Article
Chemistry, Physical
Yeol Kyo Choi, Nathan R. Kern, Seonghan Kim, Krishan Kanhaiya, Yaser Afshar, Sun Hee Jeon, Sunhwan Jo, Bernard R. Brooks, Jumin Lee, Ellad B. Tadmor, Hendrik Heinz, Wonpil Im
Summary: Molecular modeling and simulation are important tools for predicting properties and understanding mechanisms of nanomaterials. However, building nanomaterial-containing systems is challenging. Researchers have developed a web-based nanomaterial modeler that generates transferable nanomaterial models among different simulation packages. The modeler has been validated and can also generate complex systems of nanomaterial-biomolecule and nanomaterial-polymer interfaces.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Microbiology
Cristina Sebastia, Josep M. Folch, Maria Ballester, Jordi Estelle, Magi Passols, Maria Munoz, Juan M. Garcia-Casco, Ana I. Fernandez, Anna Castello, Armand Sanchez, Daniel Crespo-Piazuelo
Summary: The gut microbiota is closely related to the composition of short-chain fatty acids in the host, with Prevotella spp. and Akkermansia spp. potentially serving as biomarkers for acetic and n-butyric acid levels, and Rikenellaceae RC9 gut group potentially influencing the fatty acid composition in backfat and muscle of the pig.
Article
Chemistry, Multidisciplinary
Jiuye Zhao, Yuanhang Zhang, Dapeng Xue, Chunyi Cui, Wenzheng Li, Fang Liu
Summary: The failure of the interfacial transition zone is identified as the main cause of damage in cement-based materials. The interfacial composite structures exhibit lower densities in the interfacial zones compared to the bulk. Different configurations of the interfacial composite structures display diverse nanomechanical behaviors.
Article
Chemistry, Multidisciplinary
Jin Han, Yosuke Iimure, Yukihiro Okamoto, Keishi Suga, Hiroshi Umakoshi
Summary: In this study, coassemblies of lipids and polyamidoamine amphiphilic dendrons (AD) were prepared using different generations and composition ratios of AD. It was found that the generation of AD significantly influenced the structure and hydration state of the coassemblies.
Article
Biochemistry & Molecular Biology
Jean L. L. Beltran, Lila G. G. McGrath, Sophia Caruso, Richara K. K. Bain, Claire E. E. Hendrix, Hana Kamran, Hartlee G. G. Johnston, Rebecca M. M. Collings, Menkara-Chinua N. Henry, Tsega-Ab L. Abera, Valeria A. A. Donoso, Erin C. C. Carriker, Bryan H. H. Thurtle-Schmidt
Summary: Borate transporters regulate intracellular borate levels, which are essential for plant growth but toxic in excess. In yeast, borate export confers tolerance. Despite sequence and solute differences, borate transporters share structural homology with human bicarbonate transporters in the SLC4 family. This study characterizes the yeast borate transporter Bor1p and demonstrates shared properties and critical amino acids with SLC4 transporters, providing insights into their mechanisms and functional similarities.
Article
Chemistry, Multidisciplinary
Vishal Maingi, Paul W. K. Rothemund
Summary: The study found that charge neutralization of DNA scaffolds was more important than the total hydrophobic content of their modifications in achieving bulk bilayer behavior. Additionally, complete charge neutralization of DNA scaffolds enabled better lipid binding and more stable bilayers. In conclusion, the simulations provide a guide for the design of DNA-scaffolded nanodiscs suitable for studying membrane proteins.
Article
Chemistry, Multidisciplinary
Hossein Moghimianavval, Chintan Patel, Sonisilpa Mohapatra, Sung-Won Hwang, Tunc Kayikcioglu, Yashar Bashirzadeh, Allen P. Liu, Taekjip Ha
Summary: InterSpy is introduced as a synthetic biology tool for engineering membrane-membrane interfaces. It allows tracking and reconstitution of functional fluorescent protein between apposing synthetic or cell membranes, demonstrating the potential for designing non-native cellular communication pathways and creating synthetic tissues. The technology is tested using a mammalian cell-free expression system and shows promising results.
