Mechanistic modeling

A better understanding of the constitutive material behavior is imperative in predicting mechanical responses and performance of rail tracks that are usually categorized as either conventional ballasted tracks or unconventional ballastless tracks. Computational approaches such as finite element modeling and discrete element modeling have been primary methods to model rail tracks for mechanistic analysis and design. In particular, finite element modeling is advantageous as an eff rigorous tool in predicting the long-term track behavior under different loading conditions with great versatility for addressing the constitutive behavior of various materials used in rail tracks. This paper aims to recapitulate the major findings of many international studies on the finite element modeling of conventional and unconventional rail tracks and deliver a collective review of the structural configuration of rail tracks and the constitutive behavior of materials used to model rail tracks. In addition, we present the existing limitations and/or gaps in the current literature. Information presented in this study can aid the rail track engineering community with further insights on rail track performance prediction in a purely mechanistic manner, which can potentially bring a significant reduction in the complex and costly full-scale testing.

To prevent the pollution of water resources, the measurement and the limitation of wastewater discharges are required. Despite the progress in the field of data acquisition systems, sensors are subject to malfunctions that can bias the evaluation of the pollution flow. It is therefore essential to identify potential anomalies in the data before any use. The objective of this work is to deploy artificial intelligence tools to automate the data validation and to assess the added value of this approach in assisting the validation performed by an operator. To do so, we compare two state-of-the-art anomaly detection algorithms on turbidity data in a sewer network. On the one hand, we conclude that the One-class SVM model is not adapted to the nature of the studied data which is heterogeneous and noisy. The Matrix Profile model, on the other hand, provides promising results with a majority of anomalies detected and a relatively limited number of false positives. By comparing these results to the expert validation, it turns out that the use of the Matrix Profile model objectifies and accelerates the validation task while maintaining the same level of performance compared to the annotator agreement rate between two experts.

A traditional ballasted railway track, characterized by its layers of ballast, sub-ballast, and subgrade, is the most viable option for Indonesia's railway system, primarily due to its cost-effectiveness and straightforward construction process. This track type must ensure a stable train route, maintaining appropriate horizontal and vertical alignment. Each component of the system is required to fulfill its designated role effectively. However, prior research has predominantly concentrated on assessing the permanent deformation of individual layers within conventional rail tracks. It has been determined that employing a linear elastic material model is inadequate for accurately representing the behavior of ballast, sub-ballast, and subgrade. The prevailing approach in existing literature involves simulating the inelastic behavior and modeling the permanent deformation of granular and soil materials in railway tracks using elastoplastic constitutive models, such as the Mohr-Coulomb and Drucker-Prager (Elastic Perfect-Plastic) models. In this context, the present study aims to evaluate the efficacy of mechanistic modeling in predicting the overall permanent deformation of conventional rail tracks, utilizing the Modified Drucker-Prager Cap model for the ballast, sub-ballast, and subgrade layers. Additionally, this research examines the contributions of each component layer to the total permanent deformation in the design of conventional rail tracks. A key finding from this investigation is that the ballast layer plays a crucial role in the permanent deformation of the conventional track, followed by the subgrade and sub-ballast layers.

This paper presents a new mechanistic empirical model for predicting dynamic modulus of asphalt paving mixtures at a wider range of temperatures and loading frequencies, which can be shifted into a master curve for characterizing asphalt concrete. Available predictive models seem to be not capable of predicting dynamic modulus of asphalt mixtures at higher temperatures and lower loading frequencies; these models over-predict dynamic modulus by a significant deviation from laboratory-measured values. The new model is capable of accurately predicting measured dynamic modulus at a broader range of temperatures and loading frequencies. The proposed new model was derived from the law of mixtures where composite materials are modeled in a combination of parallel and series phases. For a system of purely parallel phases, the combined mechanical behavior is simply the addition of the responses from these phases. To develop the new model, asphalt mixtures with different performance grades co...

In the yeast Saccharomyces cerevisiae, the Ras/cAMP/PKA pathway plays a major role in the regulation of metabolism, stress resistance and cell cycle progression. We extend here a mechanistic model of the Ras/ cAMP/PKA pathway that we previously defined by describing the molecular interactions and posttranslational modifications of proteins, and perform a computational analysis to investigate the dynamical behaviors of the components of this pathway, regulated by different control mechanisms. We carry out stochastic simulations to consider, in particular, the effect of the negative feedback loops on the activity of both Ira2 (a Ras-GAP) and Cdc25 (a Ras-GEF) proteins. Our results show that stable oscillatory regimes for the dynamics of cAMP can be obtained only through the activation of these feedback mechanisms, and when the amount of Cdc25 is within a specific range. In addition, we highlight that the levels of guanine nucleotides pools are able to regulate the pathway, by influencing the transition between stable steady states and oscillatory regimes.

