title: Stochastic lag time in nucleated linear self-assembly.
abstract: Protein aggregation is of great importance in biology, e.g., in amyloid fibrillation. The aggregation processes that occur at the cellular scale must be highly stochastic in nature because of the statistical number fluctuations that arise on account of the small system size at the cellular scale. We study the nucleated reversible self-assembly of monomeric building blocks into polymer-like aggregates using the method of kinetic Monte Carlo. Kinetic Monte Carlo, being inherently stochastic, allows us to study the impact of fluctuations on the polymerization reactions. One of the most important characteristic features in this kind of problem is the existence of a lag phase before self-assembly takes off, which is what we focus attention on. We study the associated lag time as a function of system size and kinetic pathway. We find that the leading order stochastic contribution to the lag time before polymerization commences is inversely proportional to the system volume for large-enough system size for all nine reaction pathways tested. Finite-size corrections to this do depend on the kinetic pathway.
authors.affiliation: Group Theory of Polymers and Soft Matter, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands.
authors.forename: Nitin S
authors.initials: NS
authors.lastname: Tiwari
authors.affiliation: Group Theory of Polymers and Soft Matter, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands.
authors.forename: Paul
authors.initials: P
authors.lastname: van der Schoot
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D007700:Kinetics; D008958:Models, Molecular; D009010:Monte Carlo Method; D058105:Polymerization; D055503:Protein Multimerization; D013269:Stochastic Processes; D013997:Time Factors