Faculty Profiles - ZINCHENKO, Anatoly

Papers - ZINCHENKO, Anatoly

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Mechanism of ground improvement using biomass-derived polymers based on soil mechanics principles

Takayuki Sakai, Anatoly Zinchenko, Masaki Nakano

Transportation Geotechnics Vol. 55 2025.11

Language：English Publishing type：Research paper (scientific journal) Publisher：Transportation Geotechnics

Recently, biomass-derived polymers have been increasingly considered as eco-friendly additives and modifiers for various construction materials; however, the mechanical behavior of such systems is poorly understood. This study investigates the effectiveness of soil improvement and its mechanical behaviour using biopolymers, specifically chitosan (CS) and carboxymethyl cellulose (CMC). Laboratory tests were conducted on specimens prepared with varying degrees of compaction (D<inf>c</inf> = 75 % and 90 %), CMC concentrations (0.5 % and 1.0 %), and CS: CMC mixing ratios (1:1 and 2:1). The effects of biopolymer treatment were examined based on soil mechanics principles. In the oedometer tests, specimens with higher CS: CMC ratios exhibited greater consolidation yield stress and compressibility, whereas permeability decreased with the addition of biopolymer. Specifically, at a CS: CMC ratio of 2:1, the consolidation yield stress was approximately 2.5 times higher, and the compression index increased by about 1.3 times compared to unimproved soil. Additionally, the permeability coefficient was reduced to approximately 0.2–0.5 times that of unimproved soil due to the addition of biopolymer. In the triaxial compression tests, a higher CS: CMC ratio led to more pronounced hardening with plastic expansion and improved shear strength. For example, at CMC concentration of 1 % and D<inf>c</inf> = 75 %, the maximum deviator stress for CS: CMC = 2:1 was approximately three times greater than that of the unimproved soil. These mechanical behaviours suggest an increase in overconsolidation ratio (OCR). Furthermore, the addition of biopolymers altered not only the soil skeleton structure but also fundamental physical properties such as the liquid limit and compression index, indicating a change in the “type” of soil itself. The upward shift of the normal consolidation line (NCL) caused by biopolymer treatment contributes to an increase in the OCR. These findings provide important insights into the mechanisms of biopolymer-based soil improvement from a geotechnical perspective, enabling the design of more efficient and sustainable soil reinforcement systems.

DOI： 10.1016/j.trgeo.2025.101670

Scopus

Hydrochars of mixed marine biomass and plastic wastes: Carbonization scenarios and the performance as ketoprofen adsorbents. Reviewed International coauthorship

Khonekeo Kingkhambang, Kayee Chan, Anatoly Zinchenko

Waste management Vol. 198 page： 66 - 76 2025.5

Upcycling of Waste PET Fibers and Fabrics via Surface Engineering: Surface Aminolysis-Assisted Functionalization with Catalytic Nanoparticles Reviewed International coauthorship Open Access

Miku Nakanishi, Kayee Chan, Anatoly Zinchenko

Chemical Engineering Journal Vol. 511 page： 161839 2025.5

Hydrothermal preparation of pharmaceuticals adsorbents from chitin and chitosan: Optimization and mechanism Reviewed

Xin Lin, Kayee Chan, Khonekeo Kingkhambang, Hideki Hayashi, Anatoly Zinchenko

Bioresource Technology Vol. 414 page： 131583 2024.10

Polyion Hydrogels of Polymeric and Nanofibrous Carboxymethyl Cellulose and Chitosan: Mechanical Characteristics and Potential Use in Environmental Remediation. Reviewed

Taisei Kawate, Yehao Wang, Kayee Chan, Nobuyuki Shibata, Yuya Doi, Yuichi Masubuchi, Anatoly Zinchenko

Gels Vol. 10 ( 9 ) 2024.9

Functional upcycling of waste PET plastic to the hybrid magnetic microparticles adsorbent for cesium removal. Reviewed

Kayee Chan, Anatoly Zinchenko

Chemosphere Vol. 354 page： 141725 2024.4

Multi-color polymer carbon dots synthesized from waste polyolefins through phenylenediamine-assisted hydrothermal processing Reviewed

Yusei Takahashi, Kayee Chan, Anatoly Zinchenko

Chemosphere Vol. 354 page： 141685 2024.4

Soil Improvement by Biomass Polyions and Compaction: Reinforcement, Biodegradation Resistance, and Retention of Heavy Metal Ions Reviewed

Vol. 12 ( 1 ) page： 111676 2023.12

Removal of Copper Ions Using a Waste Plastic-Derived Hydrogel Prepared via Microwave-assisted PET Aminolysis Reviewed

Chan Kayee, Kawai Masami, Yamake Mina, Zinchenko Anatoly

Gels Vol. 9 ( 11 ) page： 874 2023.11

Authorship：Last author,　Corresponding author Language：English Publishing type：Research paper (scientific journal) Publisher：Nanomaterials

Ubiquitous on Earth DNA and other nucleic acids are being increasingly considered as promising biomass resources. Due to their unique chemical structure, which is different from that of a more common carbohydrate biomass polymers, materials based on nucleic acids may exhibit new attractive characteristics. In this study, fluorescent nanoparticles (biodots) were prepared by a hydrothermal (HT) method from various nucleic acids (DNA, RNA, nucleotides, and nucleosides) to establish the relationship between the structure of precursors and fluorescent properties of biodots and to optimize conditions for preparation of the most fluorescent product. HT treatment of nucleic acids results in decomposition of sugar moieties and depurination/depyrimidation of nucleobases, while their consequent condensation and polymerization gives fluorescent nanoparticles. Fluorescent properties of DNA and RNA biodots are drastically different from biodots synthesized from individual nucleotides. In particular, biodots synthesized from purine-containing nucleotides or nucleosides show up to 50-fold higher fluorescence compared to analogous pyrimidine-derived biodots. The polymeric nature of a precursor disfavors formation of a bright fluorescent product. The reported effect of the structure of the nucleic acid precursor on the fluorescence properties of biodots should help designing and synthesizing brighter fluorescent nanomaterials with broader specification for bioimaging, sensing, and other applications.

