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

To investigate the optimum layouts of small vertical axis wind turbines, a two-dimensional analysis of dynamic fluid body interaction is performed via computational fluid dynamics for a rotor pair in various configurations. The rotational speed of each turbine rotor (diameter: D = 50 mm) varies based on the equation of motion. First, the dependence of rotor performance on the gap distance (gap) between two rotors is investigated. For parallel layouts, counter-down (CD) layouts with blades moving downwind in the gap region yield a higher mean power than counter-up (CU) layouts with blades moving upwind in the gap region. CD layouts with gap/D = 0.5–1.0 yield a maximum average power that is 23% higher than that of an isolated single rotor. Assuming isotropic bidirectional wind speed, co-rotating (CO) layouts with the same rotational direction are superior to the combination of CD and CU layouts regardless of the gap distance. For tandem layouts, the inverse-rotating configuration (IR) shows an earlier wake recovery than the CO configuration. For 16-wind-direction layouts, both the IR and CO configurations indicate similar power distribution at gap/D = 2.0. For the first time, this study demonstrates the phase synchronization of two rotors via numerical simulation.

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.

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

Fog computing is a potential solution to overcome the shortcomings of the cloud computing processing of IoT tasks. These drawbacks can be high latency, location awareness and security, and it is attributed to the distance between IoT devices and servers, network congestion and other variables. Although fog computing has evolved as a solution to these challenges, it is known for having limited resources that need to be consciously utilised, or any of its ad-vantages would be lost. Computational offloading and resource management are critical concerns to be considered to get maximum benefit of the available resource at fog computing systems and benefit from its advantages. Computational offloading and resource management are important issues to be considered to get maximum benefit of the available resource at fog computing systems and benefit from its advantages. In this article, in vehicular traffic applications, we introduce a dynamic online offloading scheme that involves the execution of delay-sensitive ac-tivities. This paper proposes an architecture of a fog node that enables a fog node to adjust its offloading threshold dynamically (i.e., the criteria by which a fog node decides whether tasks should be offloaded rather than executed locally) using two algorithms: dynamic task scheduling (DTS) and dynamic energy control (DEC). These algorithms seek to solve an optimisation problem aimed at minimising overall delay, improving throughput, and minimising energy consumption at the fog layer, while maximising the use of resource-constrained fog nodes. Compared with other benchmarks, our approach can reduce the delay by up to 95.38% and reduce energy consumption by up to 67.71% in fog nodes. Additionally, this approach enhances throughput by 71.08%.

The epithelial-mesenchymal (E/M) hybrid state has emerged as an important mediator of elements of cancer progression, facilitated by epithelial mesenchymal plasticity (EMP). We review here evidence for the presence, prognostic significance, and therapeutic potential of the E/M hybrid state in carcinoma. We further assess modelling predictions and validation studies to demonstrate stabilised E/M hybrid states along the spectrum of EMP, as well as computational approaches for characterising and quantifying EMP phenotypes, with particular attention to the emerging realm of single-cell approaches through RNA sequencing and protein-based techniques.

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.

RAS oncogenes are amongst the most commonly mutated proteins in human cancers. They regulate a wide range of effector pathways that control cell proliferation, survival, differentiation, migration and metabolic status. Including aberrations in these pathways, RAS dependent signaling is altered in more than half of human cancers. Targeting mutant RAS proteins and their downstream oncogenic signaling pathways has been elusive. However, recent results comprising detailed molecular studies, large scale omics studies and computational modeling have painted a new and more comprehensive portrait of RAS signaling that helps us to understand the intricacies of RAS, how its physiological and pathophysiological functions are regulated, and how we can target them. Here, we review these efforts particularly trying to relate the detailed mechanistic studies with global functional studies. We highlight the importance of computational modeling and data integration to derive an actionable understanding of RAS signaling that will allow us to design new mechanism based therapies for RAS mutated cancers.

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

This paper presents a discrete compartmental Susceptible-Exposed-Infected-Recovered/Dead (SEIR/D) model to address the expansion of Covid-19 pandemic. When time passes, the status of the cells is determined by binary rules that update following both a neighbourhood and a delay pattern. The model assumes the environmental parameters have a crucial impact on the expansion of the disease so a grid is assigned to each parameter to model the single effect caused by this parameter. The expansion is then the weighted sum of all the grids. This proposal shows how the grid architecture, along with an update rule and a neighbourhood pattern is a valuable tool to model the pandemic expansion. This model has already been analyzed in previous works and compared with the corresponding continuous models solved by ordinary differential equations (ODE), coming to find the homologous parameters between both approaches. Thus, it has been possible to prove that the combination neighborhood-update rule is responsible for the rate of expansion and recovering/death of the illness. The delays (between Susceptible and Asymptomatic, Asymptomatic and Infected, Infected and Recovered/Dead) may have a crucial impact on both the peak of Infected and the Recovery/Death rate. This theoretical model has been successfully tested in the case of the dissemination of information through mobile social networks and in the case of plant pests.

