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» Stochastic Simulation Algorithms for Chemical Reactions
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BMCBI
2010
259views more  BMCBI 2010»
13 years 3 months ago
Rule-based spatial modeling with diffusing, geometrically constrained molecules
Background: We suggest a new type of modeling approach for the coarse grained, particle-based spatial simulation of combinatorially complex chemical reaction systems. In our appro...
Gerd Gruenert, Bashar Ibrahim, Thorsten Lenser, Ma...
ICCAD
2010
IEEE
117views Hardware» more  ICCAD 2010»
13 years 6 months ago
A synthesis flow for digital signal processing with biomolecular reactions
Abstract--We present a methodology for implementing digital signal processing (DSP) operations such as filtering with biomolecular reactions. From a DSP specification, we demonstra...
Hua Jiang, Aleksandra P. Kharam, Marc D. Riedel, K...
FPGA
2004
ACM
174views FPGA» more  FPGA 2004»
14 years 1 months ago
A compiled accelerator for biological cell signaling simulations
The simulation of large systems of biochemical reactions is a key part of research into molecular signaling and information processing in biological cells. However, it can be impr...
John F. Keane, Christopher Bradley, Carl Ebeling
ACSD
2008
IEEE
130views Hardware» more  ACSD 2008»
14 years 2 months ago
BAM: BioAmbient machine
In recent years it has become clear that techniques developed for concurrent programming are in fact very useful for the analysis of complex systems in biology. To some level of i...
Vinod A. Muganthan, Andrew Phillips, Maria Grazia ...
ANTSW
2010
Springer
13 years 6 months ago
Evaluating the Robustness of Activator-Inhibitor Models for Cluster Head Computation
Activator-inhibitor models have been widely used to explain several morphogenetic processes. They have also been used to engineer algorithms for computer graphics, distributed syst...
Lidia Yamamoto, Daniele Miorandi