  Throughout our history, we, humans, have sought to better control and
understand our environment. To this end, we have extended our natural senses
with a host of sensors-tools that enable us to detect both the very large, such
as the merging of two black holes at a distance of 1.3 billion light-years from
Earth, and the very small, such as the identification of individual viral
particles from a complex mixture. This dissertation is devoted to studying the
physical mechanisms that govern a tiny, yet highly versatile sensor: the
biological nanopore. Biological nanopores are protein molecules that form
nanometer-sized apertures in lipid membranes. When an individual molecule
passes through this aperture (i.e., "translocates"), the temporary disturbance
of the ionic current caused by its passage reveals valuable information on its
identity and properties. Despite this seemingly straightforward sensing
principle, the complexity of the interactions between the nanopore and the
translocating molecule implies that it is often very challenging to
unambiguously link the changes in the ionic current with the precise physical
phenomena that cause them. It is here that the computational methods employed
in this dissertation have the potential to shine, as they are capable of
modeling nearly all aspects of the sensing process with near atomistic
precision.
  Beyond familiarizing the reader with the concepts and state-of-the-art of the
nanopore field, the primary goals of this dissertation are fourfold: (1)
Develop methodologies for accurate modeling of biological nanopores; (2)
Investigate the equilibrium electrostatics of biological nanopores; (3)
Elucidate the trapping behavior of a protein inside a biological nanopore; and
(4) Mapping the transport properties of a biological nanopore.
  In the first results chapter of this thesis (Chapter 3), we used 3D
equilibrium simulations [...]
