The sensitivity analysis of atomic force microscope (AFM) based manipulation of gold spherical nanoparticles in air medium has been carried out in previous research works. In the AFM-based manipulations conducted in various biological liquid mediums, the new environmental parameters associated with these biological fluids also affect the dynamics of the manipulation process. Therefore in this r...

Excitability is an attribute of life, and is a driving force in the descent of complexity. Cellular electrical activity as realized by membrane proteins that act as either channels or transporters is the basis of excitability. Electrical signaling is mediated by a wave of action potentials, which consist of synchronous redistribution of ionic gradients down ion channels. Ion channels select for...

Declaration I hereby declare that this thesis is entirely my own work except where otherwise indicated. I have used only the resources given in the list of references. Abstract An astonishing diversity of biological concepts and processes can be represented by the relatively simple formalism of networks, which consist of nodes connected by edges. Examples range from neuron communication to meta...

This chapter aims to introduce some of the basics of modeling with ODEs in biology. We focus on computational, numerical techniques, rather than on symbolic ones. We restrict our attention to reaction-based models, where the biological interactions are mechanistically described in terms of reactions, reactants and products. We discuss how to build the ODE model associated to a reaction-based mo...

It is argued that multiscale approaches are necessary for an explanatory modeling of biological systems. A first step, besides common to the multiscale modeling of physical and living systems, is a bottom-up integration based on the notions of effective parameters and minimal models. Top-down effects can be accounted for in terms of effective constraints and inputs. Biological systems are essen...