1
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Wang P, Tao W, Zhou T, Wang J, Zhao C, Zhou G, Yamauchi Y. Nanoarchitectonics in Advanced Membranes for Enhanced Osmotic Energy Harvesting. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024:e2404418. [PMID: 38973652 DOI: 10.1002/adma.202404418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 05/24/2024] [Indexed: 07/09/2024]
Abstract
Osmotic energy, often referred to as "blue energy", is the energy generated from the mixing of solutions with different salt concentrations, offering a vast, renewable, and environmentally friendly energy resource. The efficacy of osmotic power production considerably relies on the performance of the transmembrane process, which depends on ionic conductivity and the capability to differentiate between positive and negative ions. Recent advancements have led to the development of membrane materials featuring precisely tailored ion transport nanochannels, enabling high-efficiency osmotic energy harvesting. In this review, ion diffusion in confined nanochannels and the rational design and optimization of membrane architecture are explored. Furthermore, structural optimization of the membrane to mitigate transport resistance and the concentration polarization effect for enhancing osmotic energy harvesting is highlighted. Finally, an outlook on the challenges that lie ahead is provided, and the potential applications of osmotic energy conversion are outlined. This review offers a comprehensive viewpoint on the evolving prospects of osmotic energy conversion.
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Affiliation(s)
- Peifang Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China
| | - Weixiang Tao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China
| | - Tianhong Zhou
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China
| | - Jie Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China
- Australian Institute for Bioengineering and Nanotechnology (AIBN) and School of Chemical Engineering, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Chenrui Zhao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China
| | - Gang Zhou
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China
| | - Yusuke Yamauchi
- Australian Institute for Bioengineering and Nanotechnology (AIBN) and School of Chemical Engineering, The University of Queensland, Brisbane, QLD, 4072, Australia
- Department of Materials Process Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Aichi, 464-8603, Japan
- Department of Plant & Environmental New Resources, College of Life Sciences, Kyung Hee University, 1732 Deogyeong-daero, Giheung-gu, Yongin-si, Gyeonggi-do, 17104, South Korea
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2
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Cui Y, Ying C, Huang XY, Ye Q, Tian J, Liu Z. Electrical Transport and Dynamics of Confined DNA through Highly Conductive 2D Graphene Nanochannels. NANO LETTERS 2024; 24:4485-4492. [PMID: 38578031 DOI: 10.1021/acs.nanolett.4c00403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
Confining DNA in nanochannels is an important approach to studying its structure and transportation dynamics. Graphene nanochannels are particularly attractive for studying DNA confinement due to their atomic flatness, precise height control, and excellent mechanical strength. Here, using femtosecond laser etching and wetting transfer, we fabricate graphene nanochannels down to less than 4.3 nm in height, with the length-to-height ratios up to 103. These channels exhibit high stability, low noise, and self-cleaning ability during the long-term ionic current recording. We report a clear linear relationship between DNA length and the residence time in the channel and further utilize this relationship to differentiate DNA fragments based on their lengths, ranging widely from 200 bps to 48.5 kbps. The graphene nanochannel presented here provides a potential platform for label-free analyses and reveals fundamental insights into the conformational dynamics of DNA and proteins in confined space.
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Affiliation(s)
- Yangjun Cui
- The Key Laboratory of Weak Light Nonlinear Photonics, Ministry of Education, School of Physics and Teda Applied Physics Institute, Nankai University, Tianjin 300071, China
| | - Cuifeng Ying
- Advanced Optics & Photonics Laboratory, Department of Engineering, School of Science & Technology, Nottingham Trent University, Nottingham NG11 8NS, U.K
| | - Xiao-Yu Huang
- The Key Laboratory of Weak Light Nonlinear Photonics, Ministry of Education, School of Physics and Teda Applied Physics Institute, Nankai University, Tianjin 300071, China
| | - Qing Ye
- The Key Laboratory of Weak Light Nonlinear Photonics, Ministry of Education, School of Physics and Teda Applied Physics Institute, Nankai University, Tianjin 300071, China
| | - Jianguo Tian
- The Key Laboratory of Weak Light Nonlinear Photonics, Ministry of Education, School of Physics and Teda Applied Physics Institute, Nankai University, Tianjin 300071, China
- Renewable Energy Conversion and Storage Center, Nankai University, Tianjin 300071, China
| | - Zhibo Liu
- The Key Laboratory of Weak Light Nonlinear Photonics, Ministry of Education, School of Physics and Teda Applied Physics Institute, Nankai University, Tianjin 300071, China
- Renewable Energy Conversion and Storage Center, Nankai University, Tianjin 300071, China
- The Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
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3
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Liu P, Kong XY, Jiang L, Wen L. Ion transport in nanofluidics under external fields. Chem Soc Rev 2024; 53:2972-3001. [PMID: 38345093 DOI: 10.1039/d3cs00367a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Nanofluidic channels with tailored ion transport dynamics are usually used as channels for ion transport, to enable high-performance ion regulation behaviors. The rational construction of nanofluidics and the introduction of external fields are of vital significance to the advancement and development of these ion transport properties. Focusing on the recent advances of nanofluidics, in this review, various dimensional nanomaterials and their derived homogeneous/heterogeneous nanofluidics are first briefly introduced. Then we discuss the basic principles and properties of ion transport in nanofluidics. As the major part of this review, we focus on recent progress in ion transport in nanofluidics regulated by external physical fields (electric field, light, heat, pressure, etc.) and chemical fields (pH, concentration gradient, chemical reaction, etc.), and reveal the advantages and ion regulation mechanisms of each type. Moreover, the representative applications of these nanofluidic channels in sensing, ionic devices, energy conversion, and other areas are summarized. Finally, the major challenges that need to be addressed in this research field and the future perspective of nanofluidics development and practical applications are briefly illustrated.
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Affiliation(s)
- Pei Liu
- Henan Institute of Advanced Technology, Zhengzhou University, Zhengzhou 450052, P. R. China
- College of Materials Science and Engineering, Zhengzhou University, Zhengzhou 450052, P. R. China
| | - Xiang-Yu Kong
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China.
- School of Future Technology, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
- Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou, Jiangsu 215123, P. R. China
| | - Lei Jiang
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China.
- School of Future Technology, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
- Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou, Jiangsu 215123, P. R. China
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, P. R. China
| | - Liping Wen
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China.
- School of Future Technology, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
- Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou, Jiangsu 215123, P. R. China
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, P. R. China
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4
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Mei T, Liu W, Xu G, Chen Y, Wu M, Wang L, Xiao K. Ionic Transistors. ACS NANO 2024. [PMID: 38285731 DOI: 10.1021/acsnano.3c06190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2024]
Abstract
Biological voltage-gated ion channels, which behave as life's transistors, regulate ion transport precisely and selectively through atomic-scale selectivity filters to sustain important life activities. By this inspiration, voltage-adaptable ionic transistors that use ions as signal carriers may provide an alternative information processing unit beyond solid-state electronic devices. This review provides a comprehensive overview of the first generation of biomimetic ionic transistors, including their operating mechanisms, device architecture development, and property characterizations. Despite its infancy, significant progress has been made in the applications of ionic transistors in fields such as DNA detection, drug delivery, and ionic circuits. Challenges and prospects of full exploitation of ionic transistors for a broad spectrum of practical applications are also discussed.
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Affiliation(s)
- Tingting Mei
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Institute of Innovative Materials, Southern University of Science and Technology, Southern University of Science and Technology, Shenzhen 518055, P.R. China
| | - Wenchao Liu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Institute of Innovative Materials, Southern University of Science and Technology, Southern University of Science and Technology, Shenzhen 518055, P.R. China
| | - Guoheng Xu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Institute of Innovative Materials, Southern University of Science and Technology, Southern University of Science and Technology, Shenzhen 518055, P.R. China
| | - Yuanxia Chen
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Institute of Innovative Materials, Southern University of Science and Technology, Southern University of Science and Technology, Shenzhen 518055, P.R. China
| | - Minghui Wu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Institute of Innovative Materials, Southern University of Science and Technology, Southern University of Science and Technology, Shenzhen 518055, P.R. China
| | - Li Wang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Institute of Innovative Materials, Southern University of Science and Technology, Southern University of Science and Technology, Shenzhen 518055, P.R. China
| | - Kai Xiao
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Institute of Innovative Materials, Southern University of Science and Technology, Southern University of Science and Technology, Shenzhen 518055, P.R. China
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5
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Hidayat R, Pradana JS, Fariz A, Komalasari S, Chalimah S, Bahar H. Dual plasmonic modes in the visible light region in rectangular wave-shaped surface relief plasmonic gratings. Sci Rep 2023; 13:5274. [PMID: 37002239 PMCID: PMC10066186 DOI: 10.1038/s41598-023-30083-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 02/15/2023] [Indexed: 04/03/2023] Open
Abstract
Rectangular wave-shaped surface-relief plasmonic gratings (RSR-PGs) have been fabricated from a hybrid polymer by employing a simple nanoimprint photocuring lithography technique using a silicon template, followed by gold nanolayer metallization on top of the formed replica structure. By forming a one-dimensional (1D) plasmonic grating with a periodicity of approximately 700 nm, a reflectance spectral dip was experimentally observed in the visible light region, from 600 to 700 nm, with increasing incident angle from 45° to 60°. This dip can be associated with surface plasmon resonance (SPR) wave excitation, which is coupled with the diffraction order m = - 2. The calculations of reflectance spectra simulation using the rigorous coupled wave analysis (RCWA) method have also been carried out, resulting in the appearance of an SPR dip in the range of 600-700 nm, for incident angles in the range of 45°-65°, which agrees with the experimental results. Interestingly, these RSR-PGs show richer plasmon characteristics than the sine-wave-shaped plasmonic gratings. The experimental and spectral simulation results revealed two different plasmonic excitation modes: long-range SPR and quasi-localized SPR (LSPR). While the long-range SPR was formed above the ridge sections along the grating structure surface, the quasi-localized SPR was locally formed inside the groove. In addition, for RSR-PGs with a narrow groove section, the long-range SPR seems to be coupled with the periodic structure of the grating, resulting in the appearance of plasmonic lattice surface resonance (LSR) that is indicated by a narrower plasmon resonance dip. These characteristics are quite different from those found in the sine wave-shaped plasmonic gratings. The present results may thus provide better insights for understanding the plasmon excitations in this type of rectangular plasmonic grating and might be useful for designing their structure for certain practical applications.