MAMANI D., SPORLEDER M, KROSCHEL J. 2011. Effect of inert materials of bioinsecticides formula to protect stored tubers of potato against the potato moths. Rev. peru. entomol. 46(2): 43-49. In Peruvian potato production zones two species of potato tuber moths prevail: Phthorimaea operculella Zeller (Lepidoptera: Gelechiidae) and Symmetrischema tangolias Gyen (Gelechiidae). For avoiding damage by these pests farmers dust their home-stored potatoes (Solanum tuberosum Linneo) with inert materials or talcum formulations with a granulovirus that attacks P. operculella (PoGV). The objective of this study was to determine the protective capacity of inert materials (talc, kaolin, lime and sand) applied to potato tubers against larvae of both species and to define the optimal application dose. Potato tubers (cv. Peruanita) impregnated with these materials at a dose of 5g/kg potatoes (experiment 1) and at different doses: 0,625; 1,25; 2,5; 5; 10 and 15 g/kg potatoes (experiment 2) were inocul...

Model parameters must be exact in order to employ mechanistic models in chromatography. Cleared cell harvest is particularly difficult feedstock for mechanistic models to simulate. A lack of specimen complex and time to establish all of the desirable criteria is also a big hindrance in the way. Therefore, the research's purpose was to build a process that initiates with complicated feedstock including monoclonal antibodies and uses an automated liquid handling system. It was put to the test by comparing separate data sets with estimates produced by the mechanical typical employing all parameters determined in this work. The method was backed up by a near-perfect match between predicted and actual results. The 200 L bed volume of Robo Columns may therefore be effectively used to regulate isotherm parameters for bigger scale column predictions. Mechanistic chromatographic modelling of complex biological feedstocks can benefit greatly from this approach since it provides a new way of finding crucial model input parameters.

Modeling and simulation in computational neuroscience is currently a research enterprise to better understand neural systems. It is not yet directly applicable to the problems of patients with brain disease. To be used for clinical applications, there must not only be considerable progress in the field but also a concerted effort to use best practices in order to demonstrate model credibility to regulatory bodies, to clinics and hospitals, to doctors, and to patients. In doing this for neuroscience, we can learn lessons from long-standing practices in other areas of simulation (aircraft, computer chips), from software engineering, and from other biomedical disciplines. In this manuscript, we introduce some basic concepts that will be important in the development of credible clinical neuroscience models: reproducibility and replicability; verification and validation; model configuration; and procedures and processes for credible mechanistic multiscale modeling. We also discuss how ga...

To avoid the existing limitations of the PCA process for the precipitation of proteins and polar polymers a new approach based on the use of water to modify the phase behaviour of the system DMSO-CO 2 was developed. The addition of water to the DMSO displaces the mixture critical pressure of the solution-CO 2 system to higher pressures and produces a new operating region in which the PCA process can be carried out. Following this approach, it was possible to develop a process to produce 1-10 m particles of N-trimethylchitosan chloride (TMC) suitable for inhalation. Encapsulation of proteins in TMC using this technique could also be successfully achieved.

The latitudinal diversity gradient (LDG) is one of the most widely studied patterns in ecology, yet no consensus has been reached about its underlying causes. We argue that the reasons are the verbal nature of existing hypotheses, the failure to mechanistically link interacting ecological and evolutionary processes to the LDG, and the fact that empirical patterns are often consistent with multiple explanations. To address this issue, we synthesize current LDG hypotheses, uncovering their eco-evolutionary mechanisms, hidden assumptions, and commonalities. Furthermore, we propose mechanistic eco-evolutionary modeling and an inferential approach that makes use of geographic, phylogenetic, and trait-based patterns to assess the relative importance of different processes for generating the LDG.

Monte Carlo simulation has proven to be an effective means of incorporating reliability analysis into the Mechanistic-Empirical (M-E) design process for flexible pavements. Nigerian Empirical-Mechanistic Pavement Analysis and Design System procedure for Nigeria Environments has been proposed. This work aimed at providing most appropriate number of Monte Carlo simulation cycles that should be adopted for used to provide enough sufficient repeatability for damage reliability relationship in the Nigerian environments. Two selected fatigue distress models and a selected rutting distress models were evaluated for Nigerian environment. It was observed that Monte Carlo simulation cycle of 2, 500 thresholds were enough to be used to provide sufficient repeatability for damage reliability relationship and that axle weight has an overwhelming effect on the output variability as an increase in applied load was highly noticed in the reliability values.

