Related papers: Computer Simulation of Biological Processes at the…
One popular assumption regarding biological systems is that traits have evolved to be optimized with respect to function. This is a standard goal in evolutionary computation, and while not always embraced in the biological sciences, is an…
Computer-aided design for synthetic biology promises to accelerate the rational and robust engineering of biological systems; it requires both detailed and quantitative mathematical and experimental models of the processes to (re)design,…
A computer simulation has to be fast to be helpful, if it is employed to study the behavior of a multicomponent dynamic system. This paper discusses modeling concepts and algorithmic techniques useful for creating such fast simulations.…
Generative models are now capable of producing natural language text that is, in some cases, comparable in quality to the text produced by people. In the computing education context, these models are being used to generate code, code…
Probabilistic inference provides a language for describing how organisms may learn from and adapt to their environment. The computations needed to implement probabilistic inference often require specific representations, akin to having the…
Computation, the use of a computer to solve, simulate, or visualize a physical problem, has revolutionized how physics research is done. Computation is used widely to model systems, to simulate experiments, and to analyze data. Yet, in most…
We develop a qualitative model of decision making with two aims: to describe how people make simple decisions and to enable computer programs to do the same. Current approaches based on Planning or Decisions Theory either ignore uncertainty…
Computer simulations have become a very powerful tool for scientific research. Given the vast complexity that comes with many open scientific questions, a purely analytical or experimental approach is often not viable. For example,…
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…
An agent-based computer simulation of death by inheritable mutations in a changing environment shows a maximal population, or avoids extinction, at so intermediate mutation rate of the individuals. Thus death seems needed to al for…
A simple evolutionary model for biological ageing is modified such that it requires a minimum population for survival, like in human society. This social effect leads to a transition between extinction and survival of the species.
An invitation to simulation is made into a realizable challenge: the reader is taken from scratch to games with words, to mathematical models, to statistical analysis, to simulation of evolution. No special requirements are needed: we work…
Student simulation presents a transformative approach to enhance learning outcomes, advance educational research, and ultimately shape the future of effective pedagogy. We explore the feasibility of using large language models (LLMs), a…
Everyday we increasingly rely on machine learning models to automate and support high-stake tasks and decisions. This growing presence means that humans are now constantly interacting with machine learning-based systems, training and using…
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…
Metabolic cybergenetics is a promising concept that interfaces gene expression and cellular metabolism with computers for real-time dynamic metabolic control. The focus is on control at the transcriptional level, serving as a means to…
Despite major advances in quantitative approaches to natural resource management, there has been resistance to using these tools in the actual practice of managing ecological populations. Given a managed system and a set of assumptions,…
Living organisms rely on molecular networks, such as gene circuits and signaling pathways, for information processing and robust decision-making in crowded, noisy environments. Recent advances show that interacting biomolecules…
Decisions by humans depend on their estimations given some uncertain sensory data. These decisions can also be influenced by the behavior of others. Here we present a mathematical model to quantify this influence, inviting a further study…
Over the last century, a large number of physical and mathematical developments paired with rapidly advancing technology have allowed the field of quantum chemistry to advance dramatically. However, the lack of computationally efficient…