DOI： doi.org/10.3390/gels9110874

Design and Synthesis of Functional Materials by Chemical Recycling of Waste Polyethylene Terephthalate (PET): Opportunities and Challenges Reviewed

Kayee Chan, Anatoly Zinchenko

Journal of Cleaner Production Vol. 433 page： 139828 2023.11

Authorship：Last author,　Corresponding author Language：English Publishing type：Research paper (scientific journal) Publisher：Waste Management

The progressive accumulation of discarded plastic in the environment demands further development of waste management of plastic waste and conversion technologies of such waste to value-added materials. Recently, the conversion of plastic waste to functional materials via chemical recycling has attracted considerable attention. In this report, plastic waste (PET) was utilized for the preparation of a hydrogel-based catalyst via a cross-linking reaction of PET-derived oligo(terephthalamide)s followed by the electroless metallization. The polymeric matrix of PET-derived hydrogel plays multiple roles of (i) an adsorption media for noble metal ions such as Au3+ and Ag+, (ii) a reducing agent of Au3+ and Ag+ ions to Au0 and Ag0, and (iii) a matrix for the controlled growth of Au and Ag nanoparticles (AuNPs and AgNPs). The obtained hybrid hydrogels after metallization contained well-dispersed AuNPs and AgNPs of 6.1 ± 3.7 nm or 6.1 ± 1.4 nm size, respectively. The catalytic activities of the hybrid hydrogels with metal nanoparticles were studied in a model system of p-nitrophenol reduction in an aqueous solution. The hybrid materials of both Au@hydrogel and Ag@hydrogel were catalytically active for the reduction of p-nitrophenol, obeying the first-order kinetics. Importantly, the AuNPs or AgNPs in the hydrogel matrix preserved the original catalytic activity after multiple p-nitrophenol reduction reactions, showing a promising reusability of the catalysts. The proposed here approach aims to broaden the scope of conversion routes of plastic waste to value-added materials as well as to develop new types of polymeric matrices for templating and growth of metal nanoparticles for catalytic applications.

DOI： 10.1016/j.jclepro.2023.139828

Electrochemical extraction of methanol from lignin under mild conditions Reviewed International coauthorship

Hibino Takashi, Kobayashi Kazuo, Zhou Dongwen, Chen Siyuan, Zinchenko Anatoly, Teranishi Shinya, Miyawaki Aki, Sawada Yoshiharu

Applied Catalysis B: Environmental Vol. 341 2023.10

Language：English Publishing type：Research paper (scientific journal) Publisher：Applied Catalysis B: Environmental

We report an electrochemical approach to extract methanol from lignin with a maximum efficiency of 95% under mild conditions of ambient pressure and a temperature of 75 °C. Hydroxyl radicals were generated from water over a platinum-sputtered anode and attacked the syringyl and guaiacyl units of the lignin. Methoxy groups in the units were demethylated to methanol with a yield greater than 40% through the formation of hemiketal intermediates. The electro-oxidation was coupled to cathode reactions that generated hydrogen in a helium flow and electric power in an air flow. Another important aspect of this approach is that no extra energy or effort was required to separate methanol from the reaction system. This technology can accelerate the replacement of fossil organic resources with renewable biomass resources.

DOI： 10.1016/j.apcatb.2023.123328

Scopus

Templating of catalytic gold and silver nanoparticles by waste plastic PET-derived hydrogel playing a dual role of a reductant and a matrix Reviewed

Kayee Chan, Anatoly Zinchenko

Waste Management Vol. 164 page： 20 - 28 2023.6

Authorship：Last author,　Corresponding author Language：English Publishing type：Research paper (scientific journal) Publisher：Waste Management

DOI： 10.1016/j.wasman.2023.03.037

Scopus

Reconstituted TAD-size chromatin fibers feature heterogeneous nucleosome clusters Reviewed International coauthorship

Korolev Nikolay, Zinchenko Anatoly, Soman Aghil, Chen Qinming, Wong Sook Yi, Berezhnoy Nikolay V, Basak Rajib, van der Maarel Johan R. C., van Noort John, Nordenskiold Lars

Scientific Reports Vol. 12 ( 1 ) page： 15558 2022.9

Language：English Publishing type：Research paper (scientific journal) Publisher：Scientific Reports

Large topologically associated domains (TADs) contain irregularly spaced nucleosome clutches, and interactions between such clutches are thought to aid the compaction of these domains. Here, we reconstituted TAD-sized chromatin fibers containing hundreds of nucleosomes on native source human and lambda-phage DNA and compared their mechanical properties at the single-molecule level with shorter ‘601’ arrays with various nucleosome repeat lengths. Fluorescent imaging showed increased compaction upon saturation of the DNA with histones and increasing magnesium concentration. Nucleosome clusters and their structural fluctuations were visualized in confined nanochannels. Force spectroscopy revealed not only similar mechanical properties of the TAD-sized fibers as shorter fibers but also large rupture events, consistent with breaking the interactions between distant clutches of nucleosomes. Though the arrays of native human DNA, lambda-phage and ‘601’ DNA featured minor differences in reconstitution yield and nucleosome stability, the fibers’ global structural and mechanical properties were similar, including the interactions between nucleosome clutches. These single-molecule experiments quantify the mechanical forces that stabilize large TAD-sized chromatin domains consisting of disordered, dynamically interacting nucleosome clutches and their effect on the condensation of large chromatin domains.