The aim of this work was to evaluate reliability index (RI) with respect to fatigue and rutting within the different seasons peculiar to Nigeria, in order to improve Empirical-Mechanistic flexible pavement design approach, using First Order Reliability Method (FORM). Flexible pavement design involves many uncertainties, variabilities, and approximations regarding the input parameters like material properties, traffic loads. Others include subgrade strength, drainage conditions, construction, compaction procedures and climatic factors such as temperature, rainfall, and snowfall, etc. The combination of the variances associated with input parameters contributes to components and system uncertainty, and this combination of variances can have a significant effect on the predicted performance of the pavement. Reliability in pavement design is introduced to consider these uncertainties. Layers thicknesses, material properties, and Equivalent Standard Axle Load (ESAL) were entered into a multi-layer elastic theory software, ELSYM-5, which in turn were used to calculate strains and stresses for different seasons. The results obtained were entered into Nigerian fitted transfer function distress models to compute allowable ESALS. Miner's hypothesis theory equation was used to calculate the cumulative damage due to stress and strains generated. A Framework was generated for finding individual reliability index (RI), systemic reliability index (SRI), and probability of failure. The findings showed that Season I (Winter) recorded the highest component reliability index for fatigue (5.63 for Normal Distribution). Season II (Summer) recorded the lowest component reliability index (β) for rutting (5.4 for Normal Distribution). Season III (Spring) recorded the lowest component reliability index for fatigue (1.85 for Normal Distribution)

While Wesley Salmon attributes the debate on scientific explanation between Carl Hempel and Peter Railton (or between the epistemic and ontic conceptions of scientific explanation, more generally) as one over which conception of explanation is correct, I claim that Hempel and Railton were responding to two different questions altogether. Hempel was addressing a question akin to ‘what is scientific explanation?’, while Railton was focused on a question more similar to ‘what is scientific explanation?’. In this paper I discuss the different questions Hempel and Railton were addressing, and how distinguishing these two questions can aid in the discussion of the requirements and adequacy of models of scientific explanation. While these two questions are clearly inter-related, I claim that we should not judge the adequacy of an answer to one of these questions on the basis of the adequacy of an answer to the other. The Epistemic and Ontic Conceptions of Scientific Explanation Kaetlin Dia...

In the yeast Saccharomyces cerevisiae, the Ras/cAMP/PKA pathway plays a major role in the regulation of metabolism, stress resistance and cell cycle progression. We extend here a mechanistic model of the Ras/ cAMP/PKA pathway that we previously defined by describing the molecular interactions and posttranslational modifications of proteins, and perform a computational analysis to investigate the dynamical behaviors of the components of this pathway, regulated by different control mechanisms. We carry out stochastic simulations to consider, in particular, the effect of the negative feedback loops on the activity of both Ira2 (a Ras-GAP) and Cdc25 (a Ras-GEF) proteins. Our results show that stable oscillatory regimes for the dynamics of cAMP can be obtained only through the activation of these feedback mechanisms, and when the amount of Cdc25 is within a specific range. In addition, we highlight that the levels of guanine nucleotides pools are able to regulate the pathway, by influencing the transition between stable steady states and oscillatory regimes.

This is one of a pair of discussion notes comparing some features of the account of causation in Wolfgang Spohn's Laws of Belief with the "interventionist" account in James Woodward's Making Things Happen. This note locates the core difference of the accounts in the fact that Woodward's account follows an epistemological order, while Spohn's follows a conceptual order. This unfolds in five further differences: (i) type-versus token-level causation, (ii) reference to time, (iii) actual/counterfactual intervention versus epistemic/suppositional wiggling, (iv) a circular versus a circle-free conception of the circumstances of a direct causal relation, and (v) absolute versus model-relative causation.

In this paper, I examine two idealized models in astrophysics, with the aim of showing that the idealizations in these models play an important explanatory role. I argue, against many representationalists, that it is because of the idealizations in these models, rather than in spite of them, that the models turn out to have explanatory power. In many cases, this claim can be extended to the use of idealized models in the sciences more generally, and thus it gives important insight into the nature of model explanation.

This volume forms the proceedings of one of eight co-located symposia held at the AISB Convention 2013 that took place 3rd-5th April 2013 at the University of Exeter, UK. The convention consisted of these symposia together in four parallel tracks with five plenary talks; all papers other than the plenaries were given as talks within the symposia. This symposium-based format, which has been the standard for AISB conventions for many years, encourages collaboration and discussion among a wide variety of disciplines. Although each symposium is self contained, the convention as a whole represents a diverse array of topics from philosophy, psychology, computer science and cognitive science under the common umbrella of artificial intelligence and the simulation of behaviour. We would like to thank the symposium organisers and their programme committees for their hard work in publicising their symposium, attracting and reviewing submissions and compiling this volume. Without these interesting, high quality symposia the convention would not be possible.

This volume forms the proceedings of one of eight co-located symposia held at the AISB Convention 2013 that took place 3rd-5th April 2013 at the University of Exeter, UK. The convention consisted of these symposia together in four parallel tracks with five plenary talks; all papers other than the plenaries were given as talks within the symposia. This symposium-based format, which has been the standard for AISB conventions for many years, encourages collaboration and discussion among a wide variety of disciplines. Although each symposium is self contained, the convention as a whole represents a diverse array of topics from philosophy, psychology, computer science and cognitive science under the common umbrella of artificial intelligence and the simulation of behaviour. We would like to thank the symposium organisers and their programme committees for their hard work in publicising their symposium, attracting and reviewing submissions and compiling this volume. Without these interesting, high quality symposia the convention would not be possible.