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Affiliation(s)
- Rahmat Hidayat
- Physics of Magnetism and Photonics Research Division, Physics Study Program, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha 10, Bandung, 40132, West Java, Indonesia.
| | - Jalu Setiya Pradana
- Physics of Magnetism and Photonics Research Division, Physics Study Program, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha 10, Bandung, 40132, West Java, Indonesia
- Department of Biosystems, Biosensors Group, KU Leuven, 3001, Leuven, Belgium
| | - Alvin Fariz
- Physics of Magnetism and Photonics Research Division, Physics Study Program, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha 10, Bandung, 40132, West Java, Indonesia
| | - Susi Komalasari
- Physics of Magnetism and Photonics Research Division, Physics Study Program, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha 10, Bandung, 40132, West Java, Indonesia
| | - Siti Chalimah
- Physics of Magnetism and Photonics Research Division, Physics Study Program, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha 10, Bandung, 40132, West Java, Indonesia
| | - Herman Bahar
- Physics of Magnetism and Photonics Research Division, Physics Study Program, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha 10, Bandung, 40132, West Java, Indonesia
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6
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Gautam D, Pandey S, Chen J. Effect of Flow Rate and Ionic Strength on the Stabilities of YOYO-1 and YO-PRO-1 Intercalated in DNA Molecules. J Phys Chem B 2023; 127:2450-2456. [PMID: 36917775 PMCID: PMC10088364 DOI: 10.1021/acs.jpcb.3c00777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Single-molecule DNA studies have improved our understanding of the DNAs' structure and their interactions with other molecules. A variety of DNA labeling dyes are available for single-molecule studies, among which the bis-intercalating dye YOYO-1 and mono-intercalating dye YO-PRO-1 are widely used. They have an extraordinarily strong affinity toward DNA and are bright with a high quantum yield (>0.5) when bound to DNAs. However, it is still not clear how these dyes behave in DNA molecules under higher ionic strength and strong buffer flow. Here, we have studied the effect of ionic strength and flow rate of buffer on their binding in single DNA molecules. The larger the flow rate and the higher the ionic strength, the faster the intercalated dyes are washed away from the DNAs. In the buffer with 1 M ionic strength, YOYO-1 and YO-PRO-1 are mostly washed away from DNA within 2 min of moderate buffer flow.
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Affiliation(s)
- Dinesh Gautam
- Department of Chemistry and Biochemistry, Nanoscale & Quantum Phenomena Institute, Ohio University, Athens, OH 45701, USA
| | - Srijana Pandey
- Department of Chemistry and Biochemistry, Nanoscale & Quantum Phenomena Institute, Ohio University, Athens, OH 45701, USA
| | - Jixin Chen
- Department of Chemistry and Biochemistry, Nanoscale & Quantum Phenomena Institute, Ohio University, Athens, OH 45701, USA
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7
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Fauvel M, Trybala A, Tseluiko D, Starov VM, Bandulasena HCH. Foam-Based Electrophoretic Separation of Charged Dyes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:13935-13942. [PMID: 36322953 PMCID: PMC9671044 DOI: 10.1021/acs.langmuir.2c02228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 10/25/2022] [Indexed: 06/16/2023]
Abstract
Electrophoretic separation of a fluorescent dye mixture, containing rhodamine B (RB) and fluorescein, in liquid foams stabilized by anionic, cationic, or non-ionic surfactants in water-glycerol mixtures was studied in a custom-designed foam separation device. The effects of the external electric field applied across the foam and the initial pH of the solution on the effectiveness of separation were also studied. The fluid motion due to electroosmosis and the resulting back pressure within the foam and local pH changes were found to be complex and affected the separation. Fluorescein dye molecules, which have a positive or negative charge depending on the solution pH, aggregated in the vicinity of an electrode, leaving a pure band of neutral dye RB. The effectiveness of the separation was quantified by the percentage width of the pure RB band, which was found to be between 29 and 42%. This study demonstrates the potential of liquid foam as a platform for electrophoretic separation.
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Affiliation(s)
- Matthieu Fauvel
- Department
of Chemical Engineering, Loughborough University, Loughborough, Leicestershire LE11 3TU, U.K.
| | - Anna Trybala
- Department
of Chemical Engineering, Loughborough University, Loughborough, Leicestershire LE11 3TU, U.K.
| | - Dmitri Tseluiko
- Department
of Mathematics, Loughborough University, Loughborough, Leicestershire LE11 3TU, U.K.
| | - Victor Mikhilovich Starov
- Department
of Chemical Engineering, Loughborough University, Loughborough, Leicestershire LE11 3TU, U.K.
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8
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Magill M, Nagel AM, de Haan HW. Parallel computing for mobilities in periodic geometries. Phys Rev E 2022; 106:045304. [PMID: 36397582 DOI: 10.1103/physreve.106.045304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 09/24/2022] [Indexed: 06/16/2023]
Abstract
We examine methods for calculating the effective mobilities of molecules driven through periodic geometries in the context of particle-based simulation. The standard formulation of the mobility, based on the long-time limit of the mean drift velocity, is compared to a formulation based on the mean first-passage time of molecules crossing a single period of the system geometry. The equivalence of the two definitions is derived under weaker assumptions than similar conclusions obtained previously, requiring only that the state of the system at subsequent period crossings satisfy the Markov property. Approximate theoretical analyses of the computational costs of estimating these two mobility formulations via particle simulations suggest that the definition based on first-passage times may be substantially better suited to exploiting parallel computation hardware. This claim is investigated numerically on an example system modeling the passage of nanoparticles through the slit-well device. In this case, the traditional mobility formulation is found to perform best when the Péclet number is small, whereas the mean first-passage time formulation is found to converge much more quickly when the Péclet number is moderate or large. The results suggest that, given relatively modest access to modern GPU hardware, this alternative mobility formulation may be an order of magnitude faster than the standard technique for computing effective mobilities of biomolecules through periodic geometries.
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Affiliation(s)
- Martin Magill
- Faculty of Science, University of Ontario Institute of Technology, 2000 Simcoe St N, Oshawa, Ontario L1H7K4, Canada
| | - Andrew M Nagel
- Faculty of Science, University of Ontario Institute of Technology, 2000 Simcoe St N, Oshawa, Ontario L1H7K4, Canada
| | - Hendrick W de Haan
- Faculty of Science, University of Ontario Institute of Technology, 2000 Simcoe St N, Oshawa, Ontario L1H7K4, Canada
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9
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Nagel AM, Magill M, de Haan HW. Studying first passage problems using neural networks: A case study in the slit-well microfluidic device. Phys Rev E 2022; 106:025311. [PMID: 36109883 DOI: 10.1103/physreve.106.025311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 07/28/2022] [Indexed: 06/15/2023]
Abstract
This study presents deep neural network solutions to a time-integrated Smoluchowski equation modeling the mean first passage time of nanoparticles traversing the slit-well microfluidic device. This physical scenario is representative of a broader class of parametrized first passage problems in which key output metrics are dictated by a complicated interplay of problem parameters and system geometry. Specifically, whereas these types of problems are commonly studied using particle simulations of stochastic differential equation models, here the corresponding partial differential equation model is solved using a method based on deep neural networks. The results illustrate that the neural network method is synergistic with the time-integrated Smoluchowski model: together, these are used to construct continuous mappings from key physical inputs (applied voltage and particle diameter) to key output metrics (mean first passage time and effective mobility). In particular, this capability is a unique advantage of the time-integrated Smoluchowski model over the corresponding stochastic differential equation models. Furthermore, the neural network method is demonstrated to easily and reliably handle geometry-modifying parameters, which is generally difficult to accomplish using other methods.
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Affiliation(s)
- Andrew M Nagel
- Faculty of Science, University of Ontario Institute of Technology, 2000 Simcoe St N, Oshawa, Ontario, Canada L1H7K4
| | - Martin Magill
- Faculty of Science, University of Ontario Institute of Technology, 2000 Simcoe St N, Oshawa, Ontario, Canada L1H7K4
| | - Hendrick W de Haan
- Faculty of Science, University of Ontario Institute of Technology, 2000 Simcoe St N, Oshawa, Ontario, Canada L1H7K4
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10
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Fauvel M, Trybala A, Tseluiko D, Starov VM, Bandulasena HCH. Stability of Two-Dimensional Liquid Foams under Externally Applied Electric Fields. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:6305-6321. [PMID: 35546544 PMCID: PMC9134501 DOI: 10.1021/acs.langmuir.2c00026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 04/26/2022] [Indexed: 06/15/2023]
Abstract
Liquid foams are highly complex systems consisting of gas bubbles trapped within a solution of surfactant. Electroosmotic effects may be employed to induce fluid flows within the foam structure and impact its stability. The impact of external electric fields on the stability of a horizontally oriented monolayer of foam (2D foam) composed of anionic, cationic, non-ionic, and zwitterionic surfactants was investigated, probing the effects of changing the gas-liquid and solid-liquid interfaces. Time-lapse recordings were analyzed to investigate the evolution of foam over time subject to varying electric field strengths. Numerical simulations of electroosmotic flow of the same system were performed using the finite element method. Foam stability was affected by the presence of an external electric field in all cases and depended on the surfactant type, strength of the electric field, and the solid material used to construct the foam cell. For the myristyltrimethylammonium bromide (MTAB) foam in a glass cell, the time to collapse 50% of the foam was increased from ∼25 min under no electric field to ∼85 min under an electric field strength of 2000 V/m. In comparison, all other surfactants trialed exhibited faster foam collapse under external electric fields. Numerical simulations provided insight as to how different zeta potentials at the gas-liquid and solid-liquid interfaces affect fluid flow in different elements of the foam structure under external electric fields, leading to a more stable or unstable foam.
