Article
Chemistry, Multidisciplinary
Kui Wang, Xin Meng, Xue-Jiao Zhang
Summary: In this study, calixpyridinium was identified as a suitable component for constructing an artificial dissipative system. By utilizing an alkali as the fuel, the structural evolution of the calixpyridinium-indigo carmine system from disorder to fibrous assembly was achieved via a dual visual dissipative pathway. Moreover, this method was successfully applied to mimic the alkaline biological molecule-driven dissipative process in real samples.
MATERIALS CHEMISTRY FRONTIERS
(2023)
Article
Chemistry, Multidisciplinary
Jose A. Sainz-Aja, Marcos Sanchez, Laura Gonzalez, Pablo Tamayo, Gilberto Garcia del Angel, Ali Aghajanian, Soraya Diego, Carlos Thomas
Summary: This research explores the valorisation of polyethylene waste as recycled fibres for reinforcement of concrete and achieves promising results. The findings indicate that the addition of these recycled fibres enhances the mechanical properties of concrete, particularly the tensile strength, and effectively controls cracking in concrete.
APPLIED SCIENCES-BASEL
(2022)
Article
Multidisciplinary Sciences
Tatsuya Ide, Asuka Koyama
Summary: Insect galls often have complex structures that are believed to be adaptive for the survival of insects. A unique internal structure was discovered in a new species of cynipid, Belizinella volutum, where the larval chamber can roll freely within the gall. Micro-computed tomography observations revealed the formation process of the gall.
SCIENTIFIC REPORTS
(2023)
Article
Physics, Applied
Chensen Lin, Shuo Chen, Lanlan Xiao, Dongxiao Zhao
Summary: Molecular combing allows for the investigation of single DNA molecules by immobilizing them on a solid surface using a moving water-air interface. This study utilized dissipative particle dynamics to model the deposition process and linearization of DNA molecules in a three-phase system with complex fluids. The research also explored the impact of substrate properties on combing results, proposing a chemical heterogeneous stripe-patterned substrate for better linearization.
JOURNAL OF APPLIED PHYSICS
(2022)
Article
Chemistry, Multidisciplinary
Willi R. Berg, Jonathan F. Berengut, Changzhuang Bai, Laura Wimberger, Lawrence K. Lee, Felix J. Rizzuto
Summary: In this study, we demonstrate a method to achieve dynamics in DNA nanostructures without DNA modification. By using protonated DNA strands and a small molecule pH regulator, we successfully assemble DNA origami into one-dimensional fibrils, which can be reversibly assembled and disassembled by visible light activation.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Multidisciplinary
Jie Deng, Wei Liu, Mo Sun, Andreas Walther
Summary: The development of synthetic non-equilibrium systems has opened doors for man-made life-like materials. Through ATP-driven dynamic covalent DNA assembly, we have successfully achieved ATP-fueled transient organization and ATP-fueled DNAzymes for substrate cleavage.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Construction & Building Technology
Cesare Signorini, Antonella Sola, Beatrice Malchiodi, Andrea Nobili
Summary: Synthetic fibers, especially polypropylene fibers, are being considered as a potential reinforcement for concrete due to their durability, affordability, and other properties. However, the chemical nature of polypropylene hampers the development of strong bonds with the concrete matrix, affecting the mechanical performance. To overcome this issue, researchers have chemically attacked or coated the fibers to enhance their affinity with the hydration products in the binder. The results show that surface functionalization, particularly nanosilica coating, improves the interaction between the binder and fibers, resulting in a significant increase in energy dissipation at failure. Additionally, these treatments induce a hardening response, contrasting with the softening behavior of low-dosage fiber-reinforced concrete.
