Abstract
Particle-based Monte-Carlo simulations are an important tool for the analysis of microscopic molecular physiology. One of the major challenges in the field is how to accurately simulate molecular diffusion, interaction, and multi-protein complex assembly in the cellular environment. Here we present a novel event-driven simulation scheme (Cellular Dynamics Simulator, CDS) that can address how volume exclusion and molecular crowding impact signaling cascades in small subcellular compartments such as dendritic spines. We contend that the exact molecular collision detection scheme used in this simulator is essential to understand the spatio-temporal pattern of Ca2+-CaM activation during synaptic stimulations. from Seventeenth Annual Computational Neuroscience Meeting: CNS*2008 Portland, OR, USA. 19–24 July 2008
Highlights
Results from a novel Cellular Dynamics Simulator reveal a quantitative mechanism for Ca2+-CaM activation in dendritic spines
FCiag2u+-rCea1M Activation domain Ca2+-CaM Activation domain. (A) A snapshot of a simulation showing that CaM molecules become fully Ca2+ saturated only within close proximity of ion channels with low Ca2+ injection rates
BMC Neuroscience 2008, 9(Suppl 1):P107. Combining this novel simulator and a detailed kinetic model of Ca2+-CaM-CaMKII interactions, we investigate how the rate of Ca2+ injection and the spatial localization of Ca2+ channels impact the spatio-temporal patterns of Ca2+/CaM and CaMKII activations in a simplified dendritic spine
Summary
Results from a novel Cellular Dynamics Simulator reveal a quantitative mechanism for Ca2+-CaM activation in dendritic spines Published: 11 July 2008 BMC Neuroscience 2008, 9(Suppl 1):P107 doi:10.1186/1471-2202-9-S1-P107 We present a novel event-driven simulation scheme (Cellular Dynamics Simulator, CDS) that can address how volume exclusion and molecular crowding impact signaling cascades in small subcellular compartments such as dendritic spines.
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