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Teusink B.,VU University Amsterdam | Teusink B.,Netherlands Institute Systems Biology NISB | Teusink B.,Kluyver Center for Genomics of Industrial Fermentation | Westerhoff H.V.,Netherlands Institute Systems Biology NISB | And 5 more authors.
Wiley Interdisciplinary Reviews: Systems Biology and Medicine

Comparative analyses, as carried out by comparative genomics and bioinformatics, have proven extremely powerful to obtain insight into the identity of specific genes that underlie differences and similarities across species. The central concept developed in this chapter is that important aspects of the functional differences between organisms derive not only from the differences in genetic components (which underlies comparative genomics) but also from dynamic, molecular (physical) interactions. Approaches that aim at identifying such networkbased rather than component-based homologies between species we shall call Comparative Systems Biology. It will be illustrated by a number of examples from metabolic networks from prokaryotes, via yeast, to man. The potential for species comparisons, at the genome-scale using classical approaches and at the more detailed level of dynamic molecular networks will be illustrated. In our opinion, comparative systems biology, as a marriage between bioinformatics and systems biology, will offer new insights into the nature of organisms for the benefit of medicine, biotechnology, and drug design. As dynamic modeling is becoming more mainstream in cell biology, the potential of comparative systems biology will become more evident. © 2010 John Wiley & Sons, Inc. Source

Camporeale E.,Center for Mathematics and Computer Science Amsterdam | Zimbardo G.,University of Calabria
Physics of Plasmas

We present a self-consistent Particle-in-Cell simulation of the resonant interactions between anisotropic energetic electrons and a population of whistler waves, with parameters relevant to the Earth's radiation belt. By tracking PIC particles and comparing with test-particle simulations, we emphasize the importance of including nonlinear effects and time evolution in the modeling of wave-particle interactions, which are excluded in the resonant limit of quasi-linear theory routinely used in radiation belt studies. In particular, we show that pitch angle diffusion is enhanced during the linear growth phase, and it rapidly saturates well before a single bounce period. This calls into question the widely used bounce average performed in most radiation belt diffusion calculations. Furthermore, we discuss how the saturation is related to the fact that the domain in which the particles pitch angle diffuses is bounded, and to the well-known problem of 90° diffusion barrier. © 2015 AIP Publishing LLC. Source

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