Consumer products contain the chemical substances that threaten human health. The modeling methods and experimental methods have been used to estimate the inhalation exposure concentration by the consumer products. The model and measurement methods have the spatial property problem and time/cost consuming problem, respectively. For solving the problems due to the conventional methodology, this study performed the feasibility of applying CFD for evaluation of inhalation exposure by comparing the experiment results and the zero-dimensional results with CFD results. To calculate the aerosol concentration, the CFD was performed by combined the 3D Reynolds averaged Navier Stoke’s equation and discrete phased model using ANSYS FLUENT. As a result of comparing the three methodologies performed under the same simulation/experimental conditions, we found the zero-dimensional spray model shows approximately 5 times underestimated inhalation exposure concentration when compared with the CFD results and measurement results in near field. Also, the results of the measured concentration of aerosols at five locations and the CFD results at the same location were compared to show the possibility of evaluating inhalation exposure at various locations using CFD instead of experimental method. The CFD results according to measurement positions can predict rationally the measurement results with low error. In conclusion, in the field of exposure science, a guideline for exposure evaluation using CFD was found that complements the shortcomings of the conventional methodology, the zero-dimensional spray model and measurement method.

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

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

Many cellular functions important for tumor initiation and progression are mediated by members of the integrin family, a diverse family of cell adhesion receptors. With recent studies emphasising on the role of the tumor microenvironment (TME) in tumor initiation and progression, it is not surprising that a lot of attention is being given to integrins. Several integrins are under trial with many demonstrating appealing activity in patients with different cancers. A deeper knowledge of the functions of integrins within the tumor microenvironment is still required, and might lead to better inhibitors being discovered. Integrin expression is commonly dysregulated in many tumors with integrins playing key roles in signaling as well as promotion of tumor cell invasion and migration. This review report new data on the differential expression of integrins within solid tumors using two publicly available resources: The Cancer Genomic Atlas (TCGA) and Gene Expression Profiling Interactive Analysis (GEPIA). In this analysis, I investigated the expression of integrin alpha 2 (ITGα2), ITGα3, ITGβ4 and ITGβ6 in tumor tissues versus adjacent normal tissues. This analysis showed that integrins were differentially expressed in cervical squamous cell carcinoma (CESC), head and neck squamous cell carcinoma (HNSC), esophageal carcinoma (ESCA) and lung adenocarcinoma (LUAD). This analysis showed that ITGα2 and ITGβ6 expression are upregulated in CESC and ESCA, ITGα3 is upregulated in HNSC and ESCA whilst ITGβ4 is highly expressed in CESC, HNSC, ESCA and LUAD tumor tissues compared to adjacent normal tissues. Integrins also play a major role in adhesion of circulating tumor cells to new sites and the resulting formation of secondary tumors. Furthermore, integrins have demonstrated the ability to promoting stem cell-like properties in tumor cells as well as drug resistance. Anti-integrin therapies rely heavily on the doses or concentrations used as these determine whether the drugs act as antagonists or as integrin agonists. This review offers the latest synthesis in terms of current knowledge of integrins functions within the tumor microenvironment and potential targets for different cancers.

Genome sequencing is enabling precision medicine—tailoring treatment to the unique constellation of variants in an individual’s genome. The impact of recurrent pathogenic variants is often understood, leaving a long tail of rare genetic variants that are uncharacterized. The problem of uncharacterized rare variation is especially acute when it occurs in genes of known clinical importance with functionally consequent frequent variants and associated mechanisms. Variants of unknown significance (VUS) in these genes are discovered at a rate that outpaces current ability to classify them using databases of previous cases, experimental evaluation, and computational predictors. Clinicians are thus left without guidance about the significance of variants that may have actionable consequences. Computational prediction of the impact of rare genetic variation is increasingly becoming an important capability. In this paper, we review the technical and ethical challenges of interpreting the function of rare variants in two settings: inborn errors of metabolism in newborns, and pharmacogenomics. We propose a framework for a genomic learning healthcare system with an initial focus on early-onset treatable disease in newborns and actionable pharmacogenomics. We argue that (1) a genomic learning healthcare system must allow for continuous collection and assessment of rare variants, (2) emerging machine learning methods will enable algorithms to predict the clinical impact of rare variants on protein function, and (3) ethical considerations must inform the construction and deployment of all rare-variation triage strategies, particularly with respect to health disparities arising from unbalanced ancestry representation.

