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Mechanobiology is gaining more and more traction as the fundamental role of physical forces in biological function becomes clearer. Forces at the microscale are often measured indirectly using inverse problems such as Traction Force…
We have developed a coarse-grained formulation for modeling the dynamic behavior of cells quantitatively, based on stochasticity and heterogeneity, rather than on biochemical reactions. We treat each reaction as a continuous-time stochastic…
Wet-lab experiments, in which the dynamics within living cells are observed, are usually costly and time consuming. This is particularly true if single-cell measurements are obtained using experimental techniques such as flow-cytometry or…
Application of Microelectronic to bioanalysis is an emerging field which holds great promise. From the standpoint of electronic and system design, biochips imply a radical change of perspective, since new, completely different constraints…
Single-cell analysis is currently one of the most high-resolution techniques to study biology. The large complex datasets that have been generated have spurred numerous developments in computational biology, in particular the use of…
Using bioimaging technology, biologists have attempted to identify and document analytical interpretations that underlie biological phenomena in biological cells. Theoretical biology aims at distilling those interpretations into knowledge…
Optics is an important subfield of physics required for instrument design and used in a variety of other disciplines, including materials science, physics, and life sciences such as developmental biology and cell biology. It is important to…
The molecular biology revolution of the last seventy five years has transformed our view of living systems. Scientific explanations of biological phenomena are now synonymous with the identification of the genes, proteins, and signaling…
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…
This review was written for the Encyclopedia of Complexity and System Science (Springer-Verlag, Berlin, 2008), and is intended as a guide to the growing literature which approaches the phenomena of cell biology from a more theoretical point…
We present a collection of biophysics examination problems that focus on electrodiffusion, the superposition principle, and currents in RC circuits, leading towards an understanding of the Hodgkin-Huxley model of action potentials. These…
Stochastic simulation can make the molecular processes of cellular control more vivid than the traditional differential-equation approach by generating typical system histories instead of just statistical measures such as the mean and…
This paper deals with the derivation of a collective model of cell populations out of an individual-based description of the underlying physical particle system. By looking at the spatial distribution of cells in terms of time-evolving…
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…
Experiments performed in the Physics Laboratory play a significant role in understanding the concepts taught in the theory. A good accompanying laboratory manual serves as a concise guideline which students can use to complete the…
Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with…
To illustrate the power of the biophysical approach in solving important problems in life science, I present here one of our current research projects as an example. We have developed special biophotonic techniques to study the dynamic…
Theory and empirical science should be in constant dialogue, but often find it hard to understand one another. Here we describe a graduate-level university course we developed to improve matters. The course was designed to help…
The research documents the impact of a teaching experiment designed in order to make students consider not only the spectral composition of light but also its intensity when they interpret colour phenomena. The analysis of eight recorded…
This study describes a vision, how technology can help improving the efficiency in research. We propose a new clean-slate design, where more emphasis is given on the correctness and up-to-dateness of the scientific results, it is more open…