JOURNAL OF MATERIALS IN CIVIL ENGINEERING
(2022)
Article
Microbiology
Sinil Kim, Hyerang Eom, Rutuja Nandre, Yeon Jae Choi, Hwayong Lee, Hojin Ryu, Hyeon-Su Ro
Summary: The variation of mitochondrial DNA in Lentinula edodes strains was investigated in this study. The results showed that the size variation of mtDNA was mainly due to the number of introns, repeated sequences, transposable elements, and plasmid-related sequences. The insertion and deletion of introns, as well as the presence of repetitive sequences and transposable elements, contributed to the dynamic evolution of mtDNA at the strain level. The findings highlight the importance of understanding mtDNA variation in eukaryotic cells.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemical Research Methods
Andrey V. Bzikadze, Pavel A. Pevzner
Summary: This study introduces UniAligner, a computational method that efficiently and accurately aligns extra-long tandem repeats, allowing for analysis of their variation and evolution. Traditional alignment approaches fail to adequately align these sequences, but UniAligner prioritizes matches of rare substrings, providing a better understanding of the evolutionary relationship between two sequences. The researchers apply UniAligner to estimate mutation rates in human centromeres, revealing high rates of large duplications and deletions, suggesting that centromeres may be among the most rapidly evolving regions of the human genome in terms of their structural organization.
Article
Biochemistry & Molecular Biology
Lucas C. Wheeler, Joseph F. Walker, Julienne Ng, Rocio Deanna, Amy Dunbar-Wallis, Alice Backes, Pedro H. Pezzi, M. Virginia Palchetti, Holly M. Robertson, Andrew Monaghan, Loreta Brandao de Freitas, Gloria E. Barboza, Edwige Moyroud, Stacey D. Smith
Summary: The relationship between gene function and substitution rates is crucial for understanding molecular evolution. Our study on the flavonoid pigment pathway in the Petunieae clade of the Solanaceae family reveals that transcription factors evolve faster, with MYB genes exhibiting the highest evolutionary rates. Despite weak correlations with changes in coding regions, there is a strong relationship between floral pigmentation shifts and the presence/absence patterns of MYB transcripts.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Engineering, Civil
Salvatore Lopez
Summary: A second-order accurate single-step time integration method is developed for nonlinear structural dynamics, incorporating algorithmic dissipation of higher modes and conservation of linear and angular momentum. The method consists of two phases, computing a solution point in the first phase and hypothesizing a correction in the second phase. The conservation of linear and angular momentum is imposed through a correction of the computed solution point, differentiating this integration scheme from others.
INTERNATIONAL JOURNAL OF STRUCTURAL STABILITY AND DYNAMICS
(2021)
Article
Multidisciplinary Sciences
Jae Young Lee, Heeyuen Koh, Do-Nyun Kim
Summary: This study presents a computational framework for analyzing the equilibrium and non-equilibrium dynamics of structured DNA assemblies. The framework successfully simulates the dynamic reconfiguration of DNA structures in response to changes in ion concentration. This research offers a rational method for designing responsive and reconfigurable DNA machines.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Jeong Ryeol Choi
Summary: The characteristics of nonextensivity for a general quantum dissipative oscillatory system in the SU(1,1) coherent states are investigated using the invariant operator method. The effects of nonextensivity on the parametric evolution of the SU(1,1) coherent states are elucidated. The advantage of the methodology which adopts the linear invariant operator is addressed by comparing the results with those of previous researches. The nonextensive behaviors associated with the fluctuations of canonical variables and the dissipation of quantum energy are analyzed in detail regarding their dependence on q. The properties of SU(1,1) coherent states adopted in this study can be utilized in quantum-information processes such as cloning, swapping, and teleportation of state information.
SCIENTIFIC REPORTS
(2022)
Article
Chemistry, Physical
Marcus Johansen, Johanna Xu, Pui Lam Tam, Leif E. Asp, Fang Liu
Summary: Structural batteries are multifunctional devices that store energy and carry mechanical load. This study explores the interaction between lithium and carbon fibers in polyacrylonitrile-based carbon fibers using Auger electron spectroscopy (AES). The distribution of lithium in the fiber is found to be influenced by charge/discharge rates, with slow rates resulting in uniform distribution and fast rates leading to lithium trapping in the fiber core. This research provides insights that can improve the performance of structural batteries and guide AES analysis of carbonaceous electrode materials.