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

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

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

Fibroblasts, the most abundant cells in the connective tissue, are key modulators of the extracellular matrix (ECM) composition. These spindle-shaped cells are capable of synthesizing various extracellular matrix proteins and collagen. They also provide the structural framework (stroma) for tissues and play a pivotal role in the wound healing process. While they are maintainers of the ECM turnover and regulate several physiological processes, they can also undergo transformations responding to certain stimuli and display aggressive phenotypes that contribute to disease pathophysiology. In this review, we focus on the metabolic pathways of glucose and highlight metabolic reprogramming as a critical event that contributes to the transition of fibroblasts from quiescent to activated and aggressive cells. We also cover the emerging evidence that allows us to draw parallels between fibroblasts in autoimmune disorders and more specifically in rheumatoid arthritis and cancer. We link the metabolic changes of fibroblasts to the toxic environment created by the disease condition and discuss how targeting of metabolic reprogramming could be employed in the treatment of such diseases. Lastly, we discuss Systems Biology approaches, and more specifically, computational modelling, as a means to elucidate pathogenetic mechanisms and accelerate the identification of novel therapeutic targets.

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

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.

Microbes do not live in isolation but in microbial communities. The relevance of microbial communities is increasing due to the awareness about their biotechnological influences in a huge number of environmental, health and industrial processes. Hence, being able to control and engineer the output of both natural and synthetic communities would be of great interest. However, most of the available methods and biotechnological applications (both in vivo and in silico) have been developed in the context of isolated microbes. In vivo microbial consortia development, i.e. to reproduce the community life conditions in the wet-lab, is extremely difficult and expensive requiring of computational approaches to advance knowledge about microbial communities, mainly with descriptive modelling, and further with engineering modelling. In this review we provide a detailed compilation of available examples of engineered microbial communities as a launch pad for an exhaustive and historical revision of those computational methods devoted so far toward the better understanding, and rational engineering of natural and synthetic microbial communities.

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

The 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.

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

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.

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

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.

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

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

Computationally modelling a nuclear reactor startup core for a benchmark against the existing models is highly desirable for an independent assessment informing nuclear engineers and energy policymakers. This work presents a startup core model of the UK’s first Evolutionary Pressurised Water Reactor (EPR) based on Monte Carlo simulations of particle collisions using Serpent 2, a continuous-energy Monte Carlo reactor physics burnup code. Coupling between neutronics and thermal-hydraulic conditions with the fuel depletion is incorporated into the multi-dimensional branches, obtaining the thermal flux and fission rate (power) distributions radially and axially from the three dimensional (3D) single assembly level to a 3D full core. Shannon entropy is employed to characterise the convergence of the fission source distribution, with 3 billion neutron histories tracked by parallel computing. Source biasing is applied for the variance reduction. Benchmarking the proposed Monte Carlo 3D full-core model against the traditional deterministic transport computation suite used by the UK Office for Nuclear Regulation (ONR), a reasonably good agreement within statistics is demonstrated for the safety-related reactivity coefficients, which creates trust in the EPR safety report.

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

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.

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).

The 'big data revolution' has enabled novel types of analyses in the life sciences, facilitated by public sharing and reuse of datasets. Here, we review the prodigious potential of reusing publicly available datasets and the challenges, limitations and risks associated with it. Possible solutions to issues and research integrity considerations are also discussed. Due to the prominence, abundance and wide distribution of sequencing data, we focus on the reuse of publicly available sequence datasets. We define ‘successful reuse’ as the use of previously published data to enable novel scientific findings and use selected examples of such reuse from different disciplines to illustrate the enormous potential of the practice, while acknowledging their respective limitations and risks. A checklist to determine the reuse value and potential of a particular dataset is also provided. The open discussion of data reuse and the establishment of the practice as a norm has the potential to benefit all stakeholders in the life sciences.

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 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.

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.

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.

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

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

Solid tumors display complex biology and most therapies including chemotherapy cannot prevent therapy resistance and relapse. Most therapeutics target cancer cells, but recent data suggest the presence of cancer stem cells as cells with self-renewal and tumorigenic abilities. Cancer stem cell markers have been suggested to have prognostic value and can be targeted during cancer treatment and in resistant disease. CSCs have been postulated to play significant contextual roles in tumor initiation, progression, therapy resistance and metastasis. CSCs have thus been targeted by new generation cancer drugs. The transcriptional expression of several CSC markers in different cancers was evaluated by searching publicly available The Cancer Genome Atlas (TCGA) and Gene Expression Profiling Interactive Analysis (GEPIA) databases. We report here new findings on expression and prognostic significance of CSC markers in several cancers by examining the expression of CSCs markers in tumor tissues versus the adjacent normal tissues. We found that CSC markers were mostly highly expressed various tumors such as colon, lung, pancreatic and esophageal cancers. No CSC marker is expressed in the same pattern in all cancers and individual CSC marker expression was not linked to patient survival. This analysis calls for continued research on CSCs and clinical evaluation of the CSC markers in relation to prognosis of cancers in large population samples. Novel cancer drugs ought to target CSCs, cancer cells and tumor microenvironment variations.

