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We describe a new program package that is designed to perform numerical Molecular Dynamics (MD) and Monte Carlo (MC) simulations for a broad class of soft matter systems in a parallel computing environment. Our main concept in developing ESPResSo was to provide a user friendly and fast simulation tool which serves at the same time as a research platform(More)
Autophagy has been established as a player in host defense against viruses. The mechanisms by which the host induces autophagy during infection are diverse. In the case of HSV type 1 (HSV-1), dsRNA-dependent protein kinase is essential for induction of autophagy in fibroblasts through phosphorylation of eukaryotic initiation factor 2α (eIF2α). HSV-1(More)
The innate immune system senses infection by detecting either evolutionarily conserved molecules essential for the survival of microbes or the abnormal location of molecules. Here we demonstrate the existence of a previously unknown innate detection mechanism induced by fusion between viral envelopes and target cells. Virus-cell fusion specifically(More)
We present a new method, in the following called MMM2D, to accurately calculate the electrostatic energy and forces on charges being distributed in a two dimensional periodic array of finite thickness. It is not based on an Ewald summation method and as such does not require any fine-tuning of an Ewald parameter for convergence. We transform the Coulomb sum(More)
The purpose of this study was to analyze the expression of the two proinflammatory cytokines IL-20 and IL-24 and their shared receptors in rheumatoid arthritis and spondyloarthropathy. IL-20 was increased in plasma of rheumatoid arthritis patients compared with osteoarthritis patients and IL-24 was increased in synovial fluid and plasma of rheumatoid(More)
Based on a parallel scalable library for Coulomb interactions in particle systems, a comparison between the fast multipole method (FMM), multigrid-based methods, fast Fourier transform (FFT)-based methods, and a Maxwell solver is provided for the case of three-dimensional periodic boundary conditions. These methods are directly compared with respect to(More)
c 2004 by John von Neumann Institute for Computing Permission to make digital or hard copies of portions of this work for personal or classroom use is granted provided that the copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. To copy otherwise requires prior(More)
We study the mechanism underlying the attraction between nucleosomes, the fundamental packaging units of DNA inside the chromatin complex. We introduce a simple model of the nucleosome, the eight-tail colloid, consisting of a charged sphere with eight oppositely charged, flexible, grafted chains that represent the terminal histone tails. We demonstrate that(More)
Theoretical estimates for the cutoff errors in the Ewald summation method for dipolar systems are derived. Absolute errors in the total energy, forces and torques, both for the real and reciprocal space parts, are considered. The applicability of the estimates is tested and confirmed in several numerical examples. We demonstrate that these estimates can be(More)