DOI： 10.1038/s41598-022-19471-3

Web of Science

Scopus

PubMed

Aminolysis-assisted hydrothermal conversion of waste PET plastic to N-doped carbon dots with markedly enhanced fluorescence Reviewed

Journal of Environmental Chemical Engineering Vol. 10 ( 3 ) page： 107749 2022.6

Conversion of waste bottle PET to magnetic microparticles adsorbent for dye-simulated wastewater treatment Reviewed

Chan Kayee, Zinchenko Anatoly

Journal of Environmental Chemical Engineering Vol. 10 ( 3 ) page： 108055 2022.6

Authorship：Last author,　Corresponding author Language：English Publishing type：Research paper (scientific journal) Publisher：Journal of Environmental Chemical Engineering

Mass production and consequent accumulation of plastic wastes in the environment urges the development of technologies for the efficient plastic wastes utilization and valorization to materials and products to support circular economy. Here, we report a novel conversion of PET plastic to a magnetic microparticles adsorbent prepared by co-precipitation of Fe3O4 nanoparticles with oligomeric products of PET aminolysis. The obtained adsorbent represents highly water-dispersible oligo(terephthalamide) particles of several tens μm size embedding magnetic nanoparticles randomly distributed in the organic matrix. The PET-derived magnetic adsorbent was used for the rapid and facile magnetic separation of an anionic dye (Congo Red, CR) from dye simulated water samples. The adsorbent containing plenty of amine groups showed superb adsorption capacity for CR of ca. 780 mg/g which is pH dependent and optimal at pH 6.5. Furthermore, the microparticular, non-aggregative state of the adsorbent coupled with its magnetic functionality provided rapid saturation of the adsorbent with dye by ca. 70% of the equilibrium adsorption capacity within 5 min and possibility of instantaneous removal from solution by a magnet. The proposed here material design addresses simultaneously the problem of plastic wastes utilization and preparation of cost-effective and efficient adsorbents for environmental cleaning purposes.

DOI： 10.1016/j.jece.2022.108055

Web of Science

Scopus

Efficient Stabilization of Soil, Sand, and Clay by a Polymer Network of Biomass-Derived Chitosan and Carboxymethyl Cellulose Reviewed

Anatoly Zinchenko, Takayuki Sakai, Kohki Morikawa, Masaki Nakano

Journal of Environmental Chemical Engineering Vol. 10 ( 1 ) 2022.2

Authorship：Lead author,　Corresponding author Language：English Publishing type：Research paper (scientific journal) Publisher：Journal of Environmental Chemical Engineering

Biomass-derived polymers are being increasingly utilized as eco-friendly functional materials in fields ranging from medicine and food to agriculture and environmental engineering. In this report, we developed a novel efficient method for improvement of soil materials based on in situ gelation of a polyion complex formed by biomass-derived carboxymethyl cellulose (CMC) and chitosan (CS). Self-organized network of polymer films and microfibers assembled via electrostatic interactions between oppositely-charged polyions interconnects particles of soil material and imparts the resulted composite with a considerable mechanical strength. Treatment of soil even with a high water content (ca. 30%) by a mixture of CMC and CS at m(CMC + CS)/m(soil) ratio of ca. 1% is sufficient to gain up to 150 kPa compression strength that further increases up to ca. 1 MPa after drying. Similar reinforcement effect by CMC-CS complex was observed for sand, and much higher yield strengths were measured for clay. Mechanical properties of soil materials strengthened by CMC-CS complex depended on structure and stability of CMC-CS polyion network and controlled by the polymerization degrees of macromolecules and the charge ratio between them. Being composed entirely of biomass-derived polymers, the proposed soil treatment system is particularly attractive due to environmental friendliness and sustainability and it can be utilized not only for the soil improvement but also for the construction of functional platforms for soil pollution control and remediation.

DOI： 10.1016/j.jece.2021.107084

Scopus

DNA-Chitosan Aerogels and Regenerated Hydrogels with Extraordinary Mechanical Properties Reviewed International coauthorship

Postnova Irina, Sarin Sergey, Zinchenko Anatoly, Shchipunov Yury

ACS Applied Polymer Materials Vol. 4 ( 1 ) page： 663 - 671 2021.12

Language：English Publishing type：Research paper (scientific journal) Publisher：ACS Applied Polymer Materials

It has recently been shown that native ds-DNA and chitosan can coassemble without common phase separation and precipitation, forming a translucent homogeneous hydrogel. This simple approach consists of progressive charging of the polysaccharide through gradual acidification of a solution in the presence of DNA, which slowly strengthens the electrostatic interactions between them, ruling out fast and uncontrolled cooperative association, which is a well-known problem associated with coacervation. Homogeneous hydrogels thus fabricated demonstrated mechanical properties characteristic of quite strong physical hydrogels. Extraordinary mechanical strength and elasticity have been observed in aerogels prepared from an original hydrogel and also in hydrogels, which were restored by the rehydration of aerogels. Aerogels match highly cross-linked synthetic polyurethane foams despite DNA with chitosan being bound only via electrostatic interactions without using a toxic cross-linking agent. Owing to their biocompatibility, biodegradability, and available renewable resources, hydrogels and aerogels might replace typical synthetic polymers. The fabrication of bionanocomposites with luminescent, sensing, and photocatalytic functionalities by entrapping quantum dots, titania nanoparticles, and dyes demonstrates some possible applications.

DOI： 10.1021/acsapm.1c01585

Web of Science

Scopus

Conversion of waste bottles' PET to a hydrogel adsorbent via PET aminolysis Reviewed

Kayee Chan, Anatoly Zinchenko

Journal of Environmental Chemical Engineering Vol. 9 ( 5 ) page： 106129 2021.10

Authorship：Last author,　Corresponding author Language：English Publishing type：Research paper (scientific journal) Publisher：Journal of Environmental Chemical Engineering

To ensure sustainable use of natural resources and circulation of materials, efficient methods of waste plastic conversion into value chemicals and scenarios for utilization of the latter are increasingly demanded. Here, we propose a method of waste PET bottles conversion to cross-linked hydrogels through PET aminolysis using tri- and tetraamines as a method of plastic waste valorization. Water-soluble oligomeric products of PET aminolysis were cross-linked in water using diglycidyl ether to get mechanically stable hydrogels that show typical polyelectrolyte behavior of polycations. PET-derived hydrogels abundant with amino groups and aromatic moieties were tested as adsorbents for an anionic dye such as Congo Red, and their absorption capacity towards dye was found to be ca. 500 mg/g. Beside demonstrated here application of PET-derived hydrogels for water cleaning from an industrial dye, utilization of such hydrogel materials in fields of environment, agriculture, separation, etc. are also anticipated.

