scholarly journals Coordinated Detection of Micro- and Nanoparticles using Tuneable Resistive Pulse Sensing and Optical Spectroscopy

2021 ◽  
Author(s):  
◽  
Peter Hauer

<p>The detection and characterisation of micro- and nanoscale particles has become increasingly important in many scientific fields, spanning from colloidal science to biomedical applications. Resistive Pulse Sensing (RPS) and its derivative Tuneable Resistive Pulse Sensing (TRPS), which both use the Coulter principle, have proven to be useful tools to detect and analyse particles in solution over a wide range of sizes. While RPS uses a fixed size pore, TRPS uses a dynamically stretchable pore in a polyurethane membrane, which has the advantages that the pore geometry can be tuned to increase the device's sensitivity and range of detection. The technique has been used to accurately determine the size, concentration and charge of many different analytes.  However, the information obtained using TRPS does not give any insight into the particle's composition. In an attempt to overcome this, an experimental technique was developed in order to obtain simultaneous, time-resolved, high-resolution optical spectra of particles passing through the pore. Due to the ordered and controllable fashion in which the particles are guided through the sensing region, this approach has an advantage over diffusion based optical techniques. The experimental setup for the coordinated electrical and optical measurements involves many underlying physical phenomena, e.g. microuidics, electrokinetic effects, and Gaussian beam optics. A significant proportion of this work was therefore devoted to the development and the optimisation of the experimental setup by adapting a commercial TRPS device and a spectrometer with an attached microscope. Methods to engineer the spot size of a Gaussian beam to account for the different pore diameters, and the development of algorithms to filter, analyse and coordinate the recorded data are essential to the technique.  The results using fluorescently labelled polystyrene particle sets with diameters from 190nm to 2 µm show that matching rates between the electrical and optical measurements of over 90% can repeatedly be achieved. Mixtures of particle species with similar diameters but with different fluorescent labels were used to demonstrate the technique's capability to characterise the analyte on a particle-by-particle basis and extend the information that can be obtained by TRPS alone. It was also shown that the data acquired with the electrical and optical measurements complement each other and can be used to better understand the TRPS technique itself. The influence of experimental parameters, such as the particle velocity, the beam size and the optical detection volume, on the intensity of the optical signals and the matching rates was studied intensively. These studies showed that the technique requires a careful experimental design to achieve the best results. Overall, the developed technique enhances the particle-by-particle specificity of conventional RPS measurements, and could be useful for a range of particle characterization and bio-analysis applications.  Alongside the experiments, semi-analytic modelling and simulations using the Finite Element Method (FEM) were used to understand the particle motion through the pores, to interpret the experimental data, and predict the optical signals. The models were also used to assist the design and the optimization of the experiments. The FEM models were implemented with increasing physical detail and show superior understanding of the TRPS signals compared to the semi-analytic model, which is conventionally used in the TRPS field. The physical phenomena considered included o -axis trajectories, particle-field interactions for both fluid and electric fields, and the non-homogeneous distribution of ions close to the charged membrane and particle interfaces. Several effects which have been observed experimentally could be explained, including the intrinsic pulse height distribution, the current rectification, and the occurrence of bi-phasic pulses, demonstrating the benefits of FEM methods for RPS.</p>

