16,621 research outputs found
Compartmental Modeling for the Neophyte: An Application of Berkeley Madonna
Compartmental modeling serves as a necessary framework in many fields, especially biomathematics and ecology. This article introduces readers to a user-friendly approach to constructing compartmental models and solving the resulting systems of differential equations to simulate real-world applications. The platform used is Berkeley Madonna, a software package that has an intuitive graphical interface which empowers usersāeven those with limited mathematical and programming backgroundsāto focus on modeling concepts rather than mathematical or programming intricacies. This makes Berkeley Madonna an ideal platform for students, educators, and researchers
Berkeley Madonna Version 10-A simulation package for solving mathematical models.
Berkeley Madonna is a software program that provides an easy and intuitive environment for graphically building and numerically solving mathematical equations. Our users range from college undergraduates with little or no mathematical experience to academic researchers and professionals building and simulating sophisticated mathematical models that represent complex systems in the biological, chemical, and engineering fields. Here we briefly describe our recent advances including a new Java-based user interface introduced in Version 9 and our transition from a 32- to 64-bit architecture with the release of Version 10. We take the reader through an example tutorial that illustrates how to construct a mathematical model in Berkeley Madonna while highlighting some of the recent changes to the software. Specifically, we construct a standard pharmacokinetic model of the antifungal medication amphotericin B taken from the literature and discuss aspects related to model building, key numerical considerations, data fitting, and graphical visualization. We end by discussing planned functionality and features intended for future releases
Renaissance theories of vision
A collection of essays by leading art and architectural historians which examine treatises and works of art produced throughout Europe during the Renaissance in order to understand how artists and writers conceived of processes of vision and perception, and how those conceptions influenced the works of art.
Keywords: Renaissance, vision, perception, optics, Plato (Meno, Republic, Symposium, Timaeus), Aristotle (De anima, Metaphysics, Nicomachean Ethics, Physics), Plotinus (Enneads), Saint Augustine (De Civitate Dei), Ibn Sina (Avicenna, Liber canonis), Ibn al-Haytham (Alhazen, De Aspectibus), Ibn Sahl, Marsilio Ficino (De amore, Theologia Platonica), Nicholas of Cusa (On Conjecture, On Learned Ignorance, On the Vision of God), Leon Battista Alberti (De pictura), Gian Paolo Lomazzo (Trattato della pittura), Gregorio Comanini (Il Figino), John Davies (Nosce Teipsum, Orchestra), RenĆ© Descartes (Optics), Samuel van Hoogstraten, George Berkeley (A New Theory of Vision), Florence, Rome, Venice, England, Austria, Netherlands, Fra Angelico (Annunciation, Lamentation, Lamentation Over the Dead Christ), Donatello (Chellini Madonna, Coronation of the Virgin, Crucifix, Piot Madonna), Leonardo da Vinci (Last Supper, Notebooks, Treatise on Painting, Two Views of the Skull, Uffizi Annunciation, Vitruvian Man), Filippino Lippi (Delphic Sibyl), Giovanni Bellini (Agony in the Garden, Coronation of the Virgin), Raphael (Disputa, Holy Family, Jurisprudence, Madonna di Foligno, Parnassus, School of Athens, Sistine Madonna), Parmigianino (Self Portrait in a Convex Mirror), Titian (Assunta, Salome), Bronzino (Pygmalion and Galatea), Johannes Gumpp (Self Portrait), Rembrandt van Rijn (Bathsheba at Her Bath, Jeremiah Lamenting the Destruction of Jerusalem, The Jewish Bride, Lucretia, The Night Watch, Salome, Self Portrait, The Syndics, Titus, A Woman Bathing), Svetlana Alpers (The Art of Describing, Rembrandtās Enterprise, The Vexations of Art), Thomas Aquinas (Summa Theologica, Commentary on the Sentences), Roger Bacon, Francesco Barozzi, Celeste Brusati (Artifice and Illusion), Norman Bryson (Looking at the Overlooked, Vision and Painting), Baldessare Castiglione (Libro del cortegiano), catoptrics, dioptrics, extramission, intromission, Benvenuto Cellini (Perseus), Giovanni Chellini, Antonio Correggio (Assumption of the Virgin), Georges Didi-Huberman (Fra Angelico), Samuel Edgerton (The Heritage of Giottoās Geometry), Euclid (Elements of Geometry, Optica), KamÄl