DOI： 10.1016/j.jece.2021.106129

Web of Science

Scopus

Fluorescent Nanoparticles Synthesized from DNA, RNA, and Nucleotides Reviewed International coauthorship

Wang Maofei, Tsukamoto Masaki, Sergeyev Vladimir G., Zinchenko Anatoly

Nanomaterials Vol. 11 ( 9 ) page： 2265 2021.9

Authorship：Last author,　Corresponding author Language：English Publishing type：Research paper (scientific journal) Publisher：Nanomaterials

DOI： 10.3390/nano11092265

Web of Science

Scopus

PubMed

Metal Ions Sensing by Biodots Prepared from DNA, RNA, and Nucleotides. Reviewed International coauthorship International journal

Maofei Wang, Masaki Tsukamoto, Vladimir G Sergeyev, Anatoly Zinchenko

Biosensors Vol. 11 ( 9 ) page： 333 2021.9

Authorship：Last author,　Corresponding author Language：English Publishing type：Research paper (scientific journal)

Nucleic acids that exhibit a high affinity toward noble and transition metal ions have attracted growing attention in the fields of metal ion sensing, toxic metal ion removal, and the construction of functional metal nanostructures. In this study, fluorescent nanoparticles (biodots) were synthesized from DNA, RNA, and RNA nucleotides (AMP, GMP, UMP, and CMP) using a hydrothermal (HT) method, in order to study their metal ion sensing characteristics. The fluorescent properties of biodots differ markedly between those prepared from purine and pyrimidine nucleobases. All biodots demonstrate a high sensitivity to the presence of mercury cations (Hg2+), while biodots prepared from DNA, RNA, and guanosine monophosphate (GMP) are also sensitive to Ag+ and Cu2+ ions, but to a lesser extent. The obtained results show that biodots inherit the metal ion recognition properties of nucleobases, while the nucleobase composition of biodot precursors affects metal ion sensitivity and selectivity. A linear response of biodot fluorescence to Hg2+ concentration in solution was observed for AMP and GMP biodots in the range 0-250 μM, which can be used for the analytic detection of mercury ion concentration. A facile paper strip test was also developed that allows visual detection of mercury ions in solutions.

DOI： 10.3390/bios11090333

Web of Science

Scopus

PubMed

Adsorptive Removal of Heavy Metal Ions, Organic Dyes, and Pharmaceuticals by DNA-Chitosan Hydrogel Invited Reviewed

Chan K., Morikawa K., Shibata N., Zinchenko A.

Gels Vol. 7 ( 3 ) page： 112 2021.8

DNA-Chitosan Hydrogels: Formation, Properties, and Functionalization with Catalytic Nanoparticles Reviewed International coauthorship

Morikawa K., Masubuchi Y., Shchipunov Y., Zinchenko A.

ACS Applied Bio Materials Vol. 4 page： 1823 - 1832 2021.1

Internal Motion of Chromatin Fibers Is Governed by Dynamics of Uncompressed Linker Strands. Reviewed International coauthorship

Biophysical Journal Vol. 119 ( 11 ) page： 2326 - 2334 2020.12

Compaction and self-association of megabase-sized chromatin are induced by anionic protein crowding Reviewed International coauthorship

Zinchenko Anatoly, Chen Qinming, Berezhnoy Nikolay V, Wang Sai, Nordenskiold Lars

Sort Matter Vol. 16 ( 18 ) page： 4366 - 4372 2020.5

Amino Acid Sequence of Oligopeptide Causes Marked Difference in DNA Compaction and Transcription Reviewed

Zinchenko Anatoly, Hiramatsu Hiroyuki, Yamaguchi Hideaki, Kubo Koji, Murata Shizuaki, Kanbe Toshio, Hazemoto Norio, Yoshikawa Kenichi, Akitaya Tatsuo

Biophysical Journal Vol. 116 ( 10 ) page： 1836 - 1844 2019.5

Small DNA Additives to Polyelectrolyte Multilayers Promote Formation of Ultrafine Gold Nanoparticles with Enhanced Catalytic Activity Invited Reviewed

Nagahama C., Zinchenko A.

Colloid and Polymer Science Vol. 297 page： 363–369 2019.3

Hybrid porous magnetic bentonite-chitosan beads for selective removal of radioactive cesium in water. Reviewed

Wang K, Ma H, Pu S, Yan C, Wang M, Yu J, Wang X, Chu W, Zinchenko A

Journal of Hazardous Materials Vol. 362 page： 160 - 169 2019.1

Encapsulation of Long Genomic DNA into a Confinement of a Polyelectrolyte Microcapsule: A Single-Molecule Insight Reviewed

Zinchenko Anatoly, Inagaki Eisuke, Murata Shizuaki

ACS OMEGA Vol. 4 ( 1 ) page： 458 - 464 2019.1

A highly efficient magnetic chitosan “fluid” adsorbent with a high capacity and fast adsorption kinetics for dyeing wastewater purification Reviewed

Ma Hui, Pu Shengyan, Hou Yaqi, Zhu Rongxin, Zinchenko Anatoly, Chu Wei

Chemical Engineering Journal Vol. 345 page： 556 - 565 2018.8

Language：English Publishing type：Research paper (scientific journal) Publisher：Elsevier B.V.

A novel magnetic fluid adsorbent (magnetic chitosan “fluid” MCF) was prepared via a one-step in situ co-precipitation procedure using inexpensive and environmentally friendly chitosan (CS) and iron precursor. The resultant ultrafine colloid was characterized using transmission electron microscopy (TEM), X-ray powder diffraction (XRD), thermogravimetric analysis (TGA), and Fourier transform infrared spectroscopy (FTIR). The sorption and desorption characteristics of the composite were studied using a common Congo Red (CR) anionic dye to evaluate the suitability of the MCF for anionic dye wastewater purification. As an important advantage, the dye adsorption could be achieved in a wide alkaline pH range and reached the equilibrium within 5 min demonstrating the superior properties of our material compared the previously reported CS-based adsorbents. The adsorption obeyed the Langmuir isotherm model with the remarkable maximum adsorption capacity of approx. 1700 mg/g for CR under neutral pH. NaOH treatment was utilized to desorb and regenerate MCF, while the removal rate still remained above 90% after recycling five times, demonstrating that the MCF could be employed for repeated use without significant capacity loss. MCF could be readily separated from water within 30 s under a low magnetic field (&lt
0.035 T). Overall, the ultrafine colloidal state of the synthesized MCF enabled a rapid pollutant uptake, high adsorption capacity, and reusability. The above characteristics of MCF and its environmentally friendly composition make it a very promising material for practical dyeing wastewater purification.

