Meredys, a multi-compartment reaction-diffusion simulator using multistate realistic molecular complexes

<p>Abstract</p> <p>Background</p> <p>Most cellular signal transduction mechanisms depend on a few molecular partners whose roles depend on their position and movement in relation to the input signal. This movement can follow various rules and take place in different compartments. Additionally, the molecules can form transient complexes. Complexation and signal transduction depend on the specific states partners and complexes adopt. Several spatial simulator have been developed to date, but none are able to model reaction-diffusion of realistic multi-state transient complexes.</p> <p>Results</p> <p><it>Meredys </it>allows for the simulation of multi-component, multi-feature state molecular species in two and three dimensions. Several compartments can be defined with different diffusion and boundary properties. The software employs a Brownian dynamics engine to simulate reaction-diffusion systems at the reactive particle level, based on compartment properties, complex structure, and hydro-dynamic radii. Zeroth-, first-, and second order reactions are supported. The molecular complexes have realistic geometries. Reactive species can contain user-defined feature states which can modify reaction rates and outcome. Models are defined in a versatile NeuroML input file. The simulation volume can be split in subvolumes to speed up run-time.</p> <p>Conclusions</p> <p><it>Meredys </it>provides a powerful and versatile way to run accurate simulations of molecular and sub-cellular systems, that complement existing multi-agent simulation systems. <it>Meredys </it>is a Free Software and the source code is available at <url>http://meredys.sourceforge.net/</url>.</p

Crossing chronic total occlusions with the Ocelot system: the initial European experience

Aims: The aim of the study was to determine the safety, efficacy and feasibility of a new chronic total occlusion (CTO) device using optical coherence tomography (OCT) technology, the Ocelot catheter (Avinger, Inc., Redwood City, CA, USA), for crossing of SFA CTOs following guidewire failure.Methods and results: Prospective, multicentre, market preference testing. Thirty-three patients with confirmed CTO (99-100% stenosis by visual estimate) of their superficial femoral artery (SFA) were treated between September 28, 2011, and December 9, 2011, at three European centres. Ocelot crossed 94% (31/33) of CTOs, allowing guidewire placement in the distal true lumen. All (100%) lesions were treated without any major adverse safety events. Procedural time and contrast dose were significantly reduced (p&lt;0.0001) when compared with a similar, non-OCT-guided CTO crossing device (Wildcat catheter; Avinger, Inc.). Overall physician feedback on the catheter performance was positive with an 87% average rating of excellent or good across seven categories. Performance ratings of Ocelot's OCT imaging guidance were consistently positive with an 86% average rating of excellent or good across five OCT categories.Conclusions: The Ocelot catheter combines advanced CTO crossing technology with real-time OCT guidance. When compared with a similar non-OCT-guided catheter, crossing efficacy and safety profile improved. Total procedure time and contrast volumes were significantly reduced. The Ocelot is a safe, efficient and effective tool for crossing CTOs