@article {23355,
	title = {Computational modeling of subcellular transport and signaling},
	journal = {Current Opinion in Structural Biology},
	volume = {25},
	year = {2014},
	month = {Feb},
	pages = {92{\textendash}97},
	publisher = {Department of Bioengineering and Medicine, University of California San Diego, CA, USA.},
	abstract = {Numerous signaling processes in the cell are controlled in microdomains that are defined by cellular structures ranging from nm to μm in size. Recent improvements in microscopy enable the resolution and reconstruction of these micro domains, while new computational methods provide the means to elucidate their functional roles. Collectively these tools allow for a biophysical understanding of the cellular environment and its pathological progression in disease. Here we review recent advancements in microscopy, and subcellular modeling on the basis of reconstructed geometries, with a special focus on signaling microdomains that are important for the excitation contraction coupling in cardiac myocytes.},
	doi = {10.1016/j.sbi.2014.01.006},
	url = {http://dx.doi.org/10.1016/j.sbi.2014.01.006},
	author = {Johan Elon {Hake} and Peter M. {Kekenes-Huskey} and Andrew D. {McCulloch}}
}
@inproceedings {23356,
	title = {A Markov-State Model for the Regulation of the Sarcoplasmic Reticulum Ca2+ ATPase by Phospholamban},
	journal = {Annual meeting in Biophysical society},
	volume = {106},
	year = {2014},
	month = {01/2014},
	publisher = {Elsevier},
	abstract = {Compelling evidence suggests that reduced sarcoplasmic reticulum (SR) Ca 2+ uptake via\&nbsp;the SR Ca 2+ ATPase (SERCA) is a major contributor to the development of Ca 2+ signaling\&nbsp;abnormalities in heart failure, and equally important as other known contributors to impaired\&nbsp;Ca 2+ handling.},
	author = {Peter M. {Kekenes-Huskey} and Andrew G {Edwards} and Johan Elon {Hake} and Anushka P. {Michailova} and Andrew J. {McCammon} and Andrew D. {McCulloch}}
}
@article {Simula.simula.2284,
	title = {Molecular and Subcellular-Scale Modeling of Nucleotide Diffusion in the Cardiac Myofilament Lattice},
	journal = {Biophysical Journal},
	volume = {105},
	number = {9},
	year = {2013},
	pages = {2130},
	doi = {10.1016/j.bpj.2013.09.020},
	author = {Peter M. {Kekenes-Huskey} and Liao, Tao and Andrew K. {Gillette} and Johan Elon {Hake} and Zhang, Yongjie and Anushka P. {Michailova} and Andrew D. {McCulloch} and Andrew J. {McCammon}}
}
@article {Simula.simula.1664,
	title = {Finite-Element Estimation of Protein-ligand Association Rates With Post-Encounter Effects: Applications to Calcium Binding in Troponin C and SERCA},
	journal = {Computational Science \& Discovery},
	volume = {5},
	number = {1},
	year = {2012},
	pages = {014015},
	abstract = {We introduce a computational pipeline and suite of software tools for the approximation of diffusion-limited binding based on a recently developed theoretical framework. Our approach handles molecular geometries generated from high-resolution structural data and can account for active sites buried within the protein or behind gating mechanisms. Using tools from the FEniCS library and the APBS solver, we implement a numerical code for our method and study two Ca2+-binding proteins: troponin C and the sarcoplasmic reticulum Ca2+ ATPase. We find that a combination of diffusional encounter and internal {\textquoteright}buried channel{\textquoteright} descriptions provides superior descriptions of association rates, improving estimates by orders of magnitude.},
	author = {Peter M. {Kekenes-Huskey} and Andrew K. {Gillette} and Johan Elon {Hake} and Andrew J. {McCammon}}
}
@misc {Simula.simula.1428,
	title = {Modeling Calcium Dynamics in Realistic Rabbit Ventricular Myocytes With Several Transverse Tubules},
	year = {2012},
	author = {Peter M. {Kekenes-Huskey} and Johan Elon {Hake} and Cheng, Yuhui and Michael J. {Holst} and Frank B. {Sachse} and John H. {Bridge} and Andrew D. {McCulloch} and Andrew J. {McCammon} and Anushka P. {Michailova}}
}
@misc {Simula.simula.1410,
	title = {Modeling Calcium Sparks in a Three-Dimensional Reconstruction of a Cardiac Calcium Release Unit},
	year = {2012},
	author = {Johan Elon {Hake} and Andrew G {Edwards} and Yu, Z. and Peter M. {Kekenes-Huskey} and Anushka P. {Michailova} and Andrew J. {McCammon} and Michael J. {Holst} and Hoshijima, Masahiko and Andrew D. {McCulloch}}
}
@article {Simula.simula.1318,
	title = {Modeling Cardiac Calcium Sparks in a Three-Dimensional Reconstruction of a Calcium Release Unit},
	journal = {The Journal of Physiology},
	volume = {590},
	number = {18},
	year = {2012},
	month = {Sept},
	pages = {4403-4422},
	author = {Johan Elon {Hake} and Andrew G {Edwards} and Yu, Z. and Peter M. {Kekenes-Huskey} and Anushka P. {Michailova} and Andrew J. {McCammon} and Michael J. {Holst} and Hoshijima, Masahiko and Andrew D. {McCulloch}}
}
@article {Simula.simula.1722,
	title = {Modeling Effects of L-Type Ca2+ Current and Na+-Ca2+ Exchanger on Ca2+ Trigger Flux in Rabbit Myocytes With Realistic T-Tubule Geometries},
	journal = {Frontiers in Physiology},
	volume = {3},
	year = {2012},
	pages = {351},
	keywords = {Workshop},
	author = {Peter M. {Kekenes-Huskey} and Cheng, Yuhui and Johan Elon {Hake} and Frank B. {Sachse} and John H. {Bridge} and Michael J. {Holst} and Andrew J. {McCammon} and Andrew D. {McCulloch} and Anushka P. {Michailova}}
}
@article {Chen-2012-15002,
	title = {Multi-Scale Continuum Modeling of Biological Processes: From Molecular Electro-Diffusion to Sub-Cellular Signaling Transduction},
	journal = {Computational Science \& Discovery},
	volume = {5},
	number = {1},
	year = {2012},
	pages = {015002},
	keywords = {Conference},
	author = {Cheng, Y. and Peter M. {Kekenes-Huskey} and Johan Elon {Hake} and Michael J. {Holst} and Andrew J. {McCammon} and Anushka P. {Michailova}}
}
@misc {Simula.simula.966,
	title = {Contributions of Multiple T-Tubules and Membrane Ca2+ Flux Localization to Sub-Cellular Ca2+ Signaling in Rabbit Ventricular Myocytes},
	year = {2011},
	author = {Peter M. {Kekenes-Huskey} and Johan Elon {Hake} and Cheng, Yuhui and Sachse, Frank and Bridge, John and Andrew J. {McCammon} and Anushka P. {Michailova}}
}
@misc {Simula.simula.968,
	title = {Contributions of Structural T-Tubule Heterogeneities and Membrane Ca2+ Flux Localization to Local Ca2+ Signaling in Rabbit Ventricular Myocytes},
	year = {2011},
	author = {Peter M. {Kekenes-Huskey} and Johan Elon {Hake} and Cheng, Yuhui and Sachse, Frank and Bridge, John and Andrew J. {McCammon} and Anushka P. {Michailova}}
}