DOI： 10.1016/j.cej.2018.03.115

Web of Science

Scopus

Efficient prevention of nanomaterials transport in the porous media by treatment with polyelectrolytes Reviewed

Soenaryo T., Murata S., Zinchenko A.

Chemosphere Vol. 210 page： 567-576 2018.8

Compaction of Single Molecule Megabase-Long Chromatin under the Influence of Macromolecular Crowding Reviewed

Zinchenko A., Berezhnoy N., Chen Q., Nordenskiöld L.

Biophysical Journal Vol. 114 page： 2326–2335 2018.5

Stretch and Dynamics of Single Chromatin Molecules Confined in Nano-fluidic Channels

William M. Rosencrans, Fan Liu, Nikolay V. Berezhnoy, Anatoly Zinchenko, Lars Nordenskiold, Johan R. C. van der Maarel

BIOPHYSICAL JOURNAL Vol. 114 ( 3 ) page： 599A - 599A 2018.2

Removal of Carbon Nanomaterials by Co-Precipitation with Chitosan: A Facile Method for Water Pre-Treatment Reviewed

Soenaryo T., Zinchenko A., Murata S.

Environmental Science: Water Research Technolology Vol. 4 page： 265-271 2018.1

Single-Molecule Compaction of Megabase-Long Chromatin Molecules by Multivalent Cations Reviewed

Zinchenko A., Berezhnoy N., Wang S, Rosencrans W., Korolev N., van der Maarel J., Nordenskiöld L.

Nucleic Acids Research Vol. 2 page： 635-649 2018.1

Formation of Multi-Layered Chitosan Honeycomb Spheres via Breath-Figure-Like Approach in Combination with Co-Precipitation Processing Reviewed

Ma H., Pu S.Y., Ma J., Yan C., Zinchenko A., Pei X., Chu W.

Materials Letters Vol. 211 page： 91-95 2018.1

DNA-based materials as chemical reactors for synthesis of metal nanoparticles

Zinchenko A., Sergeyev V. G.

Polymer Science Series C Vol. 59 ( 1 ) page： 18-28 2017.9

Novel highly porous magnetic hydrogel beads composed of chitosan and sodium citrate: an effective adsorbent for the removal of heavy metals from aqueous solutions Reviewed

Pu S.Y., Ma H., Zinchenko A., Chu W.

Environmental Science and Pollution Research Vol. 24 ( 19 ) page： 16520-16530 2017.7

Photoinduced Fusion of Lipid Bilayer Membranes Reviewed

Suzuki Y., Nagai K., Zinchenko A., Hamada T.

Languir Vol. 33 ( 10 ) page： 2671-2676 2017.3

An efficient heterogeneous fenton catalyst based on modified diatomite for degradation of cationic dye simulated wastewater Reviewed

Pu S.Y., Xiang C., Zhu R., Ma H., Zinchenko A., Chu W.

Desalination Water Treat. Vol. 79 page： 378-385 2017

大学の廃棄物のキャンパスマインとしての活用への提言（１） ─ 名古屋大学における廃試薬の調査に基づく考察 Reviewed

ジンチェンコアナトーリ, 竹田裕哉, 三品太志, 村田静昭, 陳寧

環境と安全 Vol. 7 page： 17 2016.4

Gold Nanoparticles in DNA-Based Multilayer Films: Synthesis, Size Control, and Influence of the Multilayer Structure on Au NP Catalytic Properties Reviewed

Zinchenko A, Nagahama C, Murata. S

ChemNanoMat Vol. 2016 ( 2 ) page： 125-132 - 132 2016.1

Language：English Publishing type：Research paper (scientific journal) Publisher：WILEY-V C H VERLAG GMBH

A method to prepare DNA-based multilayered microcapsules as a host matrix for synthesizing ultrasmall gold nanoparticles of 2-4 nm in size is presented. Utilizing the intrinsic affinity of DNA for transition metal ions, ionic gold was first efficiently concentrated inside the DNA-based multilayers assembled on a CaCO3 sacrificial template. Further reduction of ionic gold inside the multilayers resulted in the formation of high-density, well-dispersed 2-4 nm gold nano-particles distributed evenly and exclusively inside the polyelectrolyte multilayers. Metallized multilayers containing ultrafine gold nanoparticles showed a good performance in catalytic reduction of nitroaromatic compounds and the catalytic activity of gold nanoparticles was enhanced with a decrease of host multilayer thickness. The influence of the multilayer structure and composition on size and catalytic activity of gold nanoparticles is discussed.

DOI： 10.1002/cnma.201600012

Web of Science

DNA Conformational Behavior and Compaction in Biomimetic Systems: Toward Better Understanding of DNA Packaging in Cel Reviewed

Zinchenko A.

Adv. Colloid. Interface Sci. Vol. 2016 ( 232 ) page： 70-79 2016.1

Decoration of DNA scaffold by gold nanoparticles formed in aqueous solutions Reviewed

Lopatina L.I., Karpushkin E.A., Zinchenko A., Sergeyev V.G.

Mendeleyev Comm. Vol. 26 page： 291‐292 2016

Fabrication of Bimetallic Core-Shell and Alloy Ag-Au Nanoparticles on a DNA Template Reviewed

Taniguchi S., Zinchenko A., Murata. S.

Chem.Lett. Vol. 45 page： 610‐611 2016

Divalent cation shrinks DNA but inhibits its compaction with trivalent cation Reviewed

Tongu C., Kenmotsu T., Yoshikawa Y., Zinchenko A., Chen N., Yoshikawa K.*

J. Chem. Phys. Vol. 144 page： 205101 2016

Metallization of DNA Hydrogel - Application of Soft Matter Host for Preparation and Nesting of Catalytic Nanoparticles Reviewed

Zinchenko A., Che Y., Taniguchi S., Lopatina L.I., Sergeyev V.G.,Murata S.