A systematic method has been proposed to estimate the two-phase flow properties of horizontal fractures under normal deformation condition. Based on Gaussian aperture distributions and-2-the assumption of local parallel plate model, a simple model was obtained in closed form to predict the capillary pressure-saturation relationships for both wetting and non-wetting phases. Three conceptual models were also developed to characterize the relative permeability behaviors. In order to investigate the effect of normal deformation on two-phase flow properties, the normal deformation could be represented with the maximum void space closure on the basis of penetration model. A rigorous successive random addition (SRA) method was used to generate the aperture-based fractures and a numerical approach based on invasion percolation (IP) model was employed to model capillary-dominated displacements between wetting and non-wetting phases. The proposed models were partially verified by a laboratory dataset and numerical calculations without consideration of deformation. Under large normal deformations, it was found that the macroscopic model is in better agreement with simulated observations. The simulation results demonstrated that the two-phase flow properties including the relationships between capillary pressure, relative permeability and saturation, phase interference, phase structures, residual-saturationrated parameters and tortuosity factor, were highly sensitive to the spatial correlation of aperture distribution and normal deformation.

Empirical pharmacokinetic models are used to explain the pharmacokinetics of the antiviral drug tenofovir (TFV) and its metabolite TFV diphosphate (TFV-DP) in peripheral blood mononuclear cells. These empirical models lack the ability to explain differences between the disposition of TFV-DP in HIV-infected patients vs. healthy individuals. Such differences may lie in the mechanisms of TFV transport and phosphorylation. Therefore, we developed an exploratory model based on mechanistic mass transport principles and enzyme kinetics to examine the uptake and phosphorylation kinetics of TFV. TFV-DP median C max from the model was 38.5 fmol/10 6 cells, which is bracketed by two reported healthy volunteer studies (38 and 51 fmol/10 6 cells). The model presented provides a foundation for exploration of TFV uptake and phosphorylation kinetics for various routes of TFV administration and can be updated as more is known on actual mechanisms of cellular transport of TFV.

The uniqueness and sensitivity of foam modeling parameters are crucial for simulating foam flow through porous media. In the absence of oil in the porous medium, the local-equilibrium foam model investigated in this work uses three parameters to describe the foam quality dependence: f mmob, f mdr y, and epdr y. Even for a specified value of epdr y, in some cases, two pairs of f mmob and f mdr y values can experimentally match measured transition foam quality (f t g) and transition foam apparent viscosity (μ t foam,app). This non-uniqueness can be broken by limiting the solution such that f mdr y is smaller than the transition water saturation (S t w). In addition, a three-parameter fit using all experimental data of apparent viscosity versus foam quality was developed to simultaneously estimate f mmob, f mdr y, and epdr y. However, a better strategy is to conduct and match a transient experiment, in addition to steady-state experiments, in which a gas displaces the surfactant solution at 100 % water saturation. This transient foam quality scans the entire range of fractional flow, and the values of the foam parameters that best match the experiment can be uniquely determined. The numerical artifact of pressure oscillations in simulating this transient foam process was investigated by comparing the finite difference algorithm with the method of characteristics. Sensitivity analyses indicated that the estimated foam parameters were highly dependent on the parameters used for the water and gas relative permeabilities. In particular, the water relative permeability exponent and connate water saturation are important.

The application of mechanistic models for chromatography requires accurate model parameters. Especially for complex feedstocks such as a clarified cell harvest, this can still be an obstacle limiting the use of mechanistic models. Another commonly encountered obstacle is a limited amount of sample material and time to determine all needed parameters. Therefore, this study aimed at implementing an approach on a robotic liquid handling system that starts directly with a complex feedstock containing a monoclonal antibody. The approach was tested by comparing independent experimental data sets with predictions generated by the mechanistic model using all parameters determined in this study. An excellent agreement between prediction and experimental data was found verifying the approach. Thus, it can be concluded that RoboColumns with a bed volume of 200 lL can well be used to determine isotherm parameters for predictions of larger scale columns. Overall, this approach offers a new way to determine crucial model input parameters for mechanistic modelling of chromatography for complex biological feedstocks. V

This paper concerns the assessment of direct causal effects from a combination of: (i) non-experimental data, and (ii) qualitative domain knowledge. Domain knowledge is encoded in the form of a directed acyclic graph (DAG), in which all interactions are assumed linear, and some variables are presumed to be unobserved. The paper establishes a sufficient criterion for the identifiability of all causal effects in such models as well as a procedure for estimating the causal effects from the observed covariance matrix.

This book addresses the challenge of understanding human life. We compare our life experience with the attempts to grasp it by astrologers, eugenicists, psychologists, social scientists, and philosophers. How have these various disciplines sought to give substance to an experience at once so intimate and so universal?
The main opposition in the list above lies between understanding and misunderstanding. For example, the astrologers’ and eugenicists’ approach, fully accepted in their day, is now largely viewed as a form of misunderstanding. To show why this is so, we examine their methodology. For practitioners of the other disciplines, their understanding may be limited by various methodological problems they encounter but are trying to overcome. We shall explore these issues as well.

