Maria E. Gracheva

Simulation of the electric response of DNA translocation through a semiconductor nanopore-capacitor

A multi-scale/multi-material computational model for simulation of the electric signal detected on the electrodes of a metal–oxide–semiconductor (MOS) capacitor forming a nanoscale artificial membrane, and containing a nanopore with translocating DNA, is presented. The multi-scale approach is based on the incorporation of a molecular dynamics description of a translocating DNA molecule in the nanopore within a three-dimensional Poisson equation self-consistent scheme involving electrolytic and semiconductor charges for the electrostatic potential calculation. The voltage signal obtained from the simulation supports the possibility for single nucleotide resolution with a nanopore device. The electric signal predicted on the capacitor electrodes complements ongoing experiments exploring the use of nanopores in a MOS capacitor membrane for DNA sequencing.

A Model of Fibroblast Motility on Substrates with Different Rigidities

To function efficiently in the body, the biological cells must have the ability to sense the external environment. Mechanosensitivity toward the extracellular matrix was identified as one of the sensing mechanisms affecting cell behavior. It was shown experimentally that a fibroblast cell prefers locomoting over the stiffer substrate when given a choice between a softer and a stiffer substrate. In this article, we develop a discrete model of fibroblast motility with substrate-rigidity sensing. Our model allows us to understand the interplay between the cell-substrate sensing and the cell biomechanics. The model cell exhibits experimentally observed substrate rigidity sensing, which allows us to gain additional insights into the cell mechanosensitivity.

Electrically tunable solid-state silicon nanopore ion filter

We show that a nanopore in a silicon membrane connected to a voltage source can be used as an electrically tunable ion filter. By applying a voltage between the heavily doped semiconductor and the electrolyte, it is possible to invert the ion population inside the nanopore and vary the conductance for both cations and anions in order to achieve selective conduction of ions even in the presence of significant surface charges in the membrane. Our model based on the solution of the Poisson equation and linear transport theory indicates that in narrow nanopores substantial gain can be achieved by controlling electrically the width of the charge double layer.

Pores with Longitudinal Irregularities Distinguish Objects by Shape

The resistive-pulse technique has been used to detect and size objects which pass through a single pore. The amplitude of the ion current change observed when a particle is in the pore is correlated with the particle volume. Up to date, however, the resistive-pulse approach has not been able to distinguish between objects of similar volume but different shapes. In this manuscript, we propose using pores with longitudinal irregularities as a sensitive tool capable of distinguishing spherical and rod-shaped particles with different lengths. The ion current modulations within resulting resistive pulses carry information on the length of passing objects. The performed experiments also indicate the rods rotate while translocating, and displace an effective volume that is larger than their geometrical volume, and which also depends on the pore diameter.

Simulation of ionic current through the nanopore in a double-layered semiconductor membrane

We study the effects of different nanopore geometries (double-conical, single-conical, cylindrical) on the electrostatic potential distribution and ionic conductivity in a double-layered semiconductor nanopore device as functions of the applied membrane bias. Ionic current-voltage characteristics as well as their rectification ratios are calculated using a simple ion transport model. Based on our calculations, we find that the double-layered semiconductor membrane with a single-conical nanopore with a narrow opening in the n-Si layer exhibits the largest range of available potential variations in the pore and, thus, may be better suited for control of polymer translocation through the nanopore.

Electrolytic charge inversion at the liquid–solid interface in a nanopore in a doped semiconductor membrane

The electrostatics of a nanopore in a doped semiconductor membrane immersed in an electrolyte is studied with a numerical model. Unlike dielectric membranes that always attract excess positive ion charges at the electrolyte/membrane interface whenever a negative surface charge is present, semiconductor membranes exhibit more versatility in controlling the double layer at the membrane surface. The presence of dopant charge in the semiconductor membrane, the shape of the nanopore and the negative surface charge resulting from the pore fabrication process have competing influences on the double layer formation. The inversion of the electrolyte surface charge from negative to positive is observed for n-Si membranes as a function of the membrane surface charge density, while no such inversion occurs for dielectric and p-Si membranes.

Slowing down and stretching DNA with an electrically tunable nanopore in a p–n semiconductor membrane

We have studied single-stranded DNA translocation through a semiconductor membrane consisting of doped p and n layers of Si forming a p-n-junction. Using Brownian dynamics simulations of the biomolecule in the self-consistent membrane-electrolyte potential obtained from the Poisson-Nernst-Planck model, we show that while polymer length is extended more than when its motion is constricted only by the physical confinement of the nanopore. The biomolecule elongation is particularly dramatic on the n-side of the membrane where the lateral membrane electric field restricts (focuses) the biomolecule motion more than on the p-side. The latter effect makes our membrane a solid-state analog of the α-hemolysin biochannel. The results indicate that the tunable local electric field inside the membrane can effectively control dynamics of a DNA in the channel to either momentarily trap, slow down or allow the biomolecule to translocate at will.

Coarse-grained Ginzburg–Landau free energy for Lennard-Jones systems

We discuss the application of Monte Carlo methods to the self-consistent calculation of a Ginzburg–Landau free energy functional for Lennard-Jones systems in three dimensions. Following this discussion, we demonstrate that the parameters in the coarse-grained free energy can be extracted from a multivariate distribution of energies and particle densities which, when suitably reweighted, permit one to extrapolate the results to other nearby points in the thermodynamic parameter space. For the purposes of illustration, both single-phase and liquid–gas coexistence are considered here with the aim of describing various regions of the phase diagram with a single function and, in doing so, providing a link between atomistic and mesoscopic length scales.

Filtering of Nanoparticles with Tunable Semiconductor Membranes

Translocation dynamics of nanoparticles permeating through the nanopore in an n-Si semiconductor membrane is studied. With the use of Brownian Dynamics to describe the motion of the charged nanoparticles in the self-consistent membrane-electrolyte electrostatic potential, we asses the possibility of using our voltage controlled membrane for the macroscopic filtering of the charged 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 larger nanoparticles due to their stronger interaction with the membrane while in the nanopore. By extracting the membrane permeability from our microsopic simulations, we compute the macroscopic sieving factors and show that the size selectivity of the membrane can be tuned by the applied voltage.

Charged particle separation by an electrically tunable nanoporous membrane

We study the applicability of an electrically tunable nanoporous semiconductor membrane for the separation of nanoparticles by charge. We show that this type of membrane can overcome one of the major shortcomings of nanoporous membrane applications for particle separation: the compromise between membrane selectivity and permeability. The computational model that we have developed describes the electrostatic potential distribution within the system and tracks the movement of the filtered particle using Brownian dynamics while taking into consideration effects from dielectrophoresis, fluid flow, and electric potentials. We found that for our specific pore geometry, the dielectrophoresis plays a negligible role in the particle dynamics. By comparing the results for charged and uncharged particles, we show that for the optimal combination of applied electrolyte and membrane biases the same membrane can effectively separate same-sized particles based on charge with a difference of up to 3 times in membrane permeability.