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Flow in filopodia: re-organization and the representation of biological entities as computational objects

COMPUTATIONAL & APPLIED MATHEMATICS 2025年第1期44卷 1-27页

作者： Leal, Thiago Franco de Moura, Carlos Antonio Kritz, Mauricio Vieira Prokop, Andreas Rio de Janeiro Fed Inst Rio De Janeiro Brazil Univ Estado Rio De Janeiro Rio De Janeiro Brazil Natl Lab Sci Comp Petropolis Brazil Univ Manchester Manchester England

Actin is the most abundant protein in eukaryotic cells. They form filamentous polymers that are organized in different ways within the cell to perform various functions. For instance, prominent parallel bundles of F-actins mediate the formation and dynamics of filopodia that are long, finger-like protrusions of cell membrane occurring in certain cells, like growing neurons. Understanding actin organization dynamics and its regulation is a crucial problem for biologists that cannot be solved exclusively by biological methods, requiring the support of mathematical and computational modelling. In this work, grounded on a previous hypothesis of ours about the cytosol flow within filopodia, we address several modelling challenges posed by the growth of filopodia in neurons. We use alternative stochastic models and particle-centered numerical methods for transport and elongations, as well as an innovative object-oriented modelling-strategy to represent chemical transformations, polymerization, and their regulation. These modelling strategies allowed for simulating elongations 20 times longer than the typical ranges attained by commonly used filopodia diffusion models, and show that our hypothesis is feasible, acting as a proof-of-concept about the importance of considering organization as a key element in biological explanations.

关键词： Filopodia Actin dynamics Transport phenomena Stochastic model object-oriented programming 70-10 Mathematical modeling orsimulation for problems pertaining to mechanics of particles and systems 92-10Mathematical modeling or simulation for problems pertaining to biology

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Towards Reactive programming for object-oriented Applications

Towards Reactive Programming for Object-Oriented Application...

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12th International Conference on Modularity and Aspect-oriented Software Development

作者： Salvaneschi, Guido Mezini, Mira Tech Univ Darmstadt Software Technol Grp Darmstadt Germany

ISBN: (纸本)9783642550997;9783642550980

Reactive applications are difficult to implement. Traditional solutions based on event systems and the Observer pattern have a number of inconveniences, but programmers bear them in return for the benefits of OO design. On the other hand, reactive approaches based on automatic updates of dependencies - like functional reactive programming and dataflow languages - provide undoubted advantages but do not fit well with mutable objects. In this paper, we provide a research roadmap to overcome the limitations of the current approaches and to support reactive applications in the OO setting. To establish a solid background for our investigation, we propose a conceptual framework to model the design space of reactive applications and we study the flaws of the existing solutions. Then we highlight how reactive languages have the potential to address those issues and we formulate our research plan.

关键词： Reactive programming Functional-reactive programming object-oriented programming Incremental Computation

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Perceptions of computer programming students on interactive environments for teaching object-oriented concepts using Java

Perceptions of computer programming students on interactive ...

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作者： PATRICK MWANSA Cape Peninsula University of Technology

学位级别：硕士

The skill of programming necessitates knowing programming tools, problem solving and effective techniques of program design and implementation. Most students are incapable of fully understanding and utilising the feature set of Integrated Development Environments (IDEs). The feature set of certain IDEs comes with a lot of functionalities and students have to spend a lot of their time studying the features of the IDE without paying much attention to the syntax and semantics of the programming language. The main objective of this study was to examine the perceptions of students on interactive environments for teaching object-oriented concepts using the Java programming language in two integrated development environments. This was done by adopting the ISO 9126 model to select generic external system quality characteristics and sub-characteristics that might influence student evaluation of an IDE. The proposed model was applied on NetBeans and JCreator LE 5.0 as IDEs for teaching Java programming using OOP concepts. The study adopted a mixed method research approach using interviews and questionnaires. A single-case study was used for data collection and analysis. The approaches collected data from two groups of students using either NetBeans or JCreator and who were learning OOP concepts. The study further looked at the students' class tests and exam results in an effort to have an objective overview of how students performed. These groups of students were at two different campuses of the selected University. Each group had already been exposed to the Java syntax. The result from this study was general guidelines to establish an interactive OOP development environment for teaching and learning of Java programming that enhances OOP comprehension. This research study involved human subjects. It was, therefore, a requirement to seek ethics approval. Additionally, the objects involved were students of a selected University and as such a consent letter was sought from the U

关键词： object-oriented programming Java NetBeans JCreator 5.0 IDE

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SYMBOLIC-NUMERICAL object-oriented FINITE ELEMENT programming

SYMBOLIC-NUMERICAL OBJECT-ORIENTED FINITE ELEMENT PROGRAMMIN...

