Article
Mathematics, Applied
Andrew Cleary, Jacob Page
Summary: This paper presents a new method for systematically exploring the free-energy landscape in the study of superfluids. It discovers new equilibrium states and evaluates the likelihood of observing certain states in experiments. Additionally, it investigates the dynamics near the minimizing state.
Article
Chemistry, Physical
Ruinan Li, Qingsong Liu, Rupeng Zhang, Yaqi Li, Yulin Ma, Hua Huo, Yunzhi Gao, Pengjian Zuo, Jiajun Wang, Geping Yin
Summary: This study presents a novel design of passivation-free magnesium alloy anode for high-energy-density magnesium/sulfur batteries. By utilizing an alloy with lithium that undergoes a substitution reaction with magnesium ions in the electrolyte, the passivation reaction on the anode is hindered, resulting in improved interfacial reaction kinetics and reduced impedance. The magnesium/sulfur battery with this passivation-free Mg-Li alloy anode achieves an enhanced discharge voltage platform and higher energy density.
ENERGY STORAGE MATERIALS
(2022)
Article
Multidisciplinary Sciences
Korak Kumar Ray, Colin D. Kinz-Thompson, Jingyi Fei, Bin Wang, Qiao Lin, Ruben L. Gonzalez
Summary: Biomolecular machines utilize thermal and chemical energy to perform cellular processes, and they require dynamic rearrangements of structural components. The physical and structural mechanisms through which ligands achieve repurposing of these dynamics remain unknown.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Materials Science, Ceramics
T. Odagaki, Y. Saruyama, T. Ishida
Summary: The free energy landscape is reorganized with temperature modulation, impacting the relaxation process and physical properties. The relaxation time of dielectric response depends on the relaxation of the FEL, converging to equilibrium in the long term. In temperature modulation spectroscopy, the dynamics are influenced by the relaxation time of FEL.
JOURNAL OF NON-CRYSTALLINE SOLIDS
(2021)
Review
Biochemistry & Molecular Biology
Lin Deng, Xiaofeng Han, Ziping Wang, Xiaowei Nie, Jinsong Bian
Summary: This review summarizes the research on the classification, biogenesis, biological functions, and molecular mechanisms of noncoding RNA transcripts involved in pulmonary vascular remodeling in pulmonary hypertension (PH). It highlights the utility and challenges of using these noncoding RNAs as biomarkers and therapeutics in PH.
Article
Biochemistry & Molecular Biology
Hisashi Ishida, Hidetoshi Kono
Summary: Nucleosome reconstitution is crucial for cellular functions, and the displacement of the H2A-H2B dimer is a key step. In this study, adaptive biased molecular dynamics and umbrella sampling simulations were used to investigate the free energy landscape of the dimer displacement. The docking domain of H2A and the C-terminal of H4 were identified as the main contributors to the free energy. The extent of nucleosomal DNA wrapping determined the different paths for the dimer displacement, suggesting that external factors such as histone chaperones can modulate the displacement path. Additionally, key residues involved in the free energy were found to be related to nucleosome assembly, reassembly, and posttranslational modifications (PTMs) in cancer cells.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Richard Giege, Gilbert Eriani
Summary: tRNAs play a crucial role in ribosome-dependent protein synthesis and their accuracy relies on specific identity elements within tRNA molecules. Although the understanding of these identity elements has expanded, the increasing number of reported functional differences has caused confusion. Furthermore, other processes involving tRNAs have been discovered, revealing multiple novel identities on the same tRNA molecule. This review highlights the mechanistic and evolutionary aspects of tRNA and tRNA-like identities, as well as new methods for identifying multiple identities on a single tRNA.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Abrahan Hernandez-Hernandez, Tayde Lopez-Santaella, Aranxa Torres-Caballero, Amarantha Serrato, Ulises Torres-Flores, Diego Montesinos-Valencia, Fernando Chico-Ponce De Leon, Vicente Gonzalez-Carranza, Samuel Torres-Garcia, Rosa Rebollar-Vega, Inti Alberto De la Rosa-Velazquez, Rosario Ortiz, Monserrat Perez-Ramirez, Normand Garcia-Hernandez, Antonio Garcia-Mendez, Francisco Arenas-Huertero
Summary: Central nervous system tumors are common in childhood and contribute to cancer-related mortality. This study explored the transcriptomic landscape of pediatric astrocytoma, focusing on the genetic alterations associated with tumorigenesis. The findings provide insights into the biological functions and pathways involved in astrocytoma, and establish a transcriptional signature for identifying different grades of the tumor.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Chak Kui Wong, Jonathan P. K. Doye
Summary: Molecular simulations using coarse-grained models provide insights into the structure, dynamics, and mechanics of DNA origamis. In this study, the focus is on the free-energy landscape of a jointed DNA origami, where the predicted results differ from experimental observations, possibly due to assembly defects affecting the ensemble of structures.
