Results for 'Computer simulations in biochemistry'

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  1.  31
    Computer simulations and experiments: in vivo–in vitro conditions in biochemistry.Pio Garcia - 2015 - Foundations of Chemistry 17 (1):49-65.
    Scientific practices have been changed by the increasing use of computer simulations. A central question for philosophers is how to characterize computer simulations. In this paper, we address this question by analyzing simulations in biochemistry. We propose that simulations have been used in biochemistry long before computers arrived. Simulation can be described as a surrogate relationship between models. Moreover, a simulative aspect is implicit in the classical dichotomy between in vivo–in vitro conditions. (...)
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  2. Computer Simulations in Science and Engineering. Concept, Practices, Perspectives.Juan Manuel Durán - 2018 - Springer.
    This book addresses key conceptual issues relating to the modern scientific and engineering use of computer simulations. It analyses a broad set of questions, from the nature of computer simulations to their epistemological power, including the many scientific, social and ethics implications of using computer simulations. The book is written in an easily accessible narrative, one that weaves together philosophical questions and scientific technicalities. It will thus appeal equally to all academic scientists, engineers, and (...)
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  3.  60
    Computer Simulation in the Physical Sciences.Fritz Rohrlich - 1990 - PSA: Proceedings of the Biennial Meeting of the Philosophy of Science Association 1990:507-518.
    Computer simulation is shown to be philosophically interesting because it introduces a qualitatively new methodology for theory construction in science different from the conventional two components of "theory" and "experiment and/or observation". This component is "experimentation with theoretical models." Two examples from the physical sciences are presented for the purpose of demonstration but it is claimed that the biological and social sciences permit similar theoretical model experiments. Furthermore, computer simulation permits theoretical models for the evolution of physical systems (...)
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  4. Computer Simulations in Science.Eric Winsberg - forthcoming - Stanford Encyclopedia of Philosophy.
  5.  15
    Complexity Computer Simulation in the Study of the Overall Playing Method of Campus Football.Zhao Dai - 2021 - Complexity 2021:1-9.
    With the mutual exchange and integration of world football, modern football is in an increasingly comprehensive direction. This research mainly discusses complexity computer simulation in the study of the overall play of campus football. Complexity computer simulation is used to design the background of the simulated football field, and the area is divided according to the size ratio of the actual football field. Then, it uses drawing software to draw the football and player controls. The construction of the (...)
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  6.  11
    Computer Simulation in the Physical Sciences.Fritz Rohrlich - 1990 - PSA Proceedings of the Biennial Meeting of the Philosophy of Science Association 1990 (2):507-518.
    The central claim of this paper is that computer simulation provides (though not exclusively) a qualitatively new and different methodology for the physical sciences, and that this methodology lies somewhere intermediate between traditional theoretical physical science and its empirical methods of experimentation and observation. In many cases it involves a new syntax which gradually replaces the old, and it involves theoretical model experimentation in a qualitatively new and interesting way. Scientific activity has thus reached a new milestone somewhat comparable (...)
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  7.  37
    Collaborative computer simulations in climate science.Anouk Barberousse, Henri Galinon & Marion Vorms - unknown
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  8.  65
    Introduction: Computer Simulations in Social Epistemology.Igor Douven - 2009 - Episteme 6 (2):107-109.
    Over recent decades, computer simulations have become a common tool among practitioners of the social sciences. They have been utilized to study such diverse phenomena as the integration and segregation of different racial groups, the emergence and evolution of friendship networks, the spread of gossip, fluctuations of housing prices in an area, the transmission of social norms, and many more. Philosophers of science and others interested in the methodological status of these studies have identified a number of distinctive (...)
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  9.  72
    Computer simulations in game theory.Paul Weirich - manuscript
    A computer simulation runs a model generating a phenomenon under investigation. For the simulation to be explanatory, the model has to be explanatory. The model must be isomorphic to the natural system that realizes the phenomenon. This paper elaborates the method of assessing a simulation's explanatory power. Then it illustrates the method by applying it to two simulations in game theory. The first is Brian Skyrms's (1990) simulation of interactive deliberations. It is intended to explain the emergence of (...)
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  10.  24
    Computer simulations in metaphysics: Possibilities and limitations.Billy Wheeler - 2019 - Manuscrito 42 (3):108-148.
    Computer models and simulations have provided enormous benefits to researchers in the natural and social sciences, as well as many areas of philosophy. However, to date, there has been little attempt to use computer models in the development and evaluation of metaphysical theories. This is a shame, as there are good reasons for believing that metaphysics could benefit just as much from this practice as other disciplines. In this paper I assess the possibilities and limitations of using (...)
