From the article...
Biological tissues serve as model factories for the production of macromolecular structures, where the processes of molecular self-assembly and macroscopic growth are integrated in robust systems, which display self-healing and adaptivity. Growth occurs as nutrients, amino acids, and enzymes undergo mass transport and react to increase tissue mass. At the molecular scale, there is considerable understanding of the reactions for self-assembly of tissue components such as collagen. There is less understanding of the thermodynamic driving forces and of how these interact with growth processes to form multicellular tissue. These processes are also influenced by mechanics at the continuum scale.
One of the things that has been driving me batty in the quest for knowledge in building a whole cell model and simulation is coming up with techniques to verify the resulting simulations are accurate. Obviously an entire model can't be built all at once. It has to be broken down and tackled in pieces and unit tests will be needed for each step of the process and or portion of the model. The timeframes of chemical pathways are so minute and extensive in regards to the number of steps that they are not observable nor testable by simple observation other than evaluating the final outputs of the reactions, which usually are immediate inputs to others. Taking snapshots of cellular activity with a camera at the femptosecond level aren't possible. If I'm wrong, someone please point me to the Amazon link to purchase one [sfty]. Unlike the pathways the cellular scaffolding isn't nearly as transient. While there are ongoing changes to the cytoskeleton (e.g. actin filamants treadmilling), in general, the majority of the cellular cytoskeletal proteins either through the assistance of helper proteins or through self assembly tend to gravitate towards their ultimate role in a macrostructure.
Protein folding will eventually reach a point where secondary through quarternary structures can be much more easily predicted. The next steps will be to model those that the self assemble into larger cellular structures. Assuming the thermodynamic forces and entropical effects of water are accurately accounted for, the in silico behavior of these proteins should match self assembled structures we see ex silico. The assumptions here are not trivial as mixture theory and the various forces involved are not fully understood as the article below points out.
Link: Simulating Self-assembly and Growth of Biological
Other research keywords:
mixture theory
Darcy's Law
Lattice Boltzmann calculations
Law of Mass Balance
Edited by maestro949, 10 March 2006 - 01:53 AM.
