Methodology of the research
A powerful computational instrument will be created to modelate
and simulate the molecular dynamics of the bioparticles placed in a
variable electric and/or magnetic field. The molecular dynamics
assumes the integration of the movement equations for dozens of
millions of particles (including solvent molecules) and the extraction
of the equilibrium/transition equations. In these simulations the ions
and water molecules are represented by extended point charges, for
which the far interactions are given by Coulomb’s law, and the short
range forces derive from a Lennard-Jones or Born-Mayer-Huggins. The
molecule can be rigid or flexible; the charges can be constant
(non-polarized model) or fluctuant (polarized model).
Stage 2. During this stage, highly predictive theoretical
models are developed for the evaluation of electro-magnetic properties
of the nano-biosystems; fast converging algorithms are developed as a
part of the virtual investigation instrument. The two activities
contribute to the choice of promising directions to be followed in the
3rd stage. Also, the experimenter identifies the preliminary models
accessible to the experiment, experimental and observation methods.
During this faze we will model and design the microelectrodes for
dielectrophoresis; micromagnets and spin valves for magnetophoresis.
By using the impedance modification when a cell passes through a small
opening, we will develop a new flow cytometer in order to model the
particle transport in blood. We will also study the influence of cell
dimensions on the drag.
Stage 3. In order to set the optimum dimensions and position of
the microelectrodes we will use specialized software packages; ANSYS,
DL_POLY and CHARMM/Amber. The AFM measurements will be done to study
the topography and cartography of the surfaces. The controlled surface
modification will be done by ion bombardment in a reactive ion etching
plasma, in Ar, O2, SF6 or CF4 atmosphere. The microfabrication and
nanopaterning allow the creation of different geometries of
microchannels and the surface functionalization in order to facilitate
the separation and sorting of the molecules. The ion implant of the
surfaces increase the degree of adherence and thus the surface
activation energy increases also.
Stage 4. Fast converging numerical algorithms will be
elaborated in order to reduce the computational effort during the
simulation of the nanometric properties. The classic quantum mechanics
must be adapted to the open systems with mixt spectrum and variable
mass. From the point of view of nanometric structure simulations, the
semiclassic approximations of the hydrodynamic Schrodinger equation
are widely used coupled with the Navier-Stokes equations, the Pradl
equations for the boundary layer and the Poisson equation. An
important limitation in applying these methods is the computational
effort while solving numerically, usually realized by finite elements
or finite difference methods. The simulation is nothing but an
interface between the theory and the experiment. The high costs of a
micro-nanotechnological experiment recommends the use of simulations.
Stage 5. The partial computational results are summed and the
optimized numerical code of the simulator is written. We will realize
final theoretical models of the dielectrophoretic and magnetophoretic
devices. We will elaborate numerical models and we will implement them
in a simulator. We will optimize the numerical algorithms in order to
diminish the computational effort. By comparison with the simulations,
we will validate the theoretical models we have had elaborated. The
research activities bound to the bio/semiconductor interface are done
only up to the simulation, without direct experiments with live cells.