Solid-State Quad-Nanopore Array for High-Resolution Single-Molecule Analysis and Discrimination

The ability to detect and distinguish biomolecules at the single-molecule level is at the forefront of today's biomedicine and analytical chemistry research. Increasing the dwell time of individual biomolecules in the sensing spot can greatly enhance the sensitivity of single-molecule methods. This is particularly important in solid-state nanopore sensing, where the detection of small molecules is often limited by the transit dwell time and insufficient temporal resolution. Here, a quad-nanopore is introduced, a square array of four nanopores (with a space interval of 30-50 nm) to improve the detection sensitivity through electric field manipulation in the access region. It is shown that dwell times of short DNA strands (200 bp) are prolonged in quad-nanopores as compared to single nanopores of the same diameter. The dependence of dwell times on the quad-pore spacing is investigated and it is found that the "retarding effect" increases with decreasing space intervals. Furthermore, ultra-short DNA (50 bp) detection is demonstrated using a 10 nm diameter quad-nanopore array, which is hardly detected by a single nanopore. Finally, the general utility of quad-nanopores has been verified by successful discrimination of two kinds of small molecules, metal-organic cage and bovine serum albumin (BSA).

Topographic de-adhesion in the viscoelastic limit

The superiority of many natural surfaces at resisting soft, sticky biofoulants have inspired the integration of dynamic topography with mechanical instability to promote self-cleaning artificial surfaces. The physics behind this novel mechanism is currently limited to elastic biofoulants where surface energy, bending stiffness and topographical wavelength are key factors. However, the viscoelastic nature of many biofoulants causes a complex interplay between these factors with time-dependent characteristics such as material softening and loading rate. Here, we enrich the current elastic theory of topographic de-adhesion using analytical and finite-element models to elucidate the nonlinear, time-dependent interaction of three physical, dimensionless parameters: biofoulant's stiffness reduction, the product of relaxation time and loading rate, and the critical strain for short-term elastic de-adhesion. Theoretical predictions, in good agreement with numerical simulations, provide insight into tuning these control parameters to optimize surface renewal via topographic de-adhesion in the viscoelastic regime.

On Modeling Diversity in Electrical Cellular Response: Data-Driven Approach

Electrical properties of biological cells and tissues possess valuable information that enabled numerous applications in biomedical engineering. The common foundation behind them is a numerical model that can predict electrical response of a single cell or a network of cells. We analyzed the past empirical observations to propose the first statistical model that accurately mimics biological diversity among animal cells, yeast cells, and bacteria. Based on membrane elasticity and cell migration mechanisms, we introduce a more realistic three-dimensional geometry generation procedure that captures membrane protrusions and retractions in adherent cells. Together, they form a model of diverse electrical response across multiple cell types. We experimentally verified the model with electrical impedance spectroscopy of a single human cervical carcinoma (HeLa) cell on a microelectrode array. The work is of particular relevance to medical diagnostic and therapeutic applications that involve exposure to electric and magnetic fields.

Three-dimensional analytical poromechanical solutions for an arbitrarily inclined borehole subjected to fluid injection

Hydraulic fracturing is the primary method of stimulation in unconventional reservoirs, playing a significant role in oil and gas production enhancement. A key issue for the analysis of hydraulic fracture initiation is to accurately determine the stress distributions in the vicinity of the borehole caused by the injection of pressurized fluids. This paper develops an exact, three-dimensional, poroelastic coupled analytical solution for such stress analysis of an arbitrarily inclined borehole subjected concurrently to a finite-length fluid discharge and in situ stresses, using Fourier expansion theorem and the Laplace-Fourier integral transform technique. The complicated boundary conditions, which involve the mixed boundary values at the borehole surface and the coupling between the total radial stress and injection-induced pore pressure over the sectioned borehole interval, as well as the fully three-dimensional far field in situ stresses, are addressed in a novel way and deliberately/elegantly decomposed into five fundamental, easier to handle modes. The rigour and definitive nature of the proposed analytical methodology facilitates fundamental understanding of the mechanism underlying the stress responses of the borehole and porous medium. It can be and is used here as a benchmark for the numerical solutions obtained from the finite-element analysis commercial program (ABAQUS).

