Organization in the cytoplasm across space and time
Living organisms are characterized by a high degree of spatial organization across a broad range of scales – whether at the level of a protein, an organelle, or a limb, form provides the basis for function and mechanism. Despite this basic biological fact, we tend often to describe the biochemical processes that take place in the cytoplasm as though they are governed by well-defined rate and dissociation constants, even though such mathematical tools originate from idealized models of chemical reactions in well-mixed, dilute solutions. A great deal of experimental evidence now suggests that the cytoplasm is not a mere inchoate jumble of occasionally colliding components, but rather an extremely crowded and exquisitely organized medium, in which the correlated transport, co-localization, and catalytic coordination of various macromolecular components underlies an astounding degree of functional complexity. Our goal is to provide the first systematic characterization of cytosolic organization using the formalism of stochastic reaction-diffusion equations. We are currently in the planning stages of an extensive collaboration with live-cell microscopy experts in the lab of Dan Kaganovich at Hebrew University in Jerusalem. By applying the correlation-function techniques of non-equilibrium statistical mechanics to data from the cutting edge of confocal microscopy, we intend to give a rigorous account of the difference between native and non-native cytosol.