The effects of velocity and gas type on foam flow through porous media have yet to be completely elucidated. Pressure drop and capillary pressure measurements were made at ambient conditions during a series of foam quality scan experiments in a homogenous sandpack while foam texture was simultaneously visualized. New insights into foam-flow behavior in porous media were discovered. Previously accepted “limiting” capillary pressure theory is challenged by the findings in this work, and the “limiting” terminology is replaced with the word “plateau” to reflect these novel observations. Plateau capillary pressure $${(P}_{c})$$ ( P c ) and transition foam quality were found to increase with velocity. Transition foam quality was found to depend mostly on liquid velocity rather than gas velocity and is physically linked to foam type (continuous vs. discontinuous) and texture (fine vs. coarse). Distinct rheological behaviors also arose in the low- and high-quality foam regimes as a function...

The debate over the explanatory nature of cognitive models has been waged mostly between two factions: the mechanists and the dynamical systems theorists. The former hold that cognitive models are explanatory only if they satisfy a set of mapping criteria, particularly the 3M/3M* requirement. The latter have argued, pace the mechanists, that some cognitive models are both dynamical and constitute covering-law explanations. In this paper, I provide a minimal model interpretation of dynamical cognitive models, arguing that this both provides needed clarity to the mechanist versus dynamicist divide in cognitive science and also paves the way towards further insights about scientific explanation generally.

Climate change is driving worldwide shifts in the distribution of biodiversity, and fundamental changes to global avian migrations. Some arctic-nesting species may shorten their migration distance as warmer temperatures allow them to winter closer to their high-latitude breeding grounds. However, such decisions are not without risks, since this intensifies pressure on resources when they are used for greater periods of time. In this study, we used an individual-based model to predict how future changes in food abundance, winter ice coverage, and human disturbance could impact an Arctic/sub-Arctic breeding goose species, black brant (Branta bernicla nigricans, Lawrence 1846), and their primary food source, common eelgrass (Zostera marina L.), at the Izembek Lagoon complex in southwest Alaska. Brant use the site during fall and spring migrations, and increasingly, for the duration of winter. The model was validated by comparing predictions to empirical observations of proportion of geese surviving, proportion of geese emigrating, mean duration of stay, mean rate of mass gain/loss, percentage of time spent feeding, number of bird days, peak population numbers, and distribution across the complex. The model predicted that reductions >50% of the current decadal (2007-2015) mean of eelgrass biomass, which have been observed in some years, or increases in the number of brant, could lead to a reduction in the proportion of birds that successfully migrate to their breeding grounds from the site. The model also predicted that access to eelgrass in lagoons other than Izembek was critical for overwinter survival and spring migration of brant, if overall eelgrass biomass was 50% of the decadal mean biomass. Geese were typically predicted to be more vulnerable to environmental change during winter and spring, when eelgrass biomass is lower, and thermoregulatory costs for the geese are higher than in fall. We discuss the consequences of these predictions for goose population trends in the face of natural and human drivers of change.

Mechanisms in Science: Method or Metaphysics?. 1 It includes not only clear and concise philosophical argument and detailed yet digestible scientific case studies, but some fascinating history of the mechanical philosophy. Especially interesting is the authors' comparison of Newton's disagreement with Leibniz over mechanical explanation with their own disagreement with New Mechanists. Mechanistic philosophers of science must certainly grapple with this book. I have some reservations about the historical comparison, but here I focus on what I take to be the central philosophical theses of the book. These are 1) that much contemporary mechanistic philosophy of science contains metaphysical commitments that are unnecessary to understand the concept of mechanism used in scientific practice and 2) that an account of that concept as a causal pathwayunderstood merely as a sequence of difference-makers linked by relations of counterfactual dependencecaptures its use without the unnecessary metaphysical commitments. Although I think both theses are mostly true, I take this opportunity to register some points of disagreement. Which work in contemporary mechanistic philosophy of science is metaphysically profligate and why? Two (among others) of the book's main antagonists here are Carl Craver and Stuart Glennan, to each of whom a critical chapter is devoted. Briefly, Craver's metaphysical extravagance is his concept of constitutive relevance, and Glennan's is his concept of activity. Constitutive relevance is the relation Craver, following Salmon (1984), takes to hold between an explanandum phenomenon and the explanatorily relevant parts of the mechanism responsible for it. When the phenomenon to be explained is the end product of a causal sequence, such as the

The article presents the comparative analysis of the concept of organizational mechanism by foreign and domestic scholars in the field of management, economics and organizational studies. The article summarizes the main theoretical views, models and empirical findings on this topic based on a wide range of scientific sources, including books, professional articles, monographs, conference papers. The article highlights the similarities and differences in the approaches of different scholars to this topic, as well as identifies the key debates and controversies around the definition, scope and functions of the organizational mechanism. The article highlights common themes and trends in the study of organizational mechanism, compares and contrasts the perspectives of domestic and foreign scientists on the subject. There are different interpretations and definitions of this concept, but a common thread is that it refers to the various elements and processes that an organization uses to ...