An empirical measure of nonlinear strain for soft tissue indentation

Indentation is a primary tool in the investigation of the mechanical properties of very soft tissue such as the brain. However, the usual material characterization protocols are not applicable because the resulting deformation is inhomogeneous, with even the identification of the amount of strain ambiguous and uncertain. Focusing on spherical indentation only, a standard is needed to quantify the amount of strain in terms of the probe radius and displacement so that different indentation experiments can be compared and contrasted. It is shown here that the minimum axial value of the Eulerian logarithmic strain tensor has many desirable properties of such a standard, such as invariance under the choice of material model, and experimental conditions for a given probe displacement. The disadvantage of this measure is that sophisticated finite element techniques need to be used in its determination. An empirical relation is obtained between this strain and the probe radius and displacement to circumvent this problem, and it is shown that this relationship is an excellent predictor of the strain measure. Two essential features of this empirical measure for nonlinear strains are that the exact strain measure for the linear theory is recovered on restriction to infinitesimal deformations and that the simulations use models based on reliable and accurate indentation data obtained from freshly harvested murine brains using a bespoke micro-indentation device.

A computational study of cancer hyperthermia based on vascular magnetic nanoconstructs

The application of hyperthermia to cancer treatment is studied using a novel model arising from the fundamental principles of flow, mass and heat transport in biological tissues. The model is defined at the scale of the tumour microenvironment and an advanced computational scheme called the embedded multiscale method is adopted to solve the governing equations. More precisely, this approach involves modelling capillaries as one-dimensional channels carrying flow, and special mathematical operators are used to model their interaction with the surrounding tissue. The proposed computational scheme is used to analyse hyperthermic treatment of cancer based on systemically injected vascular magnetic nanoconstructs carrying super-paramagnetic iron oxide nanoparticles. An alternating magnetic field is used to excite the nanoconstructs and generate localized heat within the tissue. The proposed model is particularly adequate for this application, since it has a unique capability of incorporating microvasculature configurations based on physiological data combined with coupled capillary flow, interstitial filtration and heat transfer. A virtual tumour model is initialized and the spatio-temporal distribution of nanoconstructs in the vascular network is analysed. In particular, for a reference iron oxide concentration, temperature maps of several different hypothesized treatments are generated in the virtual tumour model. The observations of the current study might in future guide the design of more efficient treatments for cancer hyperthermia.

Development of a training phantom for compression breast elastography-comparison of various elastography systems and numerical simulations

The elastic properties of tissue are related to tissue composition and pathological changes. It has been observed that many pathological processes increase the elastic modulus of soft tissue compared to normal. Ultrasound compression elastography is a method of characterization of elastic properties that has been the focus of many research efforts in the last two decades. In medical radiology, compression elastography is provided as an additional tool with ultrasound B-mode in the existing scanners, and the combined features of elastography and echography act as a promising diagnostic method in breast cancer detection. However, the full capability of the ultrasound elastography technique together with B-mode has not been utilized by novice radiologists due to the nonavailability of suitable, appropriately designed tissue-mimicking phantoms. Since different commercially available ultrasound elastographic scanners follow their own unique protocols, training novice radiologists is becoming cumbersome. The main focus of this work is to develop a tissue-like agar-based phantom, which mimics breast tissue with common abnormal lesions like fibroadenoma and invasive ductal carcinoma in a clinically perceived way and compares the sonographic and elastographic appearances using different commercially available systems. In addition, the developed phantoms are simulated using the finite-element method, and ideal strain images are generated. Strain images from experiment and simulation are compared based on image contrast parameters, namely contrast transfer efficiency (CTE) and observed strain, and they are in good agreement. The strain image contrast of malignant inclusions is significantly improved compared to benign inclusions, and the trend of CTE is similar for all elastographic scanners under investigation.

Ion Transport within High Electric Fields in Nanogap Electrochemical Cells

Ion transport near an electrically charged electrolyte/electrode interface is a fundamental electrochemical phenomenon that is important in many electrochemical energy systems. We investigated this phenomenon using lithographically fabricated thin-layer electrochemical cells comprising two Pt planar electrodes separated by an electrolyte of nanometer thickness (50-200 nm). By exploiting redox cycling amplification, we observed the influence of the electric double layer on transport of a charged redox couple within the confined electrolyte. Nonclassical steady-state peak shaped voltammograms for redox cycling of the ferrocenylmethyltrimethylammonium redox couple (FcTMA(+/2+)) at low concentrations of supporting electrolyte (≤10 mM) results from electrostatic interactions between the redox ions and the charged Pt electrodes. This behavior contrasts to sigmoidal voltammograms with a diffusion-limited plateau observed in the same electrochemical cells in the presence of sufficient electrolyte to screen the electrode surface charge (200 mM). Moreover, steady-state redox cycling was depressed significantly within the confined electrolyte as the supporting electrolyte concentration was decreased or as the cell thickness was reduced. The experimental results are in excellent agreement with predictions from finite-element simulations coupling the governing equations for ion transport, electric fields, and the redox reactions. Double layer effects on ion transport are generally anticipated in highly confined electrolyte and may have implications for ion transport in thin layer and nanoporous energy storage materials.