Diffusion and reaction in complex media

In this talk I will illustrate some of the theoretical and computational approaches that we are developing in our group to investigate basic problems in biology and chemistry.
After a first general overview of our activities, I will describe more in detail some theoretical and computational models that we designed to study reaction-diffusion dynamics and equilibria in complex systems.
In all chemical and biochemical reactions occurring in solution, reactants have to form an encounter complex before the specific chemical step. Typically, in order to reach their binding partners, the reactants have to diffuse in complex environments. In living media, for example, the allowed space is (i) crowded with all sorts of biomolecules and organelles and (ii) confining, due to the presence of different membranes and cytoskeletal structures that strongly compartimentalize the available space. Likewise, in modern nano-technological applications, reactions are often realized in confining media, such as nano-reactors of different sort.
As a first application, I will talk about Brownian dynamics simulations of antibodies (IgG) binding to surface-immobilized antigens, such as in kinetics measurements based on surface plasmon resonance (Biacore). The objective of this work is to assess the role of internal flexibility of IgGs and of excluded-volume interactions occurring at the surface on the binding kinetics. Comparison of the simulations with micro-fluidics experiments will also be discussed.
In the last part of the talk, I will illustrate a general theoretical paradigm that we developed to compute the reaction rate constant of a ligand binding to an arbitrary three-dimensional array of spheres, endowed with an arbitrary set of intrinsic reactivities. This allows us to model diffusion-reaction landscapes of arbitrary complexity, made of obstacles (reflecting spheres, i.e. vanishing reactivity) and reactive surfaces of arbitrary strength, both in open and closed domains.
I will discuss several applications, ranging from the diffusion to a binding pocket in a coarse-grained model of protein to reactions occurring in vesicles and other kinds of
nano-reactors.