J.Nanopart. Res. Vol. 18 page： 179 2016

Suggestion on application of campus wastes as valuable resources, a campus mine (1) — Study and discussion on chemical wastes of Nagoya University Reviewed

Zinchenko Anatoly, Takeda Yuuya, Mishina Taiji, Murata Shizuaki, Chen Ning

Journal of Environment and Safety Vol. 7 ( 1 ) page： 17 - 23 2016

Language：Japanese Publishing type：Research paper (scientific journal) Publisher：Academic Consociation of Environmental Safety and Waste Management, Japan

In order to reduce the amount of wastes and to promote their reuse and recycle, valuable materials, such as minor and noble metals and their compounds, which were included in disposed reagents generated by academic activities in Nagoya University during the period of 2009 to 2012, have been investigated. Closed up herein were many problems, such as dumping hazardous materials without special care, the absence of a recycling system of valuable chemical wastes and wasting research budgets due to disposing reagents without opening bottles. In addition, establishment of a chemical library of minor elements as well as an exchanging system of information about chemical stocks in each laboratory for the purpose of their sharing.

DOI： 10.11162/daikankyo.15g1101

CiNii Research

Size Dependent Catalytic Activity of Gold Nanoparticles in DNA Hydrogels Reviewed

Zinchenko A. Taniguchi S., Murata. S.

Macromolecular Symposia Vol. 2015 ( 129 ) page： 106-111 2015.12

DNAの資源化

ジンチェンコアナトーリ

化学と工業 Vol. 68 ( 9 ) page： 804-805 2015.9

Solubilization of MWCNT by DNA and Construction of DNA-MWCNT Hybrid Hydrogels Reviewed

Zinchenko A, Taki Y, Sergeyev V.G, Murata S

Nanomaterials Vol. 2015 ( 5 ) page： 270-283 2015.2

Uptake of Aromatic Compounds by DNA: Toward the Environmental Application of DNA for Cleaning Water Reviewed

Fernández-Solis C, Kuroda Y, Zinchenko A, Murata S

Colloids Surf., B. Vol. 2015 ( 129 ) page： 146–153 2015.2

Compaction of Double-Stranded DNA by Negatively Charged Proteins and Colloids Reviewed

Zinchenko A, Yoshikawa K

Curr. Opin. Colloid Interface Sci. Vol. 2015 ( 20 ) page： 60-65 2015.1

Control of a Catalytic Activity of Gold Nanoparticles Embedded in DNA Hydrogel by Swelling/Shrinking the Hydrogel's Matrix Reviewed

Che Y, Zinchenko A, Murata S

J. Colloid Interface Sci. Vol. 2015 ( 445 ) page： 364-370 2015.1

Entrapment and Removal of Carbon Nanotubes and Fullerenes by Co-Precipitation with Calcium Carbonate Beads Reviewed

Pu S.Y, Zinchenko A.A, Chen N, Murata S

ACS Sustainable Chem. Eng. Vol. 2014 ( 2 ) page： 2275-2282 2014.9

Photochemical metallization to fabricate DNA-templated gold nanorings Reviewed

Pu S.Y, Zinchenko A.A., Qina L., Xua M., M. Xu., Murata S.

Mater. Lett. Vol. 130 page： 168-171 2014

DNA Hydrogel as a Template for Synthesis of Ultrasmall Gold Nanoparticles for Catalytic Applications Reviewed

Zinchenko A. A., Miwa, Y., Lopatina L.I., Sergeyev V.G., Murata S.

ACS Appl. Mater. Interfaces Vol. 6 ( 5 ) page： 3226–3232. 2014

Crowding by anionic nanoparticles causes DNA double-strand instability and compaction Reviewed

Zinchenko, A.; Tsumoto, K.; Murata, S.; Yoshikawa, K.

J. Phys. Chem. Vol. 118 ( 5 ) page： 1256-1262 2014

Size Control of Gold Nanoparticles Synthesized in a DNA Hydrogel Reviewed

Miwa, Y, Zinchenko A. A, Lopatina L.I, Sergeyev V.G, Murata S

Polym. Int. Vol. 63 ( 9 ) page： 1566-1571 2014

Extraction of Noble and Rare-Earth Metals from Aqueous Solutions by DNA Cross-Linked Hydrogel Reviewed

Maeda Y., Zinchenko A. A., Murata S.

ChemPlusChem Vol. 78 ( 7 ) page： 619-622 2013

Entrapping of Fullerenes, Nanotubes, and Inorganic Nanoparticles by a DNA-Chitosan Complex: A Method for Nanomaterials Removal Reviewed

Zinchenko A. A, Maeda N, Pu S.Y, Murata S

Environ. Sci. Technol. Vol. 47 ( 9 ) page： 4489-4496 2013

Facile Control of DNA-Templated Inorganic Nanoshell Size Reviewed

Vol. 12 page： 635-641 2012

Templating of inorganic nanomaterials by biomacromolecules and their assemblies Invited Reviewed

Vol. 54 ( 7 ) page： 1048-1055 2012

Photochemical Modulation of DNA Conformation by Organic Dications Reviewed

Zinchenko A. A, Tanahashi M, Murata S

ChemBioChem Vol. 13 page： 105-111 2012

Thiol-Mediated Anchoring of Silver Cations to DNA for Construction of Nanofibers on DNA Scaffold Reviewed

Zinchenko A. A, Chen N, Baigl D, Lopatina L, Sergeyev V. G

Biomacromolecules Vol. 13 ( 6 ) page： 1787-1793 2012

A Facile Method for the Assessment of DNA Damage Induced by UV-Activated Nanomaterials Reviewed

Yamazaki Y, Zinchenko A. A, Murata S

Nanoscale Vol. 3 ( 7 ) page： 2909-2915 2011

Effects of Cationic and Anionic Nanoparticles on the Stability of the Secondary Structure of DNA Reviewed

Kamata H., Zinchenko A. A., Murata S.

Colloid Polym. Sci. Vol. 289 page： 1329-1335 2011

Conformational behavior of DNA-templated CdS inorganic nanowiren of Hollow Meshed Inorganic Nanoshells Reviewed

Pu S. Y., Zinchenko A. A., Murata S.