A dynamic modulus master curve for asphalt concrete is a critical input for flexible pavement design in the Mechanistic–Empirical Pavement Design Guide developed in NCHRP Project 1-37A, which has drawn much attention among asphalt technologists. The objectives in this study were ( a) to consider and compare different analysis techniques for construction of the master curve and ( b) to measure and analyze the effect of permanent strain on samples that have been evaluated with one of the simple performance tests, dynamic modulus. It was found that differences existed in the calculated asymptote values and the shape of the master curve, depending upon which method was adopted. Recommendations are made for modifications to the testing protocol and for further work to determine the effect of permanent strain at higher test temperatures.

Bee declines are driven by multiple combined stresses, making it exceedingly difficult to identify experimentally the most critical threats to bees and their pollination services. We highlight here the too often ignored potential of mechanistic models in identifying critical stress combinations. Advanced bee models are now available as open access tools and offer an unprecedented opportunity for bee biologists to explore bee resilience tipping points in a variety of environmental contexts. We provide general guidelines on how to run bee models to help detect a priori critical stress combinations to be targeted in the field. This so-called funnel analysis should be performed in tight conjunction with the recent development of large-scale field monitoring programs for bee health surveillance. Apis mellifera / field monitoring program / honeybees / mechanistic modeling / agent-based models

A review of the different mathematical methodologies for calculating energy efficiency in boilers was carried out in this work, considering both the methods included in standards and the proposals and applications published in research works. The classification was delimited in analytical methods, mechanistic modeling, and empirical modeling; moreover, the main equations for each of the methodologies are presented, which allows building a compilation that is expected to be useful for a first approach to the subject. It is displayed that those mechanistic models are used to evaluate subsystems or specific cases that require a high level of detail, while analytical models are used to make a first approximation to the systems described, and empirical models stand out in terms of their use at the industrial level if there is access to a starting database to adjust them.

Mechanistic explanations satisfy widely held norms of explanation: the ability to control and answer counterfactual questions about the explanandum. A currently debated issue is whether any non-mechanistic explanations can satisfy these explanatory norms. Weiskopf (2011) argues that the models of object recognition and categorization, JIM, SUSTAIN, and ALCOVE, are not mechanistic, yet satisfy these norms of explanation. In this paper I will argue that these models are sketches of mechanisms. My argument will make use of model-based fMRI, a novel neuroimaging approach whose significance for current debates on psychological models and mechanistic explanation has yet to be explored.

This paper draws on biology, evolution and cognitive science to formulate a mechanistic and consequentialist explanation of human behavior that resolves the traditional conflicts between behaviorism and cognitivism. Animals are biological information processing systems that input environmental data through their senses, interpret it, and output behaviors that advance their goals. Communication extends the capabilities of individual organisms by serving an input (sensing) function for receivers and an output (manipulating) function for senders. Higher animals build internal models of the physical world that are collections of representations of, or truth claims about, its contents and its cause-and-effect rules, which they use as guides to manipulating the world to induce desired physical effects. They use other animals as agents by sending them truth claims intended to influence their behavior selection. Humans (at least) also selectively accept and reject truth claims to manipulate their own affective states. Sensory and cognitive restrictions limit the completeness and accuracy with which our internal representations can mirror their physical referents. These impediments to faithful representation, along with functional biases, make representational errors and omissions resistant to correction and enable latitude in the construction of social reality (the shared models of the world that govern the distribution of social rewards and penalties). The displacement of unmediated physical effects in the human environment by anthropogenic effects over the course of social and technological evolution reduced the general frequency with and degree to which truth claims need to be true in order to lead to effects intended by their claimants.

A review of the different mathematical methodologies for calculating energy efficiency in boilers was carried out in this work, considering both the methods included in standards and the proposals and applications published in research works. The classification was delimited in analytical methods, mechanistic modeling, and empirical modeling; moreover, the main equations for each of the methodologies are presented, which allows building a compilation that is expected to be useful for a first approach to the subject.

This paper presents results concerning mechanistic modeling to describe the dynamics and interactions between biomass growth, glucose
consumption and ethanol production in batch culture fermentation by Kluyveromyces marxianus (K. marxianus). The mathematical model was formulated based on the biological assumptions underlying each variable and is given by a set of three coupled nonlinear first-order Ordinary Differential Equations. The model has ten parameters, and their values were fitted from the experimental data of 17 K. marxianus strains by  means of a computational algorithm design in Matlab. The latter allowed us to determine that seven of these parameters share the same value among all the strains, while three parameters concerning biomass maximum growth rate, and ethanol production due to biomass and glucose had specific values for each strain. These values are presented with their corresponding standard error and 95% confidence interval.
The goodness of fit of our system was evaluated both qualitatively by in silico experimentation and quantitative by means of the coefficient of determination and the Akaike Information Criterion. Results regarding the fitting capabilities were compared with the classic model given by the logistic, Pirt, and Luedeking–Piret Equations. Further, nonlinear theories were applied to investigate local and global dynamics of the system, the Localization of Compact Invariant Sets Method was applied to determine the so-called localizing domain, i.e., lower and upper bounds for each variable; whilst Lyapunov’s stability theories allowed to establish sufficient conditions to ensure asymptotic stability in the nonnegative octant, i.e., R3
+,0. Finally, the predictive ability of our mechanistic model was explored through several numerical simulations with expected results according to microbiology literature on batch fermentation.
This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY

This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.

