Related papers: Integrative biological simulation praxis: Consider…
Artificial life is a research field studying what processes and properties define life, based on a multidisciplinary approach spanning the physical, natural and computational sciences. Artificial life aims to foster a comprehensive study of…
The aim of this paper is to give an overview of brain organoid computing, its characteristics, challenges, as well as possible advantages for future applications in the field of artificial intelligence. An important part is the extensive…
For decades, researchers have been applying computer simulation to address problems in biology. However, many of these "grand challenges" in computational biology, such as simulating how proteins fold, remained unsolved due to their great…
Deep learning is transforming many areas in science, and it has great potential in modeling molecular systems. However, unlike the mature deployment of deep learning in computer vision and natural language processing, its development in…
We advocates here the use of (mathematical) logic for systems biology, as a unified framework well suited for both modeling the dynamic behaviour of biological systems, expressing properties of them, and verifying these properties. The…
We will review some of the theoretical progresses that have been in the study of complex systems in physics and of their applications to biology.
Computational biology is on the verge of a paradigm shift in its research practice - from a data-based (computational) paradigm to an information-based (cognitive) paradigm. As in the other research fields, this transition is impeded by…
Biological systems are generally complicated and/or complex. In the former approach, one sets up a model with a large number of parameters to describe the system in detail. The latter approach focuses on understanding the universal aspects…
Computer modeling and simulation is used to analyze system behavior and evaluate strategies for operating in descriptive or predictive modes. In this part of the book, modeling and simulation approaches that have been proposed since the…
Modellers of complex biological or social systems are often faced with an invidious choice: to use simple models with few mechanisms that can be fully analysed, or to construct complicated models that include all the features which are…
System and synthetic biology are rapidly evolving systems, but both lack tools such as those used in engineering environments to shift the their focus from the design of parts (details) to the design of systems (behaviors); to aggravate,…
Undergraduate physics education has greatly benefited from the introduction of computational activities. However, despite the benefits computation has delivered, we still lack a complete understanding of the computationally integrated…
Computational models of how users perceive and act within a virtual or physical environment offer enormous potential for the understanding and design of user interactions. Cognition models have been used to understand the role of attention…
Philosophers frequently struggle with the relation of metaphysics to the everyday world, with its practical value, and with its relation to empirical science. This paper distinguishes several different models of the relation between…
While experiments and computer simulations to study biological phenomena are usually performed in diluted in vitro conditions, such phenomena happen inside the cell, an environment densely packed with diverse macromolecules. Here, we revise…
Computer simulations of coarse-grained molecular models for amphiphilic systems can provide insight into the the structure of amphiphiles at interfaces. They can help to identify the factors that determine the phase behavior, and they can…
Bioinformatics has witnessed a paradigm shift with the increasing integration of artificial intelligence (AI), particularly through the adoption of foundation models (FMs). These AI techniques have rapidly advanced, addressing historical…
Research in cell biology is steadily contributing new knowledge about many different aspects of physiological processes like polymerization, both with respect to the involved molecular structures as well as their related function.…
Recent advances in machine learning, coupled with low-cost computation, availability of cheap streaming sensors, data storage and cloud technologies, has led to widespread multi-disciplinary research activity with significant interest and…
The chapter supports educators and postgraduate students in understanding the role of simulation in software engineering research based on the authors' experience. This way, it includes a background positioning simulation-based studies in…