al-DÄ«n al-FÄrisÄ« (The Revision of Optics), Giovan Ambrogio Figino, Fra Bartolommeo, Fra Filippo Lippi (Annunciation), Piero della Francesca (De prospectiva pingendi), Galileo (Sidereus Nuncius), Galleria degli Uffizi, Galleria Doria Pamphili, Lorenzo Ghiberti (Commentaries), Domenico Ghirlandaio (Annunciation), Giles of Viterbo, Giorgione (Adoration of the Shepherds), Herbert Grabes (The Mutable Glass), Anthony Grafton (Leon Battista Alberti), Martin Heidegger (Poetry, Language, Thought), Edmund Husserl, Cristiaan Huygens, Immanuel Kant (Critique of Pure Reason), Martin Kemp (The Science of Art), Johannes Kepler, Alkindi (De Aspectibus), Murray Krieger (Ekphrasis), Diogenes Laertius (On the Lives of Philosophers), John Locke, Andrea Mantegna (Friedsam Madonna, St. Sebastion, Trivulzio Altarpiece), Giambattista Marino (La galeria), Masaccio (Tribute Money, Trinity), Museo San Marco, Narcissus, Neoplatonism, Agrippa von Nettesheim (De occulta philosophia), Erwin Panofsky, Platonic Academy, Pliny the Elder, Proclus (Commentary on the First Book of Euclidās Elements), Ptolemy, Pythagoras, Peter Paul Rubens (Judith with the Head of Holofernes), William Shakespeare (The Rape of Lucrece, Venus and Adonis), Stanza della Segnatura, Giorgio Vasari (Vite), Vatican, Diego VelĆ”zquez (The Spinners), Johannes Vermeer (The Artist in His Studio, Girl with a Pearl Earring, View of Delft), Ernst van de Wetering (Rembrandt), Joost van den Vondel, Erasmus Witelo (Perspectivae), Heinrich Wƶlfflin (Principles of Art History
Teaching mathematical modelling: a research based approach
A collaborative, research based laboratory experiment in mathematical modelling was included in a bioprocess engineering laboratory module, taught as part of an interdisciplinary program in biotechnology. The class was divided into six groups of three students and given the task of investigating a novel diafiltration process that is currently the focus of international research. Different aspects of the problem were assigned to each group and inter-group communication via email was required to ensure that there was a coherent set of objectives for each group and for the class as a whole. The software package, Berkeley Madonna, was used for all calculations. As well as giving the students an introduction to mathematical modelling and computer programming, this approach helped to illustrate the importance of research in bioprocess engineering.
In general, the experiment was well received by the students and the fact that they were discovering new knowledge generated a degree of enthusiasm. However, many students were consumed by the technical demands of computer programming, especially the attention to detail required. Thus, they did not think too deeply about the physical aspects of the system they were modelling. In future years, therefore, consideration will be given to giving the student prior instruction in the use of the software
FluxSimulator: An R Package to Simulate Isotopomer Distributions in Metabolic Networks
The representation of biochemical knowledge in terms of fluxes (transformation rates) in a metabolic network is often a crucial step in the development of new drugs and efficient bioreactors. Mass spectroscopy (MS) and nuclear magnetic resonance spectroscopy (NMRS) in combination with ^13C labeled substrates are experimental techniques resulting in data that may be used to quantify fluxes in the metabolic network underlying a process. The massive amount of data generated by spectroscopic experiments increasingly requires software which models the dynamics of the underlying biological system. In this work we present an approach to handle isotopomer distributions in metabolic networks using an object-oriented programming approach, implemented using S4 classes in R. The developed package is called FluxSimulator and provides a user friendly interface to specify the topological information of the metabolic network as well as carbon atom transitions in plain text files. The package automatically derives the mathematical representation of the formulated network, and assembles a set of ordinary differential equations (ODEs) describing the change of each isotopomer pool over time. These ODEs are subsequently solved numerically. In a case study FluxSimulator was applied to an example network. Our results indicate that the package is able to reproduce exact changes in isotopomer compositions of the metabolite pools over time at given flux rates.