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  11.  25
    Mapping an expanding territory: computer simulations in evolutionary biology.Philippe Huneman - 2014 - History and Philosophy of the Life Sciences 36 (1):60-89.
    The pervasive use of computer simulations in the sciences brings novel epistemological issues discussed in the philosophy of science literature since about a decade. Evolutionary biology strongly relies on such simulations, and in relation to it there exists a research program (Artificial Life) that mainly studies simulations themselves. This paper addresses the specificity of computer simulations in evolutionary biology, in the context (described in Sect. 1) of a set of questions about their scope as (...)
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  12.  96
    Computer Simulations, Machine Learning and the Laplacean Demon: Opacity in the Case of High Energy Physics.Florian J. Boge & Paul Grünke - forthcoming - In Andreas Kaminski, Michael Resch & Petra Gehring (eds.), The Science and Art of Simulation II.
    In this paper, we pursue three general aims: (I) We will define a notion of fundamental opacity and ask whether it can be found in High Energy Physics (HEP), given the involvement of machine learning (ML) and computer simulations (CS) therein. (II) We identify two kinds of non-fundamental, contingent opacity associated with CS and ML in HEP respectively, and ask whether, and if so how, they may be overcome. (III) We address the question of whether any kind of (...)
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  13. Explanation by computer simulation in cognitive science.Jordi Fernández - 2003 - Minds and Machines 13 (2):269-284.
    My purpose in this essay is to clarify the notion of explanation by computer simulation in artificial intelligence and cognitive science. My contention is that computer simulation may be understood as providing two different kinds of explanation, which makes the notion of explanation by computer simulation ambiguous. In order to show this, I shall draw a distinction between two possible ways of understanding the notion of simulation, depending on how one views the relation in which a computing (...)
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  14.  38
    Multiplex and Unfolding: Computer Simulation in Particle Physics.Martina Merz - 1999 - Science in Context 12 (2):293-316.
    The ArgumentWhat kind of objects are computer programs used for simulation purposes in scientific settings? The current investigation treats a special case. It focuses on “event generators,” the program packages that particle physicists construct and use to simulate mechanisms of particle production. The paper is an attempt to bring the multiplex and unfolding character of such knowledge objects to the fore: Multiple meanings and functions are embodied in the object and can be drawn out selectively according to the requirements (...)
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  15.  16
    Epistemological Framework for Computer Simulations in Building Science Research: Insights from Theory and Practice.Amos Kalua & James Jones - 2020 - Philosophies 5 (4):30.
    Computer simulations are widely used within the area of building science research. Building science research deals with the physical phenomena that affect buildings, including heat and mass transfer, lighting and acoustic transmission. This wide usage of computer simulations, however, is characterized by a divergence in thought on the composition of an epistemological framework that may provide guidance for their deployment in research. This paper undertakes a fundamental review of the epistemology of computer simulations within (...)
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  16. Tools for Evaluating the Consequences of Prior Knowledge, but no Experiments. On the Role of Computer Simulations in Science.Eckhart Arnold - manuscript
    There is an ongoing debate on whether or to what degree computer simulations can be likened to experiments. Many philosophers are sceptical whether a strict separation between the two categories is possible and deny that the materiality of experiments makes a difference (Morrison 2009, Parker 2009, Winsberg 2010). Some also like to describe computer simulations as a “third way” between experimental and theoretical research (Rohrlich 1990, Axelrod 2003, Kueppers/Lenhard 2005). In this article I defend the view (...)
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  17.  16
    Re-evaluating semi-empirical computer simulations in quantum chemistry.María Silvia Polzella & Penélope Lodeyro - 2019 - Foundations of Chemistry 21 (1):83-95.
    Usually within the context of computer simulations in quantum chemistry practices, there is a distinction between ab initio and semi-empirical methods. Related to this, a controversy within the scientific and philosophical communities came about regarding the superiority of the ab initio methods due to their theoretical rigor. In this article we re-evaluate the condition of the semi-empirical simulations in this area of research. We examine some of the aspects of this debate that have been considered in philosophy (...)
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  18.  21
    Gluing life together. Computer simulation in the life sciences: an introduction.Janina Wellmann - 2018 - History and Philosophy of the Life Sciences 40 (4):70.
    Over the course of the last three decades, computer simulations have become a major tool of doing science and engaging with the world, not least in an effort to predict and intervene in a future to come. Born in the context of the Second World War and the discipline of physics, simulations have long spread into most diverse fields of enquiry and technological application. This paper introduces a topical collection focussing on simulations in the life sciences. (...)
