Article
Chemistry, Multidisciplinary
Jigneshkumar Dahyabhai Prajapati, Sushil Pangeni, Mehmet Alphan Aksoyoglu, Mathias Winterhalter, Ulrich Kleinekathoefer
Summary: The voltage-dependent transport through biological and artificial nanopores is widely used in applications such as DNA sequencing and sensing. The dependence of the electroosmotic flow (EOF) on the concentration of the buffer salt and its interplay with other factors such as pH, temperature, and pore diameter remain poorly understood. In this study, the concentration-dependent EOF and its correlation with experimental kinetic constants for the translocation of alpha-cyclodextrin through the Delta CymA nanopore were investigated, revealing non-monotonic and nonlinear changes in net ionic flux and EOF.
Article
Nanoscience & Nanotechnology
Tomoki Hayashida, Makusu Tsutsui, Sanae Murayama, Tomoko Nakada, Masateru Taniguchi
Summary: This study systematically characterized the effect of dielectric coatings on the capture-to-translocation dynamics of single particles in solid-state pores. By covering SiNx membranes with different coatings, the researchers were able to change the zeta-potential at the pore wall, leading to easier particle capture and slower translocation motion in the channel. These findings serve as a guide for engineering pore wall surfaces to optimize translocation dynamics for efficient sensing of particles and molecules.
ACS APPLIED MATERIALS & INTERFACES
(2021)
Article
Mechanics
Ali Shafiei Souderjani, Mostafa Bakouei, Mohammad Hassan Saidi, Mojtaba Taghipoor
Summary: The electrophoretic motion of hydrophobic particles in solid-state nanopores is numerically investigated. The Poisson, Stokes, and Nernst-Planck equations are simultaneously solved using the Newton-Raphson algorithm. The hydrophobic surface characteristics are described using the Navier-slip boundary condition with a wide range of slip lengths. The study examines the effects of electric field intensity, electrolyte concentration, and particle size on electrophoretic velocity, and manipulates the nanopore's size and surface charge density to separate hydrophobic and hydrophilic particles based on their slip lengths. The resistive pulse properties of particles with different slip lengths are also studied, showing potential application for resistive pulse sensing to determine particle slip length.
Article
Chemistry, Multidisciplinary
Turash Haque Pial, Harnoor Singh Sachar, Parth Rakesh Desai, Siddhartha Das
Summary: This study uses molecular dynamics simulations to investigate the possibility of changing the direction of electroosmotic liquid flow in nanochannels by adjusting the electric field strength. The research explores the behavior of nanoconfined polyelectrolyte brushes, revealing an overscreening effect, specific ion distributions, and changes in brush height that lead to a reversal in the direction of electroosmotic transport.
Review
Chemistry, Multidisciplinary
Weichen Wei, Xiaojuan Chen, Xuejiao Wang
Summary: Nanopore sensing technique, as an emerging method for detecting single molecules, has been extensively researched in various fields, including nanopore sequencing and other applications of single-molecule studies. Recently, researchers have explored specific ion effects in nanopore channels, which provide a unique understanding of the Hofmeister effect at the single-molecule level. This review summarizes the recent advances in using nanopore sensing techniques to study the Hofmeister effect and attempts to elucidate the physicochemical mechanism involved. The challenges and future goals in this field are also discussed.
Article
Chemistry, Physical
Meng Yu, Wei Si, Tao Zeng, Chang Chen, Xiaojing Lin, Zhouxiang Ji, Fei Guo, Yuxiang Li, Jingjie Sha, Yuliang Dong
Summary: This research used all-atom molecular dynamic simulations to uncover the microscopic mechanism behind current variation when single-stranded DNA passes through the MspA nanopore. It was found that nucleotide orientation and the region below the constriction of the nanopore play crucial roles in inducing current variation. These findings provide valuable insights for developing low-cost, high-throughput nanopore DNA sequencing technology.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Electrochemistry
Amin Alinezhad, Mahdi Khatibi, Seyed Nezameddin Ashrafizadeh
Summary: This article examines the use of nanofluidic membranes containing straight nanopores as nanotransistors, focusing on the PNP nanotransistor with its three regions representing the emitter, base, and collector. Applying voltage to the base region increases the current flowing between the emitter and collector regions. The study investigates the effect of electrolyte concentrations on the PNP nanotransistor's performance and suggests that adjusting these concentrations can enhance the device's functionality and open up new opportunities for nanoscale electronics.