Article
Chemistry, Physical
Farzad Khorrami, Mohammad H. Kowsari
Summary: This research uses molecular dynamics simulations to study the behavior of ionic liquids confined in nanopores. The results reveal heterogeneous local structures and dynamics, with significant differences depending on the position of the ions relative to the pore walls. The interaction between the ionic liquid and different wall materials, such as rutile and graphite, also affects the behavior of the confined system.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Review
Biochemistry & Molecular Biology
Jie Gao, Ruihan Hou, Long Li, Jinglei Hu
Summary: Integral or peripheral membrane proteins, or protein oligomers often interact closely on cell membranes and perform biological tasks collectively. In addition to electrostatic and van der Waals interactions, these proteins also experience membrane-mediated interactions, which are crucial for their functionality and originate from perturbation of lipid membranes by protein inclusions. This type of interaction has been the subject of intensive research in membrane biophysics, with both theoretical and numerical studies conducted for membrane proteins and nanoparticles bound to lipid membranes.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Chemistry, Multidisciplinary
Dmitry V. Averyanov, Ivan S. Sokolov, Igor A. Karateev, Alexander N. Taldenkov, Oleg E. Parfenov, Andrey M. Tokmachev, Vyacheslav G. Storchak
Summary: The study demonstrates that the structure of the oxide/Si interface does not depend on the type of the template, its symmetry, and stoichiometry. Chemical transformations of the templates converging into the same 2D product are detected in situ by electron diffraction, and the common interfacial structure of 1D periodicity is visualized by high-resolution electron microscopy.
ADVANCED FUNCTIONAL MATERIALS
(2021)
Article
Construction & Building Technology
Ratan K. Mishra, Krishan Kanhaiya, Jordan J. Winetrout, Robert J. Flatt, Hendrik Heinz
Summary: The article introduces an atomistic force field for all calcium sulfate phases that performs well in reproducing a wide range of experimental data and outperforms prior force fields and DFT methods. It provides new insights into (hkl) cleavage energies, water interface dynamics, and crystal-facet specific hydration and solubility, showing impressive agreement between computed and experimentally measured hydration energies.
CEMENT AND CONCRETE RESEARCH
(2021)
Article
Multidisciplinary Sciences
Zifan Ye, Aleksander Prominski, Bozhi Tian, Giulia Galli
Summary: This study focuses on investigating the behavior of hydrogenated Si surfaces in contact with water, with applications in transient electronics and photoelectrochemical modulation of biological cells and tissues. By using first principles molecular dynamics simulations and experimental measurements, they found that voltage-dependent capacitive currents are present at the Si/water interface, while Faradaic currents are weakly dependent on the applied bias due to surface defects in newly prepared samples.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Victor Vasquez-Montes, Vivek Tyagi, Eden Sikorski, Alexander Kyrychenko, J. Alfredo Freites, Damien Thevenin, Douglas J. Tobias, Alexey S. Ladokhin
Summary: The study investigates the effects of PS, Ca2+, and peptide protonation state on the interactions of pHLIP with lipid membranes. Cellular experiments demonstrate that exposed PS on the plasma membrane promotes pHLIP targeting and the magnitude of this effect depends on extracellular Ca2+ concentration. The mechanism of targeting is further explored through a combination of fluorescence and molecular dynamics simulations.
Article
Environmental Sciences
Xianghao Meng, Duoji Luosang, Shujuan Meng, Rui Wang, Wenhong Fan, Dawei Liang, Xiaohu Li, Qian Zhao, Linyan Yang
Summary: The spatial configuration of polysaccharide foulant is significant in membrane fouling, controlling the resistance of gel layer formed on the membrane. Polysaccharides with different properties show distinct fouling mechanisms in accordance with Hermia's models. Cations may change the interaction of polysaccharide foulant, leading to structural changes in the gel layer.
Review
Biochemistry & Molecular Biology
Rebekah Rakotonirina-Ricquebourg, Vitor Costa, Vitor Teixeira
Summary: Lipid droplets (LDs) are crucial organelles involved in various cellular processes and linked to health and disease. Membrane contact sites play a key role in controlling lipid exchange and important cellular functions.
