Article
Multidisciplinary Sciences
Prabhat Tripathi, Abdelkrim Benabbas, Behzad Mehrafrooz, Hirohito Yamazaki, Aleksei Aksimentiev, Paul M. Champion, Meni Wanunu
Summary: The study investigates the electric-field-driven translocation behavior of cytochrome c through ultrathin silicon nitride solid-state nanopores. Results show that protein can pass through narrow pores either by squeezing or by threading after fully unfolding, depending on the pore diameter and unfolding driving force.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Chemistry, Physical
Zhan Wang, Rui Hu, Rui Zhu, Wenlong Lu, Guanghao Wei, Jing Zhao, Zhi-Yuan Gu, Qing Zhao
Summary: This study employs a metal-organic cage as a carrier to enhance the sensitivity and selectivity of solid-state nanopores for small analytes. The carrier itself is undetectable unless bound with the target analytes, and oligonucleotides are used as linkers for attachment. Two small analytes are successfully distinguished using the molecular carrier. Selectivity of nanopore detection is achieved by attaching the carrier to oligonucleotide-tailed aptamers, and successful detection of a human alpha-thrombin sample is demonstrated. The highly designable metal-organic cage shows potential as a versatile carrier for biomolecules and enables single-molecule screening of clinically relevant biomolecules via solid-state nanopores.
Article
Chemistry, Multidisciplinary
Rui Hu, Rui Zhu, Guanghao Wei, Zhan Wang, Zhi-Yuan Gu, Meni Wanunu, Qing Zhao
Summary: The ability to detect and distinguish biomolecules at the single-molecule level is essential in biomedicine and analytical chemistry. The sensitivity of single-molecule methods can be enhanced by increasing the dwell time of biomolecules. A quad-nanopore, a square array of four nanopores, is introduced to improve the detection sensitivity through electric field manipulation in the access region. The quad-nanopore shows prolonged dwell times for short DNA strands and enables the detection of ultra-short DNA.
ADVANCED MATERIALS
(2023)
Article
Chemistry, Multidisciplinary
Liqun He, Martin Charron, Philipp Mensing, Kyle Briggs, Jonathan Adams, Hendrick de Haan, Vincent Tabard-Cossa
Summary: DNA nanostructures can be characterized by solid-state nanopores, providing information on their geometrical dimensions, mechanical properties, assembly yield, and stability.
Article
Multidisciplinary Sciences
Ke Xia, James T. Hagan, Li Fu, Brian S. Sheetz, Somdatta Bhattacharya, Fuming Zhang, Jason R. Dwyer, Robert J. Linhardt
Summary: The application of solid-state nanopore devices for analyzing synthetic heparan sulfate GAG chains is feasible, with clear differences between signals generated by different GAGs detected through machine learning and data analysis. These findings suggest that ultrasensitive GAG analysis could be achieved using SS nanopore detection and well-characterized molecular training sets.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Chemistry, Multidisciplinary
Jasper P. Fried, Jacob L. Swett, Binoy Paulose Nadappuram, Jan A. Mol, Joshua B. Edel, Aleksandar P. Ivanov, James R. Yates
Summary: Solid-state nanopore fabrication techniques have advanced significantly, allowing for the rapid and simple creation of nanopores with diameters down to a few nanometres in electrolyte environments, enabling applications in DNA sequencing, protein analysis, and more.
CHEMICAL SOCIETY REVIEWS
(2021)
Article
Chemistry, Multidisciplinary
Arthur Rand, Philip Zimny, Roland Nagel, Chaitra Telang, Justin Mollison, Aaron Bruns, Emily Leff, Walter W. Reisner, William B. Dunbar
Summary: In this study, an electronic mapping of a bacterial genome using solid-state nanopore technology was presented. The method involves a dual-nano-pore architecture and active control logic to produce single-molecule data and estimate distances between physical tags on double-stranded DNA. Custom analysis methods were developed to generate consensus alignments from multiple scans, and this approach was applied to map the E. coli chromosome. The results showed a significant increase in alignment length with the recapture method, and the intertag resolution was determined to be around 150-166 bp.
