Self-assembly is an equilibrium process, i.e. the individual and assembled components exist in equilibrium. In addition, the flexibility and the lower free energy conformation is usually a result of a weaker intermolecular force between self-assembled moieties and is essentially enthalpic in nature.
The thermodynamics of the self-assembly process can be represented by a simple Gibbs free energy equation:
where if  is negative, self-assembly is a spontaneous process.  is the enthalpy change of the process and is largely determined by the potential energy/intermolecular forces between the assembling entities.  is the change in entropy associated with the formation of the ordered arrangement. In general, the organization is accompanied by a decrease in entropy and in order for the assembly to be spontaneous the enthalpy term must be negative and in excess of the entropy term. This equation shows that as the value of  approaches the value of  and above a critical temperature, the self-assembly process will become progressively less likely to occur and spontaneous self-assembly will not happen.
The self-assembly is governed by the normal processes of nucleation and growth. Small assemblies are formed because of their increased lifetime as the attractive interactions between the components lower the Gibbs free energy. As the assembly grows, the Gibbs free energy continues to decrease until the assembly becomes stable enough to last for a long period of time. The necessity of the self-assembly to be an equilibrium process is defined by the organization of the structure which requires non-ideal arrangements to be formed before the lowest energy configuration is found.
Kinetics
The ultimate driving force in self-assembly is energy minimization and the corresponding evolution towards equilibrium, but kinetic effects can also play a very strong role. These kinetic effects, such as trapping in metastable states, slow coarsening kinetics, and pathway-dependent assembly, are often viewed as complications to be overcome in, for example, the formation of block copolymers.
Amphiphile self-assembly is an essential bottom-up approach of fabricating advanced functional materials. Self-assembled materials with desired structures are often obtained through thermodynamic control. Here, we demonstrate that the selection of kinetic pathways can lead to drastically different self-assembled structures, underlining the significance of kinetic control in self-assembly.