Related papers: Computer Simulation of Biological Processes at the…
Systems Biology has emerged in the last years as a new holistic approach based on the global understanding of cells instead of only being focused on their individual parts (genes or proteins), to better understand the complexity of human…
The gradual accumulation of damage and dysregulation during the aging of living organisms can be quantified. Even so, the aging process is complex and has multiple interacting physiological scales -- from the molecular to cellular to whole…
Predicting long-term outcomes of interventions is necessary for educational and social policy-making processes that might widely influence our society for the long-term. However, performing such predictions based on data from large-scale…
This paper introduces two ongoing research projects which seek to apply computer modelling techniques in order to simulate human behaviour within organisations. Previous research in other disciplines has suggested that complex social…
Systems biology models are useful models of complex biological systems that may require a large amount of experimental data to fit each model's parameters or to approximate a likelihood function. These models range from a few to thousands…
We represent a process of learning by using bit strings, where 1-bits represent the knowledge acquired by individuals. Two ways of learning are considered: individual learning by trial-and-error; and social learning by copying knowledge…
Experimental evolution has yielded surprising insights into human history and evolution by shedding light on the roles of chance and contingency in history and evolution, and on the deep evolutionary roots of cooperation, conflict and kin…
Machine Learning techniques have been used to teach computer programs how to play games as complicated as Chess and Go. These were achieved using powerful tools such as Neural Networks and Parallel Computing on Supercomputers. In this…
To maintain homeostasis, living cells process information with networks of interacting molecules. Traditional models for cellular information processing have focused on networks of chemical reactions between molecules. Here, we describe how…
Determining the different conformational states of a protein and the transition paths between them is key to fully understanding the relationship between biomolecular structure and function. This can be accomplished by sampling protein…
Motivated by the results of recent laboratory experiments (Yoshida et al. Nature, 424, 303-306 (2003)) as well as many earlier field observations that evolutionary changes can take place in ecosystems over relatively short ecological time…
We investigate the ability of a genetic algorithm to design cellular automata that perform computations. The computational strategies of the resulting cellular automata can be understood using a framework in which ``particles'' embedded in…
The processes taking place inside the living cell are now understood to the point where predictive computational models can be used to gain detailed understanding of important biological phenomena. A key challenge is to extrapolate this…
Computational modeling is becoming a widely used methodology in modern neuroscience. However, as the complexity of the phenomena under study increases, the analysis of the results emerging from the simulations concomitantly becomes more…
Simulations of the coevolution of many interacting species are performed using the Webworld model. The model has a realistic set of predator-prey equations that describe the population dynamics of the species for any structure of the food…
Genetic algorithms, computer programs that simulate natural evolution, are increasingly applied across many disciplines. They have been used to solve various optimisation problems from neural network architecture search to strategic games,…
Like other types of computational research, modeling and simulation of biological processes (biomodels) is still largely communicated without sufficient detail to allow independent reproduction of results. But reproducibility in this area…
Many mathematical models of synaptic plasticity have been proposed to explain the diversity of plasticity phenomena observed in biological organisms. These models range from simple interpretations of Hebb's postulate, which suggests that…
A primary motivation for our research in Digital Ecosystems is the desire to exploit the self-organising properties of biological ecosystems. Ecosystems are thought to be robust, scalable architectures that can automatically solve complex,…
Simple memorizing tasks have been chosen such as a binary code on a matrix. After the establishment of an appropriate protocol, the codified matrices were individually presented to 150 university students who had to memorize them. A…