Life-science phenomena are often explained by specifying the mechanisms that bring them about. The new mechanistic philosophers have done much to substantiate this claim, and to provide us with a better understanding of what mechanisms are and how they explain. While there is disagreement among current mechanists on various issues, they share a common core position and a seeming commitment to some form of scientific realism. But is such a commitment necessary? Is it the best way to go about mechanistic explanation? In this paper, we propose an alternative antirealist account that also fits explanatory practice in the life sciences. We pay special attention to mechanistic models, i.e. scientific models that involve a mechanism, and to the role of coherence considerations in building such models. To illustrate our points, we consider the mechanism for the action potential. 1 Introduction 2 Some Core Features of Mechanistic Explanation 3 Scientific Realism and Mechanistic Explanation 4 Antirealist Mechanistic Explanation. The Case of the Action Potential 5 Some Outstanding Issues for the Antirealist Mechanist 6 Two Problems for the Realist Mechanist 7 Conclusions

Nitrogen gas drive and foam drive are commonly adopted for practical production in fractured carbonate reservoirs. A systematic study on nitrogen gas drive and foam assisted nitrogen gas drive in varying-aperture fractures is a practical and essential method to understand the EOR mechanism. In this study, we designed and fabricated similarity models and microscopic visual models. The fluid flow mechanisms were discussed combining the pressure response and dynamic displacement phenomenon. Experimental results show that the effective time of nitrogen gas drive was longer in decreasing-aperture fractures than that in increasing-aperture fractures. After water flooding, 0.8 PV nitrogen gas injection lead to gas channeling in decreasing-aperture fracture of 1 mm-0.2 mm while 0.6 PV nitrogen gas injection by reverse displacement direction. Both production rate and average pressure appeared discrete in narrow fracture compared to wide fracture. Enhanced oil recovery efficiency by foam drive was average 5% higher than that by nitrogen gas drive in single fracture. The displacement front of foam varies in four forms: micro-scale foam accumulation, small-scale foam accumulation, mesoscale foam slight deformation and large-scale foam serious deformation. This study could provide a theoretical basis for enhance oil recovery and further dig the potential of remaining oil in fractured carbonate reservoirs.

Gas injection leads to foam formation in porous media in the presence of surfactant solutions, which is used for flow diversion and enhanced oil recovery. We present here laboratory experiments of co-injecting nitrogen and sodium C 14−16 alpha olefin sulfonate with two concentrations: 20× the critical micelle concentration (CMC) in an unconsolidated sandpack of 1860 Darcy and at the CMC for a Bentheimer sandstone of 3 Darcy. The steady state profile for the unconsolidated sandpack is achieved after 1.3 pore volumes, whereas for Bentheimer sandstone, steady state is obtained after injection of 12-15 pore volume. A model that leads to four equations, viz., a pressure equation, a water saturation equation, a bubble density equation and a surfactant transport-adsorption equation, is used to explain the experimental pressure drop. It is asserted that the experimental pressure drop across the measurement points can be used to obtain a first estimate of the average bubble density, which can be further used to obtain part of the source term in the bubble density equation. If we consider flowing fraction of foam, the rate of change of bubble density during transient state can be equated to the bubble density generation-coalescence function plus the terms accounted for bubble transport by convection and diffusion divided by porosity and saturation.

There has been much criticism of the idea that Friston's free-energy principle can unite the life and mind sciences. Here, we argue that perhaps the greatest problem for the totalizing ambitions of its proponents is a failure to recognize the importance of evolutionary dynamics and to provide a convincing adaptive story relating free-energy minimization to organismal fitness.

Tenofovir (TFV) is used in combination with other antiretroviral drugs for human immunodeficiency virus (HIV) treatment and prevention. TFV requires two phosphorylation steps to become pharmacologically active; however, the kinases that activate TFV in cells and tissues susceptible to HIV infection have yet to be identified. Peripheral blood mononuclear cells (PBMC), vaginal, and colorectal tissues were transfected with siRNA targeting nucleotide kinases, incubated with TFV, and TFV-monophosphate (TFV-MP) and TFV-diphosphate (TFV-DP) were measured using mass spectrometry-liquid chromatography. Adenylate kinase 2 (AK2) performed the first TFV phosphorylation step in PBMC, vaginal, and colorectal tissues. Interestingly, both pyruvate kinase isozymes, muscle (PKM) or liver and red blood cell (PKLR), were able to phosphorylate TFV-MP to TFV-DP in PBMC and vaginal tissue, while creatine kinase, muscle (CKM) catalyzed this conversion in colorectal tissue. In addition, next-generation sequencing of the Microbicide Trials Network MTN-001 clinical samples detected 71 previously unreported genetic variants in the genes encoding these kinases. In conclusion, our results demonstrate that TFV is activated in a compartment-specific manner. Further, genetic variants have been identified that could negatively impact TFV activation, thereby compromising TFV efficacy in HIV treatment and prevention.