Nanotechnology Vol. 22 page： 375604 2011

Facile Control of DNA-Templated Inorganic Nanoshell Size Reviewed

Pu S. Y., Zinchenko A. A., Murata S.

J. Nanosci. Nanotechnol. page： in press 2011

DNA-Assisted "Double-Templating" Approach for the Construction of Hollow Meshed Inorganic Nanoshells Reviewed

Pu S. Y., Zinchenko A. A., Murata S.

Langmuir Vol. 27 ( 8 ) page： 5009-5013 2011

DNA Compaction on Histone Mimics Prepared from Silica Nanoparticles

TAKENAKA Toshio, ZINCHENKO Anatoly A., YOSHIKAWA Kenichi, MURATA Shizuaki

Vol. 39 ( 1 ) page： 72 - 73 2010.1

DNA Compaction on Histone Mimics Prepared from Silica Nanoparticles Reviewed

Takenaka T., Zinchenko A. A., Yoshikawa K., Murata S.

Chemistry Letters Vol. 39 page： 72-73 2010

Quantum dot probes for observation of single molecule DNA and a synthetic polyelectrolyte higher-order structure Reviewed

Chen N., Zinchenko A. A., Yamazaki Y., Yoshikawa Y., Murata S., Yoshikawa K.

Soft Matter Vol. 6 page： 2834 - 2841 2010

Roles of Mono- and Divalent Cations in DNA Compaction Induced by Histone-Mimic Nanoparticles Reviewed

Takenaka T., Zinchenko A. A., Yoshikawa K., Murata S.

Bulletin of the Chemical Society of Japan Vol. 83 page： 643-650 2010

Thermo-Switching of the Conformation of Genomic DNA in Solutions of Poly(N-isopropylacrylamide) Reviewed

Chen N, Zinchenko A. A, Kidoaki S, Murata S, Yoshikawa K

Langmuir Vol. 26 ( 5 ) page： 2995-2998 2010

*Application of DNA condensation for removal of mercury ions from aqueous solutions Reviewed

Zinchenko A. A, Sakai H, Matsuoka S, Murata S

Journal of Hazardous Materials Vol. 168 ( 1 ) page： 38-43 2009

Removal of heavy metal ions from aqueous solutions by complexation with DNA and precipitation with cationic surfactant Reviewed

Sakai H., Matsuoka S., Zinchenko A. A., Murata S.

Colloids Surf., A. Vol. 347 page： 210–214 2009

Assessment of the DNA damage using the fluorescence microscope Reviewed

Yamazaki Y., Zinchenko A. A., Murata S.

Nucleic Acids Symp. Ser. Vol. 53 page： 47-48 2009

ATP-induced shrinkage of DNA with MukB protein and MukBEF complex of Escherichia coli Reviewed

Chen N, Zinchenko A.A, Yoshikawa Y, Araki S, Adachi S, Yamazoe M, Hiraga S, Yoshikawa K

Journal of Bacteriology Vol. 190 ( 10 ) page： 3731-3737 2008

Language：English Publishing type：Research paper (scientific journal)

Fluorescence microscopic observation on individual T4 DNA molecules revealed that MukBEF complex (bacterial condensin) and its subunit MukB (a member of SMC superfamily) homodimer of Escherichia coli shrunk markedly large DNA molecules in the presence of hydrolysable ATP. Contrary, in the presence of ADP or ATP-γS, the conformation of DNA was almost not changed. This suggests that the ATPase activity of subunit MukB is essential to shrink large DNA molecules. Stretching experiment on the shrunken DNA in the presence of ATP and MukBEF indicated cross bridging interaction between DNA molecules.

Photochemical Metallization of DNA Reviewed

Zinchenko A. A, Chen N, Murata S

Chemistry Letters Vol. 37 page： 1096-1097 2008

Conformational Behavior of Giant DNA through Binding with Ag+ and Metallization Reviewed

Zinchenko A. A., Baigl D, Chen N., Pyshkina O. A., Endo K., Sergeyev V. G., Yoshikawa K.

Biomacromolecules Vol. 9 page： 1981-1987 2008

A Novel Type Cationic Silica Nanoparticles and its Potential Application in Biomedicine Reviewed

Li L., Takenaka T., Zinchenko A., Chen N., Ma Y., Yoshikawa K.

Proceedings of International Conference on Bioinformatics and Biomedical Engineering (ICBBE) 2008 page： 1539-1542 2008

Single-Molecule Observations of Giant DNA and Synthetic Polyelectrolyte by Labeling with Semiconductor "Quantum Dots" Reviewed

Chen N., Yamazaki Y., Zinchenko A., Yoshikawa Y., Murata S., Yoshikawa K.

Proceedings of International Symposium on Micro-Nano Mechatronics and Human Science page： 140-144 2008

Transcription of Giant DNA Complexed with Cationic Nanoparticles as a Simple Model of Chromatin Reviewed

Zinchenko A. A., Luckel F., Yoshikawa K.

Biophysical Journal Vol. 92 page： 1318-1325 2007

Dynamic Conformational Behavior and Molecular Interaction Discrimination of DNA/Binder Complexes by Single-Chain Stretching in a MicroDevice Reviewed

Huang W.-H., Zinchenko A. A., Pawlak C., Chen Y., Baigl D.

ChemBioChem Vol. 8 ( 15 ) page： 1771-1774 2007

Visualization of Different Pathways of DNA Release from Interpolyelectrolyte Complex Reviewed

Ayoubi M. A., Zinchenko A. A., Philippova O. E, Khokhlov A. R., Yoshikawa K.

Journal of Physical Chemistry B Vol. 111 page： 8378-8378 2007

Language：English Publishing type：Research paper (scientific journal)

Fluorescence microscopy is used for visualizing the release of double-stranded DNA from its interpolyelectrolyte complex with positively charged poly(allylamine hydrochloride) though exchange reaction with added polyanion, poly(sodium styrenesulfonate). The switching of pathway of DNA release is due to the screening of electrostatic repulsion in charged sequences of naked DNA and the decrease of the osmotic pressure of counterions.

