Local characterization of hindered Brownian motion by using digital video microscopy and 3D particle tracking

This is the author accepted manuscript. The final version is available from the publisher via the DOI in this record.In this article we present methods for measuring hindered Brownian motion in the confinement of complex 3D geometries using digital video microscopy. Here we discuss essential features of automated 3D particle tracking as well as diffusion data analysis. By introducing local mean squared displacement-vs-time curves, we are able to simultaneously measure the spatial dependence of diffusion coefficients, tracking accuracies and drift velocities. Such local measurements allow a more detailed and appropriate description of strongly heterogeneous systems as opposed to global measurements. Finite size effects of the tracking region on measuring mean squared displacements are also discussed. The use of these methods was crucial for the measurement of the diffusive behavior of spherical polystyrene particles (505 nm diameter) in a microfluidic chip. The particles explored an array of parallel channels with different cross sections as well as the bulk reservoirs. For this experiment we present the measurement of local tracking accuracies in all three axial directions as well as the diffusivity parallel to the channel axis while we observed no significant flow but purely Brownian motion. Finally, the presented algorithm is suitable also for tracking of fluorescently labeled particles and particles driven by an external force, e.g., electrokinetic or dielectrophoretic forces.S.L.D. acknowledges funding from the German Academic Exchange Service (DAAD) and the German National Academic Foundation. S.P. and U.F.K. were supported by an ERC starting grant. S.P. also acknowledges the support from the Leverhulme Trust and the Newton Trust through an Early Career Fellowship

Channel-facilitated diffusion boosted by particle binding at the channel entrance

This is the final version of the article. Available from the publisher via the DOI in this record.We investigate single-file diffusion of Brownian particles in arrays of closely confining microchannels permeated by a variety of attractive optical potentials and connecting two baths with equal particle concentration. We simultaneously test free diffusion in the channel, diffusion in optical traps coupled in the center of the channel, and diffusion in traps extending into the baths. We found that both classes of attractive optical potentials enhance the translocation rate through the channel with respect to free diffusion. Surprisingly, for the latter class of potentials we measure a 40-fold enhancement in the translocation rate with respect to free diffusion and find a sublinear power law dependence of the translocation rate on the average number of particles in the channel. Our results reveal the function of particle binding at the channel entrances for diffusive transport and open the way to a better understanding of membrane transport and design of synthetic membranes with enhanced diffusion rate.S. P. acknowledges support from the Leverhulme and Newton Trust through an Early Career Fellowship. S. L. D. acknowledges funding from the German Academic Exchange Service (DAAD) and the German National Academic Foundation. U. F. K. was supported by an ERC starting grant

Quantifying Nanomolar Protein Concentrations Using Designed DNA Carriers and Solid-State Nanopores

Designed "DNA carriers" have been proposed as a new method for nanopore based specific protein detection. In this system, target protein molecules bind to a long DNA strand at a defined position creating a second level transient current drop against the background DNA translocation. Here, we demonstrate the ability of this system to quantify protein concentrations in the nanomolar range. After incubation with target protein at different concentrations, the fraction of DNA translocations showing a secondary current spike allows for the quantification of the corresponding protein concentration. For our proof-of-principle experiments we use two standard binding systems, biotin-streptavidin and digoxigenin-antidigoxigenin, that allow for measurements of the concentration down to the low nanomolar range. The results demonstrate the potential for a novel quantitative and specific protein detection scheme using the DNA carrier method.The authors thank Howarth Lab, Oxford for providing the monovalent streptavidin sample, Yizhou Tan for the help with Labview programs, and Dr. Janet Kumita for the help with FP measurement. J. Kong acknowledges funding from Chinese Scholarship Council and Cambridge Trust. N.A.W.B. acknowledges funding from an EPSRC doctoral prize award and an ERC starting grant (Passmembrane 261101); U.F.K. acknowledges support from an ERC starting grant (Passmembrane 261101)

Anisotropic diffusion of spherical particles in closely confining microchannels

This is the author accepted manuscript. The final version is available from the publisher via the DOI in this record.We present here the measurement of the diffusivity of spherical particles closely confined by narrow microchannels. Our experiments yield a two-dimensional map of the position-dependent diffusion coefficients parallel and perpendicular to the channel axis with a resolution down to 129 nm. The diffusivity was measured simultaneously in the channel interior, the bulk reservoirs, as well as the channel entrance region. In the channel interior we found strongly anisotropic diffusion. While the perpendicular diffusion coefficient close to the confining walls decreased down to approximately 25% of the value on the channel axis, the parallel diffusion coefficient remained constant throughout the entire channel width. In addition to the experiment, we performed finite element simulations for the diffusivity in the channel interior and found good agreement with the measurements. Our results reveal the distinctive influence of strong confinement on Brownian motion, which is of significance to microfluidics as well as quantitative models of facilitated membrane transport.S.L.D. acknowledges funding from the German Academic Exchange Service (DAAD) and the German National Academic Foundation. S.P. and U.F.K. were supported by an ERC starting grant. S.P. also acknowledges support from the Leverhulme Trust and the Newton Trust through an Early Career Fellowship

Ionic and molecular transport in aqueous solution through 2D and layered nanoporous membranes

