Archives
Please see the NSR Physiome Model Wiki for up-to-date physiological models.
Cellular and Molecular Physiology
- Cellular Diffusion and Transport: Molecular movement inside cytosol, on cell membranes, and transport through nuclear pores are essential cellular processes. These processes were studied in the past by various laboratory biophysical methods combined with computational models based on either the diffusion equation or stochastic Brownian motion. Examples for such models are the theories of fluorescence photobleaching recovery (FPR) and single-particle tracking (SPT).
- Cellular and Tissue Mechanics: Cytoskeleton is responsible for the main mechanical properties of cells and their motilities. Mechanical studies of cells range from microrheology to micropipett asporation and cell indentation (cell poker). There are a wide range of computational models for cell mechanics, ranging from actin filament based models for cell shape and motility to finite-element based models for cell deformation.
- Cellular Energetics: Energy metabolism is one of the most important processes of an intact cell. The key enzymes in the energy metabolism as well as major energy consuming components (i.e. Myosin II, microtuble polymerization, ionic pumping etc) have been characterized in sufficient detail. Specific cells such as muscles and E. Coil's are even better understood. The models for cell energetics are primarily integrated kinetic models.
- Cellular Electrophysiology: Electrophysiology, based on the work of Hodgkin-Huxley and Neher-Sakmann, is one of most well understood components of a cell. The detailed data on channels and their interaction with cell membrane electric potential, provide molecular mechanisms by which computational models have been developed. These models range from simple compartmental models (like that of Hodgkin-Huxley model) to spatially distributed ion movements. Calcium dynamics is also a major modeling subject.
- Cell Homeostasis: Models of cellular metabolism, ionic regulation, energetics, and redox state are examples of systems involved in responses to changes in local environment. These models need to maintain exact mathematical balances of mass, charge, energy and so on. The most primitive models of this sort will serve a starting points for details models for metabolism, signaling, energy, and gene transcription regulation. The principles are described in "The modeling of the primitive 'sustainable' conservative cell." by J. Bassingthwaighte in Phil Trans Roy Soc Lond A 369: 1055-1072, 2001.
- Cellular Signal Transduction: Signal transduction is the "central nervous system" of a cell. The discoveries of transmembrane ligand activation, phosphorylation, and key second messengers have shown an intricate network of signaling and regulation of cell functions in terms of protein-protein interactions and biochemical kinetics.
- Cellular Genetics: Studying genetics in terms of cellular processes of replication, transcription and translation is one of the highest achievement of molecular biology. These cellular processes have been extensively studied in the past 20 years and large molecular machinary were discovered for assisting the highly accurate molecular processes. Modeling in this area ranges from protein-DNA interaction and their thermodynamics, to DNA looping, to RNA polymerase moving as a motor protein along the DNA templet. Mathematical studies of DNA elasticity and topology have also contributed significant insights into the nature of molecular biological processes.
[This page was last modified 04Feb08, 4:10 pm.]
Model development and archiving support at physiome.org provided by the following grants: NIH/NHLBI T15 HL88516-01 Modeling for Heart, Lung and Blood: From Cell to Organ, 4/1/07-3/31/11; NSF BES-0506477 Adaptive Multi-Scale Model Simulation, 8/15/05-7/31/08; NIH/NHLBI R01 HL073598 Core 3: 3D Imaging and Computer Modeling of the Respiratory Tract, 9/1/04-8/31/09; as well as prior support from NIH/NCRR P41 RR01243 Simulation Resource in Circulatory Mass Transport and Exchange, 12/1/1980-11/30/01 and NIH/NIBIB R01 EB001973 JSim: A Simulation Analysis Platform, 3/1/02-2/28/07.