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Affiliation(s)
- Matthieu Fauvel
- Department
of Chemical Engineering, Loughborough University, Loughborough, Leicestershire, LE11 3TU, United Kingdom
| | - Anna Trybala
- Department
of Chemical Engineering, Loughborough University, Loughborough, Leicestershire, LE11 3TU, United Kingdom
| | - Dmitri Tseluiko
- Department
of Mathematics, Loughborough University, Loughborough, Leicestershire, LE11 3TU, United Kingdom
| | - Victor Mikhilovich Starov
- Department
of Chemical Engineering, Loughborough University, Loughborough, Leicestershire, LE11 3TU, United Kingdom
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11
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Lamontagne M, Levy S. Nonlinear electrophoretic velocity of DNA in slitlike confinement. Phys Rev E 2022; 105:054503. [PMID: 35706241 DOI: 10.1103/physreve.105.054503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 04/20/2022] [Indexed: 06/15/2023]
Abstract
We have applied zero-time-averaged alternating electric fields to DNA molecules in a cross-shaped nanofluidic slit. We observed a net drift of DNA molecules, the magnitude of which depends on the square of the electric field amplitude. From the rate of accumulation of DNA at the center of the device, we derive an estimate for the second-order electrophoretic mobility, μ_{2}. We observe that focusing is absent at a dipole rotation frequency >20 Hz, which suggests that μ_{2} depends on the frequency of the alternating fields. The observation of a nonzero μ_{2} raises the possibility of frequency-dependent electrophoretic DNA separation by length achievable in the absence of a sieving matrix.
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Affiliation(s)
- Michael Lamontagne
- Department of Physics, Applied Physics and Astronomy, Binghamton University, 4400 Vestal Parkway East, P.O. Box 6000, Binghamton, New York 13902-6000, USA
| | - Stephen Levy
- Department of Physics, Applied Physics and Astronomy, Binghamton University, 4400 Vestal Parkway East, P.O. Box 6000, Binghamton, New York 13902-6000, USA
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12
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Verma N, Pandya A. Challenges and opportunities in micro/nanofluidic and lab-on-a-chip. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 186:289-302. [PMID: 35033289 DOI: 10.1016/bs.pmbts.2021.07.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Fluidic systems are prevalent in many areas of science due to its advantage in miniaturization, development of unique tools for diseases diagnosis and biomolecule separation. In the chapter, we will describe some of the key features of microfluidic/nanofluidic (MF/NF) and lab-on-a-chip system in diverse field over the past years. In addition, we will highlight the major challenges for the microfluidic/nanofluidic and lab-on-a-chip system. All-purpose and universal micro/nanofluidic platforms that can perform multiplexed assays on real biological samples are in high demand. However, the adoption of novel microfluidic devices has been carried out at a slow pace due to translation gap in development of new devices to realization into commercialization. By addressing the challenges of system integration, low-cost technology availability, rapid regulatory approval, and clinical acceptance, a pipeline of promising microdevice technologies can be developed.
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Affiliation(s)
- Nidhi Verma
- Department of Engineering and Physical Sciences, Institute of Advanced Research, Gandhinagar, Gujarat, India
| | - Alok Pandya
- Department of Engineering and Physical Sciences, Institute of Advanced Research, Gandhinagar, Gujarat, India.
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13
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Ching T, Toh YC, Hashimoto M. Design and fabrication of micro/nanofluidics devices and systems. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 186:15-58. [PMID: 35033282 DOI: 10.1016/bs.pmbts.2021.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This chapter provides an overview of the science, engineering, and design methods required in the development of micro/nanofluidic devices. Section 2 provides the scientific background of fluid mechanics and physical phenomena in micro/nanoscale. Section 3 gives a brief overview of the existing fabrication techniques employed in micro/nanofluidics. The techniques are grouped into three categories: (1) subtractive manufacturing, (2) formative manufacturing, and (3) additive manufacturing. The advantages and disadvantages of each manufacturing technique are also discussed. Implementation of the fluidic devices beyond laboratory demonstrations is not trivial, which requires a good understanding of the problems of interest and the end-users. To that end, Section 4 introduces the design thinking approach and its application to develop micro/nanofluidic devices. Finally, Section 5 concludes the chapter with future outlooks.
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Affiliation(s)
- Terry Ching
- Pillar of Engineering Product Development, Singapore University of Technology and Design, Singapore, Singapore; Digital Manufacturing and Design Centre, Singapore University of Technology and Design, Singapore, Singapore; Department of Biomedical Engineering, National University of Singapore, Singapore, Singapore
| | - Yi-Chin Toh
- School of Mechanical, Medical and Process Engineering, Queensland University of Technology, Brisbane, QLD, Australia; Centre for Biomedical Technologies, Queensland University of Technology, Kelvin Grove, QLD, Australia
| | - Michinao Hashimoto
- Pillar of Engineering Product Development, Singapore University of Technology and Design, Singapore, Singapore; Digital Manufacturing and Design Centre, Singapore University of Technology and Design, Singapore, Singapore.
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Bucci G, Gadelrab K, Spakowitz AJ. Free Energy and Dynamics of Annihilation of Topological Defects in Nanoconfined DNA. Macromolecules 2021. [DOI: 10.1021/acs.macromol.1c01164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Giovanna Bucci
- Robert Bosch LLC, 384 Santa Trinita Ave, Sunnyvale, California 94085, United States
| | - Karim Gadelrab
- Robert Bosch LLC, 1 Kendall Square, Suite 7-101, Cambridge, Massachusetts 02139, United States
| | - Andrew J. Spakowitz
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
- Department of Materials Science and Engineering, Stanford University, Stanford, California 94305, United States
- Department of Applied Physics, Stanford University, Stanford, California 94305, United States
- Biophysics Program, Stanford University, Stanford, California 94305, United States
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15
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Ma M, Xu Z, Zhang L. Ion transport in electrolytes of dielectric nanodevices. Phys Rev E 2021; 104:035307. [PMID: 34654206 DOI: 10.1103/physreve.104.035307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 09/09/2021] [Indexed: 06/13/2023]
Abstract
Ion transport in electrolytes with nanoscale confinements is of great importance in many fields such as nanofluidics and electrochemical energy devices. The mobility and conductance for ions are often described by the classical Debye-Hückel-Onsager (DHO) theory but this theory fails for ions near dielectric interfaces. We propose a generalized DHO theory by using the Wentzel-Kramers-Brillouin techniques for the solution of the Onsager-Fuoss equation with variable coefficients. The theory allows to quantitatively measure physical quantities of ion transport in nanodevices and is demonstrated to well explain the abnormal increase or decrease of the ionic mobility tuned via the dielectric mismatch. By numerical calculations, our theory unravels the crucial role of the size of confinements and the ionic concentration on the ion transport, and demonstrates that the dielectric polarization can provide a giant enhancement on the conductance of electrolytes in nanodevices. This mechanism provides a practical guide for related nanoscale technologies with controllable transport properties.
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Affiliation(s)
- Manman Ma
- School of Mathematical Sciences, Tongji University, Shanghai 200092, China
| | - Zhenli Xu
- School of Mathematical Sciences, Institute of Natural Sciences, and MoE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Liwei Zhang
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
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16
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Chen G, Li T, Chen C, Kong W, Jiao M, Jiang B, Xia Q, Liang Z, Liu Y, He S, Hu L. Scalable Wood Hydrogel Membrane with Nanoscale Channels. ACS NANO 2021; 15:11244-11252. [PMID: 34269048 DOI: 10.1021/acsnano.0c10117] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Many efforts have been dedicated to exploring nanofluidic systems for various applications including water purification and energy generation. However, creating robust nanofluidic materials with tunable channel orientations and numerous nanochannels or nanopores on a large scale remains challenging. Here, we demonstrate a scalable and cost-effective method to fabricate a robust and highly conductive nanofluidic wood hydrogel membrane in which ions can transport across the membrane. The ionically conductive balsa wood hydrogel membrane is fabricated by infiltrating poly(vinyl alcohol) (PVA)/acrylic acid (AA) hydrogel into the inherent bimodal porous wood structure. The balsa wood hydrogel membrane demonstrates a 3 times higher strength (52.7 MPa) and 2 orders of magnitude higher ionic conductivity compared to those of natural balsa both in the radial direction (coded as R direction) and along the longitudinal direction (coded as L direction). The ionic conductivity of the balsa wood hydrogel membrane is 1.29 mS cm-1 along the L direction and nearly 1 mS cm-1 along the R direction at low salt concentrations (up to 10 mM). In addition, the surface-charge-governed ion transport also renders the balsa wood hydrogel membrane able to harvest electrical energy from salinity gradients. A current density of up to 17.65 μA m-2 and an output power density of 0.56 mW m-2 are obtained under a 1000-fold salt concentration gradient, which can be further improved to 2.7 mW m-2 by increasing the AA content from 25 wt % to 50 wt %. These findings make contributions to develop energy-harvesting systems and other nanofluidic devices from sustainable wood materials.
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Affiliation(s)
- Gegu Chen
- Department of Materials Science and Engineering, University of Maryland, College Park, Maryland 20742, United States
| | - Tian Li
- Department of Materials Science and Engineering, University of Maryland, College Park, Maryland 20742, United States
| | - Chaoji Chen
- Department of Materials Science and Engineering, University of Maryland, College Park, Maryland 20742, United States
| | - Weiqing Kong
- Department of Materials Science and Engineering, University of Maryland, College Park, Maryland 20742, United States
| | - Miaolun Jiao
- Department of Materials Science and Engineering, University of Maryland, College Park, Maryland 20742, United States
| | - Bo Jiang
- Department of Materials Science and Engineering, University of Maryland, College Park, Maryland 20742, United States
| | - Qinqin Xia
- Department of Materials Science and Engineering, University of Maryland, College Park, Maryland 20742, United States
| | - Zhiqiang Liang
- Department of Materials Science and Engineering, University of Maryland, College Park, Maryland 20742, United States
| | - Yang Liu
- Department of Materials Science and Engineering, University of Maryland, College Park, Maryland 20742, United States
| | - Shuaiming He
- Department of Materials Science and Engineering, University of Maryland, College Park, Maryland 20742, United States
| | - Liangbing Hu
- Department of Materials Science and Engineering, University of Maryland, College Park, Maryland 20742, United States
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Soh BW, Doyle PS. Equilibrium Conformation of Catenated DNA Networks in Slitlike Confinement. ACS Macro Lett 2021; 10:880-885. [PMID: 35549205 DOI: 10.1021/acsmacrolett.1c00299] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A kinetoplast is a planar network of catenated DNA rings with topology that resembles that of chain mail armor. In this work, we use single-molecule experiments to probe the conformation of kinetoplasts confined to slits. We find that the in-plane size of kinetoplasts increases with degree of confinement, akin to the slitlike confinement of linear DNA. The change in kinetoplast size with channel height is consistent with the scaling prediction from a Flory-type approach for a 2D polymer. With an increase in extent of confinement, the kinetoplasts appear to unfold and take on more uniform circular shapes, in contrast to the broad range of conformations observed for kinetoplasts in bulk.