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  19.  87
    Why computer simulations are not inferences, and in what sense they are experiments.Florian J. Boge - 2018 - European Journal for Philosophy of Science 9 (1):1-30.
    The question of where, between theory and experiment, computer simulations (CSs) locate on the methodological map is one of the central questions in the epistemology of simulation (cf. Saam Journal for General Philosophy of Science, 48, 293–309, 2017). The two extremes on the map have them either be a kind of experiment in their own right (e.g. Barberousse et al. Synthese, 169, 557–574, 2009; Morgan 2002, 2003, Journal of Economic Methodology, 12(2), 317–329, 2005; Morrison Philosophical Studies, 143, 33–57, (...)
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  20. Tools or toys? On specific challenges for modeling and the epistemology of models and computer simulations in the social sciences.Eckhart Arnold - manuscript
    Mathematical models are a well established tool in most natural sciences. Although models have been neglected by the philosophy of science for a long time, their epistemological status as a link between theory and reality is now fairly well understood. However, regarding the epistemological status of mathematical models in the social sciences, there still exists a considerable unclarity. In my paper I argue that this results from specific challenges that mathematical models and especially computer simulations face in the (...)
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  21.  10
    Prediction and Application of Computer Simulation in Time-Lagged Financial Risk Systems.Hui Wang, Runzhe Liu, Yang Zhao & Xiaohui Du - 2021 - Complexity 2021:1-10.
    Based on the existing financial system risk models, a set of time-lag financial system risk models is established considering the influence brought by time-lag factors on the financial risk system, and the dynamical behavior of this system is analyzed by using chaos theory. Through Matlab simulation, the bifurcation diagram and phase diagram of time-lag risk intensity and control intensity are plotted. The analysis shows that this kind of time-lag financial system risk model has complex dynamic behavior, different motion states will (...)
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  22.  17
    Application of molecular dynamics computer simulations in the design of a minimal self-replicating molecular machine.Paweł Weroński, Yi Jiang & Steen Rasmussen - 2008 - Complexity 13 (4):10-17.
  23.  12
    Computer Simulations as Fiction in Science.Miloš Agatonović - 2022 - Balkan Journal of Philosophy 14 (1):5-10.
    The present paper intends to show that computer simulations used in science are akin to fiction. Starting from the problem of defining computer simulation, the paper discusses the uses and disadvantages of simulations in science. Computer simulations have a representational function, but they do not resemble the phenomena that they purport to represent. Computer simulations do not preserve the content of the models, input data, and theories from which they proceed, since the (...)
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  24. Computational Explorations in Cognitive Neuroscience: Understanding the Mind by Simulating the Brain.Axel Cleeremans - manuscript
    The goal of computational cognitive neuroscience is to understand how the brain embodies the mind by using biologically based computational models comprised of networks of neuronlike units. This text, based on a course taught by Randall O'Reilly and Yuko Munakata over the past several years, provides an in-depth introduction to the main ideas in the field. The neural units in the simulations use equations based directly on the ion channels that govern the behavior of real neurons and the neural (...)
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  25.  3
    Epistemological aspects of computer simulation in the social sciences: second International Workshop, EPOS 2006, Brescia, Italy, October 5-6, 2006: revised selected and invited papers.Flaminio Squazzoni (ed.) - 2009 - New York: Springer.
    This book constitutes the revised versions of the invited and selected papers from the Second Epistemological Perspectives on Simulation Workshop, EPOS 2006, which was held in Brescia, Italy, during October 5-6, 2006. The 11 papers presented together with 2 invited papers were carefully reviewed and selected from 35 submissions. The topics addressed were epistemological and methodological contents, such as the relevance of empirical foundations for agent-based simulations, the role of theory, the concepts and meaning of emergence, the trade-off between (...)
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  26.  78
    Computer Simulations as Scientific Instruments.Ramón Alvarado - 2022 - Foundations of Science 27 (3):1183-1205.
    Computer simulations have conventionally been understood to be either extensions of formal methods such as mathematical models or as special cases of empirical practices such as experiments. Here, I argue that computer simulations are best understood as instruments. Understanding them as such can better elucidate their actual role as well as their potential epistemic standing in relation to science and other scientific methods, practices and devices.
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  27.  49
    Complexity of a modelling exercise: A discussion of the role of computer simulation in complex system science.Fabio Boschetti, David McDonald & Randall Gray - 2008 - Complexity 13 (6):21-28.