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.

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%.

We construct a family of two-step optimal fourth order iterative methods for finding single root of non-linear equations. We generalize these methods to simultaneous iterative methods for determining all the distinct as well as multiple roots of single variable non-linear equations. Convergence analysis is present for both cases to show that the order of convergence is four in case of single root finding method and is twelve for simultaneous determination of all roots of non-linear equation. The computational cost, Basin of attraction, efficiency, log of residual and numerical test examples shows, the newly constructed methods are more efficient as compared to the existing methods in literature.

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.

Biomolecular structure drives function, and computational capabilities have progressed such that the prediction and computational design of biomolecular structures is increasingly feasible. Because computational biophysics attracts students from many different backgrounds and with different levels of resources, teaching the subject can be challenging. One strategy to teach diverse learners is with interactive multimedia material that promotes self-paced, active learning. We have created a hands-on education strategy with a set of fifteen modules that teach topics in biomolecular structure and design, from fundamentals of conformational sampling and energy evaluation to applications like protein docking, antibody design, and RNA structure prediction. Our modules are based on PyRosetta, a Python library that encapsulates all computational modules and methods in the Rosetta software package. The workshop-style modules are implemented as Jupyter Notebooks that can be executed in the Google Colaboratory, allowing learners access with just a web browser. The digital format of Jupyter Notebooks allows us to embed images, molecular visualization movies, and interactive coding exercises. This multimodal approach may better reach students from different disciplines and experience levels as well as attract more researchers from smaller labs and cognate backgrounds to leverage PyRosetta in their science and engineering research. All materials are freely available at https://github.com/RosettaCommons/PyRosetta.notebooks.

Metabolomics analysis generates vast arrays of data, necessitating comprehensive workflows involving expertise in analytics, biochemistry and bioinformatics, in order to provide coherent and high-quality data that enables discovery of robust and biologically significant metabolic findings. In this protocol article, we introduce NoTaMe, an analytical workflow for non-targeted metabolic profiling approaches utilizing liquid chromatography–mass spectrometry analysis. We provide an overview of lab protocols and statistical methods that we commonly practice for the analysis of nutritional metabolomics data. The paper is divided into three main sections: the first and second sections introducing the background and the study designs available for metabolomics research, and the third section describing in detail the steps of the main methods and protocols used to produce, preprocess and statistically analyze metabolomics data, and finally to identify and interpret the compounds that have emerged as interesting.

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.

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.

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.

As of today, 20 disease modifying drugs (DMD) have been approved for the treatment of relapsing multiple sclerosis (MS) and, based on their efficacy, they can be grouped into moderate-efficacy DMDs and high-efficacy DMDs. The choice of the drug mostly relies on the judgement and experience of neurologists and the evaluation of therapeutic response can only be obtained by monitoring clinical and magnetic resonance imaging (MRI) status during follow up. In an era where therapies are focused on personalization, the aim of this study is to develop a modeling infrastructure to predict the evolution of relapsing MS and the response to treatments. We built a computational modeling infrastructure named UISS (Universal Immune System Simulator) able to simulate the main features and dynamics of the immune system activities. We extended UISS to simulate all the underlying MS pathogenesis and its interaction with the host immune system. This simulator is a multi-scale, multi-organ, agent based simulator with an attached module capable of simulating the dynamics of specific biological pathways at the molecular level. We simulated six MS patients with different relapsing-remitting courses. These patients were characterized on the basis of their age, sex, presence of oligoclonal bands, therapy and MRI lesion load at onset. The simulator framework is made freely available and can be used following the links provided in the availability section. Even though the model can be further personalized employing immunological parameters and genetic information, based on the available data we generated a few simulation scenarios for each patient, including those who matched the real clinical and MRI history. Moreover, for two patients, the simulator anticipated the timing of subsequent relapses, which really occurred, suggesting that UISS may have the potential to assist MS specialists in predicting the course of the disease and the response to treatment.

Current therapeutic strategies targeting cancer cells within solid tumors have displayed limited success owing to the presence of non-cancer components referred to as the tumor stroma within the tumor microenvironment (TM). These stromal cells, extracellular matrix and blood vessels influence cancer cell response to therapy and play key roles in tumor relapse and resistance. Of the stromal cells present in the TM, a lot of attention has been given to cancer-associated fibroblasts (CAFs) as they are the most abundant and are important in cancer initiation, progression and therapy resistance. In this updated review I emphasize the role of CAFs in the regulation of tumor cell behaviour and reveal how CAF-derived factors and signaling influence tumor cell heterogeneity and development of novel strategies to combat cancer. To investigate the expression of CAF markers in tumor tissues versus normal tissues, transcriptomic data from The Cancer Genome Atlas (TCGA) and the Gene Expression Profiling Interactive Analysis (GEPIA) databases was used. Bioinformatic analysis reveals differential expression of CAF markers in several cancer types, underscoring the need for further multiomics and biochemical studies on CAFs, CAF subsets and markers. Differences in CAF markers’ expression could be due to different cellular origins as well as the effect of cancer-specific tumor microenvironmental effect on CAFs. Lastly, I present recent advances in therapeutic targeting of CAFs and the success of such endeavours or its lack thereof. It is recommended that for patients’ outcomes to improve, cancer treatment be combinatorial in nature, targeting both cancer cells and stromal cells and interactions.