Review
Engineering, Manufacturing
Muhammad Refatul Haq, Bong Jae Lee, Jungchul Lee
Summary: Solid-state nanopores, especially those made of semiconductor materials, have emerged as a powerful platform for single molecule bio-detection. The most common method for molecular detection is measuring the temporal variations of ionic current within the nanopore. This review discusses the principles of SSNP, device performance improvement, and various experimental aspects in detail, providing insights for current research trends and advancements in molecular sensing through synthetic nanopores.
INTERNATIONAL JOURNAL OF PRECISION ENGINEERING AND MANUFACTURING
(2021)
Article
Chemistry, Multidisciplinary
Chalmers Chau, Fabio Marcuccio, Dimitrios Soulias, Martin Andrew Edwards, Andrew Tuplin, Sheena E. Radford, Eric Hewitt, Paolo Actis
Summary: This study presents a polymer-electrolyte solid-state nanopore system for analyzing biomolecular conformation under physiological conditions. By using specific salts, the system's performance is enhanced, allowing for the analysis of Chikungunya virus RNA conformation.
Article
Chemistry, Multidisciplinary
Simon King, Kyle Briggs, Robert Slinger, Vincent Tabard-Cossa
Summary: Single-molecule detection methods play a crucial role in diagnostic applications. This article presents the use of solid-state nanopores as digital sensors for a PCR-based assay targeting strep A, demonstrating their reliability in identifying strep A in clinical samples. Methodological best practices for adapting PCR-based assays to solid-state nanopore readout and determining sample status are also discussed.
Article
Biochemistry & Molecular Biology
Yao Cai, Baocai Zhang, Liyuan Liang, Sen Wang, Lanjun Zhang, Liang Wang, Hong-Liang Cui, Yihua Zhou, Deqiang Wang
Summary: This research developed a single-molecule approach for identifying plant polysaccharides using a solid-state nanopore sensor, which could detect low concentrations of xylans and differentiate between different types of modifications. The study further demonstrated the method's capability in distinguishing between different xylans in monocot and dicot plants.
PLANT COMMUNICATIONS
(2021)
Article
Physics, Multidisciplinary
William S. Huxter, Martin F. Sarott, Morgan Trassin, Christian L. Degen
Summary: Using a scanning nitrogen-vacancy (NV) microscope, we are able to visualize domain patterns in piezoelectric and improper ferroelectric materials by measuring their electric fields. This electric field detection method enables discrimination between different types of surface charge distributions and reconstruction of three-dimensional electric field vector and charge density maps.
Article
Multidisciplinary Sciences
Lauren S. Lastra, Y. M. Nuwan D. Y. Bandara, Michelle Nguyen, Nasim Farajpour, Kevin J. Freedman
Summary: This article investigates the translocation mechanism, pulse direction, and shape in nanopore sensing, and proposes the role of electroosmosis in driving DNA events and conductive events.
NATURE COMMUNICATIONS
(2022)
Review
Chemistry, Multidisciplinary
Jasper P. Fried, Yanfang Wu, Richard D. Tilley, J. Justin Gooding
Summary: Nanopore sensors are widely studied for their ability to detect clinically important biomarkers with single-molecule resolution. There has been recent interest in using optical readout strategies for quantitative analysis, as they can monitor multiple nanopores in a high-density array and increase statistical power, enabling the analysis of analytes at ultralow concentrations.
Article
Chemistry, Analytical
Quentin Palomar, Anna Svard, Shuangshuang Zeng, Qitao Hu, Funing Liu, Daniel Aili, Zhen Zhang
Summary: Accurate, robust, and rapid diagnostics are essential for well-functioning healthcare. Proteases, specifically gingipains, play a crucial role in the onset and progression of periodontal disease, making them promising biomarkers. A novel nanopore-based biosensor strategy for monitoring protease activity was developed, demonstrating high sensitivity and a broad dynamic range. This sensor technology shows potential for diagnosing periodontal disease and monitoring other disease-related proteases.