PROGRESS IN LIPID RESEARCH
(2022)
Article
Biophysics
Hayato Takase, Keishi Suga, Hideki Matsune, Hiroshi Umakoshi, Koichiro Shiomori
Summary: In this study, chiral selective adsorption of L-amino acid tryptophan was achieved using phospholipid membrane-coated porous polymer particles. The results showed that the phospholipid membrane-coated particles exhibited similar properties to lipid membranes, and demonstrated significant adsorption of L-Trp. The deposited phospholipid membranes on the particles acted as chiral selectors for L-Trp, leading to improved adsorption performance and potential application in chiral separation.
COLLOIDS AND SURFACES B-BIOINTERFACES
(2022)
Article
Biotechnology & Applied Microbiology
Nimatul Izza, Nozomi Watanabe, Yukihiro Okamoto, Yusuf Wibisono, Hiroshi Umakoshi
Summary: This study successfully encapsulated polyphenols with antioxidant activity using nanostructured lipid carriers as a drug delivery system. The results demonstrate that the polyphenols-incorporated NLCs exhibit good performance in terms of particle stability, drug loading capacity, and antioxidant activity.
JOURNAL OF BIOSCIENCE AND BIOENGINEERING
(2022)
Article
Engineering, Chemical
Diyana Kamarudin, N. Awanis Hashim, Boon Hoong Ong, Miftah Faried, Keishi Suga, Hiroshi Umakoshi, Wan Adibah Wan Mahari
Summary: This study utilizes silver nanoparticles incorporated in PVDF membranes for membrane fouling analysis. The quantification of foulant using Raman spectroscopy and thermogravimetric analysis shows the occurrence of fouling phenomena on the membrane. The presence of AgNPs effectively reduces fouling and enhances surface enhancement in Raman spectroscopy analysis.
JOURNAL OF MEMBRANE SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Yukihiro Okamoto, Kaito Hamaguchi, Mayo Watanabe, Nozomi Watanabe, Hiroshi Umakoshi
Summary: Lipid membranes form nanodomains with heterogeneous properties that play significant roles in various cell functions. However, the analysis of these nanodomains has been challenging due to their small size and limited height difference with the surrounding membrane. This study aimed to overcome these limitations by using solvatochromic dye and the phase mode of scanning probe microscopy (SPM). The combination method successfully provided information on the phase state of lipid membranes at both micro and macro scales, enabling analysis of heterogeneous lipid membranes.
Article
Nanoscience & Nanotechnology
Ni 'matul Izza, Nozomi Watanabe, Yukihiro Okamoto, Keishi Suga, Yusuf Wibisono, Naoko Kajimura, Kaoru Mitsuoka, Hiroshi Umakoshi
Summary: Nanostructured lipid carriers (NLCs) are a new generation of lipid vectors for drug delivery systems (DDSs) that have a complex structure composed of solid and liquid lipids. This study provides molecular and physicochemical characterizations of the NLC core region. The study found that NLCs have a more rigid shell and a less rigid core, and also exhibit a crystal-like lamellar structure. The concentration of solid lipids affects the structure of the NLCs. By adjusting the lipid composition, an optimized design of NLCs with high efficacy for DDSs can be achieved.
ACS APPLIED NANO MATERIALS
(2022)
Article
Chemistry, Multidisciplinary
Tomokazu Yasuda, Hirofumi Watanabe, Koichiro M. Hirosawa, Kenichi G. N. Suzuki, Keishi Suga, Shinya Hanashima
Summary: Exosomes are small extracellular vesicles involved in cell-cell communication and cancer migration. This study investigated the properties of exosome membranes and found that they have ordered phases and asymmetric topologies, possibly enriching raft-like functional domains.
Article
Chemistry, Multidisciplinary
Hayato Takase, Nozomi Watanabe, Koichiro Shiomori, Yukihiro Okamoto, Hideki Matsune, Hiroshi Umakoshi
Summary: This study investigates a two-step preparation method that combines the inverse Leidenfrost effect and cryogelation technique to prepare macroporous polymer particles. The method involves dropping polymer precursors into liquid nitrogen to create frozen droplets through the inverse Leidenfrost effect, followed by cryo-polymerizing the frozen droplets and preparing cryogel particles after thawing. The resulting macroporous polymer particles exhibit similar characteristics, with slight differences depending on the type of monomers used. The method has the potential to be used for the preparation and design of tailor-made macroporous polymer particles for various applications.