Filtration steps are ubiquitous in biotech processes due to the simplicity of operation, ease of scalability and the myriad of operations that they can be used for. Microfiltration, depth filtration, ultrafiltration and diafiltration are some of the most commonly used biotech unit operations. For clean feed streams, when fouling is minimal, scaling of these unit operations is performed linearly based on the filter area per unit volume of feed stream. However, for cases when considerable fouling occurs, such as the case of harvesting a therapeutic product expressed in Pichia pastoris, linear scaling may not be possible and current industrial practices involve use of 20-30% excess filter area over and above the calculated filter area to account for the uncertainty in scaling. In view of the fact that filters used for harvest are likely to have a very limited lifetime, this oversizing of the filters can add considerable cost of goods for the manufacturer. Modeling offers a way out of this conundrum. In this paper, we examine feasibility of using the various proposed models for filtration of a therapeutic product expressed in Pichia pastoris at constant pressure. It is observed that none of the individual models yield a satisfactory fit of the data, thus indicating that more than one fouling mechanism is at work. Filters with smaller pores were found to undergo fouling via complete pore blocking followed by cake filtration. On the other hand, filters with larger pores were found to undergo fouling via intermediate pore blocking followed by cake filtration. The proposed approach can be used for more accurate sizing of microfilters and depth filters.

A mechanistic model considering the significant catalytic effects of Na+ on fast pyrolysis of glucose-based carbohydrates was developed in Part 1 of this study. A computational framework based on continuous distribution kinetics and mass action kinetics was constructed to solve the mechanistic model. Agreement between model yields of various pyrolysis products with experimental data from fast pyrolysis of glucose-based carbohydrates dosed with NaCl ranging from 0-0.34 mmol/g at 500 °C validated the model and demonstrated the robustness and extendibility of the mechanistic model. The model was able to capture the yields of major and minor products as well as their trends across NaCl concentrations. Modeling results showed that Na+ accelerated the rate of decomposition and reduced the time for complete thermoconversion of carbohydrates. The sharp reduction in the yield of levoglucosan (LVG) from fast pyrolysis of cellulose in the presence of NaCl was mainly caused by reduced decomposition of cellulose chains via end-chain initiation and depropagation due to Na+ favoring competing dehydration reactions. Analysis of the contributions of reaction pathways showed that the decomposition of LVG made a minor contribution to its yield reduction and contributed less than 0.5% to the final yield of glycolaldehyde from fast pyrolysis of glucose-based carbohydrates in the presence of NaCl.

This study performed the 2-dimensional modeling of Indonesia's conventional track and the asphaltic underlayment track according to four different cyclic loading conditions by varying the train speeds and bogie load of Indonesia’s Argo Jati passenger trains set. Three different mechanical responses were considered, i.e., horizontal strains, vertical stress, and deformation, to investigate and compare the performance of Indonesia's conventional track and the asphaltic underlayment track and to seek the possibility of Indonesia’s passenger trains to travel with higher speed and heavier axle load in the future. The numerical simulation results conclude that the asphaltic underlayment track capable of serving Argo Jati passenger trains set with the medium speed, 240 km/h, or 100 % higher than the existing operating speed. In addition, the application of a 20 cm asphalt layer below ballast will allow each passenger coach to carry the maximum payload up to 30 tons, or 50 % higher than the existing maximum payload. Furthermore, asphaltic underlayment track utilization in Indonesia's railway systems could be beneficial for the optimization of the life cycle cost of the rail track since it could reduce the structure's height, minimize the maintenance needs, and decrease track deterioration especially the mud pumping and deformation.

Disagreement about how best to think of the relation between theories and the realities they represent has a longstanding and venerable history. We take up this debate in relation to the free energy principle (FEP) a contemporary framework in computational neuroscience, theoretical biology and the philosophy of cognitive science. The FEP is very ambitious, extending from the brain sciences to the biology of self-organisation. In this context, some find apparent discrepancies between the map (the FEP) and the territory (target systems) a compelling reason to defend instrumentalism about the FEP. We take this to be misguided. We identify an important fallacy made by those defending instrumentalism about the FEP. We call it the literalist fallacy: this is the fallacy of inferring the truth of instrumentalism based on the claim that the properties of FEP models do not literally map onto real-world, target systems. We conclude that scientific realism about the FEP is a live and tenable o...