Related papers: Incorporating Computational Challenges into a Mult…
Stochastic fluctuations of molecule numbers are ubiquitous in biological systems. Important examples include gene expression and enzymatic processes in living cells. Such systems are typically modelled as chemical reaction networks whose…
Computational problems can be classified according to their algorithmic complexity, which is defined based on how the resources needed to solve the problem, e.g. the execution time, scale with the problem size. Many problems in…
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…
To model combinatorial decision problems involving uncertainty and probability, we introduce stochastic constraint programming. Stochastic constraint programs contain both decision variables (which we can set) and stochastic variables…
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 developed a pilot course focused on mathematical modeling within the tertiary education framework, with a distinct emphasis on sustainability and sustainable development. While an applicable textbook exists for this liberal arts course,…
In this chapter, I discuss teaching mathematical tools specifically tailored for economics students. A typical one-semester course in this area seeks to blend a range of topics: from foundational elements of subjects such as linear algebra…
Quantum Computing is an exciting field that draws from information theory, computer science, mathematics, and quantum physics to process information in fundamentally new ways. There is an ongoing race to develop practical quantum computers…
The ubiquity of technology in our daily lives and the economic stability of the technology sector in recent years, especially in areas with a computer science footing, has led to an increase in computer science enrollment in many parts of…
Both experimental and computational biology is becoming increasingly automated. Laboratory experiments are now performed automatically on high-throughput machinery, while computational models are synthesized or inferred automatically from…
The stochastic simulation of large-scale biochemical reaction networks is of great importance for systems biology since it enables the study of inherently stochastic biological mechanisms at the whole cell scale. Stochastic Simulation…
This book contains a large number of exercises related to different stochastic disciplines. Difficulty of the problems varies from the basic level in the first chapter up to the analysis of articles in Probability, Statistics and Computer…
This article addresses the logistics of implementing projects in an undergraduate mathematics class and is intended both for new instructors and for instructors who have had negative experiences implementing projects in the past. Project…
Bayesian statistics has gained great momentum since the computational developments of the 1990s. Gradually, advances in Bayesian methodology and software have made Bayesian techniques much more accessible to applied statisticians and, in…
Computational methods and associated software implementations are central to every field of scientific investigation. Modern biological research, particularly within systems biology, has relied heavily on the development of software tools…
Much of the research done by modern physicists would be impossible without the use of computation. And yet, while computation is a crucial tool of practicing physicists, physics curricula do not generally reflect its importance and utility.…
Due to the interdisciplinary nature of complex systems as a field, students studying complex systems at University level have diverse disciplinary backgrounds. This brings challenges (e.g. wide range of computer programming skills) but also…
This note presents reflections drawn from my recent experiences in teaching a course on mathematics and sustainability, with a particular emphasis on raising awareness of the topic and its broader implications. The lectures were structured…
As the frontiers of biology become increasingly interdisciplinary, the physics education community has engaged in ongoing efforts to make physics classes more relevant to life sciences majors. These efforts are complicated by the many…
This is lecture notes on the course "Stochastic Processes". In this format, the course was taught in the spring semesters 2017 and 2018 for third-year bachelor students of the Department of Control and Applied Mathematics, School of Applied…