We are developing a novel method to interrogate proteins and their behavior, through electrical manipulation of a single protein molecule on-chip without chemical tethering while simultaneously optically monitoring its physical properties (mass, hydrodynamic radius and low-frequency polarizability) in a label-free fashion. The heart of our approach is controlling the position of the single molecule through dielectrophoresis (the actuation of a polarizable object by a highly inhomogeneous electric field) applied using nanoelectrodes, which can generate sufficiently strong electric fields.
The first part of this assignment is simulation of gold nanoelectrodes in COMSOL (AC field). These fields will be later on used to simulate the motion of a protein in such a trap. Figure 1 shows the sample simulation of sandwich dual hot spot electrodes we are planning to optimize for our use.
Figure 1. (A) 3D rendered image of gold nanoelectrode structures. (B,C) Electric field predicted in the electrodes upon applying AC voltage of 100kHz frequency of 0.5V amplitude in a solution of 1mM ionic strength. The simulation was done in the AC/DC module of COMSOL
The second part of this assignment is transient analysis of electric fields in the nanoelectrode trap/dual nanoelectrode trap. Aim: develop strategies for trapping and actuation of the molecules and beads in the trap
The third part of this assignment is coupling the fields simulated in COMSOL to a python-coded 3D simulation of protein motion(Figure 2) using Langevin equation. These simulations will render multitude of protein trajectories , which will be studied to optimize stability of protein trapping and actuation in such a geometry.
Figure 2. Python simulation of the trajectory of a 50nm particle in the COMSOL-generated potential for a 4-electrode trap