We present a computational modeling and numerical simulation framework that enables the integration of multiple physics and spatiotemporal scales in models of physiological systems. This framework is the foundation of the IUPS (International Union of Physiological Sciences) Physiome Project. One novel aspect is the use of CellML, an annotated mathematical representation language, to specify mod...

MOTIVATION The Physiome Model Repository 2 (PMR2) software was created as part of the IUPS Physiome Project (Hunter and Borg, 2003), and today it serves as the foundation for the CellML model repository. Key advantages brought to the end user by PMR2 include: facilities for model exchange, enhanced collaboration and a detailed change history for each model. AVAILABILITY PMR2 is available unde...

The validity of death certification of stroke was studied in the general population cohort at Framingham, MA. During the last 30 years, 5106 people aged 30 to 62 and free of CHD and stroke at entry have been followed for the development of cardiovascular disease including stroke. Of the 280 decedents with certified stroke 113 (40% false negative rate) had no mention of stroke on the death certi...

We investigate the accuracy of the recently proposed centroid molecular dynamics ~CMD! method @J. Cao and G. A. Voth, J. Chem. Phys. 100, 5106 ~1994!# in the presence of highly anharmonic steep short range repulsive potentials. Such potentials are often present in condensed phases and govern collisions between solvent particles. We compare the results of CMD simulations with exact quantum resul...

Teun P. de Boer, Sape van der Werf, Bas Hennekam, David P. Nickerson, Alan Garny, Michèle Gerbrands, Rianne A. M. Bouwmeester, Anne-Petra Rozendal, Ellen Torfs, and Harold V. M. van Rijen Department of Medical Physiology, Division Heart and Lungs, University Medical Center, Utrecht, The Netherlands; Center for Research and Development of Education, Education Center, University Medical Center, U...

The Poh et al. (2012) paper describes the first biophysically based computational model of human jejunal smooth muscle cell (hJSMC) electrophysiology. ionic currents are described by either a traditional Hodgkin-Huxley (HH) formalism or deterministic multi-state Markov (MM) formalism. We create modularized CellML implementation model, which is able to reproduce clamping behaviours individual an...

We propose a method which uses centroid molecular dynamics ~CMD! @J. Cao and G. A. Voth, J. Chem. Phys. 100, 5106 ~1994!# real-time data in conjunction with the imaginary-time data generated using path integral Monte Carlo simulations in a numerical analytic continuation scheme based on the maximum entropy approach. We show that significant improvement is achieved by including short-time CMD da...