APPLIED SURFACE SCIENCE
(2023)
Article
Biochemical Research Methods
Miyuki Sakuma, Xiao Wang, Felix Ellett, Jon F. Edd, Kehinde Adebayo Babatunde, Adam Viens, Michael K. Mansour, Daniel Irimia
Summary: Neutrophils are the most abundant white blood cells in circulation, capable of releasing NETs to capture microbes, and can release NETs in various pathological conditions. Measuring the concentration of NETs in blood is increasingly important for monitoring patients, assessing treatment efficacy, and understanding the pathology of different diseases.
Article
Chemistry, Multidisciplinary
Tyler M. Brown, Hassan H. Fakih, Daniel Saliba, Jathavan Asohan, Hanadi F. Sleiman
Summary: A barrier for biological applications of DNA structures is their instability to nucleases. This study explores the use of UV-mediated thymine dimerization to crosslink and stabilize DNA nanostructures. The researchers compare different methods of DNA irradiation and show that all approaches can achieve nuclease protection, but with varying levels of off-target crosslinking and damage. They also demonstrate a mild irradiation condition that enhances serum stability while maintaining DNA function. This methodology has potential applications in nucleic acid therapy and nanotechnology.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Multidisciplinary
Laura Wimberger, Felix J. Rizzuto, Jonathon E. Beves
Summary: We control the formation of dissipative assemblies built from DNA by using a merocyanine photoacid that responds to visible light. The operation and species distribution in our system are regulated by irradiation time, initial pH value, and the concentration of a small-molecule binder that inhibits the reaction cycle. This modular approach, which does not require DNA modification, can be applied to various DNA sequences and lengths. Our system design enables waste-free control of dissipative DNA nanotechnology, contributing to the development of nonequilibrium, life-like nanodevices.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Multidisciplinary
Aya Sakaya, Isabel O. L. Bacellar, Jose Luis Fonseca, Andres M. Durantini, Julia McCain, Laiyi Xu, Mariana Vignoni, Andres H. Thomas, Mauricio S. Baptista, Gonzalo Cosa
Summary: A sensitive fluorogenic probe is developed to quantify the arrival of singlet oxygen (1O2) on lipid membranes, allowing for the study of membrane dynamics. The probe shows remarkable intensity enhancement upon 1O2 trapping and enables the visualization of membrane expansion dynamics.
Article
Chemistry, Multidisciplinary
Muhammad Ghufran Rafique, Jacob M. M. Remington, Finley Clark, Haochen Bai, Violeta Toader, Dmytro F. F. Perepichka, Jianing Li, Hanadi F. F. Sleiman
Summary: The study focuses on the systematic research of polymer structure, pathway mechanism, and supramolecular morphology in order to assemble water-soluble block copolymers into two-dimensional structures. By using sequence-defined triblock DNA amphiphiles, the researchers successfully polymerized free-standing DNA nanosheets in water. They found that the alkyl chain core formed a cell membrane-like structure, and the distal pi-stacking chromophore block folded back to interact with the hydrophilic DNA block on the nanosheet surface. This interaction was crucial for sheet formation and showed sensitivity to DNA sequence. The findings open up possibilities for applications in cell sensing, nucleic acid therapeutic delivery, and enzyme arrays.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Multidisciplinary
Christophe Lachance-Brais, Mostafa Rammal, Jathavan Asohan, Adam Katolik, Xin Luo, Daniel Saliba, Antranik Jonderian, Masad J. Damha, Matthew J. Harrington, Hanadi F. Sleiman
Summary: DNA hydrogels are programmable and biocompatible materials that can respond to complex stimuli, making them valuable in various applications. However, the existing DNA hydrogels are soft and lack functionality. In this study, a DNA/small-molecule motif is used to create stiff hydrogels, reaching high storage modulus. These hydrogels have tunable mechanical properties, self-healing ability, and respond to multiple stimuli. They can be used for delivering antisense oligonucleotides and enhancing gene silencing efficacy. This work extends the capabilities of DNA hydrogels and provides promising materials for various applications.