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Affiliation(s)
- Beatrice W. Soh
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Patrick S. Doyle
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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Peyravian N, Malekzadeh Kebria M, Kiani J, Brouki Milan P, Mozafari M. CRISPR-Associated (CAS) Effectors Delivery via Microfluidic Cell-Deformation Chip. MATERIALS (BASEL, SWITZERLAND) 2021; 14:3164. [PMID: 34207502 PMCID: PMC8226447 DOI: 10.3390/ma14123164] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 05/26/2021] [Accepted: 05/30/2021] [Indexed: 12/26/2022]
Abstract
Identifying new and even more precise technologies for modifying and manipulating selectively specific genes has provided a powerful tool for characterizing gene functions in basic research and potential therapeutics for genome regulation. The rapid development of nuclease-based techniques such as CRISPR/Cas systems has revolutionized new genome engineering and medicine possibilities. Additionally, the appropriate delivery procedures regarding CRISPR/Cas systems are critical, and a large number of previous reviews have focused on the CRISPR/Cas9-12 and 13 delivery methods. Still, despite all efforts, the in vivo delivery of the CAS gene systems remains challenging. The transfection of CRISPR components can often be inefficient when applying conventional delivery tools including viral elements and chemical vectors because of the restricted packaging size and incompetency of some cell types. Therefore, physical methods such as microfluidic systems are more applicable for in vitro delivery. This review focuses on the recent advancements of microfluidic systems to deliver CRISPR/Cas systems in clinical and therapy investigations.
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Affiliation(s)
- Noshad Peyravian
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran 1449614535, Iran; (N.P.); (M.M.K.)
- Department of Tissue Engineering and Regenerative Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran
| | - Maziar Malekzadeh Kebria
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran 1449614535, Iran; (N.P.); (M.M.K.)
- Department of Tissue Engineering and Regenerative Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran
| | - Jafar Kiani
- Department of Molecular Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran;
- Oncopathology Research Center, Iran University of Medical Sciences, Tehran 1449614535, Iran
| | - Peiman Brouki Milan
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran 1449614535, Iran; (N.P.); (M.M.K.)
- Department of Tissue Engineering and Regenerative Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran
| | - Masoud Mozafari
- Department of Tissue Engineering and Regenerative Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran
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Kwon S, Lee H, Kim SJ. Pulsed electric field-assisted overlimiting current enhancement through a perm-selective membrane. LAB ON A CHIP 2021; 21:2153-2162. [PMID: 33908534 DOI: 10.1039/d1lc00064k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Overlimiting current through a perm-selective membrane has been actively researched not only for the fundamental advancement of electrokinetics but also for energy/environmental applications such as electrodialysis, fuel cells, etc. In particular, various strategies were reported for the enhancement of overlimiting current because these applications demand efficient mass transport through the membrane. In this work, we presented in operando visualization and rigorous numerical study for the overlimiting current density enhancement using a pulsed electric field which is one of the most cost-effective parameters to be externally controlled. We clearly demonstrated that the current density had a peak value as a function of the pulse frequency and would suggest its correlation to a concentration profile and diffusion relaxation time ([small tau, Greek, tilde]diff). As the pulse frequency was chosen which is similar to ([small tau, Greek, tilde]diff)-1, the concentration profiles (i.e. established current paths) were maintained even in off-state due to remnant current paths helping the fast ion transportation. The fundamental evidence presented in this work would provide a strategical design of a perm-selective membrane system for a higher mass transportation efficiency.
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Affiliation(s)
- Soonhyun Kwon
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, Republic of Korea.
| | - Hyomin Lee
- Department of Chemical and Biological engineering, Jeju National University, 63243, Republic of Korea.
| | - Sung Jae Kim
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, Republic of Korea. and Inter-university Semiconductor Research Center, Seoul National University, Seoul, 08826, South Korea and Nano Systems Institute, Seoul National University, Seoul, 08826, South Korea
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20
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Qi S, Klushin LI, Skvortsov AM, Schmid F. Adsorption Active Diblock Copolymers as Universal Agents for Unusual Barrier-Free Transitions in Stimuli-Responsive Brushes. Macromolecules 2021. [DOI: 10.1021/acs.macromol.0c02095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Shuanhu Qi
- Key Laboratory of Bio-inspired Smart Interfacial Science and Technology of Ministry of Education, School of Chemistry, Beihang University, Beijing 100191, China
| | - Leonid I. Klushin
- Department of Physics, American University of Beirut, P.O. Box 11-0236, Beirut 1107 2020, Lebanon
- Institute for Macromolecular Compounds RAS, Bolshoi pr. 31, 1199004 St. Petersburg, Russia
| | | | - Friederike Schmid
- Institut für Physik, Johannes Gutenberg-Universität Mainz, Staudingerweg 7, D-55099 Mainz, Germany
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21
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22
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Gbadamasi S, Mohiuddin M, Krishnamurthi V, Verma R, Khan MW, Pathak S, Kalantar-Zadeh K, Mahmood N. Interface chemistry of two-dimensional heterostructures - fundamentals to applications. Chem Soc Rev 2021; 50:4684-4729. [PMID: 33621294 DOI: 10.1039/d0cs01070g] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Two-dimensional heterostructures (2D HSs) have emerged as a new class of materials where dissimilar 2D materials are combined to synergise their advantages and alleviate shortcomings. Such a combination of dissimilar components into 2D HSs offers fascinating properties and intriguing functionalities attributed to the newly formed heterointerface of constituent components. Understanding the nature of the surface and the complex heterointerface of HSs at the atomic level is crucial for realising the desired properties, designing innovative 2D HSs, and ultimately unlocking their full potential for practical applications. Therefore, this review provides the recent progress in the field of 2D HSs with a focus on the discussion of the fundamentals and the chemistry of heterointerfaces based on van der Waals (vdW) and covalent interactions. It also explains the challenges associated with the scalable synthesis and introduces possible methodologies to produce large quantities with good control over the heterointerface. Subsequently, it highlights the specialised characterisation techniques to reveal the heterointerface formation, chemistry and nature. Afterwards, we give an overview of the role of 2D HSs in various emerging applications, particularly in high-power batteries, bifunctional catalysts, electronics, and sensors. In the end, we present conclusions with the possible solutions to the associated challenges with the heterointerfaces and potential opportunities that can be adopted for innovative applications.
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23
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Park S, Hong S, Kim J, Son SY, Lee H, Kim SJ. Eco friendly nanofluidic platforms using biodegradable nanoporous materials. Sci Rep 2021; 11:3804. [PMID: 33589696 PMCID: PMC7884701 DOI: 10.1038/s41598-021-83306-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 02/02/2021] [Indexed: 11/09/2022] Open
Abstract
Splendid advancement of micro/nanofluidic researches in the field of bio- and chemical-analysis enables various ubiquitous applications such as bio-medical diagnostics and environmental monitoring, etc. In such devices, nanostructures are the essential elements so that the nanofabrication methods have been major issues since the last couple of decades. However, most of nanofabrication methods are sophisticated and expensive due to the requirement of high-class cleanroom facilities, while low-cost and biocompatible materials have been already introduced in the microfluidic platforms. Thus, an off-the-shelf and biodegradable material for those nanostructures can complete the concept of an eco-friendly micro/nanofluidic platform. In this work, biodegradable materials originated from well-known organisms such as human nail plate and denatured hen egg (albumen and yolk) were rigorously investigated as a perm-selective nanoporous membrane. A simple micro/nanofluidic device integrated with such materials was fabricated to demonstrate nanofluidic phenomena. These distinctive evidences (the visualization of ion concentration polarization phenomenon, ohmic/limiting/over-limiting current behavior and surface charge-governed conductance) can fulfill the requirements of functional nanostructures for the nanofluidic applications. Therefore, while these materials were less robust than nano-lithographically fabricated structures, bio-oriented perm-selective materials would be utilized as a one of key elements of the biodegradable and eco friendly micro/nanofluidic applications.
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Affiliation(s)
- Sungmin Park
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Seongjun Hong
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Junsuk Kim
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Seok Young Son
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hyomin Lee
- Department of Chemical and Biological Engineering, Jeju National University, Jeju, 63243, Republic of Korea
| | - Sung Jae Kim
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, Republic of Korea. .,Nano System Institute, Seoul National University, Seoul, 08826, Republic of Korea. .,Inter-University Semiconductor Research Center, Seoul National University, Seoul, 08826, Republic of Korea.
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24
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Hejazi S, Pahlavanzadeh H, Elliott JAW. Thermodynamic Investigation of the Effect of Electric Field on Solid-Liquid Equilibrium. J Phys Chem B 2021; 125:1271-1281. [PMID: 33497220 DOI: 10.1021/acs.jpcb.0c08754] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this study, the thermal, mechanical, and chemical equilibrium conditions are derived for binary solid-liquid equilibrium under the effect of an electric field. As an example, the effect of an electric field on the water/glycerol solid-liquid phase diagram is computed over the complete mole fraction range. We show that the application of an electric field can affect the composition dependent freezing and precipitating processes, changing freezing and precipitating temperatures and changing the eutectic point temperature and mole fraction.
