Gracheva Research Group

Filtering of Nanoparticles

Translocation dynamics of nanoparticles permeating through the nanopore in an n-Si semiconductor membrane is studied. With the use of Browninan Dynamics to describe the motion of the charged nanoparticles in the self-consistent membrnae electrolyte electrostatic potential, we asses the possibility of using our voltage controlled membrane ofr the macroscopic filtering of the hcarged nanoparticles. The results indicate that the tunable local electric field inside the membrane can effectively control interaction of a nanoparticle with the nanopore by either blocking its passage or increasing the translocation rate. The effect is particularly strong for lager nanoparticels due to their stronger interaction with the membrane while in the nanopore. by extracting the membrane permeability from our microscopic simulations, we compute the macroscopic sieving factors and show that hte size selectivity of the membrane can be tuned by the applied voltage.

Slowing down and stretching DNA

We consider single-stranded DNA translocation through a semiconductor membrane consisting of doped p- and n-layers of Si forming a pn-junction. Using Brownian dynamics simulations of the biomolecule in the self-consistent membrane-electrolyte potential, we show that the polymer translocation through the membrane is slowed down, while polymer length is greatly extended.

Brownian dynamics of DNA

Numerical simulations can provide us with invaluable insight into the microscopic behavior of molecules as they translocate through artificial nanopores. With this in mind, we have developed a computational tool-box that allows us to examine how polymer dynamics will be affected by the electrostatic fields of semiconductor membranes submerged in electrolytic solution. To simulate the electrostatic potential and the charge carrier concentrations in the solid-state membrane and the electrolyte, we have employed the electrostatic approach which is based on the self-consistent solution of Poisson equation within the semiclassical approximation for charge carrier statistics in the membrane and electrolyte.

Protein and ion filter

We shown recently that a semiconductor membrane made of two thin layers of opposite (n- and p-) doping can perform electrically tunable ion current rectification and filtering in a nanopore. Our model is based on the solution of the 3D Poisson equation for the electrostatic potential in a double-cone nanopore combined with a transport model. It predicts that, for appropriate biasing of the membrane-electrolyte system, transitions from ohmic behavior to sharp rectification with vanishing leakage current are achievable. Furthermore, ion current rectifying and filtering regimes of the nanopore correspond to different charge states in the p-n membrane, which can be tuned with appropriate biasing of the n- and p- layers.

DNA translocation through a nanopore

We evaluate the magnitude of the electrical signals produced by DNA translocation through a 1 nm diameter nanopore in a capacitor membrane with a numerical multi-scale approach, and assess the possibility of resolving individual nucleotides as well as their types in the absence of conformational disorder. We show that the maximum recorded voltage caused by the DNA translocation is about 35 mV, while the maximum voltage signal due to the DNA backbone is about 30 mV, and the maximum voltage of a DNA base is about 8 mV. Signals from individual nucleotides can be identified in the recorded voltage traces, suggesting a 1 nm diameter pore in a capacitor can be used to accurately count the number of nucleotides in a DNA strand.

Cell biomechanics

Cell motility is extremely important for many aspects of life from embryonic development and immunity response to wound healing and diseases.

It is not fully understood how cells coordinate overall motility, but from experiments it was established that at least four different stages of locomotion can be distinguished. Cells crawl by extending pseudopodia (filopodia or lamellipodia), adhere, contract and detach the rear. Extension of both filopodia and lamellipodia of most cells is based on actin polymerization. While the protrusive event of cell locomotion is thought to be driven by actin polymerization, the mechanism of forward translocation of the cell body is not completely understood.