Article
Chemistry, Physical
Keita Hayashi, Hikaru Ota, Haruna Sugimura, Toshinori Shimanouchi, Tomoyuki Iwasaki, Sakiko Fujita, Hidemi Nakamura, Hiroshi Umakoshi
Summary: Aggregates of amphiphilic molecules can be used as drug carriers, and their properties can be modified by adding cholesterol. In this study, we investigated the effect of cholesterol on the formation and hydrophobicity of sorbitan surfactant aggregates. Cholesterol changed the formation process from micelles to vesicles and increased the hydrophobicity of the aggregates. The localization of embedded molecules was found to be related to the gradual increase in hydrophobicity.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Nanoscience & Nanotechnology
Ryota Kameda, Taisei Suzuki, Ikumi Kato, Keishi Suga, Kanako Watanabe, Kimiko Nagino, Kumiko Hayashi, Satoshi Arai, Daisuke Nagao
Summary: In recent years, many photothermal materials have been developed for efficient photothermal therapy. However, upsizing these materials for better performance hampers cellular uptake. To overcome this, an active control system was proposed to manipulate the assembly of magnetic composite particles (MCPs) at the cellular level. Different-sized MCPs were synthesized and their surfaces were modified, showing improved dispersibility and cellular uptake. The assembly and redispersal of MCPs were controlled using a direct current magnetic field (DCMF), leading to improved cytotoxicity under near-infrared laser irradiation.
ACS APPLIED NANO MATERIALS
(2023)
Review
Multidisciplinary Sciences
Thaaranni Bashkeran, Azlina Harun Kamaruddin, Trung Xuan Ngo, Kazuma Suda, Hiroshi Umakoshi, Nozomi Watanabe, Masrina Mohd Nadzir
Summary: Curcumin is widely used for cancer treatment, but its limited absorption and rapid excretion hinder its clinical use. Niosomes as a delivery system for curcumin can enhance its absorption and prolong its excretion, providing a potential solution. This review analyzes the cytotoxic effects, formulations, characterizations, and performance factors of curcumin niosomes, aiming to accelerate advances in the pharmaceutical, biotechnology, and medical industries.
Article
Chemistry, Physical
Keita Hayash, Hikaru Ota, Haruna Sugimura, Toshinori Shimanouchi, Tomoyuki Iwasaki, Sakiko Fujita, Hidemi Nakamura, Hiroshi Umakoshi
Summary: Aggregates of amphiphilic molecules can be used as drug carriers and their properties can be modified by mixing with other molecules such as cholesterol. Understanding the effects of such additives is crucial as they directly impact the material functions. This study investigates the effect of cholesterol on the formation and hydrophobicity of sorbitan surfactant aggregates, showing that cholesterol changes the formation and increases hydrophobicity, particularly in the middle regions.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Chemistry, Physical
Hayato Takase, Nozomi Watanabe, Koichiro Shiomori, Yukihiro Okamoto, Endang Ciptawati, Hideki Matsune, Hiroshi Umakoshi
Summary: Hydrophobic cryogel particles with monolithic supermacropores were prepared using poly-trimethylolpropane trimethacrylate (pTrim) by combining the inverse Leidenfrost effect and cryo-polymerization technique. The prepared particles demonstrated efficient separation of stabilized oil-in-water emulsion. Characterization of the particles showed a narrow size distribution and monolithic supermacroporous structure. The hydrophobicity of the particles was confirmed by the selective adsorption of organic droplets.
COLLOIDS AND INTERFACES
(2023)
Article
Nanoscience & Nanotechnology
Keishi Suga, Makina Murakami, Shota Nakayama, Kanako Watanabe, Sayuri Yamada, Toshikazu Tsuji, Daisuke Nagao
Summary: Polymer nanoparticles, specifically cationic polystyrene (PSt) nanoparticles synthesized via soap-free emulsion polymerization, were investigated for their surface properties and antibacterial activity. It was found that PSt nanoparticles with larger affinity values (K) exhibited antibacterial activity against Staphylococcus epidermidis. These nanoparticles disrupted the bilayer structure of model membranes, indicating their potential as contact-killing antibacterial agents.
ACS APPLIED BIO MATERIALS
(2022)