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Affiliation(s)
- Sima Hejazi
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta Canada T6G 1H9.,Faculty of Chemical Engineering, Tarbiat Modares University, Tehran 14115-336, Iran
| | - Hassan Pahlavanzadeh
- Faculty of Chemical Engineering, Tarbiat Modares University, Tehran 14115-336, Iran
| | - Janet A W Elliott
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta Canada T6G 1H9
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The Longitudinal Superdiffusive Motion of Block Copolymer in a Tight Nanopore. Polymers (Basel) 2020; 12:polym12122931. [PMID: 33302399 PMCID: PMC7762597 DOI: 10.3390/polym12122931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 11/30/2020] [Accepted: 12/03/2020] [Indexed: 11/16/2022] Open
Abstract
The structure and dynamic properties of polymer chains in a confined environment were studied by means of the Monte Carlo method. The studied chains were represented by coarse-grained models and embedded into a simple 3D cubic lattice. The chains stood for two-block linear copolymers of different energy of bead-bead interactions. Their behavior was studied in a nanotube formed by four impenetrable surfaces. The long-time unidirectional motion of the chain in the tight nanopore was found to be correlated with the orientation of both parts of the copolymer along the length of the nanopore. A possible mechanism of the anomalous diffusion was proposed on the basis of thermodynamics of the system, more precisely on the free energy barrier of the swapping of positions of both parts of the chain and the impulse of temporary forces induced by variation of the chain conformation. The mean bead and the mass center autocorrelation functions were examined. While the former function behaves classically, the latter indicates the period of time of superdiffusive motion similar to the ballistic motion with the autocorrelation function scaling with the exponent t5/3. A distribution of periods of time of chain diffusion between swapping events was found and discussed. The influence of the nanotube width and the chain length on the polymer diffusivity was studied.
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Luan B, Kuroda MA. Electrophoretic Transport of Single-Stranded DNA through a Two Dimensional Nanopore Patterned on an In-Plane Heterostructure. ACS NANO 2020; 14:13137-13145. [PMID: 32902252 DOI: 10.1021/acsnano.0c04743] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Recent advances in nanotechnology have facilitated fabrication of various solid state nanopores as a versatile alternative to biological nanopores; however, effective transport of a single-stranded DNA (ssDNA) molecule through solid state nanopores for sequencing has remained a challenge. In particular, the nonspecific interactions between the ssDNA and the engineered nanopore surface are known to impose difficulties on both transport and interrogation. Here, we show that a two-dimensional (2D) nanopore patterned on an in-plane heterostructure comprising both graphene and hexagonal boron nitride (hBN) can be utilized to transport the ssDNA electrophoretically. Energetically, a ssDNA molecule prefers to stay on the hBN domain than the graphene one since the former has a stronger van der Waals attraction with the ssDNA, as demonstrated in both classic molecular dynamics (MD) simulations and density functional theory (DFT) based calculations, which leads to the confinement of the ssDNA in the 2D nanopore. Therefore, this nanopore enables the manipulation of the conformation of a highly flexible ssDNA molecule on a flat 2D heterostructure surface, making it possible for sensing ssDNA bases using the high resolution atomic force microscopy (AFM) or scanning tunneling microscopy (STM) in the third dimension (perpendicular to the 2D surface).
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Affiliation(s)
- Binquan Luan
- Computational Biological Center, IBM Thomas J. Watson Research, Yorktown Heights, New York 10598, United States
| | - Marcelo A Kuroda
- Department of Physics, Auburn University, Auburn, Alabama 36849, United States
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27
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Bucci G, Spakowitz AJ. Systematic Approach toward Accurate and Efficient DNA Sequencing via Nanoconfinement. ACS Macro Lett 2020; 9:1184-1191. [PMID: 35653210 DOI: 10.1021/acsmacrolett.0c00423] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Coarse-grained modeling tools are employed to simulate the mechanics of DNA loading within a nanoscale confinement and predict semiflexible polymer conformations within the confinement, providing design recommendations for DNA-sequencing devices. A workflow is developed to quantify competing requirements of efficiency and accuracy and extract metrics that guide design optimization. The mean first-passage time for DNA loading is calculated as a function of the nanochannel geometry and the applied electric field. We analyze the interplay between the free energy of confinement and the electric potential energy in achieving high-throughput, base-pair detection. The single-read probability is investigated as informative metrics for sequencing accuracy and for sensing-strategy design. High cost, low throughput, and low accuracy have so far limited the adoption of nanochannel analysis and other long-read technologies. Our work directly addresses these limitations with a systematic approach that is scalable to long molecules and complex geometries.
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Affiliation(s)
- Giovanna Bucci
- Robert Bosch LLC, 384 Santa Trinita Avenue, Sunnyvale, California 94085, United States
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28
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He Z, Zhou R. Planar graphene/h-BN/graphene heterostructures for protein stretching and confinement. NANOSCALE 2020; 12:13822-13828. [PMID: 32572421 DOI: 10.1039/d0nr02271c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Protein stretching and confinement in nanochannels is critical for advancing single-molecule detection techniques. For standard nanochannels integrated with nano-sensors, reducing their cross-section is beneficial for reading highly localized signals with minimal error, but results in increasing difficulty for the initial capture of any chain molecules due to the entropy barrier. Using molecular dynamics simulations, we show that spontaneous protein stretching can be realized by a two-dimensional (2D) heterostructure composed of a hexagonal boron nitride (h-BN) nanoribbon stitched with two graphene (GRA) sheets (i.e., a sandwiched GRA/BN/GRA structure). Due to fast protein diffusion on its flat surface and adsorption potential difference between two 2D materials, this planar nanochannel permits effective capture and elongation of three representative intrinsically disordered proteins including amyloid-β (1-42), polyglutamine (42) and α-synuclein (61-95). Moreover, we found that the extremely narrow h-BN stripe can provide stronger confinement for a longer polyglutamine chain after being stretched. Our approach has the potential to facilitate the bona fide readout of single-molecule protein sequencing techniques.
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Affiliation(s)
- Zhi He
- Institute of Quantitative Biology, Zhejiang University, Hangzhou 310027, China.
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29
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Müller V, Dvirnas A, Andersson J, Singh V, Kk S, Johansson P, Ebenstein Y, Ambjörnsson T, Westerlund F. Enzyme-free optical DNA mapping of the human genome using competitive binding. Nucleic Acids Res 2019; 47:e89. [PMID: 31165870 PMCID: PMC6735870 DOI: 10.1093/nar/gkz489] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/03/2019] [Accepted: 05/22/2019] [Indexed: 01/24/2023] Open
Abstract
Optical DNA mapping (ODM) allows visualization of long-range sequence information along single DNA molecules. The data can for example be used for detecting long range structural variations, for aiding DNA sequence assembly of complex genomes and for mapping epigenetic marks and DNA damage across the genome. ODM traditionally utilizes sequence specific marks based on nicking enzymes, combined with a DNA stain, YOYO-1, for detection of the DNA contour. Here we use a competitive binding approach, based on YOYO-1 and netropsin, which highlights the contour of the DNA molecules, while simultaneously creating a continuous sequence specific pattern, based on the AT/GC variation along the detected molecule. We demonstrate and validate competitive-binding-based ODM using bacterial artificial chromosomes (BACs) derived from the human genome and then turn to DNA extracted from white blood cells. We generalize our findings with in-silico simulations that show that we can map a vast majority of the human genome. Finally, we demonstrate the possibility of combining competitive binding with enzymatic labeling by mapping DNA damage sites induced by the cytotoxic drug etoposide to the human genome. Overall, we demonstrate that competitive-binding-based ODM has the potential to be used both as a standalone assay for studies of the human genome, as well as in combination with enzymatic approaches, some of which are already commercialized.
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Affiliation(s)
- Vilhelm Müller
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Albertas Dvirnas
- Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
| | - John Andersson
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Vandana Singh
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Sriram Kk
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Pegah Johansson
- Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Yuval Ebenstein
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Tobias Ambjörnsson
- Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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Spontaneous ssDNA stretching on graphene and hexagonal boron nitride in plane heterostructures. Nat Commun 2019; 10:4610. [PMID: 31601816 PMCID: PMC6787186 DOI: 10.1038/s41467-019-12584-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 09/12/2019] [Indexed: 11/08/2022] Open
Abstract
Single-stranded DNA (ssDNA) molecules in solution typically form coiled structures, therefore stretching ssDNA is extremely crucial before applying any nanotechnology for ssDNA analysis. Recent advances in material fabrication enable the deployment of nanochannels to manipulate, stretch, sort and map double-stranded DNA (dsDNA) molecules, however nanochannels fail to stretch ssDNA molecules due to the ultra-short persistence length and the potential nonspecific-interaction-induced clogging. Given the significance of ssDNA stretching in genome analysis, here we report an ssDNA stretching platform: two dimensional in-plane heterostructure comprising graphene and hexagonal boron nitride (h-BN), and show that ssDNA can be stretched on a h-BN nanostripe sandwiched between two adjacent graphene domains (“nanochannel”). We further show that with a biasing voltage the stretched ssDNA can be electrophoretically transported along the “nanochannel”, allowing easy controls/manipulations. When being conveniently integrated with existing atomic resolution sensors, the heterostructure platform paves the way for sequencing DNA on a planar surface. Single stranded DNA analysis is of interest for a range of applications; however, natural folding of DNA can cause problems with this. Here, the authors report on the in silico analysis of graphene and hexagonal-boron-nitride structures for the stretching and unfolding of DNA to allow for analysis.