Category theory applied to a radically new but logically essential description of time and space
McTaggart's ideas on the unreality of time as expressed in "The Nature of Existence" have retained great interest for many years for scholars, academics and other philosophers. In this essay, there is a brief discussion which mentions some of the high points of this philosophical interest, and goes on to apply his ideas to modern physics and neuroscience. It does not discuss McTaggart's C and D series, but does emphasise how the use of derived versions of both his A and B series can be of great virtue in discussing both the abstract physics of time, and the present and future importance of McTaggart's ideas to the subject of time. Indeed an experiment using human volunteers and dynamic systems modelling which was carried out is described, which illustrates this fact. The Many Bubble Interpretation, which also derives from McTaggart's ideas, is discussed and various examples of its use and effectiveness are referred to. The Schrodinger Cat paradox is essentially resolved in principle, the quantum Zeno effect interpretable, Kwiat's recent result referred to, and the newly discovered reverse Stickgold effect described.\u
Mathematical modelling of bioethanol production from raw sugar beet cossettes in a horizontal rotating tubular bioreactor
Alternative to the use of fossil fuels are biofuels (e.g., bioethanol, biodiesel and biogas), which are more environmentally friendly and which can be produced from different renewable resources. In this investigation, bioethanol production from raw sugar beet cossettes (semi-solid substrate) by yeast Saccharomyces cerevisiae in a horizontal rotating tubular bioreactor (HRTB) was studied. Obtained results show that HRTB rotation mode (constant or interval) and rotation speed have considerable impact on the efficiency of bioethanol production in the HRTB. The main goal of this research was to develop a non-structural mathematical model of bioethanol production from raw sugar beet cossettes in the HRTB. The established mathematical model of bioethanol production in the HRTB describes substrate utilization and product formation (glycerol, ethanol and acetate) and presumes negative impact of high substrate concentration on the working microorganism (substrate inhibition) by using Andrews inhibition kinetics. All simulations of bioethanol production in the HRTB were performed by using Berkeley Madonna software, version 8.3.14 (Berkeley Madonna, Berkeley, CA, USA). The established non-structural bioprocess model describes relatively well the bioethanol production from raw sugar beet cossettes in the HRTB
Toward a simulation approach for alkene ring-closing metathesis : scope and limitations of a model for RCM
A published model for revealing solvent effects on the ring-closing metathesis (RCM) reaction of di-Et diallylmalonate 7 has been evaluated over a wider range of conditions, to assess its suitability for new applications. Unfortunately, the model is too flexible and the published rate consts. do not agree with exptl. studies in the literature. However, by fixing the values of important rate consts. and restricting the concn. ranges studied, useful conclusions can be drawn about the relative rates of RCM of different substrates, precatalyst concn. can be simulated accurately and the effect of precatalyst loading can be anticipated. Progress has also been made toward applying the model to precatalyst evaluation, but further modifications to the model are necessary to achieve much broader aims
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Gendered spaces and practice,relationality, emotion and affect at the Marian shrine of Ta Pinu, Gozo, Malta
In this chapter the case study of Taā Pinu, Gozo, a site of pilgrimage for Marian devotion and the national shrine of Malta, is analysed as a gendered assemblage and an example of the intersection of gender and religion, with attention to the spatial and power relations associated with these flows and processes. Islands have functioned as places of spiritual retreat and subsequent pilgrimage throughout the history of the Christian faith, the liminal character of their coastal landscapes and environments creating particular intertwinings of experience and spiritual practice; yet, whilst this experiential nexus may be extraordinary for visitors, it is the everyday context of daily life for inhabitants (see Maddrell 2011, 2013,
Maddrell and della Dora 2013, Maddrell et al 2015, Maddrell and Scriven (forthcoming)). Here my attention is turned to the island of Gozo in Malta, analysing the Roman Catholic shrine of Taā Pinu, in order to offer a spatial perspective on gender and religion within this specific
context and arena. Whilst the journeys to this island shrine can have significance, drawing on feminist theories of embodiment, my focus here is less on the journey per se and more on the spaces and practices of religious performance and related geographies of spiritual encounter,
emotion and affect, with particular attention to the gendered dimensions of these practices at Taā Pinu. This will be set within the wider context of an overarching analysis of faith practices as embodied in everyday spaces and practices, reflecting a need for more scholarly
attention to examining those pilgrimages which are embedded in everyday practice rather than a stand-alone extraordinary event (Maddrell 2013). It is hoped that this meshing of perspectives and themes will yield fresh understanding of the specific place-time dynamics of
gender and religion at Taā Pinu, and in turn contribute to a spiritually-inflected understanding of gendered discourses and practices. Before turning to the core discussion, Marian veneration as a form of pilgrimage practice and the history of the Taā Pinu shrine are briefly
outlined, and fieldwork methodologies explained
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