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Li C, Chen Q, Ding M. Escape dynamics of active ring polymers in a cylindrical nanochannel. SOFT MATTER 2024; 20:1719-1724. [PMID: 38284326 DOI: 10.1039/d3sm01524f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
We explore the escape dynamics of active ring polymers confined in a cylindrical nanochannel using Brownian dynamics. Our simulation results show that the escape time decreases with the increase of the Péclet number, which is not noticeable between the two stages of the escape process, based on whether the center of mass of the polymer is inside or outside the nanochannel. However, the monomer motion trajectory of the active polymer is very different from that of the passive polymer, similar to the snake-like motion with uniform velocity. The passive polymer, however, is in constant fugitive motion with increased velocity at the tail end of the escape. Our work is vital for understanding the escape dynamics of active ring polymers in the confined nanochannel, which provides new perspectives on their characterization and analysis.
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Affiliation(s)
- Chuqiao Li
- Xinjiang Laboratory of Phase Transitions and Microstructures in Condensed Matter Physics, College of Physical Science and Technology, Yili Normal University, Yining 835000, China
| | - Qiaoyue Chen
- Xinjiang Laboratory of Phase Transitions and Microstructures in Condensed Matter Physics, College of Physical Science and Technology, Yili Normal University, Yining 835000, China
| | - Mingming Ding
- Xinjiang Laboratory of Phase Transitions and Microstructures in Condensed Matter Physics, College of Physical Science and Technology, Yili Normal University, Yining 835000, China
- School of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou 510006, China.
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Buglakov AI, Vasilevskaya VV. Fibril Assembly and Gelation of Macromolecules with Amphiphilic Repeating Units. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:12377-12387. [PMID: 34637315 DOI: 10.1021/acs.langmuir.1c01953] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
This paper reports the self-assembly of the fibrillar network in a concentrated solution of macromolecules with an amphiphilic structure of repeating units. The investigation of amphiphilic homopolymers and alternating copolymers with the linear and cyclic topologies, the solution with different polymer concentrations and solvent qualities, allows us to conclude that the ability to form a fibrillar gel with branched fibrils and regular subchain thickness is inherent for macromolecules with the solvophobic backbone and solvophilic pendants. The elements of the gel structure, such as the mesh size and fibrillar thickness, the number of cross-links, and their functionality, can be tuned and customized according to the requirements of their application. The results could be helpful for the directed design of the synthetic analogue of the relevant extracellular matrix, in tissue engineering, for fibrotic disease treatment and cell encapsulation.
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Affiliation(s)
- Aleksandr I Buglakov
- A. N. Nesmeyanov Institute of Organoelement Compounds RAS, Vavilova ul., 28, Moscow 119991, Russia
- Faculty of Physics, M. V. Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia
| | - Valentina V Vasilevskaya
- A. N. Nesmeyanov Institute of Organoelement Compounds RAS, Vavilova ul., 28, Moscow 119991, Russia
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Alexiou TS, Alatas PV, Tsalikis DG, Mavrantzas VG. Conformational and Dynamic Properties of Short DNA Minicircles in Aqueous Solution from Atomistic Molecular Dynamics Simulations. Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c00821] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Terpsichori S. Alexiou
- Department of Chemical Engineering, University of Patras & FORTH-ICE/HT, Patras, GR 26504, Greece
| | - Panagiotis V. Alatas
- Department of Chemical Engineering, University of Patras & FORTH-ICE/HT, Patras, GR 26504, Greece
| | - Dimitrios G. Tsalikis
- Department of Chemical Engineering, University of Patras & FORTH-ICE/HT, Patras, GR 26504, Greece
| | - Vlasis G. Mavrantzas
- Department of Chemical Engineering, University of Patras & FORTH-ICE/HT, Patras, GR 26504, Greece
- Department of Mechanical and Process Engineering, Particle Technology Laboratory, ETH Zürich, CH-8092 Zürich, Switzerland
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Hirano K, Iwaki T, Ishido T, Yoshikawa Y, Naruse K, Yoshikawa K. Stretching of single DNA molecules caused by accelerating flow on a microchip. J Chem Phys 2018; 149:165101. [PMID: 30384753 DOI: 10.1063/1.5040564] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
DNA elongation induced by fluidic stress was investigated on a microfluidic chip composed of a large inlet pool and a narrow channel. Through single-DNA observation with fluorescence microscopy, the manner of stretching of individual T4 DNA molecules (166 kbp) was monitored near the area of accelerating flow with narrowing streamlines. The results showed that the DNA long-axis length increased in a sigmoidal manner depending on the magnitude of flow acceleration, or shear, along the DNA chain. To elucidate the physical mechanism of DNA elongation, we performed a theoretical study by adopting a model of a coarse-grained nonlinear elastic polymer chain elongated by shear stress due to acceleration flow along the chain direction.