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作者： PISITH SAM THAMMASAT UNIVERSITY

学位级别：硕士

There are times when closed-form analysis of solids and structures is needed. When only a structural member is considered, it is certainly possible to perform this type of analysis by hand. However, when a structure with several members is to be considered, manual calculation becomes practically impossible even when closed-form solutions are theoretically obtainable. A finite element (FE) program that can symbolically analyze elasticity problems of solids and structures can therefore be quite useful. Unfortunately, symbolic computations are usually difficult to perform when problems are complex. In these cases, numerical computations are still necessary. This study presents an object-oriented FE program that can perform both symbolic and numerical computations. The program is implemented in MATLAB. The object-oriented programming (OOP) technique is used to enhance the maintainability, extendibility, and reusability of the program. The proposed program is capable of performing symbolic and numerical finite element analysis depending on the input it receives. The obtained program is tested using some engineering problems in order to demonstrate its usefulness. The results obtained from the program are found to be satisfactory.

关键词： Finite element programming Closed-form analysis Linear elasticity Symbolic computation Numerical computation Symbolic-numerical computation object-oriented programming

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Live But Not Active: Minimal Effect with Passive Live Coding 2025

Live But Not Active: Minimal Effect with Passive Live Coding

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56th Technical Symposium on Computer Science Education

作者： Watkins, Andrea Settle, Amber Miller, Craig S. Schwabe, Eric J. Univ Illinois Urbana IL 61820 USA Depaul Univ Chicago IL USA

ISBN: (纸本)9798400705328

Background: Live coding, or the process of instructors writing code in real time in front of students, is an alternative teaching method to showing students static code examples. Variations of live coding tightly coupled with more active learning approaches are common, which can make it difficult to understand the contribution of live coding alone. Purpose: In this study, we aim to disentangle the benefits of live coding from live coding with explicit active learning approaches. We compare live coding with no added active learning components to presenting students with static code examples. Methods: We present a programming topic to over 100 students using either live coding or static code examples. To more closely parallel showing static code examples, our live coding process involves simply writing and discussing code. We compare student performance and engagement between the two session modes. Findings: Our results show no significant difference between the two presentation modes in terms of learning outcomes. This suggests that live coding in its most basic form may not be sufficiently different from showing static code examples to impact student performance. We also found that live coding students were much more likely to type code, but no more likely to display other engagement behaviors. However, of the engagement activities, only different levels of code typing corresponded with different learning outcomes. Contributions: This research highlights the need for more explicit differentiation and comparisons of live coding with and without active learning strategies.

关键词： engagement live coding object-oriented programming static code examples

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CONSTRUCTION OF AN INTERACTIVE programming ENVIRONMENT FOR CONTROL OF THEATRICAL-SET EFFECTS VIA object-oriented METHODS

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SOFTWARE-PRACTICE & EXPERIENCE 1993年第6期23卷 655-675页

作者： THIRION, B Institut de Recherche Polytechnique 34 rue Marc Seguin BP 2438 68067 Mulhouse Cedex France

This paper describes the object-oriented design of a novel application, for control of complex theatrical-set effects defined by an appropriate language. Besides giving a general description of the proposed system, the paper presents the language and its programming environment, which is intended for inexperienced users and integrates facilities to create, edit, check and run the effect scripts. The description of the implementation demonstrates the relevance of an object-oriented approach when it is associated with compiler techniques. The object paradigm is used to build support classes such as character streams, run-time values or symbols as well as syntactic objects. Each syntactic-object class models a different LL(1) grammar non-terminal and allows for an object-oriented predictive parsing. Moreover, organizing the instances of these classes as an object-based parse tree simplifies parsing, unparsing, syntax-directed editing, syntax-directed help, interpretation, etc. The description of these various operations shows the flexibility of our method, e.g. with respect to an iterative prototyping of the language and its environment.

关键词： THEATRICAL APPLICATION INTERACTIVE programming ENVIRONMENT object-oriented programming

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Application of Robot programming to the Teaching of object-oriented Computer Languages

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INTERNATIONAL JOURNAL OF ENGINEERING EDUCATION 2016年第4期32卷 1823-1832页

