scholarly journals Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models

2015 ◽  
Vol 11 (5) ◽  
pp. e1004096 ◽  
Author(s):  
Jonathan R. Karr ◽  
Alex H. Williams ◽  
Jeremy D. Zucker ◽  
Andreas Raue ◽  
Bernhard Steiert ◽  
...  
2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Joshua Rees-Garbutt ◽  
Oliver Chalkley ◽  
Sophie Landon ◽  
Oliver Purcell ◽  
Lucia Marucci ◽  
...  
Keyword(s):  

Author(s):  
GEORGE S. B. WILLIAMS ◽  
MARCO A. HUERTAS ◽  
GREGORY D. SMITH ◽  
M. SALEET JAFRI ◽  
ERIC A. SOBIE
Keyword(s):  

2015 ◽  
Vol 308 (5) ◽  
pp. H510-H523 ◽  
Author(s):  
Xiao Wang ◽  
Seth H. Weinberg ◽  
Yan Hao ◽  
Eric A. Sobie ◽  
Gregory D. Smith

Population density approaches to modeling local control of Ca2+-induced Ca2+ release in cardiac myocytes can be used to construct minimal whole cell models that accurately represent heterogeneous local Ca2+ signals. Unfortunately, the computational complexity of such “local/global” whole cell models scales with the number of Ca2+ release unit (CaRU) states, which is a rapidly increasing function of the number of ryanodine receptors (RyRs) per CaRU. Here we present an alternative approach based on a Langevin description of the collective gating of RyRs coupled by local Ca2+ concentration ([Ca2+]). The computational efficiency of this approach no longer depends on the number of RyRs per CaRU. When the RyR model is minimal, Langevin equations may be replaced by a single Fokker-Planck equation, yielding an extremely compact and efficient local/global whole cell model that reproduces and helps interpret recent experiments that investigate Ca2+ homeostasis in permeabilized ventricular myocytes. Our calculations show that elevated myoplasmic [Ca2+] promotes elevated network sarcoplasmic reticulum (SR) [Ca2+] via SR Ca2+-ATPase-mediated Ca2+ uptake. However, elevated myoplasmic [Ca2+] may also activate RyRs and promote stochastic SR Ca2+ release, which can in turn decrease SR [Ca2+]. Increasing myoplasmic [Ca2+] results in an exponential increase in spark-mediated release and a linear increase in nonspark-mediated release, consistent with recent experiments. The model exhibits two steady-state release fluxes for the same network SR [Ca2+] depending on whether myoplasmic [Ca2+] is low or high. In the later case, spontaneous release decreases SR [Ca2+] in a manner that maintains robust Ca2+ sparks.


2017 ◽  
Vol 12 (1) ◽  
pp. 45-51 ◽  
Author(s):  
Wei‐Chang Yeh ◽  
Chia‐Ling Huang ◽  
Peijie Lin ◽  
Zhicong Chen ◽  
Yunzhi Jiang ◽  
...  

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