This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Biochemical network modeling of multi-component complexes results in a combinatorial explosion of distinct molecular states (each with a particular combination of binding sites filled) and state transitions (reactions). The underlying mechanistic description, however, can often be summarized in a compact form, a description of individual interactions only enough context to quantify those dependent bindings. This compact form can be formalized as a set of elementary molecules with named binding sites (or domains) and a set of reaction rules. In collaboration with Michael Blinov of Los Alamos National Laboratory, we are investigating the integration of his BioNetGen rules-based biochemical network generator into the Virtual Cell framework. We are pursing separate funding to fully integrate the existing BioNetGen capabilities within the conceptual framework of the Virtual Cell, and to start collaborative research in other aspects of managing combinatorial complexity.
| Ron, Amit; Azeloglu, Evren U; Calizo, Rhodora C et al. (2017) Cell shape information is transduced through tension-independent mechanisms. Nat Commun 8:2145 |
| Schaff, James C; Gao, Fei; Li, Ye et al. (2016) Numerical Approach to Spatial Deterministic-Stochastic Models Arising in Cell Biology. PLoS Comput Biol 12:e1005236 |
| Semenova, Irina; Ikeda, Kazuho; Resaul, Karim et al. (2014) Regulation of microtubule-based transport by MAP4. Mol Biol Cell 25:3119-32 |
| Novak, Igor L; Slepchenko, Boris M (2014) A conservative algorithm for parabolic problems in domains with moving boundaries. J Comput Phys 270:203-213 |
| Michalski, Paul J (2014) First demonstration of bistability in CaMKII, a memory-related kinase. Biophys J 106:1233-5 |
| Azeloglu, Evren U; Hardy, Simon V; Eungdamrong, Narat John et al. (2014) Interconnected network motifs control podocyte morphology and kidney function. Sci Signal 7:ra12 |
| Ditlev, Jonathon A; Mayer, Bruce J; Loew, Leslie M (2013) There is more than one way to model an elephant. Experiment-driven modeling of the actin cytoskeleton. Biophys J 104:520-32 |
| Acker, Corey D; Loew, Leslie M (2013) Characterization of voltage-sensitive dyes in living cells using two-photon excitation. Methods Mol Biol 995:147-60 |
| Loew, Leslie M; Hell, Stefan W (2013) Superresolving dendritic spines. Biophys J 104:741-3 |
| Blasius, T Lynne; Reed, Nathan; Slepchenko, Boris M et al. (2013) Recycling of kinesin-1 motors by diffusion after transport. PLoS One 8:e76081 |
Showing the most recent 10 out of 117 publications