In order to perceive the behavior presented by the multiphase chemical reactors, the ant colony optimization algorithm was combined with computational fluid dynamics (CFD) data. This intelligent algorithm creates a probabilistic technique for computing flow and it can predict various levels of three-dimensional bubble column reactor (BCR). This artificial ant algorithm is mimicking real ant behavior. This method can anticipate the flow characteristics in the reactor using almost 30 % of the whole data in the domain. Following discovering the suitable parameters, the method is used for predicting the points not being simulated with CFD, which represent mesh refinement of Ant colony method. In addition, it is possible to anticipate the bubble-column reactors in the absence of numerical results or training of exact values of evaluated data. The major benefits include reduced computational costs and time savings. The results show a great agreement between ant colony prediction and CFD outputs in different sections of the BCR. The combination of ant colony system and neural network framework can provide the smart structure to estimate biological and nature physics base phenomena. The ant colony optimization algorithm (ACO) framework based on ant behavior can solve all local mathematical answers throughout 3D bubble column reactor. The integration of all local answers can provide the overall solution in the reactor for different characteristics. This new overview of modelling can illustrate new sight into biological behavior in nature.

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.

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.

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

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

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

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

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

The 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.

Small molecule inhibitors of adipocyte fatty-acid binding protein 4 (FABP4) have got interest following the recent publication of their pharmacologically beneficial effects. Recently it comes out that FABP4 is an attractive molecular target for the treatment of type 2 diabetes, other metabolic diseases, and some type of cancers. In the past years, hundreds of effective FABP4 inhibitors have been synthesized and discovered but, unfortunately, none of them is in the clinical research phase. The field of computer-aided drug design seems to be promising and useful for the identification of FABP4 inhibitors; hence, different structure- and ligand-based computational approaches were already performed for their identification. In this paper, we searched for new potentially active FABP4 ligands in the Marine Natural Products (MNP) database. 14,492 compounds were retrieved from this database and filtered through a statistical and computational filter. Seven compounds were suggested by our methodology to possess a potential inhibitory activity upon FABP4 in the range of 79–245 nM. ADMET properties prediction were performed to validate the hypothesis of the interaction with the intended target and to assess the drug-likeness of these derivatives; from these analyses, three molecules resulted as excellent candidates for becoming new drugs.

Design and advancement of the durable urban train infrastructures are of utmost importance for reliable mobility in the smart cities of the future. Given the importance of urban train lines, tunnels, and subway stations, these structures should be meticulously analyzed. In this research, two-dimensional modeling and analysis of the soil-structure mass of the Alan Dasht station of Mashhad Urban Train are studied. The two-dimensional modeling was conducted using Hashash’s method and displacement interaction. After calculating the free-field resonance and side distortion of the soil mass, this resonance was entered into PLAXIS finite element program, and finally, stress and displacement contours together with the bending moment, shear force and axial force curves of the structure were obtained.

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

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.

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.

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.

Tissue engineering has the potential for repairing large bone defects, which impose a heavy financial burden on the public health. However, difficulties with O₂ delivery to the cells residing in the interior of tissue engineering scaffolds make it challenging to grow artificial tissues of clinically-relevant sizes. This study uses image-based simulation in order to provide insight into how to better optimize the scaffold manufacturing parameters, and the culturing conditions, in order to resolve the O₂ bottleneck. To do this, high resolution 3D X-ray images of two common scaffold types (salt leached foam and non-woven fiber mesh) are fed into a Lattice Boltzmann Method fluid dynamics and reactive Lagrangian Scalar Tracking mass transfer solvers. The obtained findings indicate that the scaffolds should have maximal surface area-to-solid volume ratios, for higher chances of the molecular collisions with the cells. Furthermore, the cell culture media should be flown through the scaffold pores as fast as practically possible (without detaching or killing the cells). Finally, we have provided a parametric sweep that maps how the molecular transport within the scaffolds is affected by variations in rates of O₂ consumption by the cells. Ultimately, the results of this study are expected to benefit the computer-assisted design of tissue engineering scaffolds and culturing experiments.