ELECTROCHIMICA ACTA
(2023)
Article
Chemistry, Multidisciplinary
Wei Si, Xiaojing Lin, Liwei Wang, Gensheng Wu, Yin Zhang, Yunfei Chen, Jingjie Sha
Summary: This study theoretically reports a DNA-tracked nanovehicle that can move on a solid-state surface using molecular dynamics simulations. The nanovehicle is assembled with a graphene membrane as the chassis and circular ssDNAs as the wheels. By inducing electroosmotic flows through independently charged nanopores, controlled rotary motion is achieved, allowing the nanovehicle to move linearly and make turns. This design enables access to almost anywhere in the human body, leading to breakthroughs in nanoscale surgery and drug delivery. It enriches the nanorobot family and provides a new approach for nanovehicle design.
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)
Article
Multidisciplinary Sciences
Mohit Trivedi, Neelkanth Nirmalkar
Summary: This article investigates the flow, ionic mass transfer, and ionic current rectification phenomena in a single conical nanopore with viscoelastic fluids. The results show that the extensibility parameter and Deborah number facilitate the ICR phenomena at high applied voltage, while the ICR phenomena are more pronounced at low values of kappa R-t.
SCIENTIFIC REPORTS
(2022)
Article
Mechanics
Priyanka Koner, Subrata Bera, Hiroyuki Ohshima
Summary: The time-dependent electroosmotic flow (EOF) and heat transfer of a generalized Maxwell fluid through a polyelectrolyte layer (PEL) grafted nanopore is studied, considering different permittivity between the PEL and electrolyte solution. The ion partitioning effects arising from the different permittivity are taken into account. Analytical solutions for the induced potential and fluid flow distribution are established, and the energy equations for hydro-dynamically fully developed flow with constant thermophysical properties are presented. The influence of several important factors on heat transfer behavior is investigated.
Article
Chemistry, Multidisciplinary
Fei Zheng, Mohammed Alawami, Jinbo Zhu, Casey M. Platnich, Jingjie Sha, Ulrich F. Keyser, Kaikai Chen
Summary: Nanopore analysis requires high sample concentration and long turnaround time. Recapture and re-reading of the same molecule is a promising alternative to enrich the signal information. Molecular recapture can be improved by linking the target molecule to a long DNA carrier. This method accurately resolves nanostructure motifs along a DNA scaffold.
Article
Computer Science, Software Engineering
Ngan Nguyen, Ondrej Strnad, Tobias Klein, Deng Luo, Ruwayda Alharbi, Peter Wonka, Martina Maritan, Peter Mindek, Ludovic Autin, David S. Goodsell, Ivan Viola
Summary: This new technique allows for rapid modeling and construction of scientifically accurate mesoscale biological models based on a few 2D microscopy scans and the latest knowledge available about the biological entity. Utilizing statistical and rule-based modeling approaches, the 3D models are fast to author, construct, and revise. In addition to incorporating imaging evidence and statistical properties in the construction of the models, further information can be included by defining rules.
IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS
(2021)
Article
Chemistry, Multidisciplinary
Kabin Lin, Zhongwu Li, Yi Tao, Kun Li, Haojie Yang, Jian Ma, Tie Li, Jingjie Sha, Yunfei Chen
Summary: The study proposes a theoretical model to predict the surface charge density of a Si3N4 nanopore, revealing its dependence on both pH and salt concentration. It is found that while silanol groups are major determinants of surface charge, the influence of amine groups should not be neglected as even a small number can dramatically alter the isopotential point (pH(iep)) of the nanopore.
Article
Chemistry, Physical
Yuyuan Lu, Zhenhua Wang, Lijia An, An-Chang Shi
Summary: The study examines the force- and flow-induced translocation processes of linear and ring polymers, focusing on the behavior of the polymer translocation time. The scaling exponents for the translocation time are found to not be constants, with α = 1.0 for both force- and flow-induced translocations in long chains. The differences between the force- and flow-induced translocations are attributed to the distinct monomer crowding effects due to different flow patterns outside the channel.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Chemistry, Multidisciplinary
Giovanni Di Muccio, Blasco Morozzo della Rocca, Mauro Chinappi
Summary: This study introduces a purely geometrical mechanism to induce ionic selectivity and electroosmotic flow in uncharged nanopores, and develops a theoretical model for designing pore geometry. The research shows that the selectivity depends on the applied voltage, and becomes completely inverted when reversing the voltage, leading to unidirectional electroosmotic flow.
Article
Physics, Multidisciplinary
Alberto Gubbiotti, Mauro Chinappi, Carlo Massimo Casciola
Summary: Electrohydrodynamics play a crucial role in nanofluidics and biotechnology, and a mesoscale method based on the DPD model has been introduced for analyzing the dynamic behavior of ions in fluid dynamics. The model allows for a link between system dynamics and equilibrium properties, demonstrating significant effects on concentration and velocity profiles when accounting for ionic finite size.
