Showing papers by "Leslie Greengard published in 2007"
TL;DR: A fast solver for the inhomogeneous heat equation in free space, following the time evolution of the solution in the Fourier domain is described, based on a recently developed spectral approximation of the free-space heat kernel coupled with the non-uniform fast Fourier transform.
42 citations
TL;DR: The results suggest that the entire topology of the network is needed to impart stability to one portion of thenetwork at the expense of the rest, which could have significant implications for systems biology, in that large, complex pathways may have properties that are not easily replicated with simple modules.
Abstract: We have developed a mathematical approach to the study of dynamical biological networks, based on combining large-scale numerical simulation with nonlinear “dimensionality reduction” methods. Our work was motivated by an interest in the complex organization of the signaling cascade centered on the neuronal phosphoprotein DARPP-32 (dopamine- and cAMP-regulated phosphoprotein of molecular weight 32,000). Our approach has allowed us to detect robust features of the system in the presence of noise. In particular, the global network topology serves to stabilize the net state of DARPP-32 phosphorylation in response to variation of the input levels of the neurotransmitters dopamine and glutamate, despite significant perturbation to the concentrations and levels of activity of a number of intermediate chemical species. Further, our results suggest that the entire topology of the network is needed to impart this stability to one portion of the network at the expense of the rest. This could have significant implications for systems biology, in that large, complex pathways may have properties that are not easily replicated with simple modules.
35 citations
01 Jan 2007
Abstract: An integrated gyrokinetic particle simulation with turbulence and neoclassical physics in a diverted tokamak edge plasma has been performed. Neoclassical equilibrium gyrokinetic solutions in the whole edge plasma have been separated from the turbulence activities for the first time, using the massively parallel Jaguar XT3 computer at Oak Ridge National Laboratory. The equilibrium solutions in an H-mode-like edge plasma condition show strongly sheared global ExB and parallel flows in the entire edge plasma including the pedestal and scrape-off regions. In an L-mode-like edge plasma condition, the sheared flows in the pedestal layer are much weaker, supporting the conjecture that the neoclassical flow-shear may play a significant role in the H-mode physics.
7 citations