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31
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Hydrophobic catalysis and a potential biological role of DNA unstacking induced by environment effects. Proc Natl Acad Sci U S A 2019; 116:17169-17174. [PMID: 31413203 PMCID: PMC6717297 DOI: 10.1073/pnas.1909122116] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The main stabilizer of the DNA double helix is not the base-pair hydrogen bonds but coin-pile stacking of base pairs, whose hydrophobic cohesion, requiring abundant water, indirectly makes the DNA interior dry so that hydrogen bonds can exert full recognition power. We report that certain semihydrophobic agents depress the stacking energy (measurable in single-molecule experiments), leading to transiently occurring holes in the base-pair stack (monitorable via binding of threading intercalators). Similar structures observed in DNA complexes with RecA and Rad51, and previous observations of spontaneous strand exchange catalyzed in semihydrophobic model systems, make us propose that some hydrophobic protein residues may have roles in catalyzing homologous recombination. We speculate that hydrophobic catalysis is a general phenomenon in DNA enzymes. Hydrophobic base stacking is a major contributor to DNA double-helix stability. We report the discovery of specific unstacking effects in certain semihydrophobic environments. Water-miscible ethylene glycol ethers are found to modify structure, dynamics, and reactivity of DNA by mechanisms possibly related to a biologically relevant hydrophobic catalysis. Spectroscopic data and optical tweezers experiments show that base-stacking energies are reduced while base-pair hydrogen bonds are strengthened. We propose that a modulated chemical potential of water can promote “longitudinal breathing” and the formation of unstacked holes while base unpairing is suppressed. Flow linear dichroism in 20% diglyme indicates a 20 to 30% decrease in persistence length of DNA, supported by an increased flexibility in single-molecule nanochannel experiments in poly(ethylene glycol). A limited (3 to 6%) hyperchromicity but unaffected circular dichroism is consistent with transient unstacking events while maintaining an overall average B-DNA conformation. Further information about unstacking dynamics is obtained from the binding kinetics of large thread-intercalating ruthenium complexes, indicating that the hydrophobic effect provides a 10 to 100 times increased DNA unstacking frequency and an “open hole” population on the order of 10−2 compared to 10−4 in normal aqueous solution. Spontaneous DNA strand exchange catalyzed by poly(ethylene glycol) makes us propose that hydrophobic residues in the L2 loop of recombination enzymes RecA and Rad51 may assist gene recombination via modulation of water activity near the DNA helix by hydrophobic interactions, in the manner described here. We speculate that such hydrophobic interactions may have catalytic roles also in other biological contexts, such as in polymerases.
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Sonker M, Kim D, Egatz-Gomez A, Ros A. Separation Phenomena in Tailored Micro- and Nanofluidic Environments. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2019; 12:475-500. [PMID: 30699038 DOI: 10.1146/annurev-anchem-061417-125758] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Separations of bioanalytes require robust, effective, and selective migration phenomena. However, due to the complexity of biological matrices such as body fluids or tissue, these requirements are difficult to achieve. The separations field is thus constantly evolving to develop suitable methods to separate biomarkers and fractionate biospecimens for further interrogation of biomolecular content. Advances in the field of microfabrication allow the tailored generation of micro- and nanofluidic environments. These can be exploited to induce interactions and dynamics of biological species with the corresponding geometrical features, which in turn can be capitalized for novel separation approaches. This review provides an overview of several unique separation applications demonstrated in recent years in tailored micro- and nanofluidic environments. These include electrokinetic methods such as dielectrophoresis and electrophoresis, but also rather nonintuitive ratchet separation mechanisms, continuous flow separations, and fractionations such as deterministic lateral displacement, as well as methods employing entropic forces for separation.
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Affiliation(s)
- Mukul Sonker
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, USA;
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
| | - Daihyun Kim
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, USA;
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
| | - Ana Egatz-Gomez
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, USA;
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
| | - Alexandra Ros
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, USA;
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
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33
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Annealing of ssDNA and compaction of dsDNA by the HIV-1 nucleocapsid and Gag proteins visualized using nanofluidic channels. Q Rev Biophys 2019; 52:e2. [DOI: 10.1017/s0033583518000124] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Abstract
The nucleocapsid protein NC is a crucial component in the human immunodeficiency virus type 1 life cycle. It functions both in its processed mature form and as part of the polyprotein Gag that plays a key role in the formation of new viruses. NC can protect nucleic acids (NAs) from degradation by compacting them to a dense coil. Moreover, through its NA chaperone activity, NC can also promote the most stable conformation of NAs. Here, we explore the balance between these activities for NC and Gag by confining DNA–protein complexes in nanochannels. The chaperone activity is visualized as concatemerization and circularization of long DNA via annealing of short single-stranded DNA overhangs. The first ten amino acids of NC are important for the chaperone activity that is almost completely absent for Gag. Gag condenses DNA more efficiently than mature NC, suggesting that additional residues of Gag are involved. Importantly, this is the first single DNA molecule study of full-length Gag and we reveal important differences to the truncated Δ-p6 Gag that has been used before. In addition, the study also highlights how nanochannels can be used to study reactions on ends of long single DNA molecules, which is not trivial with competing single DNA molecule techniques.
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Krog J, Alizadehheidari M, Werner E, Bikkarolla SK, Tegenfeldt JO, Mehlig B, Lomholt MA, Westerlund F, Ambjörnsson T. Stochastic unfolding of nanoconfined DNA: Experiments, model and Bayesian analysis. J Chem Phys 2019; 149:215101. [PMID: 30525714 DOI: 10.1063/1.5051319] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Nanochannels provide a means for detailed experiments on the effect of confinement on biomacromolecules, such as DNA. Here we introduce a model for the complete unfolding of DNA from the circular to linear configuration. Two main ingredients are the entropic unfolding force and the friction coefficient for the unfolding process, and we describe the associated dynamics by a non-linear Langevin equation. By analyzing experimental data where DNA molecules are photo-cut and unfolded inside a nanochannel, our model allows us to extract values for the unfolding force as well as the friction coefficient for the first time. In order to extract numerical values for these physical quantities, we employ a recently introduced Bayesian inference framework. We find that the determined unfolding force is in agreement with estimates from a simple Flory-type argument. The estimated friction coefficient is in agreement with theoretical estimates for motion of a cylinder in a channel. We further validate the estimated friction constant by extracting this parameter from DNA's center-of-mass motion before and after unfolding, yielding decent agreement. We provide publically available software for performing the required image and Bayesian analysis.
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Affiliation(s)
- Jens Krog
- MEMPHYS-Center for Biomembrane Physics, Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Odense, Denmark
| | | | - Erik Werner
- Department of Physics, Gothenburg University, Gothenburg, Sweden
| | - Santosh Kumar Bikkarolla
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | | | - Bernhard Mehlig
- Department of Physics, Gothenburg University, Gothenburg, Sweden
| | - Michael A Lomholt
- MEMPHYS-Center for Biomembrane Physics, Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Tobias Ambjörnsson
- Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
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35
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Affiliation(s)
- W. Nowicki
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznań, Poland
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36
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Magill M, Waller E, de Haan HW. A sequential nanopore-channel device for polymer separation. J Chem Phys 2018; 149:174903. [DOI: 10.1063/1.5037449] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- Martin Magill
- Faculty of Science, University of Ontario Institute of Technology, 2000 Simcoe St N, Oshawa, Ontario L1H7K4, Canada
| | - Ed Waller
- Faculty of Energy Systems and Nuclear Science, University of Ontario Institute of Technology, 2000 Simcoe St N, Oshawa, Ontario L1H7K4, Canada
| | - Hendrick W. de Haan
- Faculty of Science, University of Ontario Institute of Technology, 2000 Simcoe St N, Oshawa, Ontario L1H7K4, Canada
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37
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Evstrapov AA. Micro- and nanofluidic systems in devices for biological, medical and environmental research. ACTA ACUST UNITED AC 2017. [DOI: 10.1088/1742-6596/917/2/022002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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38
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Roy T, Szuttor K, Smiatek J, Holm C, Hardt S. Stretching of surface-tethered polymers in pressure-driven flow under confinement. SOFT MATTER 2017; 13:6189-6196. [PMID: 28798968 DOI: 10.1039/c7sm00306d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We study the effect of pressure-driven flow on a single surface-tethered DNA molecule confined between parallel surfaces. The influence of flow and channel parameters as well as the length of the molecules on their extension and orientation is explored. In the experiments the chain conformations are imaged by laser scanning confocal microscopy. We find that the fractional extension of the tethered DNA molecules mainly depends on the wall shear stress, with effects of confinement being very weak. Experiments performed with molecules of different contour length show that the fractional extension is a universal function of the product of the wall shear stress and the contour length, a result that can be obtained from a simple scaling relation. The experimental results are in good agreement with results from coarse-grained molecular dynamics/Lattice-Boltzmann simulations.
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Affiliation(s)
- Tamal Roy
- Institute for Nano- and Microfluidics, Technische Universität Darmstadt, Darmstadt, Germany.
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39
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Qin S, Liu D, Wang G, Portehault D, Garvey CJ, Gogotsi Y, Lei W, Chen Y. High and Stable Ionic Conductivity in 2D Nanofluidic Ion Channels between Boron Nitride Layers. J Am Chem Soc 2017; 139:6314-6320. [DOI: 10.1021/jacs.6b11100] [Citation(s) in RCA: 140] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Si Qin
- Institute
for Frontier Materials (IFM), Deakin University, 75 Pigdons Road, Waurn Ponds, Victoria 3216, Australia
| | - Dan Liu
- Institute
for Frontier Materials (IFM), Deakin University, 75 Pigdons Road, Waurn Ponds, Victoria 3216, Australia
| | - Guang Wang
- Institute
for Frontier Materials (IFM), Deakin University, 75 Pigdons Road, Waurn Ponds, Victoria 3216, Australia
| | - David Portehault
- Sorbonne Universités,
UPMC Université Paris 06, CNRS, Collège de France, Laboratoire
de Chimie de la Matière Condensée de Paris (LCMCP), 11 place Marcelin Berthelot, F-75005 Paris, France
| | - Christopher J. Garvey
- Australia Nuclear Science and Technology Organization (ANSTO), Sydney, New South Wales 2232, Australia
| | - Yury Gogotsi
- A.