EUROPEAN PHYSICAL JOURNAL PLUS
(2022)
Editorial Material
Nanoscience & Nanotechnology
Mauro Chinappi, Blasco Morozzo della Rocca
NATURE NANOTECHNOLOGY
(2023)
Article
Energy & Fuels
Matteo Baldelli, Lorenzo Bartolucci, Stefano Cordiner, Giorgio D'Andrea, Emanuele De Maina, Vincenzo Mulone
Summary: This study aims to improve hydrogen production from wet residual biomass by integrating anaerobic digestion with thermochemical transformation processes. This solution is integrated into a hybrid power supply system composed of an electric grid and a photovoltaic plant, supported by a thermal energy storage system. The performance and energy demand of the plant are carefully assessed using a Simulink/Simscape model, showing good performance in terms of hydrogen yields and significant improvement in energy independence through thermal energy storage.
Article
Chemistry, Physical
Goncalo Paulo, Alberto Gubbiotti, Alberto Giacomello
Summary: Understanding intrusion and extrusion in nanoporous materials is crucial for various applications. Simulating these processes with atomistic details is challenging due to the rare event nature and long simulation times. In this work, a multiscale approach combining atomistic and coarse-grained simulations was used to study water intrusion/extrusion in a pore, reproducing experimentally relevant features and increasing simulated timescales.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Sophie Marbach, Christopher E. Miles
Summary: Transient bonds between fast linkers and slower particles are common in physical and biological systems. This paper provides a mathematical justification for the use of effective dynamics in modeling such systems, which preserves detailed balance at equilibrium. The results are verified through simulations and the application of the framework to various systems is demonstrated.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Sabine Straathof, Giovanni Di Muccio, Maaruthy Yelleswarapu, Melissa Alzate Banguero, Carsten Wloka, Nieck Jordy van der Heide, Mauro Chinappi, Giovanni Maglia
Summary: YaxAB is a large biological nanopore that can capture a wide range of proteins for folded protein analysis. The conical shape allows proteins to be trapped within the nanopore, and the time of trapping can be controlled by external bias. Unlike cylindrical nanopores, the current blockade in YaxAB decreases with the size of the trapped protein.
Article
Biotechnology & Applied Microbiology
Adina Sauciuc, Blasco Morozzo della Rocca, Matthijs Jonathan Tadema, Mauro Chinappi, Giovanni Maglia
Summary: Nanopores can be used for protein identification and fingerprinting, and the introduction of spaced charges in the nanopore lumen can generate an electroosmotic flow to induce the unidirectional transport of proteins. This approach allows for the translocation and stretching of natural polypeptides, which can be used for enzymatic and non-enzymatic protein identification and sequencing.
NATURE BIOTECHNOLOGY
(2023)
Article
Chemistry, Physical
The Hoang Ngoc Minh, Benjamin Rotenberg, Sophie Marbach
Summary: This study examines ionic fluctuations in finite volumes using Brownian dynamics and develops an analytical framework applicable to systems with pairwise interactions. The correlations between particle number and charge exhibit diverse phenomenology over time. The hyperuniform behavior of charge fluctuations is preserved over time and even becomes proportional to the box perimeter at long times. These findings pave the way for understanding fluctuations in more complex systems.
FARADAY DISCUSSIONS
(2023)
Proceedings Paper
Computer Science, Theory & Methods
Mauro Chinappi, Giovanni Di Muccio, Cristiano Giordani, Fabio Cecconi, Blasco Morozzo della Rocca
Summary: This article introduces the basic principles of nanopore-based sensors as a promising technology for single-molecule sensing, and presents the challenges and the role of modeling in the development of these sensors as biosensing devices. A hierarchical multiscale approach is proposed to efficiently calculate capture statistics, integrating pore and particle features. Possible improvements, including additional hydrodynamic/electric/chemical effects, are also discussed.
PROCEEDINGS OF 2022 IEEE INTERNATIONAL WORKSHOP ON METROLOGY FOR INDUSTRY 4.0 & IOT (IEEE METROIND4.0&IOT)
(2022)
Article
Chemistry, Multidisciplinary
Shuangshuang Zeng, Mauro Chinappi, Fabio Cecconi, Theo Odijk, Zhen Zhang
Summary: In this study, we propose a nanopore gated sub-attoliter silicon nanocavity device to investigate the behavior and properties of biopolymers in a confined environment. Single DNA molecules are electrically driven and compacted inside the nanocavity, and their dynamic fluctuations are monitored through ionic current measurements. The mechanism for DNA compaction is elucidated by varying different parameters.