2021 ◽  
Author(s):  
◽  
Peter Hauer

<p>The detection and characterisation of micro- and nanoscale particles has become increasingly important in many scientific fields, spanning from colloidal science to biomedical applications. Resistive Pulse Sensing (RPS) and its derivative Tuneable Resistive Pulse Sensing (TRPS), which both use the Coulter principle, have proven to be useful tools to detect and analyse particles in solution over a wide range of sizes. While RPS uses a fixed size pore, TRPS uses a dynamically stretchable pore in a polyurethane membrane, which has the advantages that the pore geometry can be tuned to increase the device's sensitivity and range of detection. The technique has been used to accurately determine the size, concentration and charge of many different analytes.  However, the information obtained using TRPS does not give any insight into the particle's composition. In an attempt to overcome this, an experimental technique was developed in order to obtain simultaneous, time-resolved, high-resolution optical spectra of particles passing through the pore. Due to the ordered and controllable fashion in which the particles are guided through the sensing region, this approach has an advantage over diffusion based optical techniques. The experimental setup for the coordinated electrical and optical measurements involves many underlying physical phenomena, e.g. microuidics, electrokinetic effects, and Gaussian beam optics. A significant proportion of this work was therefore devoted to the development and the optimisation of the experimental setup by adapting a commercial TRPS device and a spectrometer with an attached microscope. Methods to engineer the spot size of a Gaussian beam to account for the different pore diameters, and the development of algorithms to filter, analyse and coordinate the recorded data are essential to the technique.  The results using fluorescently labelled polystyrene particle sets with diameters from 190nm to 2 µm show that matching rates between the electrical and optical measurements of over 90% can repeatedly be achieved. Mixtures of particle species with similar diameters but with different fluorescent labels were used to demonstrate the technique's capability to characterise the analyte on a particle-by-particle basis and extend the information that can be obtained by TRPS alone. It was also shown that the data acquired with the electrical and optical measurements complement each other and can be used to better understand the TRPS technique itself. The influence of experimental parameters, such as the particle velocity, the beam size and the optical detection volume, on the intensity of the optical signals and the matching rates was studied intensively. These studies showed that the technique requires a careful experimental design to achieve the best results. Overall, the developed technique enhances the particle-by-particle specificity of conventional RPS measurements, and could be useful for a range of particle characterization and bio-analysis applications.  Alongside the experiments, semi-analytic modelling and simulations using the Finite Element Method (FEM) were used to understand the particle motion through the pores, to interpret the experimental data, and predict the optical signals. The models were also used to assist the design and the optimization of the experiments. The FEM models were implemented with increasing physical detail and show superior understanding of the TRPS signals compared to the semi-analytic model, which is conventionally used in the TRPS field. The physical phenomena considered included o -axis trajectories, particle-field interactions for both fluid and electric fields, and the non-homogeneous distribution of ions close to the charged membrane and particle interfaces. Several effects which have been observed experimentally could be explained, including the intrinsic pulse height distribution, the current rectification, and the occurrence of bi-phasic pulses, demonstrating the benefits of FEM methods for RPS.</p>


2020 ◽  
Author(s):  
Imogen Heaton ◽  
Mark Platt

<b>DNAzymes are DNA based catalysts that can undergo cleavage upon binding of the target analyte. The cleavage reaction is highly specific, and DNAzymes exists for a wide range of metal ions. The change of structure upon binding of a specific metal ion has given rise to many sensing strategies, but few exist with nanopore sensors. Resistive Pulse Sensing, RPS, is a platform that has emerged in recent years capable of identifying changes in DNA structure and sequence. Here we develop the use of DNAzymes with RPS technologies for the detection of Ca2+ ions in solution. Ca2+ plays an important role in biological processes, critical for cell signally, protein folding and catalysis. Extreme concentrations of Ca2+ within drinking water have also been linked to problems with corrosion, scaling and the taste of water. Using DNAzyme functionalised nanocarriers and RPS, it was possible follow the Ca2+ ions binding to the DNAzyme. The binding of Ca2+ caused a conformation change in the DNAzyme which was monitored as a change in translocation speed. By following the changes to the translocation speed, it is hypothesised that RPS can verify the changes in structure. In addition, the assay allowed the quantification of Ca2+ between 1 – 9 μM, and due its catalytic nature, increasing incubation time from 30 to 90 minutes allowed lower detection limits, down to 0.3 μM. We demonstrate that the speed changes are specific to Ca2+ in the presence of other metal ions, and we can quantify Ca2+ in tap and pond water samples.</b><br>


2020 ◽  
Author(s):  
Imogen Heaton ◽  
Mark Platt

<b>DNAzymes are DNA based catalysts that can undergo cleavage upon binding of the target analyte. The cleavage reaction is highly specific, and DNAzymes exists for a wide range of metal ions. The change of structure upon binding of a specific metal ion has given rise to many sensing strategies, but few exist with nanopore sensors. Resistive Pulse Sensing, RPS, is a platform that has emerged in recent years capable of identifying changes in DNA structure and sequence. Here we develop the use of DNAzymes with RPS technologies for the detection of Ca2+ ions in solution. Ca2+ plays an important role in biological processes, critical for cell signally, protein folding and catalysis. Extreme concentrations of Ca2+ within drinking water have also been linked to problems with corrosion, scaling and the taste of water. Using DNAzyme functionalised nanocarriers and RPS, it was possible follow the Ca2+ ions binding to the DNAzyme. The binding of Ca2+ caused a conformation change in the DNAzyme which was monitored as a change in translocation speed. By following the changes to the translocation speed, it is hypothesised that RPS can verify the changes in structure. In addition, the assay allowed the quantification of Ca2+ between 1 – 9 μM, and due its catalytic nature, increasing incubation time from 30 to 90 minutes allowed lower detection limits, down to 0.3 μM. We demonstrate that the speed changes are specific to Ca2+ in the presence of other metal ions, and we can quantify Ca2+ in tap and pond water samples.</b><br>