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Affiliation(s)
- Ken Hirano
- Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Takamatsu, Kagawa 761-0395 Japan
| | - Takafumi Iwaki
- Faculty of Medicine, Oita University, Yufu, Oita 879-5593, Japan
| | - Tomomi Ishido
- Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Takamatsu, Kagawa 761-0395 Japan
| | - Yuko Yoshikawa
- Faculty of Life and Medical Science, Doshisha Universiy, Kyotanabe, Kyoto 610-0321, Japan
| | - Keiji Naruse
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8558, Japan
| | - Kenichi Yoshikawa
- Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Takamatsu, Kagawa 761-0395 Japan
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Noda M, Ma Y, Yoshikawa Y, Imanaka T, Mori T, Furuta M, Tsuruyama T, Yoshikawa K. A single-molecule assessment of the protective effect of DMSO against DNA double-strand breaks induced by photo-and γ-ray-irradiation, and freezing. Sci Rep 2017; 7:8557. [PMID: 28819291 PMCID: PMC5561226 DOI: 10.1038/s41598-017-08894-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 07/14/2017] [Indexed: 11/09/2022] Open
Abstract
Dimethyl sulfoxide (DMSO) is widely used as a cryoprotectant for organs, tissues, and cell suspension in storage. In addition, DMSO is known to be a useful free radical scavenger and a radio-protectant. To date, many in vitro assays using cultured cells have been performed for analysing the protective effect of DMSO against genomic DNA damage; however, currently it has been rather difficult to detect DNA double strand breaks (DSBs) in a quantitative manner. In the present study, we aimed to observe the extent of DNA damage by use of single molecular observation with a fluorescence microscope to evaluate DSBs induced by photo- and γ-ray-irradiation, or freeze/thawing in variable concentrations of DMSO. As a result, we found that 2% DMSO conferred the maximum protective effect against all of the injury sources tested, and these effects were maintained at higher concentrations. Further, DMSO showed a significantly higher protective effect against freezing-induced damage than against photo- and γ-ray-irradiation-induced damage. Our study provides significant data for the optimization of DNA cryopreservation with DMSO, as well as for the usage of DNA as the protective agent against the injuries caused by active oxygen and radiations.
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Affiliation(s)
- Masami Noda
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, 610-0321, Japan
| | - Yue Ma
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, 610-0321, Japan
| | - Yuko Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, 610-0321, Japan
| | - Tadayuki Imanaka
- Research Organization of Science and Technology, Ritsumeikan University, Shiga, 525-8577, Japan
| | - Toshiaki Mori
- Graduate School of Engineering, Department of Quantum and Radiation Technology, Osaka Prefecture University, Osaka, 599-8570, Japan
| | - Masakazu Furuta
- Graduate School of Engineering, Department of Quantum and Radiation Technology, Osaka Prefecture University, Osaka, 599-8570, Japan
| | - Tatsuaki Tsuruyama
- Drug Discovery and Medicine, Department of Pathology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, 610-0321, Japan.
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Hoell C, Löwen H. Colloidal suspensions of C-particles: Entanglement, percolation and microrheology. J Chem Phys 2016; 144:174901. [DOI: 10.1063/1.4947237] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Christian Hoell
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, D-40225 Düsseldorf, Germany
| | - Hartmut Löwen
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, D-40225 Düsseldorf, Germany
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Ma Y, Ogawa N, Yoshikawa Y, Mori T, Imanaka T, Watanabe Y, Yoshikawa K. Protective effect of ascorbic acid against double-strand breaks in giant DNA: Marked differences among the damage induced by photo-irradiation, gamma-rays and ultrasound. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.08.054] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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