In this study, an optimization of the first blade in new test rig presented. Blade tuning is conducted using 3D geometrical parameters. Sweep and dihedral play an essential role in this study. Compressor characteristics and blades vibrational behavior are the main objective of the evaluation. Here, the attachments are designed to isolate blade dynamics from Disk. So, the Vibrational behaviors of the one's blade are tuned based on the self-excited and forced vibration phenomenon. Using a semi analytical MATLAB code instability conditions are satisfied. The code takes advantages of whitehead and force response theory to predict classically and stall flutter speeds. Beside, Forced vibrations instability is controlled using a theory presented by Campbell. Aerodynamics of new blade geometry determined using multistage simulations Computational fluid dynamics (CFD) software. Numerical results show increasing performance near the surge line and working interval along with increasing mass flow.

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.

In this research, the computational fluid dynamic (CFD) approach that has been used in wind power generation field was applied for the solution of the problems of local strong wind areas in railway fields, and the mechanism of wind generation was discussed. At the same time, the affectivity of the application of computational fluid dynamic approach to railway field was discussed. The problem of local wind that occurs on the railway line in winter was taken up in this research. A computational simulation for the prediction of wind conditions by LES was implemented and it was clarified that the local strong wind area is mainly caused by separated flows originating from the small‐scale terrain positioned at its upstream (at approximately 180.0 m above sea level). Meanwhile, the effects of the size of calculation area and spatial grid resolution on the result of calculation and the effect of atmospheric stability were also discussed. It was clarified that when the air flow characteristic of the separated flow originating from the small‐scale terrain (at altitude of approximately 180.0 m) targeted in this research is reproduced at high accuracy by computational simulation of wind conditions, approximately 10.0 m of spatial resolution of computational grid in horizontal direction is required. As a result of the computational simulation of wind conditions of stably stratified flow (Fr = 1.0), lee waves were excited at the downstream of the terrain over time. As a result, the reverse‐flow region lying behind the terrain that had been observed at a neutral time was inhibited. Consequently, local strong wind area was generated at the downstream of the terrain and the strong wind area passing through the observation mast was observed. By investigating the speed increasing rate of local strong wind area induced at the time of stable stratification, it was found that the wind was approximately 1.2 times stronger than what was generated at a neutral time.

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

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

The nuclear lamina consists of a dense fibrous meshwork made of nuclear lamins, Type V intermediate filaments, and is ~14 nm thick according to recent cryo-electron tomography studies. Recent advances in light microscopy have extended the resolution to a scale allowing for the fine structure of the lamina to be imaged in the context of the whole nucleus. We review quantitative approaches to analyze the imaging data of the nuclear lamina as acquired by structured illumination microscopy (SIM) and single molecule localization microscopy (SMLM), as well as the requisite cell preparation techniques. In particular, we discuss the application of steerable filters and graph based methods to segment the structure of the four mammalian lamin isoforms (A, C, B1, and B2) and extract quantitative information.

Machine learning (ML) methods has recently contributed very well in the advancement of the prediction models used for energy consumption. Such models highly improve the accuracy, robustness, and precision and the generalization ability of the conventional time series forecasting tools. This article reviews the state of the art of machine learning models used in the general application of energy consumption. Through a novel search and taxonomy the most relevant literature in the field are classified according to the ML modeling technique, energy type, perdition type, and the application area. A comprehensive review of the literature identifies the major ML methods, their application and a discussion on the evaluation of their effectiveness in energy consumption prediction. This paper further makes a conclusion on the trend and the effectiveness of the ML models. As the result, this research reports an outstanding rise in the accuracy and an ever increasing performance of the prediction technologies using the novel hybrid and ensemble prediction models.

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.

A study on the selection of hyperelastic constitutive model for polymeric materials is performed using a hybrid experimental-computational approach. Bis-GMA polymer is used as a case study of hyperelastic material to describe the polymer characteristics by determining its Poisson’s ratio and its valid range of the hyperelastic stress-strain curves. These two parameters are then used to determine the hyperelastic constitutive model by using the hybrid approach. Several uniaxial compression tests along with their finite element simulations are implemented in a systematic way, to identify the polymer behavior under the compressive loading conditions. Nano-indentation experiments are conducted to verify the hyperelastic behavior of the polymer. The experimental and computational evidences confirm that the Poisson’s ratio of Bis-GMA is 0.40 and the appropriate hyperelastic constitutive model for this polymer is of a second order polynomial. It is shown that, the results can be used to determine the true stress-strain curve of hyperelastic materials.

The details of antigen-antibody interactions and the identification of epitopes are critical for the development of monoclonal antibody drugs. Ab42 is a native human-derived anti-CFH monoclonal antibody. In this study, the interaction between antigen pCFH and antibody (Ab42) was theoretically demonstrated by molecular docking and MD simulation, combined with free energy calculation and computational alanine scanning (CAS), and key amino acids and epitopes were identified. Experimental alanine scanning (EAS) was then carried out to verify the results of the calculation, and our results indicated that Ab42 antibody forms hydrogen bonds and interacts hydrophobically with pCFH through the Tyr315, Ser100, Gly33, and Tyr53 residues on its CDR, while the main pCFH epitopes are located at the six sites of Pro441, Ile442, Asp443, Asn444, Ile447, and Thr448. In conclusion, this study has explored the mechanism of antigen-antibody interaction from both theoretical and experimental aspects, and our results have important theoretical significance for the design and development of relevant antibody drugs.