Abstract Two-dimensional (2D) materials provide an intriguing means to not only study physical phenomena but also serve as disruptive membranes for ionic selectivity and sensing based applications. Atomic thinness of these materials affords a unique environment in an all-surface material to unlock challenges towards improving desalination, energy harvesting and DNA sensing. This review provides an overview on some common 2D materials used in membrane applications for solving these challenges along with opportunities where 2D materials could add value to existing solutions. Following this, different types of 2D materials and structures are discussed with their relative advantages and disadvantages highlighted. Fabrication and methods of creating pores within 2D membranes are then presented with a focus on altering surface characteristics. Selected works within the field are highlighted and placed into a wider context, comparing their merits and shortfalls. A discussion of state-of-the-art performance for ionic transport, molecular sensing and power generation is then presented. This review concludes with an outlook on emerging methods and discussing exciting future directions.</jats:p

Specific Biosensing Using DNA Aptamers and Nanopores

The multiplexed biosensing of target molecules with high specificity and accuracy is of fundamental importance in both biological research and medical diagnostics. In this paper, the working range of the recent nanopore-DNA carrier based method is extended by introducing a two-step assay using specific DNA aptamers. A signal translation step allows for binding of the target in physiological conditions before the nanopore measurements. Using protein encoded DNA carriers, the simultaneous detection of three targets spanning several orders of magnitude in molecular weight is demonstrated. The single-molecule method may be integrated into nanopore sensing devices for future applied research and point-of-care applications

Nondecaying hydrodynamic interactions along narrow channels

This is the author accepted manuscript. The final version is available from the publisher via the DOI in this record.Particle-particle interactions are of paramount importance in every multibody system as they determine the collective behavior and coupling strength. Many well-known interactions such as electrostatic, van der Waals, or screened Coulomb interactions, decay exponentially or with negative powers of the particle spacing r. Similarly, hydrodynamic interactions between particles undergoing Brownian motion decay as 1/r in bulk, and are assumed to decay in small channels. Such interactions are ubiquitous in biological and technological systems. Here we confine two particles undergoing Brownian motion in narrow, microfluidic channels and study their coupling through hydrodynamic interactions. Our experiments show that the hydrodynamic particle-particle interactions are distance independent in these channels. This finding is of fundamental importance for the interpretation of experiments where dense mixtures of particles or molecules diffuse through finite length, water-filled channels or pore networks.U. F. K. was supported by an ERC starting Grant No. (PassMembrane 261101). S. P. acknowledges funding from a Leverhulme Early Career Fellowship. K. M. was supported by a grant from the EPSRC. E. L. was supported by a Marie Curie CIG grant from the EU

A label-free microfluidic assay to quantitatively study antibiotic diffusion through lipid membranes

PublishedJournal ArticleResearch Support, Non-U.S. Gov'tWith the rise in antibiotic resistance amongst pathogenic bacteria, the study of antibiotic activity and transport across cell membranes is gaining widespread importance. We present a novel, label-free microfluidic assay that quantifies the permeability coefficient of a broad spectrum fluoroquinolone antibiotic, norfloxacin, across lipid membranes using the UV autofluorescence of the drug. We use giant lipid vesicles as highly controlled model systems to study the diffusion through lipid membranes. Our technique directly determines the permeability coefficient without requiring the measurement of the partition coefficient of the antibiotic.This work was supported by a European Research Council (ERC) grant (261101 PassMembrane) to UFK. JC acknowledges support from an Internal Graduate Studentship, Trinity College, Cambridge. CC is supported by the ERC. SP acknowledges the support of the Leverhulme Trust and the Newton Trust through an Early Career Fellowship. AJ is supported by the Mexican National Council of Science and Technology. We thank Thomas Muller for help with the lithography and Tuomas Knowles for the use of his lithography facilitie

Nondeterministic self-assembly with asymmetric interactions.

We investigate general properties of nondeterministic self-assembly with asymmetric interactions, using a computational model and DNA tile assembly experiments. By contrasting symmetric and asymmetric interactions we show that the latter can lead to self-limiting cluster growth. Furthermore, by adjusting the relative abundance of self-assembly particles in a two-particle mixture, we are able to tune the final sizes of these clusters. We show that this is a fundamental property of asymmetric interactions, which has potential applications in bioengineering, and provides insights into the study of diseases caused by protein aggregation.Winton Programme for the Physics of Sustainability, Gates Cambridge, Oppenheimer PhD studentship, NanoDTC Cambridge (Grant ID: EP/L015978/1), Engineering and Physical Sciences Research Council (Grant ID: EP/L504920/1), Royal SocietyThis is the author accepted manuscript. The final version is available from the American Physical Society via http://dx.doi.org/10.1103/PhysRevE.94.02240

Free-standing graphene membranes on glass nanopores for ionic current measurements

A method is established to reliably suspend graphene monolayers across glass nanopores as a simple, low cost platform to study ionic transport through graphene membranes. We systematically show that the graphene seals glass nanopore openings with areas ranging from 180 nm2 to 20 μm2, allowing detailed measurements of ionic current and transport through graphene. In combination with in situ Raman spectroscopy, we characterise the defects formed in ozone treated graphene, confirming an increase in ionic current flow with defect density. This highlights the potential of our method for studying single molecule sensing and filtration.The authors would like to thank S. Purushothaman and K. Göpfrich for careful reading of the manuscript and V. Thacker for useful discussions. This work was supported by the EPSRC Cambridge NanoDTC, EP/G037221/1, and EPSRC grant GRAPHTED, EP/K016636/1. R.S.W. acknowledges a Research Fellowship from St. John's College, Cambridge. N.A.W.B. acknowledges an EPSRC doctoral prize award.This is the accepted manuscript. Copyright 2015 American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics. The final version is available in Applied Physics Letters 106, 023119 (2015); doi: 10.1063/1.490623