J. Drexel Nanomaterials Institute and Materials Science and Engineering
Department, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States
| | - Weiwei Lei
- Institute
for Frontier Materials (IFM), Deakin University, 75 Pigdons Road, Waurn Ponds, Victoria 3216, Australia
| | - Ying Chen
- Institute
for Frontier Materials (IFM), Deakin University, 75 Pigdons Road, Waurn Ponds, Victoria 3216, Australia
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40
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Wan M, Sun D, Wang S, Wu J, Yang Y, Wang K, He Q, Wang G, Bai J. Influence of concentration on distribution properties of stretched-DNA in the MEC studied with fluorescence imaging and drop shape analyzing. Colloids Surf B Biointerfaces 2017; 151:11-18. [PMID: 27939693 DOI: 10.1016/j.colsurfb.2016.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 11/19/2016] [Accepted: 12/01/2016] [Indexed: 11/28/2022]
Abstract
Stretching and manipulating DNA efficiently is significant for exploring the properties and applications of single DNA molecules. Here, the influence of concentrations of buffer and DNA on properties of stretched DNA molecules in the molecular evaporation combing (MEC) is investigated systematically with the single molecule fluorescence imaging microscopy and the high-precision drop shape analyzing technology. The stretched degree and uniformity of combed DNA molecules decrease as the buffer concentration are increased from 7 to 20mM. When the buffer concentration changes from 12 to 15mM, the stretched DNA molecules are apt to form a ringlike pattern. During the MEC process, there exist two kinds of evaporation modes, i.e., the constant contact angle mode and the constant contact radius mode. The former only takes effect in the lower concentration of buffer and DNA, enabling the uniform stretching. While the latter plays the leading role in the higher concentration, promoting the formation of the ringlike pattern of DNA molecules.
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Affiliation(s)
- Mengjiao Wan
- State Key Laboratory of Cultivation Base for Photoelectric Technology and Functional Materials, Laboratory of Optoelectronic Technology of Shaanxi Province, National Center for International Research of Photoelectric Technology & Nanofunctional Materials and Application, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, Shaanxi, China; School of Physics, Northwest University, Xi'an 710069, Shaanxi, China
| | - Dan Sun
- State Key Laboratory of Cultivation Base for Photoelectric Technology and Functional Materials, Laboratory of Optoelectronic Technology of Shaanxi Province, National Center for International Research of Photoelectric Technology & Nanofunctional Materials and Application, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, Shaanxi, China
| | - Shuang Wang
- State Key Laboratory of Cultivation Base for Photoelectric Technology and Functional Materials, Laboratory of Optoelectronic Technology of Shaanxi Province, National Center for International Research of Photoelectric Technology & Nanofunctional Materials and Application, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, Shaanxi, China
| | - Jianguo Wu
- State Key Laboratory of Cultivation Base for Photoelectric Technology and Functional Materials, Laboratory of Optoelectronic Technology of Shaanxi Province, National Center for International Research of Photoelectric Technology & Nanofunctional Materials and Application, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, Shaanxi, China
| | - Yuanyuan Yang
- State Key Laboratory of Cultivation Base for Photoelectric Technology and Functional Materials, Laboratory of Optoelectronic Technology of Shaanxi Province, National Center for International Research of Photoelectric Technology & Nanofunctional Materials and Application, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, Shaanxi, China
| | - Kaige Wang
- State Key Laboratory of Cultivation Base for Photoelectric Technology and Functional Materials, Laboratory of Optoelectronic Technology of Shaanxi Province, National Center for International Research of Photoelectric Technology & Nanofunctional Materials and Application, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, Shaanxi, China.
| | - Qingli He
- School of Physics, Northwest University, Xi'an 710069, Shaanxi, China
| | - Guiren Wang
- State Key Laboratory of Cultivation Base for Photoelectric Technology and Functional Materials, Laboratory of Optoelectronic Technology of Shaanxi Province, National Center for International Research of Photoelectric Technology & Nanofunctional Materials and Application, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, Shaanxi, China; Mechanical Engineering Department & Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, USA
| | - Jintao Bai
- State Key Laboratory of Cultivation Base for Photoelectric Technology and Functional Materials, Laboratory of Optoelectronic Technology of Shaanxi Province, National Center for International Research of Photoelectric Technology & Nanofunctional Materials and Application, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, Shaanxi, China; School of Physics, Northwest University, Xi'an 710069, Shaanxi, China
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41
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Friedrich R, Block S, Alizadehheidari M, Heider S, Fritzsche J, Esbjörner EK, Westerlund F, Bally M. A nano flow cytometer for single lipid vesicle analysis. LAB ON A CHIP 2017; 17:830-841. [PMID: 28128381 DOI: 10.1039/c6lc01302c] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We present a nanofluidic device for fluorescence-based detection and characterization of small lipid vesicles on a single particle basis. The device works like a nano flow cytometer where individual vesicles are visualized by fluorescence microscopy while passing through parallel nanochannels in a pressure-driven flow. An experiment requires less than 20 μl sample volume to quantify both the vesicle content and the fluorescence signals emitted by individual vesicles. We show that the device can be used to accurately count the number of fluorescent synthetic lipid vesicles down to a vesicle concentration of 170 fM. We also show that the size-distribution of the vesicles can be resolved from their fluorescence intensity distribution after calibration. We demonstrate the applicability of the assay in two different examples. In the first, we use the nanofluidic device to determine the particle concentration in a sample containing cell-derived extracellular vesicles labelled with a lipophilic dye. In the second, we demonstrate that dual-color detection can be used to probe peptide binding to synthetic lipid vesicles; we identify a positive membrane-curvature sensing behavior of an arginine enriched version of the Antennapedia homeodomain peptide penetratin. Altogether, these results illustrate the potential of this nanofluidic-based methodology for characterization and quantification of small biological vesicles and their interactors without ensemble averaging. The device is therefore likely to find use as a quantitative analytical tool in a variety of fields ranging from diagnostics to fundamental biology research. Moreover, our results have potential to facilitate further development of automated lab-on-a-chip devices for vesicle analysis.
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Affiliation(s)
- Remo Friedrich
- Department of Physics, Chalmers University of Technology, Gothenburg, Sweden.
| | - Stephan Block
- Department of Physics, Chalmers University of Technology, Gothenburg, Sweden.
| | | | - Susanne Heider
- Department of Physics, Chalmers University of Technology, Gothenburg, Sweden. and Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
| | - Joachim Fritzsche
- Department of Physics, Chalmers University of Technology, Gothenburg, Sweden.
| | - Elin K Esbjörner
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
| | - Marta Bally
- Department of Physics, Chalmers University of Technology, Gothenburg, Sweden. and Institut Curie, Centre de Recherche, CNRS, UMR168, Physico-Chimie Curie, Paris, France
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42
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Müller V, Westerlund F. Optical DNA mapping in nanofluidic devices: principles and applications. LAB ON A CHIP 2017; 17:579-590. [PMID: 28098301 DOI: 10.1039/c6lc01439a] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Optical DNA mapping has over the last decade emerged as a very powerful tool for obtaining long range sequence information from single DNA molecules. In optical DNA mapping, intact large single DNA molecules are labeled, stretched out, and imaged using a fluorescence microscope. This means that sequence information ranging over hundreds of kilobasepairs (kbp) can be obtained in one single image. Nanochannels offer homogeneous and efficient stretching of DNA that is crucial to maximize the information that can be obtained from optical DNA maps. In this review, we highlight progress in the field of optical DNA mapping in nanochannels. We discuss the different protocols for sequence specific labeling and divide them into two main categories, enzymatic labeling and affinity-based labeling. Examples are highlighted where optical DNA mapping is used to gain information on length scales that would be inaccessible with traditional techniques. Enzymatic labeling has been commercialized and is mainly used in human genetics and assembly of complex genomes, while the affinity-based methods have primarily been applied in bacteriology, for example for rapid analysis of plasmids encoding antibiotic resistance. Next, we highlight how the design of nanofluidic channels can been altered in order to obtain the desired information and discuss how recent advances in the field make it possible to retrieve information beyond DNA sequence. In the outlook section, we discuss future directions of optical DNA mapping, such as fully integrated devices and portable microscopes.
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Affiliation(s)
- Vilhelm Müller
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
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43
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Chiu DT, deMello AJ, Di Carlo D, Doyle PS, Hansen C, Maceiczyk RM, Wootton RC. Small but Perfectly Formed? Successes, Challenges, and Opportunities for Microfluidics in the Chemical and Biological Sciences. Chem 2017. [DOI: 10.1016/j.chempr.2017.01.009] [Citation(s) in RCA: 212] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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44
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Weerakoon-Ratnayake KM, O'Neil CE, Uba FI, Soper SA. Thermoplastic nanofluidic devices for biomedical applications. LAB ON A CHIP 2017; 17:362-381. [PMID: 28009883 PMCID: PMC5285477 DOI: 10.1039/c6lc01173j] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Microfluidics is now moving into a developmental stage where basic discoveries are being transitioned into the commercial sector so that these discoveries can affect, for example, healthcare. Thus, high production rate microfabrication technologies, such as thermal embossing and/or injection molding, are being used to produce low-cost consumables appropriate for commercial applications. Based on recent reports, it is clear that nanofluidics offers some attractive process capabilities that may provide unique venues for biomolecular analyses that cannot be realized at the microscale. Thus, it would be attractive to consider early in the developmental cycle of nanofluidics production pipelines that can generate devices possessing sub-150 nm dimensions in a high production mode and at low-cost to accommodate the commercialization of this exciting technology. Recently, functional sub-150 nm thermoplastic nanofluidic devices have been reported that can provide high process yield rates, which can enable commercial translation of nanofluidics. This review presents an overview of recent advancements in the fabrication, assembly, surface modification and the characterization of thermoplastic nanofluidic devices. Also, several examples in which nanoscale phenomena have been exploited for the analysis of biomolecules are highlighted. Lastly, some general conclusions and future outlooks are presented.
