Methodology of the research

Stage 1. 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.