APPLIED SCIENCES-BASEL
(2022)
Article
Chemistry, Physical
Yu-Chen Wei, Liang-Yan Hsu
Summary: This article demonstrates that quantum electrodynamic (QED) effects can significantly enhance the rate of electron transfer (ET) without the use of cavities. By incorporating the effect of infinite one-photon states into Marcus theory and introducing the concept of electron transfer overlap, the study provides new insights into the involvement of cavity-free QED effects in ET reactions.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Multidisciplinary Sciences
Julie Livingstone, Yu-Jia Shiah, Takafumi N. Yamaguchi, Lawrence E. Heisler, Vincent Huang, Robert Lesurf, Tsumugi Gebo, Benjamin Carlin, Stefan Eng, Erik Drysdale, Jeffrey Green, Theodorus van der Kwast, Robert G. Bristow, Michael Fraser, Paul C. Boutros
Summary: The study integrates telomere length, genomics, transcriptomics and proteomics in localized prostate cancer, revealing the links between telomere maintenance, disease drivers and clinical outcomes. Shorter tumor telomere lengths are associated with elevated genomic instability and genes involved in cell proliferation and signaling, while longer telomere lengths in non-tumor samples are associated with a lower rate of biochemical relapse.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Yu-Cheng Liu, Dah-Yen Yang, Sheh-Yi Sheu
Summary: G-quadruplexes have become attractive drug targets in cancer therapy, but the polymorphic nature of their structures makes understanding their conformational conversion mechanisms challenging. This study used molecular dynamics simulation to show that as salt concentration increases, the mechanism of conformational conversion shifts from multi-pathway to sequential pathways, with conformational conversion being more feasible upon K+ binding compared to Na+ binding in high-salt solutions.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Biochemistry & Molecular Biology
Piroon Jenjaroenpun, Thidathip Wongsurawat, Taylor D. Wadley, Trudy M. Wassenaar, Jun Liu, Qing Dai, Visanu Wanchai, Nisreen S. Akel, Azemat Jamshidi-Parsian, Aime T. Franco, Gunnar Boysen, Michael L. Jennings, David W. Ussery, Chuan He, Intawat Nookaew
Summary: Traditional epitranscriptomics methods rely on antibody or chemical capture of RNA modifications, which may introduce experimental artifacts. A new approach using direct sequencing of native RNA with ONT technology accurately detects RNA base modifications and predicts RNA methylation sites with the ELIGOS bioinformatic tool. Identification of the DRACH motif in mRNA highlights the potential for detailed analysis of RNA modifications at the individual base level.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Kevin Lebrigand, Joseph Bergenstrahle, Kim Thrane, Annelie Mollbrink, Konstantinos Meletis, Pascal Barbry, Rainer Waldmann, Joakim Lundeberg
Summary: SiT is an explorative method for characterizing spatial isoform variation and sequence heterogeneity using long-read sequencing. It reveals regional isoform switching and identifies differential isoform usage in the mouse brain. SiT also provides an in-depth A-to-I RNA editing map of the adult mouse brain, and data exploration can be performed through an online resource.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Chemistry, Physical
Nayara Dantas Coutinho, Hugo Gontijo Machado, Valter Henrique Carvalho-Silva, Wender Alves da Silva
Summary: Recent studies have shown that hydroxide elimination and C = C bond formation in base-promoted aldol condensation significantly impact the overall reaction rate, contrary to the widely accepted first enolization or C-C bond formation steps. By applying theoretical models to the prototypical reaction of chalcone formation, researchers have revealed how a protic solvent and a slight increase in temperature can induce the second enolization as the rate-controlling step. Additionally, observations suggest that there may not be a single step with a notably higher energy barrier than others, challenging the concept of a specific rate-controlling step.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