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.

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.

In this paper, we generalize the problems of finding simple polygons with the minimum area, maximum perimeter and maximum number of vertices so that they contain a given set of points and their angles are bounded by $\alpha+\pi$ where $\alpha$ ($0\leq\alpha\leq \pi$) is a parameter. We also consider the maximum angle of each possible simple polygon crossing a given set of points, and derive an upper bound for the minimum of these angles. The correspondence between the problems of finding simple polygons with the minimum area and maximum number of vertices is investigated from a theoretical perspective. We formulate the three generalized problems as nonlinear programming models, and then present a Genetic Algorithm to solve them. Finally, the computed solutions are evaluated on several datasets and the results are compared with those from the optimal approach.

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

This paper investigates the effects of air void topology on hydraulic conductivity in asphalt mixtures with porosity in the range 14%-31%. Virtual asphalt pore networks were generated using the Intersected Stacked Air voids (ISA) method, with its parameters being automatically adjusted by the means of a differential evolution optimisation algorithm, and then 3D printed using transparent resin. Permeability tests were conducted on the resin samples to understand the effects of pore topology on hydraulic conductivity. Moreover, the pore networks generated virtually were compared to real asphalt pore networks captured via X-ray Computed Tomography (CT) scans. The optimised ISA method was able to generate realistic 3D pore networks corresponding to those seen in asphalt mixtures in term of visual, topological, statistical and air void shape properties. It was found that, in the range of porous asphalt materials investigated in this research, the high dispersion in hydraulic conductivity at constant air void content is a function of the average air void diameter. Finally, the relationship between average void diameter and the maximum aggregate size and gradation in porous asphalt materials was investigated.

The Colebrook equation is a popular model for estimating friction loss coefficients in water and gas pipes. The model is implicit in the unknown flow friction factor . To date, the captured flow friction factor can be extracted from the logarithmic form analytically only in the term of the Lambert -function. The purpose of this study is to find an accurate and computationally efficient solution based on the shifted Lambert -function also known as the Wright -function. The Wright -function is more suitable because it overcomes the problem with the overflow error by switching the fast growing term of the Lambert -function to the series expansions that further can be easily evaluated in computers without causing overflow run-time errors. Although the Colebrook equation transformed through the Lambert -function is identical to the original expression in term of accuracy, a further evaluation of the Lambert -function can be only approximate. Very accurate explicit approximations of the Colebrook equation that contains only one or two logarithms are shown. The final result is an accurate explicit approximation of the Colebrook equation with the relative error of no more than 0.0096%. The presented approximations are in the form suitable for everyday engineering use, they are both accurate and computationally efficient.

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

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

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.

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.

In this paper, an attempt has been made to analyze the effect of spool port/ groove geometry on the pressure drop and chamber pressures which effect the performance parameters of the flow distributor valve. The work mainly involves formulation of detailed mathematical model of the valve and compare them on the same platform. For mathematical modelling, Matlab has been used. The size of the orifices is considered same throughout the model for better comparison. Initially the construction and functioning of flow distributor valve along with working principles of hydrostatic motor (Rotary Piston) is shown. Next shown the analytical analysis of area change and pressure drops due to different geometry of the spool valve ports. After that the computational fluid dynamics (CFD) analysis has been shown. A complete mathematical model to describe such flow distributor valve is developed after having a comprehensive knowledge of orifice characteristics, flow interactions based on valve geometry. Equations of flow through different orifices (fixed and variable area) of the valve have been developed based on the relationships obtained earlier.

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.

Genetic testing has expanded out of the research laboratory into medical practice and the direct-to-consumer market, and rapid analysis of the resulting genotype data can now have significant impact. We present a method for summarizing personal genotypes as ‘genotype fingerprints’ that meet these needs. Genotype fingerprints can be derived from any single nucleotide polymorphism (SNP)-based assay, and remain comparable as chip designs evolve to higher marker densities. We demonstrate that they support distinguishing types of relationships among closely related individuals and closely related individuals from individuals from the same background population, as well as high-throughput identification of identical genotypes, individuals in known background populations, and de novo separation of subpopulations within a large cohort through extremely rapid comparisons. While fingerprints do not preserve anonymity, they provide a useful degree of privacy by summarizing a genotype in a way that prevents reconstruction of individual marker states. Genotype fingerprints are therefore well-suited as a format for public aggregation of genetic information to support ancestry and relatedness determination without revealing personal health risk status.