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Affiliation(s)
- Kumuditha M Weerakoon-Ratnayake
- Department of Biomedical Engineering, University of North Carolina, Chapel Hill, NC 27599, USA and NIH Biotechnology Resource Center of Biomodular Multiscale Systems for Precision Medicine, USA
| | - Colleen E O'Neil
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA and NIH Biotechnology Resource Center of Biomodular Multiscale Systems for Precision Medicine, USA
| | - Franklin I Uba
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Steven A Soper
- Department of Chemistry and Department of Mechanical Engineering, University of Kansas, Lawrence, KS 66047, USA. and Kansas University Medical Center NIH Cancer Center, Kansas City, KS 66106, USA and NIH Biotechnology Resource Center of Biomodular Multiscale Systems for Precision Medicine, USA and Ulsan National Institute of Science and Technology, Ulsan, South Korea
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45
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Kim D, Bowman C, Del Bonis-O'Donnell JT, Matzavinos A, Stein D. Giant Acceleration of DNA Diffusion in an Array of Entropic Barriers. PHYSICAL REVIEW LETTERS 2017; 118:048002. [PMID: 28186790 DOI: 10.1103/physrevlett.118.048002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Indexed: 06/06/2023]
Abstract
We investigate with experiments and computer simulations the nonequilibrium dynamics of DNA polymers crossing arrays of entropic barriers in nanofluidic devices in a pressure-driven flow. With increasing driving pressure, the effective diffusivity of DNA rises and then peaks at a value that is many times higher than the equilibrium diffusivity. This is an entropic manifestation of "giant acceleration of diffusion." The phenomenon is sensitive to the effective energy landscape; thus, it offers a unique probe of entropic barriers in a system driven away from equilibrium.
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Affiliation(s)
- Daniel Kim
- Department of Physics, Brown University, Providence, Rhode Island 02912, USA
| | - Clark Bowman
- Division of Applied Mathematics, Brown University, Providence, Rhode Island 02912, USA
| | | | - Anastasios Matzavinos
- Division of Applied Mathematics, Brown University, Providence, Rhode Island 02912, USA
- Computational Science and Engineering Laboratory, Department of Mechanical and Process Engineering, CH-8092 ETH Zürich, Switzerland
| | - Derek Stein
- Department of Physics, Brown University, Providence, Rhode Island 02912, USA
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46
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Strelnikova N, Göllner M, Pfohl T. Direct Observation of Alternating Stretch-Coil and Coil-Stretch Transitions of Semiflexible Polymers in Microstructured Flow. MACROMOL CHEM PHYS 2016. [DOI: 10.1002/macp.201600474] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Natalja Strelnikova
- Department of Chemistry; University of Basel; Klingelbergstrasse 80 4056 Basel Switzerland
| | - Michael Göllner
- Department of Chemistry; University of Basel; Klingelbergstrasse 80 4056 Basel Switzerland
| | - Thomas Pfohl
- Department of Chemistry; University of Basel; Klingelbergstrasse 80 4056 Basel Switzerland
- Biomaterials Science Center (BMC); University of Basel; Gewerbestrasse 14 4123 Allschwil Switzerland
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47
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Müller V, Rajer F, Frykholm K, Nyberg LK, Quaderi S, Fritzsche J, Kristiansson E, Ambjörnsson T, Sandegren L, Westerlund F. Direct identification of antibiotic resistance genes on single plasmid molecules using CRISPR/Cas9 in combination with optical DNA mapping. Sci Rep 2016; 6:37938. [PMID: 27905467 PMCID: PMC5131345 DOI: 10.1038/srep37938] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 11/01/2016] [Indexed: 12/03/2022] Open
Abstract
Bacterial plasmids are extensively involved in the rapid global spread of antibiotic resistance. We here present an assay, based on optical DNA mapping of single plasmids in nanofluidic channels, which provides detailed information about the plasmids present in a bacterial isolate. In a single experiment, we obtain the number of different plasmids in the sample, the size of each plasmid, an optical barcode that can be used to identify and trace the plasmid of interest and information about which plasmid that carries a specific resistance gene. Gene identification is done using CRISPR/Cas9 loaded with a guide-RNA (gRNA) complementary to the gene of interest that linearizes the circular plasmids at a specific location that is identified using the optical DNA maps. We demonstrate the principle on clinically relevant extended spectrum beta-lactamase (ESBL) producing isolates. We discuss how the gRNA sequence can be varied to obtain the desired information. The gRNA can either be very specific to identify a homogeneous group of genes or general to detect several groups of genes at the same time. Finally, we demonstrate an example where we use a combination of two gRNA sequences to identify carbapenemase-encoding genes in two previously not characterized clinical bacterial samples.
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Affiliation(s)
- Vilhelm Müller
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Fredrika Rajer
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Karolin Frykholm
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Lena K. Nyberg
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Saair Quaderi
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
| | - Joachim Fritzsche
- Department of Applied Physics, Chalmers University of Technology, Gothenburg, Sweden
| | - Erik Kristiansson
- Department of Mathematical Sciences, Chalmers University of Technology/University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Tobias Ambjörnsson
- Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
| | - Linus Sandegren
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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Henkin G, Berard D, Stabile F, Shayegan M, Leith JS, Leslie SR. Manipulating and Visualizing Molecular Interactions in Customized Nanoscale Spaces. Anal Chem 2016; 88:11100-11107. [DOI: 10.1021/acs.analchem.6b03149] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Gil Henkin
- Department of Physics, McGill University, Montreal, Quebec, Canada H3A 2T8
| | - Daniel Berard
- Department of Physics, McGill University, Montreal, Quebec, Canada H3A 2T8
| | - Francis Stabile
- Department of Physics, McGill University, Montreal, Quebec, Canada H3A 2T8
| | - Marjan Shayegan
- Department of Physics, McGill University, Montreal, Quebec, Canada H3A 2T8
| | - Jason S. Leith
- Department of Physics, McGill University, Montreal, Quebec, Canada H3A 2T8
| | - Sabrina R. Leslie
- Department of Physics, McGill University, Montreal, Quebec, Canada H3A 2T8
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Li R, Wang J. Stretching a Semiflexible Polymer in a Tube. Polymers (Basel) 2016; 8:E328. [PMID: 30974612 PMCID: PMC6432322 DOI: 10.3390/polym8090328] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 08/09/2016] [Accepted: 08/26/2016] [Indexed: 01/26/2023] Open
Abstract
How the statistical behavior of semiflexible polymer chains may be affected by force stretching and tube confinement is a classical unsolved problem in polymer physics. Based on the Odijk deflection theory and normal mode decomposition in terms of Fourier expansion, we have derived a new compact formula for the extension of a wormlike chain of finite length strongly confined in a tube and simultaneously stretched by an external force. We have also suggested a new deflection length, which together with the force-extension relation is valid for a very extended range of the tube-diameter/persistence-length ratio comparing to the classic Odijk theory. The newly derived formula has no adjustable fitting parameters for the whole deflection regime; in contrast, the classic Odijk length needs different prefactors to fit the free energy and average extension, respectively. Brownian dynamics simulations based on the Generalized Bead-Rod (GBR) model were extensively performed, which justified the theoretical predictions.
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Affiliation(s)
- Runhua Li
- Key Laboratory of Mechanics on Disaster and Environment in Western China, Ministry of Education, College of Civil Engineering and Mechanics, Lanzhou University, Lanzhou 730000, Gansu, China.
| | - Jizeng Wang
- Key Laboratory of Mechanics on Disaster and Environment in Western China, Ministry of Education, College of Civil Engineering and Mechanics, Lanzhou University, Lanzhou 730000, Gansu, China.
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Fornander LH, Frykholm K, Fritzsche J, Araya J, Nevin P, Werner E, Çakır A, Persson F, Garcin EB, Beuning PJ, Mehlig B, Modesti M, Westerlund F. Visualizing the Nonhomogeneous Structure of RAD51 Filaments Using Nanofluidic Channels. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:8403-8412. [PMID: 27479732 DOI: 10.1021/acs.langmuir.6b01877] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
RAD51 is the key component of the homologous recombination pathway in eukaryotic cells and performs its task by forming filaments on DNA. In this study we investigate the physical properties of RAD51 filaments formed on DNA using nanofluidic channels and fluorescence microscopy. Contrary to the bacterial ortholog RecA, RAD51 forms inhomogeneous filaments on long DNA in vitro, consisting of several protein patches. We demonstrate that a permanent "kink" in the filament is formed where two patches meet if the stretch of naked DNA between the patches is short. The kinks are readily seen in the present microscopy approach but would be hard to identify using conventional single DNA molecule techniques where the DNA is more stretched. We also demonstrate that protein patches separated by longer stretches of bare DNA roll up on each other and this is visualized as transiently overlapping filaments. RAD51 filaments can be formed at several different conditions, varying the cation (Mg(2+) or Ca(2+)), the DNA substrate (single-stranded or double-stranded), and the RAD51 concentration during filament nucleation, and we compare the properties of the different filaments formed. The results provide important information regarding the physical properties of RAD51 filaments but also demonstrate that nanofluidic channels are perfectly suited to study protein-DNA complexes.
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Affiliation(s)
| | | | | | - Joshua Araya
- Department of Chemistry and Chemical Biology, Northeastern University , Boston, Massachusetts 02115, United States
| | - Philip Nevin
- Department of Chemistry and Chemical Biology, Northeastern University , Boston, Massachusetts 02115, United States
| | - Erik Werner
- Department of Physics, University of Gothenburg , 412 96 Gothenburg, Sweden
| | - Ali Çakır
- Department of Physics, University of Gothenburg , 412 96 Gothenburg, Sweden
| | - Fredrik Persson
- Department for Cell and Molecular Biology, Science for Life Laboratory, Uppsala University , 751 24 Uppsala, Sweden
| | - Edwige B Garcin
- Cancer Research Center of Marseille, CNRS UMR7258, Inserm U1068, Institut Paoli-Calmettes, Aix-Marseille Université , 13273 Marseille, France
| | - Penny J Beuning
- Department of Chemistry and Chemical Biology, Northeastern University , Boston, Massachusetts 02115, United States
| | - Bernhard Mehlig
- Department of Physics, University of Gothenburg , 412 96 Gothenburg, Sweden
| | - Mauro Modesti
- Cancer Research Center of Marseille, CNRS UMR7258, Inserm U1068, Institut Paoli-Calmettes, Aix-Marseille Université , 13273 Marseille, France
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