SENSORS AND ACTUATORS B-CHEMICAL
(2022)
Article
Biochemical Research Methods
Jugal Saharia, Y. M. Nuwan D. Y. Bandara, Min Jun Kim
Summary: Electrolyte chemistry plays a crucial role in the transport properties of analytes through nanopores. In this study, the translocation properties of human serum transferrin (hSTf) protein were investigated under different salt concentrations with positive or negative chemical gradients. The experiments showed that translocations occurred in all configurations under positive gradient conditions, while no translocations were observed under negative gradient conditions.
Article
Chemistry, Multidisciplinary
Y. M. Nuwan D. Y. Bandara, Nasim Farajpour, Kevin J. Freedman
Summary: This study presents a thorough investigation of protein sensing under low electrolyte conditions. The unfolding of proteins was found to be correlated with their isoelectric point and sensitive to the applied voltage and pH. The different forces acting on the protein movement also play a critical role.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Computer Science, Information Systems
Aminul Islam Khan, Min Jun Kim, Prashanta Dutta
Summary: This study investigates the classification of AAV vectors using deep learning methods. The researchers used fine-tuning based transfer learning to improve classification accuracy, achieving an average accuracy of 90-99% in three experiments. The results show that the accuracy depends on the applied electric field and the time frame used for data segmentation. The study also found that fine-tuning based transfer learning outperforms feature extraction-based classification.
JOURNAL OF SIGNAL PROCESSING SYSTEMS FOR SIGNAL IMAGE AND VIDEO TECHNOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Vinay Sharma, Nasim Farajpour, Lauren S. Lastra, Kevin J. Freedman
Summary: Nanopores are widely used in genome sequencing and DNA data storage, and the impact of hydrodynamic forces on DNA sensing in nanopores is still not well understood. In this study, the researchers conducted experiments and developed a computational model to analyze the effects of hydrodynamic flow on DNA transit time, capture rate, current blockade depth, and DNA folding in nanopores. The findings have important implications for DNA sensing technologies.
Article
Robotics
Neelanga Thelasingha, A. Agung Julius, Min Jun Kim
Summary: This paper introduces a method to reduce spatial variance of microbot systems through ensemble control, using motion primitives to efficiently discretize input space and optimize control trajectories, enabling faster and more effective space exploration.
INTELLIGENT SERVICE ROBOTICS
(2022)
Article
Engineering, Multidisciplinary
Anuruddha Bhattacharjee, Mehdi Jabbarzadeh, Gokhan Kararsiz, Henry C. Fu, Min Jun Kim
Summary: This paper presents the design and exploration of a bacteria-inspired soft robot that can move in highly viscous Newtonian fluids. The robot was fabricated as a tapered, hollow rod-like structure with embedded cylindrical micro-magnets for actuation. The experiments showed that the robot can perform both rolling and swimming propulsion in different locations relative to a boundary. Numerical simulations were conducted to investigate the swimming propulsion and its dependence on design parameters and fluid viscosity. The results suggest that simple geometrical asymmetry enables the robot to achieve propulsion in low Reynolds number regime.
BIOINSPIRATION & BIOMIMETICS
(2022)
Article
Robotics
Anuruddha Bhattacharjee, Yitong Lu, Aaron T. Becker, MinJun Kim
Summary: The study introduces a design of reconfigurable modular robots with high reconfigurability and controllability for mesoscale manufacturing applications. The platform can create programmable patterns through wireless control and assembly-disassembly techniques. Experimental results demonstrate robust and reproducible behavior, showing promise for mesoscale manufacturing.
IEEE TRANSACTIONS ON ROBOTICS
(2022)
Article
Chemistry, Analytical
Gokhan Kararsiz, Yasin Cagatay Duygu, Louis William Rogowski, Anuruddha Bhattacharjee, Min Jun Kim
Summary: This paper demonstrates the manipulation of snowman-shaped soft microrobots under a uniform rotating magnetic field, showing their directional controllability. Furthermore, it compares the velocity responses of microsnowmen and single alginate microrobots under the magnetic field manipulation.