Laser-induced breakdown spectroscopy (LIBS) is an important analysis technique with applications in many industrial branches and fields of scientific research. Nowadays, the advantages of LIBS are impaired by the main drawback in the analysis of collected data. This procedure is essentially based on the comparison of lines present in the spectrum with a literature database. This paper proposes the use of various computational intelligence methods to develop a reliable and fast classification of non-destructively acquired LIBS spectra into a set of predefined classes. We focus on a specific problem of classification of paper-ink samples into 30 separate, predefined classes. For each of 30 classes (10 pens of each of 5 ink types combined with 10 sheets of 5 paper types plus empty pages) 100 LIBS spectra are collected. Four variants of preprocessing, seven classifiers (Decision trees, Random forest, k-Nearest Neighbour, Support Vector Machine, Probabilistic Neural Network, Multi-Layer Perceptron, and Generalized Regression Neural Network), 5-fold stratified cross-validation and test on an independent set (for methods evaluation) scenarios are employed. Our developed system yielded an accuracy of 99.08% with average classification time of about 0.12 s is obtained using the random forest classifier. Our results clearly demonstrates that machine learning methods can be used to identify the paper-ink samples based on LIBS reliably at a faster rate.

The eighty years old empirical Colebrook function widely used as an informal standard for hydraulic resistance relates implicitly the unknown flow friction factor , with the known Reynolds number and the known relative roughness of a pipe inner surface ; . It is based on logarithmic law in the form that captures the unknown flow friction factor in a way from which it cannot be extracted analytically. As an alternative to the explicit approximations or to the iterative procedures that require at least a few evaluations of computationally expensive logarithmic function or non-integer powers, this paper offers an accurate and computationally cheap iterative algorithm based on Padé polynomials with only one -call in total for the whole procedure (expensive -calls are substituted with Padé polynomials in each iteration with the exception of the first). The proposed modification is computationally less demanding compared with the standard approaches of engineering practice, but does not influence the accuracy or the number of iterations required to reach the final balanced solution.

Synthetic Aperture RADAR (SAR) is a radar imaging technique in which the relative motion of the sensor is used to synthesize a very long antenna and obtain high spatial resolution. Standard SAR raw data processing techniques assume uniform motion of the satellite (or aerial vehicle) and a fixed antenna beam pointing sideway orthogonally to the motion path, assumed rectilinear. Despite SAR data processing is a well established imaging technology that has become fundamental in several fields and applications, in this paper a novel approach has been used to exploit coherent illumination, demonstrating the possibility of extracting a large part of the ancillary data information from the raw data itself, to be used in the focusing procedure. In this work an effort has been carried out to try to focus the raw SAR complex data matrix without the knowledge of anyof the parameters needed in standard focusing procedures as Range Doppler (RD) algorithm, ω - K algorithm and Chirp Scaling (CS) algorithm. All the literature references regarding the algorithms needed to obtain a precise image from raw data use such parameters that refer both to the SAR system acquisition geometry and its radiometric specific parameters. In [12], authors introduced a preliminary work dealing with this problem and able to obtain, in the presence of a strong point scatterer in the observed scene, good quality images, if compared to the standard processing techniques. In this work the proposed technique is described and performances parameters are extracted to compare the proposed approach to RD.

We consider the maximum entropy Markov chain inference approach to characterize the collective statistics of neuronal spike trains, focusing on the statistical properties of the inferred model. We review large deviations techniques useful in this context to describe properties of accuracy and convergence in terms of sampling size. We use these results to study the statistical fluctuation of correlations, distinguishability and irreversibility of maximum entropy Markov chains. We illustrate these applications using simple examples where the large deviation rate function is explicitly obtained for maximum entropy models of relevance in this field.

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.

Discovery of inhibitors for endothelial-related transcription factors can contribute to the development of angiogenic therapies that treat diseases ranging from cardiovascular to cancer. The role of transcription factor Vezf1 in vascular development and regulation of angiogenesis has been defined by several earlier studies. Through construction of a computational model for Vezf1, work here has identified a novel small molecule drug capable of inhibiting Vezf1 from binding to its cognate DNA binding site. Using structure-based design and virtual screening of the NCI Diversity Compound Library, 12 shortlisted compounds were tested for their ability to interfere with the binding of Vezf1 to DNA using electrophoretic gel mobility shift assays. We identified one compound, T4, which has an IC50 of 20uM. Using murine endothelial cells, MSS31, we tested the effect of T4 on endothelial cell viability and angiogenesis by using tube formation assay. Our data show that addition of T4 in cell culture medium does not affect cell viability at concentrations lower or equal to its IC 50 but strongly inhibits the network formation by MSS31 in the tube formation assays. Given its potential efficacy, this inhibitor has significant therapeutic potential in several human diseases raging from wound healing to cancer.