  28.  9
    A computer simulation study of the structures of twin boundaries in body-centred cubic crystals.P. D. Bristowe & A. G. Crocker - 1975 - Philosophical Magazine 31 (3):503-517.
  29.  68
    Computer Simulation Validation: Fundamental Concepts, Methodological Frameworks, and Philosophical Perspectives.Claus Beisbart & Nicole J. Saam (eds.) - 2019 - Springer Verlag.
    This unique volume introduces and discusses the methods of validating computer simulations in scientific research. The core concepts, strategies, and techniques of validation are explained by an international team of pre-eminent authorities, drawing on expertise from various fields ranging from engineering and the physical sciences to the social sciences and history. The work also offers new and original philosophical perspectives on the validation of simulations. Topics and features: introduces the fundamental concepts and principles related to the validation (...)
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  30. Are computer simulations experiments? And if not, how are they related to each other?Claus Beisbart - 2018 - European Journal for Philosophy of Science 8 (2):171-204.
    Computer simulations and experiments share many important features. One way of explaining the similarities is to say that computer simulations just are experiments. This claim is quite popular in the literature. The aim of this paper is to argue against the claim and to develop an alternative explanation of why computer simulations resemble experiments. To this purpose, experiment is characterized in terms of an intervention on a system and of the observation of the reaction. (...)
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  31.  26
    Computer simulation of reactions between an edge dislocation and glissile self-interstitial clusters in iron.D. J. Bacon, Y. N. Osetsky & Z. Rong - 2006 - Philosophical Magazine 86 (25-26):3921-3936.
  32.  76
    Computer simulation and philosophy of science: Eric Winsberg: Science in the age of computer simulation. Chicago: The University of Chicago Press, 2010, 168pp, $24.00 PB.Wendy S. Parker - 2011 - Metascience 21 (1):111-114.
    Computer simulation and philosophy of science Content Type Journal Article Pages 1-4 DOI 10.1007/s11016-011-9567-8 Authors Wendy S. Parker, Department of Philosophy, Ellis Hall 202, Ohio University, Athens, OH 45701, USA Journal Metascience Online ISSN 1467-9981 Print ISSN 0815-0796.
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  33.  9
    Computer simulation of the phenomenological transport coefficient in the lattice gas and Fick's First Law.I. V. Belova, M. J. Brown & G. E. Murch † - 2005 - Philosophical Magazine 85 (14):1495-1506.
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  34.  7
    Juan Manuel Durán, Computer Simulations in Science and Engineering: Concepts-Practices-Perspectives, Cham, Springer International, 2018, 209 pp. [REVIEW]Leandro Giri - 2019 - Análisis Filosófico 39 (2):231-233.
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  35.  8
    Are You in a Computer Simulation?Nick Bostrom - 2016 - In Susan Schneider (ed.), Science Fiction and Philosophy: From Time Travel to Superintelligence. Hoboken, NJ: Wiley. pp. 22–25.
    This chapter develops the issue of external world skepticism in a stunning new direction, suggesting that virtual reality science fiction thought experiments depict science fact. The author has authored an influential argument that we are, in fact, in a computer simulation. He observes that assuming that a civilization survives long enough to be technologically sophisticated, it would likely be very interested in running simulations of entire worlds. The core of the simulation argument shows that we should accept as (...)
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  36.  44
    Qualitative Models in Computational Simulative Sciences: Representation, Confirmation, Experimentation.Nicola Angius - 2019 - Minds and Machines 29 (3):397-416.
    The Epistemology Of Computer Simulation has developed as an epistemological and methodological analysis of simulative sciences using quantitative computational models to represent and predict empirical phenomena of interest. In this paper, Executable Cell Biology and Agent-Based Modelling are examined to show how one may take advantage of qualitative computational models to evaluate reachability properties of reactive systems. In contrast to the thesis, advanced by EOCS, that computational models are not adequate representations of the simulated empirical systems, it is shown (...)
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  37. Computer Simulation, Measurement, and Data Assimilation.Wendy S. Parker - 2017 - British Journal for the Philosophy of Science 68 (1):273-304.
    This article explores some of the roles of computer simulation in measurement. A model-based view of measurement is adopted and three types of measurement—direct, derived, and complex—are distinguished. It is argued that while computer simulations on their own are not measurement processes, in principle they can be embedded in direct, derived, and complex measurement practices in such a way that simulation results constitute measurement outcomes. Atmospheric data assimilation is then considered as a case study. This practice, which (...)
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  38. Layers of Models in Computer Simulations.Thomas Boyer-Kassem - 2014 - International Studies in the Philosophy of Science 28 (4):417-436.