2014 ◽  
Vol 55 (3) ◽  
pp. 197-213 ◽  
Author(s):  
G. R. WILLMOTT ◽  
B. G. SMITH

AbstractNanopore science, the study of individual nanoscale pores within thin membranes, is a fast-growing field which presents numerous interesting problems for physicists and applied mathematicians. Nanopores are most commonly applied to resistive pulse sensing (RPS) of individual particles suspended in aqueous electrolyte. The form of a resistive pulse is dependent on an array of experimental variables, including electrolyte characteristics, electrophoretic and convective transport, and (especially) pore and particle geometry. The level of analysis required depends on the application, but any broadly useful approach should be simple and flexible, due to the requirement for high data throughput and variations between different experimental systems and specimens. Here we review analytic methods for interpreting RPS experiments for particles in the approximate range 100 nm to 1 $\def \xmlpi #1{}\def \mathsfbi #1{\boldsymbol {\mathsf {#1}}}\let \le =\leqslant \let \leq =\leqslant \let \ge =\geqslant \let \geq =\geqslant \def \Pr {\mathit {Pr}}\def \Fr {\mathit {Fr}}\def \Rey {\mathit {Re}}\mu $m, focusing on calculation of resistance change as a function of the particle’s position. We detail a recently developed semi-analytical model and compare the modelled electric field with finite element results. The model can also be used to calculate particle motion, so that the experimental current–time history can be reconstructed. This approach is useful for a wide range of pore and particle geometries, and includes consideration of entrance effects. Tunable elastomeric pores with truncated linear cone geometry are used as a model system.


Author(s):  
Christian Devereux ◽  
Justin Smith ◽  
Kate Davis ◽  
Kipton Barros ◽  
Roman Zubatyuk ◽  
...  

<p>Machine learning (ML) methods have become powerful, predictive tools in a wide range of applications, such as facial recognition and autonomous vehicles. In the sciences, computational chemists and physicists have been using ML for the prediction of physical phenomena, such as atomistic potential energy surfaces and reaction pathways. Transferable ML potentials, such as ANI-1x, have been developed with the goal of accurately simulating organic molecules containing the chemical elements H, C, N, and O. Here we provide an extension of the ANI-1x model. The new model, dubbed ANI-2x, is trained to three additional chemical elements: S, F, and Cl. Additionally, ANI-2x underwent torsional refinement training to better predict molecular torsion profiles. These new features open a wide range of new applications within organic chemistry and drug development. These seven elements (H, C, N, O, F, Cl, S) make up ~90% of drug like molecules. To show that these additions do not sacrifice accuracy, we have tested this model across a range of organic molecules and applications, including the COMP6 benchmark, dihedral rotations, conformer scoring, and non-bonded interactions. ANI-2x is shown to accurately predict molecular energies compared to DFT with a ~10<sup>6</sup> factor speedup and a negligible slowdown compared to ANI-1x. The resulting model is a valuable tool for drug development that can potentially replace both quantum calculations and classical force fields for myriad applications.</p>


2021 ◽  
Vol 6 (1) ◽  
pp. 59-67
Author(s):  
Durdane Yilmaz ◽  
Dila Kaya ◽  
Kaan Kececi ◽  
Ali Dinler

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Robert Vogel ◽  
Anoop K. Pal ◽  
Siddharth Jambhrunkar ◽  
Pragnesh Patel ◽  
Sachin S. Thakur ◽  
...  

ACS Nano ◽  
2013 ◽  
Vol 7 (10) ◽  
pp. 8857-8869 ◽  
Author(s):  
Jingjie Sha ◽  
Tawfique Hasan ◽  
Silvia Milana ◽  
Cristina Bertulli ◽  
Nicholas A. W. Bell ◽  
...  

2011 ◽  
Vol 1 (2) ◽  
Author(s):  
Yuejun Zhao ◽  
David B. Bober ◽  
Chuan-Hua Chen

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