Computational cell biology: Spatiotemporal simulation of cellular events

Annual Review of Biophysics and Biomolecular Structure

Volumn 31, Issue , 2002, Pages 423-441

  Slepchenko, Boris M ^a   Schaff, James C ^a   Carson, John H ^a   Loew, Leslie M ^a  

^a UNIVERSITY OF CONNECTICUT HEALTH CENTER   (United States)

Author keywords

Cell physiology; Diffusion; Kinetics; Model; Simulation

Indexed keywords

CALCIUM; RNA;

ANALYTIC METHOD; CALCIUM SIGNALING; CELL FUNCTION; COMPUTER ANALYSIS; COMPUTER MODEL; COMPUTER PROGRAM; COMPUTER SIMULATION; LABORATORY; NONHUMAN; PRIORITY JOURNAL; REVIEW; RNA TRANSPORT;

ANIMALS; BIOPHYSICS; COMPUTER SIMULATION; COMPUTERS; CYTOLOGICAL TECHNIQUES; DIFFUSION; HUMANS; KINETICS; RNA; TIME FACTORS;

EID: 0036085765     PISSN: 10568700     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.biophys.31.101101.140930     Document Type: Review

References (50)

1. Monte Carlo simulation of miniature endplate current generation in the vertebrate neuromuscular junction
2. Inositol trisphosphate and calcium signalling
3. Neuronal calcium signaling
4. Emergent properties of networks of biological signaling pathways
5. Receptor clustering as a cellular mechanism to control sensitivity
6. The balance of power in RNA trafficking
7. RNA trafficking in oligodendrocytes
8. RNA trafficking in myelinating cells
9. Relationship between membrane excitability and single channel open-close kinetics
10. Morphological control of inositol-1,4,5-trisphosphate-dependent signals
11. An image-based model of calcium waves in differentiated neuroblastoma cells
12. A kinetic model of the conductance changes in nerve membrane
13. Exact stochastic simulation of coupled chemical reactions
14. Approximate accelerated stochastic simulation of chemically reacting systems
15. Mathematical simulation and analysis of cellular metabolism and regulation
16. An algorithmic introduction to numerical simulation of stochastic differential equations
17. The NEURON simulation environment
18. Expanding NEURON's repertoire of mechanisms with NMODL
19. A quantitative description of membrane current and its application to conduction and excitation in nerve
20. 2+ sparks
21. STOCHSIM: Modelling of stochastic biomolecular processes
22. Simulation of prokaryotic genetic circuits
23. Non-linear optimization of biochemical pathways: Applications to metabolic engineering and parameter estimation
24. Predicting temporal fluctuations in an intracellular signalling pathway
25. A free-energy-based stochastic simulation of the Tar receptor complex
26. RNA trafficking signals in human immunodeficiency virus type 1
27. The inositol phosphate-calcium signaling system in nonexcitable cells
28. SCAMP: A general-purpose simulator and metabolic control analysis program
29. A general computational framework for modeling cellular structure and function
30. The virtual cell
31. Analysis of non-linear dynamics on arbitrary geometries with the Virtual Cell
32. Physiological modeling with the Virtual Cell framework
33. Ion channel stochasticity may be critical in determining the reliability and precision of spike timing
34. Molecular model of a lattice of signalling proteins involved in bacterial chemotaxis
35. Numerical approach to fast reaction-diffusion systems: Application to buffered calcium waves in bistable models
36. Monte Carlo simulation of neurotransmitter release using MCell, a general simulator of cellular physiological processes
37. The temperature sensitivity of miniature endplate currents is mostly governed by channel gating: Evidence from optimized recordings and Monte Carlo simulations
38. Miniature endplate current rise times less than 100 microseconds from improved dual recordings can be modeled with passive acetylcholine diffusion from a synaptic vesicle
39. E-CELL: Software environment for whole-cell simulation
40. 2+ imaging of organelles, cells, tissues, and organs