Single-Chain Compaction of Long Duplex DNA by Cationic Nanoparticles: Modes of Interaction and Comparison with Chromatin Reviewed

Zinchenko A. A, Sakaue T, Araki S, Yoshikawa K, Baigl D

Journal of Physical Chemistry B Vol. 111 page： 3019 -3031 2007

Language：English Publishing type：Research paper (scientific journal)

The compaction of long duplex DNA by cationic nanoparticles (NP) used as a primary model of histone core particles has been investigated. We have systematically studied the effect of salt concentration, particle size, and particle charge by means of single-molecule observations-fluorescence microscopy (FM) and transmission electron microscopy (TEM)-and molecular dynamics (MD) simulations. We have found that the large-scale DNA compaction is progressive and proceeds through the formation of beads-on-a-string structures of various morphologies. The DNA adsorbed amount per particle depends weakly on NP concentration but increases significantly with an increase in particle size and is optimal at an intermediate salt concentration. Three different complexation mechanisms have been identified depending on the correlation between DNA and NPs in terms of geometry, chain rigidity, and electrostatic interactions: free DNA adsorption onto NP surface, DNA wrapping around NP, and NP collection on DNA chain.

Compaction of DNA on nanoscale three-dimensional templates Invited

Zinchenko A. A., Chen N.

Journal of Physics: Condensed Matter Vol. 18 page： R453-R480 2006

Na+ more strongly inhibits DNA compaction by spermidine (3+) than K+ Reviewed

Hibino K, Yoshikawa Y, Murata S, Saito T, Zinchenko A. A, Yoshikawa K

Chemical Physics Letters Vol. 426 page： 405-409 2006

Probing Biopolymer Conformation by Metallization with Noble Metals Reviewed

Chen N, Zinchenko A. A, Yoshikawa K

Nanotechnology Vol. 17 page： 5224-5232 2006

*Compaction of single-chain DNA by histone-inspired nanoparticles Reviewed

Zinchenko A. A., Yoshikawa K., Baigl D

Physical Review Letters Vol. 95 ( 22 ) page： 228101 2005

DNA-templated silver nanorings Reviewed

Zinchenko A. A., Yoshikawa K., Baigl D.

Adv. Mater. Vol. 17 ( 23 ) page： 2820-2823 2005

How Does DNA Compaction Favor Chiral Selectivity with Cationic Species? Higher Selectivity with Lower Cationic Charge Reviewed

Zinchenko A. A., Chen N., Murata S., Yoshikawa K.

ChemBioChem Vol. 6(8) page： 1419-1422 2005

Specific Formation of Beads-on-a-Chain Structures on Giant DNA Using a Designed Polyamine Derivative Reviewed

Chen N., Zinchenko A. A., Murata S., Yoshikawa K.

J. Am. Chem. Soc. Vol. 127 page： 10910-10916 2005

Na+ Shows a Markedly Higher Potential than K+ in DNA Compaction in a Crowded Environment Reviewed

Zinchenko A. A., Yoshikawa K.

Biophys. J. Vol. 88(6) page： 4118-4123 2005

DNA Compaction by the Divalent Cations: Structural Specificity Revealed by the Potentiality of the Designed Quaternary Diammonium Salts, Reviewed

Zinchenko A. A., Sergeyev V. G., Yamabe K., Murata S., Yoshikawa K.

ChemBioChem Vol. 5 ( 3 ) page： 360-368 2004

Stereoisomeric Discrimination in DNA Compaction Reviewed

Zinchenko A. A, Sergeyev V. G, Kabanov V. A, Murata S, Yoshikawa K

Angewandte Chemie International Edition Vol. 43 ( 18 ) page： 2378-2371 2004

Controlling the Intrachain Segregation on a Single DNA Molecule Reviewed

Zinchenko A. A., Sergeyev V. G., Murata S., Yoshikawa K.

J. Am. Chem. Soc. Vol. 125 ( 15 ) page： 4414 - 4415 2003

Mechanism of Interaction of DNA with Surfactants in Water-Alcohol Media and Structure of the Related Complexes Reviewed

Sergeyev V. G., Pyshkina O. A., Zinchenko A. A., Zezin S. B., Zezin A. B., Kabanov V. A.

Polymer Science, Seriya A Vol. 45 ( 5 ) page： 814 - 822 2003

Ascorbic acid induces a marked conformational change in long duplex DNA Reviewed

Yoshikawa Y., Suzuki M., Chen N., Zinchenko A. A., Murata S., Kanbe T., Nakai T., Oana H., Yoshikawa K.

European Journal of Biochemistry Vol. 270 ( 14 ) page： 3101-3106 2003

Secondary Structure of DNA is Recognized by Slightly Cross-Linked Cationic Hydrogel Reviewed

Sergeyev V. G, Novoskoltseva O. A, Zinchenko O. A, Pyshkina O. A, Rogacheva V. B, Zezin A. B, Yoshikawa K, Kabanov V. A

J. Am. Chem. Soc. Vol. 124 page： 11324-11333 2002

The secondary structure determines the character of DNA interaction with a slightly cross-linked cationic hydrogel Reviewed

Sergeyev V. G, Novoskoltseva O. A, Zinchenko A. A, Pyshkina O. A, Rogacheva V. B, Zezin A. B, Kabanov V. A

Doklady Physical Chemistry Vol. 116 page： 218-222 2001

Interplay between Folding/Unfolding and Helix/Coil Transitions in Giant DNA Reviewed

Mikhailenko S. V., Sergeyev V. G., Zinchenko A. A., Gallyamov M. O., Yaminsky I. V., Yoshikawa K.

Biomacromolecules Vol. 1 ( 4 ) page： 597-603 2000

DNA-surfactant complexes in a water/alcohol mixture Reviewed

Zinchenko A. A, Sergeyev V. G, Pyshkina O. A

Progress in Polymer and Colloid Science Vol. 116 page： 21-25 2000

Interpolyelectrolyte Complexes Formed by DNA and Astramol TM Poly(propyleneimine) Dendrimers Reviewed

Kabanov V. A, Sergeyev V. G, Pyshkina, O. A. Zinchenko A. A, Zezin A. B, Joosten J. G. H, Brackman J, Yoshikawa K

Macromolecules Vol. 33 ( 26 ) page： 9587-9593 2000

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