed to test the chamber pressure of three different types of sliders of four-way reversing valves. The maximum error of experimental tests and simulations is within 5% of engineering tolerance, so as to verify the reliability of numerical simulation. The results indicate that the chamber pressure and resistance-thrust ratio with the cutting slider are reduced, which is beneficial to the reversing of the four-way reversing valve. Compared with the straight cutting structure, the arc cutting slider four-way reversing valve has a more stable reversing process and better comprehensive reversing performance. The results can provide a theoretical basis for engineers to improve the performance of four-way reversing valves.

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.

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.

Scattering has been always considered a problem in most of the imaging and holography systems. In this project, a 3D imaging system has been developed based on scattering against common beliefs. The 3D imaging system consists of only two components namely a scattering lens, fabricated by grinding the surface of a convex lens using sandpaper and a web camera. The point spread function (PSF) in the form of speckle distribution was recorded using a laser source in the first step. A synthetic object was selected which was convolved with the PSF in a computer to generate the object intensity distribution. The image of the object was reconstructed by processing the PSF and object intensity distribution using a computational reconstruction method called non-linear reconstruction. The recorded PSF was scaled and the process was repeated for a different synthetic object. The concept was extended to 3D by summing the object intensity distributions generated using PSFs with different scaling factors. The image at different planes can be reconstructed using the PSFs corresponding to that plane.

The worldwide outbreak of SARS-CoV-2 in early 2020 caused numer- ous deaths and unprecedented measures to control its spread. We employed our Computational Analysis of Novel Drug Opportunities (CANDO) multiscale therapeutic discovery, repurposing, and design platform to identify small molecule inhibitors of the virus to treat its resulting indication, COVID-19. Initially, few experimental studies existed on SARS-CoV-2, so we optimized our drug candidate prediction pipelines using results from two independent high-throughput screens against prevalent human coronaviruses. Ranked lists of candidate drugs were generated using our open source cando.py software based on viral protein inhibition and proteomic interaction similarity. For the former viral protein inhibition pipeline, we computed interaction scores between all compounds in the corresponding candidate library and eighteen SARS-CoV proteins using an interaction scoring protocol with extensive parameter optimization which was then applied to the SARS-CoV-2 proteome for prediction. For the latter similarity based pipeline, we computed interaction scores between all compounds and human protein structures in our libraries then used a consensus scoring approach to identify candidates with highly similar proteomic interaction signatures to multiple known anti-coronavirus actives. We published our ranked candidate lists at the very beginning of the COVID-19 pandemic. Since then, 51 of our 276 predictions have demonstrated anti-SARS-CoV-2 activity in published clinical and experimental studies. These results illustrate the ability our platform to rapidly respond to emergent pathogens and provide greater evidence that treating compounds in a multitarget context more accurately describes their behavior in biological systems.

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.

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.

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.

Heart attacks and strokes are one of the leading causes of death in the world today, and heart attacks caused by clogged arteries that carry blood to the heart muscle are a significant part of these strokes. These are caused by the accumulation of fat particles in the walls of the arteries and the reduction of blood flow through it over a long process. The process of fat penetration in the underlying layers of the Artery wall has been the focus of many researchers, and various researches and Simulations have been done on it, in each of them, the effect of specific parameters has been considered. In the present study, the effect of blood flow rate on the flow pattern in a bifurcate artery with two ducts has been investigated using FLUENT software with Computation fluid dynamic Method. The effect of the angle between the two ducts of the Artery on the flow pattern has been investigated.

The current need to develop sustainable power sources has led to the development of ocean-based conversion systems. Wells turbine is a widely used converter in such systems which suffers from a lack of operational range and power production capacity under operational conditions. The profile named IFS which is concave in the post-mid-chord region, can produce significantly larger lift forces and show better separation behavior than the NACA profiles. In the present study, we tested this profile for the first time in a Wells turbine. The performance of six different blade designs with IFS and NACA profiles were evaluated and compared using a validated computational fluid dynamic model. Although the substitution of the NACA profile with the IFS profile in all cases increased the torque generated, the most efficient power generation and the largest efficient range were achieved in the design with varying thickness from the hub with a 0.15 thickness ratio reaching to the ratio of 0.2 at the tip. The operational span of this design with the IFS profile was 24.1% greater and the maximum torque generation was 71% higher than the case with the NACA profile. Therefore, the use of the IFS profile is suggested for further study and practical trials.

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.

In the pre era of synthetic antibodies, pharmaceutical companies depend on finding novel drugs from medicinal plants and other traditional resources; while in present, technological advances in biology, computer and robotics give the researchers the ability to rewrite and edit DNA in order to synthesize very large sets of drug candidates; these novel and improved candidates serves the basis for creating another library of drug candidates and so on until we find the right biomolecule for the disease of interest. all these technologies combined together to synthesize therapeutic antibodies for many types of cancer, autoimmune diseases, and infectious diseases, that can address diseases much more readily to very rapidly get therapeutics into patients so that we can potentially have an impact on disease. The antibodies mechanism is recognize and bind to disease cells and pinpoint the immune system to attack those cells effectively. Now a days, they dependent on computational approach to guide and accelerate the process of antibodies engineering by combination of selection system and use of high-throughput data acquisition and analysis to build and construct populations of next generation antibodies that are thermo-stable, non-immunogenic as possible, and to be administered to many humans as possible. In this review, I will discuss the latest in silico methods for antibodies engineering.

Electromyographic (EMG) signals provide information about a person's muscle activity. For hand movements, in particular, the execution of each gesture involves the activation of different combinations of the forearm muscles, which generate distinct electrical patterns. Conversely, the analysis of these muscle activation patterns, represented by EMG signals, allows recognizing which gesture is being performed. In this study, we aimed to implement an automatic identification system of hand or wrist gestures based on supervised Machine Learning (ML) techniques. We trained different computational models and determined which of these showed the best capacity to identify six hand or wrist gestures and generalize between different subjects. We used an open access database containing recordings of EMG signals from 36 subjects. Among the results obtained, we highlight the performance of the Random Forest model, with an accuracy of 95.39%, and the performance of a convolutional neural network with an accuracy of 94.77%.