Article
Chemistry, Multidisciplinary
Willi R. Berg, Jonathan F. Berengut, Changzhuang Bai, Laura Wimberger, Lawrence K. Lee, Felix J. Rizzuto
Summary: In this study, we demonstrate a method to achieve dynamics in DNA nanostructures without DNA modification. By using protonated DNA strands and a small molecule pH regulator, we successfully assemble DNA origami into one-dimensional fibrils, which can be reversibly assembled and disassembled by visible light activation.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Multidisciplinary
Sinan Faiad, Quentin Laurent, Alexander L. Prinzen, Jathavan Asohan, Daniel Saliba, Violeta Toader, Hanadi F. Sleiman
Summary: Nucleic acid therapeutics (NATs) are efficient tools for gene expression modulation and treating undruggable diseases. Spherical nucleic acids (SNAs) can effectively deliver small NATs to cells and protect them from degradation while improving biodistribution and reducing immune activation. Self-assembled SNAs, nanostructures made from a single DNA-polymer conjugate, have similar properties as small molecule encapsulation. A study on the factors that govern the fate of self-assembled SNAs reveals the importance of extracellular stability for recognition by membrane receptors and cellular uptake, as well as the requirement for intracellular dissociation for efficient therapeutic release. Disulfide-crosslinked SNAs combine these two properties and result in efficient and non-toxic gene silencing therapeutics. These findings will aid in the translation of self-assembled structures for in vivo gene silencing applications.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Multidisciplinary
Hugh P. Ryan, Zachary S. Fishman, Jacob T. Pawlik, Angela Grommet, Malgorzata Musial, Felix Rizzuto, James C. Booth, Christian J. Long, Kathleen Schwarz, Nathan D. Orloff, Jonathan R. Nitschke, Angela C. Stelson
Summary: The environment around a host-guest complex is determined by intermolecular interactions and plays a crucial role in their solubility and reaction rates. However, these interactions are difficult to detect with standard analytical techniques. In this study, we used microwave microfluidic measurements and principal component analysis to quantify the hydration and ion pairing of a coordination cage. The results showed that introducing guest molecules into the solution displaced the bound counterions and the solvent solubility of the guest had the greatest impact on the solvent and ion-pairing dynamics surrounding the host.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Multidisciplinary
Pierre Picchetti, Stefano Volpi, Maria Sancho-Albero, Marianna Rossetti, Michael D. Dore, Tuan Trinh, Frank Biedermann, Martina Neri, Alessandro Bertucci, Alessandro Porchetta, Roberto Corradini, Hanadi Sleiman, Luisa De Cola
Summary: Organosilica nanoparticles with responsive organic building blocks offer promising opportunities for drug formulation, biomolecule delivery, and diagnostics. In this study, the researchers combined nucleic acid interactions with sol-gel chemistry to create dynamic supramolecular bridging units in the silica-based nanoparticles. These nanoparticles exhibit programmable responses to temperature and biological inputs.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Polymer Science
Donatien de Rochambeau, Maciej Barlog, Felix J. Rizzuto, Quentin Laurent, Xin Luo, Kai Lin Lau, Hassan S. Bazzi, Hanadi F. Sleiman
Summary: The research focuses on the impact of monomer sequence on the self-assembly behavior of supramolecular materials. By precisely controlling the monomer sequence, the researchers demonstrate how small differences in sequence can lead to significant morphological changes, such as the formation of spheres or nanosheets. The ability to explore these subtle variations in polymer sequence enables the systematic study of supramolecular chemistry and the rational design of functional polymers.
Article
Chemistry, Multidisciplinary
Daniel Saliba, Xin Luo, Felix J. Rizzuto, Hanadi F. Sleiman
Summary: DNA nanotubes, built with high aspect ratio and encapsulation potential, have potential for various biological and materials applications. A systematic investigation was conducted to modulate the length, flexibility, and longitudinal patterns of wireframe DNA nanotubes through experimental and computational design. The design concepts enable fine-tuning of nanotube stiffness and may pave the way for the development of designer nanotubes for studying cellular internalization, biodistribution, and uptake mechanisms for structures of varied shapes and sizes.