作者： Corral, J. M. Rodriguez Morgado-Estevez, A. Cabrera, D. Molina Perez-Pena, F. Rodriguez, C. A. Amaya Balcells, A. Civit Sch Engn Ave Univ Cadiz 10 Puerto Real 11519 Cadiz Spain Tech Sch Comp Engn Ave Reina Mercedes S-N Seville 41012 Spain

object-oriented programming (OOP) abstract concepts are often difficult to understand for students, since it is not easy to find the equivalence of such concepts in daily life. In this paper we will study if an interdisciplinary approach based on an introduction to robotics and robot programming helps the student in acquiring the OOP concepts. For our experiments, we selected a sample of thirty individuals among students with an adequate knowledge of procedural programming. This sample was divided into two groups of fifteen students each: for the first one we used a standard introductory approach to C#, whereas for the second one we developed an experimental course that included a demonstration program that illustrated OOP basic concepts using the features of a specific type of commercial ball-shaped robot with sensing, wireless communication and output capabilities. After the courses, both groups were evaluated by completing a multiple-choice exam and a C# programming exercise. Our results show that the student group that attended the course including the robot demo showed a higher interest level (i.e. they felt more motivated) than those students that attended the standard introductory C# course. Furthermore, the students from the experimental group also achieved an overall better mark.

关键词： interdisciplinary projects mobile robots object-oriented programming robot programming teaching-learning strategies

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Improving modularity in object-oriented finite element programming

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COMMUNICATIONS IN NUMERICAL METHODS IN ENGINEERING 1997年第3期13卷 193-198页

作者： DuboisPelerin, Y Pegon, P COMMISS EUROPEAN COMMUNITIES JOINT RES CTR STRUCT MECH UNIT TP480 I-21020 ISPRA VARESE ITALY

Making a finite element code easier to maintain is achieved by further modularizing it. Due to its two levels of modularity (of procedures and data), object-oriented programming is the method of choice. Its potential is investigated in two bottlenecks of finite element programming where so far it has not proved significantly more successful than classical Fortran programming. The first of these is the lack of adequate data structures between the analysis specifications and the basic objects of the finite element method, like the element and the node. This is solved by defining two classes of objects, namely problem and domain, with clearly differentiated specifications. The second gap deals with solving linear equation systems. Introducing an intermediate class UnassembledMatrix allows alternative storage/solving schemes to be implemented in a very flexible manner. (C) 1997 by John Wiley & Sons, Ltd.

关键词： finite element method software engineering object-oriented programming

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MODULES, objectS AND DISTRIBUTED-programming - ISSUES IN RPC AND REMOTE object INVOCATION

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SOFTWARE-PRACTICE & EXPERIENCE 1991年第1期21卷 77-90页

作者： LEVY, HM TEMPERO, ED Department of Computer Science and Engineering University of Washington Seattle WA 98195 U.S.A.

Distributed programming can be greatly simplified by language support for distributed communication, such as that provided by remote procedure call (RPC) or remote object invocation. This paper examines design and implementation issues in these systems, and focuses on the influence of the communication system on a distributed program. To make the discussion concrete, we introduce a single application as implemented in two environments: Modula-2+, an extension of Modula-2 with RPC, and Emerald, an object-based language that supports remote object invocation. We show that small differences in the implementation of the communication system can have a significant impact on how distributed applications are structured.

关键词： DISTRIBUTED programming object-oriented programming programming LANGUAGES ABSTRACT DATA TYPES REMOTE PROCEDURE CALL

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object logic integration: a multiparadigm design methodology and a programming language

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COMPUTER LANGUAGES 1997年第1期23卷 25-42页

作者： Lee, JHM Pun, PKC UNIV MANCHESTER DEPT COMP SCIMANCHESTER M13 9PLLANCSENGLAND

In the past decade, there has been much research effort dedicated to combine the object-oriented programming paradigm and the logic programming paradigm. Most of this effort sheds light upon the philosophy of multiparadigm programming as a near ideal mental model for a wide class of problem domains. In this paper we propose a scheme for object and logic integration-the OLI scheme. This scheme contributes to the multiparadigm programming philosophy by putting forward a multiparadigm design methodology and describing a multiparadigm programming language. Above all, the OLI scheme integrates the object-oriented and the logic programming paradigms at the design and language levels with a precise and well-balanced interface so that each paradigm shares an equal and cooperating partnership in problem analysis and problem solving. An important property of the OLI language is that programmers can program either in one of the paradigms alone or in a mixed paradigm without sacrificing expressiveness and efficiency. We give,a formal definition of the OLI language and study its semantics both from the logical perspective and the object-oriented perspective. By viewing objects as an enrichment of the Herbrand universe, we define the declarative and operational semantics of OLI. We show that OLI's operational semantics, a generalized form of SLD-resolution, is sound and complete. From the object-oriented point of view, the logic part of OLI is simply an object with logic programs as states and methods for performing logical deduction. (C) 1997 Elsevier Science Ltd.

关键词： multiparadigm programming languages logic programming object-oriented programming

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