    I discuss here the definition of computer simulations, and more specifically the views of Humphreys, who considers that an object is simulated when a computer provides a solution to a computational model, which in turn represents the object of interest. I argue that Humphreys's concepts are not able to analyse fully successfully a case of contemporary simulation in physics, which is more complex than the examples considered so far in the philosophical literature. I therefore modify Humphreys's definition (...)
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  39. Computer Simulations as Experiments.Anouk Barberousse, Sara Franceschelli & Cyrille Imbert - 2009 - Synthese 169 (3):557 - 574.
    Whereas computer simulations involve no direct physical interaction between the machine they are run on and the physical systems they are used to investigate, they are often used as experiments and yield data about these systems. It is commonly argued that they do so because they are implemented on physical machines. We claim that physicality is not necessary for their representational and predictive capacities and that the explanation of why computer simulations generate desired information about their (...)
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  40.  45
    Computer Simulations: An Inferential Conception.Otávio Bueno - 2014 - The Monist 97 (3):378-398.
    In this paper, I offer an inferential conception of computer simulations, emphasizing the role that simulations play as inferential devices to represent empirical phenomena. Three steps are involved in a simulation: an immersion step, a derivation step, and an interpretation and correction step. After presenting the view, I mention some cases, such as simulations of the current flow between silicon atoms and buckyballs as well as of genetic regulatory systems. I argue that the inferential conception accommodates (...)
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  41. Computer simulation and the features of novel empirical data.Greg Lusk - 2016 - Studies in History and Philosophy of Science Part A 56:145-152.
    In an attempt to determine the epistemic status of computer simulation results, philosophers of science have recently explored the similarities and differences between computer simulations and experiments. One question that arises is whether and, if so, when, simulation results constitute novel empirical data. It is often supposed that computer simulation results could never be empirical or novel because simulations never interact with their targets, and cannot go beyond their programming. This paper argues against this position (...)
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  42.  15
    Computer simulation of spherical crystal surfaces: Stacking faults and partial dislocation in f.c.c. crystals.A. J. Perry & D. G. Brandon - 1968 - Philosophical Magazine 18 (152):353-359.
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  43.  19
    Computer simulation of spherical crystal surfaces : Dislocation loops and dipoles in b.c.c. and f.c.c. crystals.A. J. Perry & D. G. Brandon - 1968 - Philosophical Magazine 17 (146):255-262.
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  44. Computer simulations as a technological singularity in the empirical sciences.Juan M. Durán - forthcoming - In Jim Miller, Roman Yampolskiy, Stuart Armstrong & Vic Callaghan (eds.), The technological singularity: A pragmatic perspective.
  45. Do computer simulations support the Argument from Disagreement?Aron Vallinder & Erik J. Olsson - 2013 - Synthese 190 (8):1437-1454.
    According to the Argument from Disagreement (AD) widespread and persistent disagreement on ethical issues indicates that our moral opinions are not influenced by moral facts, either because there are no such facts or because there are such facts but they fail to influence our moral opinions. In an innovative paper, Gustafsson and Peterson (Synthese, published online 16 October, 2010) study the argument by means of computer simulation of opinion dynamics, relying on the well-known model of Hegselmann and Krause (J (...)
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  46.  6
    Computer simulation of sodium diffusion in β″-alumina.G. E. Muech & R. J. Thorn - 1977 - Philosophical Magazine 35 (2):493-502.
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  47.  7
    Computer simulation of the contrast of small dislocation loops in field-ion images of f.c.c. crystals.Kaj Stolt & Jack Washburn - 1976 - Philosophical Magazine 34 (6):1169-1184.
  48. Computer simulation and the philosophy of science.Eric Winsberg - 2009 - Philosophy Compass 4 (5):835-845.
    There are a variety of topics in the philosophy of science that need to be rethought, in varying degrees, after one pays careful attention to the ways in which computer simulations are used in the sciences. There are a number of conceptual issues internal to the practice of computer simulation that can benefit from the attention of philosophers. This essay surveys some of the recent literature on simulation from the perspective of the philosophy of science and argues (...)
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  49.  12
    A computer simulation study of the interaction of vacancies with twin boundaries in body-centred cubic crystals.K. W. Ingle, P. D. Bristowe & A. G. Crocker - 1976 - Philosophical Magazine 33 (4):663-674.
  50.  20
    Computer simulation of radiation damage in Fe3Al.Roland O. Jackson, H. P. Leighly & D. R. Edwards - 1972 - Philosophical Magazine 25 (5):1169-1193.
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