Article
Chemistry, Multidisciplinary
Lauren S. Lastra, Y. M. Nuwan, Vinay Sharma, Kevin J. Freedman
Summary: This study investigates CPS-based molecular discrimination and its voltage-dependent characteristics in nanopore sensing. The reversal of salt gradient can reinstate resistive pulses and clarify RPS-CPS transitions. Asymmetric salt conditions greatly enhance DNA configuration discrimination and are successfully utilized for the detection of a Cas9 mutant.
Article
Biochemical Research Methods
Matthew O'Donohue, Jugal Saharia, Nuwan Bandara, Georgios Alexandrakis, Min Jun Kim
Summary: A silicon nitride-based nanopore was used to characterize the human serum transferrin receptor protein (TfR). The study showed that the presence of dimeric forms of TfR decreased exponentially with increasing applied electric field, while the unfolding behaviors of monomeric TfR were positively dependent on the applied voltage. Comparison with the ligand protein hSTf demonstrated the ability to distinguish between these two protein populations using a solid-state nanopore (SSN). The excluded volumes of TfR were experimentally determined and found to be within error of their theoretical values.
Article
Chemistry, Multidisciplinary
Jugal Saharia, Yapa Mudiyanselage Nuwan Dhananjaya Yapa Bandara, Buddini Iroshika Karawdeniya, Jason Rodger Dwyer, Min Jun Kim
Summary: Stability, long lifetime, resilience against clogging, low noise, and low cost are the key features of solid-state nanopore technology. This study presents a fabrication protocol that allows for obtaining more than 1 million events from a single solid-state nanopore. Additionally, approximately 8.1 million events were reported in this work, encompassing both DNA and protein analytes. The collected data represents a significant advancement in solid-state pore performance and has potential applications in machine learning and other fields.
Article
Chemistry, Analytical
Gokhan Kararsiz, Yasin Cagatay Duygu, Zhengguang Wang, Louis William Rogowski, Sung Jea Park, Min Jun Kim
Summary: This study investigates the motion characteristics of soft alginate microrobots in complex fluidic environments utilizing wireless magnetic fields for actuation. The aim is to explore the diverse motion modes that arise due to shear forces in viscoelastic fluids by employing snowman-shaped microrobots. Microrobots are fabricated via an extrusion-based microcentrifugal droplet method, successfully demonstrating the feasibility of both wiggling and tumbling motions. Through velocity analysis, valuable insights into the relationship between applied magnetic fields and motion characteristics are obtained, facilitating a more realistic understanding of surface locomotion for targeted drug delivery purposes while accounting for swarm dynamics and non-uniform behavior.
Article
Robotics
Yitong Lu, Anuruddha Bhattacharjee, Conlan C. Taylor, Julien Leclerc, Jason M. O'Kane, MinJun Kim, Aaron T. Becker
Summary: Reconfigurable modular robots can dynamically assemble/disassemble using magnetic fields. In this study, magnetic modular cubes with embedded permanent magnets are used to self-assemble into desired 2D polyomino shapes. A closed-loop control method is presented, using computer vision feedback and re-planning, which improves the success rate of forming user-specified polyominoes. The validity of the approach is demonstrated with different cube sizes.
IEEE ROBOTICS AND AUTOMATION LETTERS
(2023)
Proceedings Paper
Engineering, Biomedical
Scott Renkes, Minjun Kim, George Alexandrakis
Summary: This study demonstrates the feasibility of using AC modulation of command voltage applied across a Self-induced Back Action Actuated Nanopore Electrophoresis (SANE) sensor to enhance the characterization of nanoparticles (NPs) and single molecules. By analyzing frequency response and electrical behavior, this method provides valuable insights into the charge and dielectric constant of analytes. The results show that different types of NPs exhibit distinctly different electrical responses.
PLASMONICS IN BIOLOGY AND MEDICINE XIX
(2022)
Proceedings Paper
Engineering, Biomedical
Homayoun Asadzadeh, Scott Renkes, MinJun Kim, George Alexandrakis
Summary: This work presents Multiphysics COMSOL simulations to analyze the contributions of optical and electrical forces acting on a 20 nm silica nanoparticle trapped by a plasmonic nanopore sensor. The simulations aim to understand the underlying forces and their impact on the optical-electric measurements.
PLASMONICS IN BIOLOGY AND MEDICINE XIX
(2022)