Article
Chemistry, Physical
Nicholas A. Jose, Jithin John Varghese, Samir H. Mushrif, Hua Chun Zeng, Alexei A. Lapkin
Summary: The study focused on the effects of different solvent environments on the structure and aggregation dynamics of two-dimensional metal organic framework nanosheets, revealing that solvent-surface interactions can control oriented attachment and impact adsorption properties. Liquid cell transmission electron microscopy provided insights into these interactions, while density functional theory calculations suggested the role of binding energy in this behavior. The research highlights the potential of solvent-mediated mechanisms in manipulating the properties of MOF nanomaterials.
JOURNAL OF PHYSICAL CHEMISTRY C
(2021)
Article
Chemistry, Multidisciplinary
Zongguang Liu, Jiang Yan, Haiguang Ma, Tiancheng Hu, Junzhuan Wang, Yi Shi, Jun Xu, Kunji Chen, Linwei Yu
Summary: The study demonstrates a novel method for manufacturing silicon nanoprobes with sharp tips, which play a critical role in recording intracellular bioelectrical signals. These probes are economically manufactured with excellent mechanical properties and sensing functionality, showing strong potential to drive and expand market implementations of intracellular sensing, monitoring, and editing applications.
Article
Chemistry, Organic
Thibaut Duhail, Tommaso Bortolato, Javier Mateos, Elsa Anselmi, Benson Jelier, Antonio Togni, Emmanuel Magnier, Guillaume Dagousset, Luca Dell'Amico
Summary: A light-driven method for the alpha-trifluoromethoxylation of ketones has been developed, showing good generality and efficiency under batch and flow conditions. The method demonstrates the potential in accessing a variety of elusive trifluoromethoxylated bioactive ingredients.
Article
Chemistry, Physical
Maria A. Syzgantseva, Nikolay F. Stepanov, Olga A. Syzgantseva
Summary: This study investigated the impact of ligand functionalization on the nonradiative electron-hole recombination process in metal-organic framework systems, revealing that ligand modification influences recombination rates and the distribution of phonon modes.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Multidisciplinary Sciences
Jeng-Yuan Tsai, Jinbo Pan, Hsin Lin, Arun Bansil, Qimin Yan
Summary: The study identifies suitable defect centers in two-dimensional transition metal dichalcogenides and assesses their potential as solid-state spin qubits through high-throughput simulations. The authors show that these atomically thin materials offer a new platform for scalable qubit fabrication and operation at room temperature. The presence of neutral antisite defects in the transition metal dichalcogenides is found to enable controllable spin qubits with a paramagnetic triplet ground state.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Inorganic & Nuclear
Jing Sun, Fang Sun, Jiaqi Tang, Xiongkai Tang, Qingyuan Wu, Rong Huo, Ayisha He, Sachurilatu, Xueli Sun, Chaolumen, Qing Tang, Hui Shen
Summary: In this work, novel copper nanoclusters co-protected by carboxylic and thioate ligands were synthesized, and their structure and surface engineering were investigated. Despite having a similar molecular structure, the two clusters exhibited significant differences in optical properties, stability, and assembly structures, highlighting the potential of carboxylates in manipulating the physicochemical properties of copper nanoclusters. This study not only provides model clusters for further research on the structure-property relationship, but also sheds light on the future development of carboxylate-stabilized metal nanoclusters.
INORGANIC CHEMISTRY FRONTIERS
(2023)
Article
Chemistry, Physical
Nils Schewe, Robin Wagner, Matthias Franzreb, Peter Thissen
Summary: The study investigates the adsorption of charged maleic acid on a graphene sheet, demonstrating that including a water layer significantly alters the conformation of charged adsorbed molecules and enhances the overall stability of the system. The experimental validation of the computational results shows good agreement with the study's findings.
JOURNAL OF PHYSICAL CHEMISTRY C
(2021)
Article
Physics, Applied
Ti Xie, Qin Wang, Robert M. Wallace, Cheng Gong
Summary: Graphene sensors show promise in gas detection due to their excellent electrical properties and large surface-to-volume ratio. The response of graphene sensors to NO2 gas depends on the initial doping level, highlighting the importance of graphene conditions in sensor performance.
APPLIED PHYSICS LETTERS
(2021)
Article
Materials Science, Multidisciplinary
M. Tyunina, J. Levoska, O. Pacherova, T. Kocourek, A. Dejneka
Summary: Oxygen vacancies have unique impacts on lattice strain in epitaxial films of ABO(3) perovskite oxides, leading to increased inhomogeneity of lattice strain under external stress.
JOURNAL OF MATERIALS CHEMISTRY C
(2022)
Article
Physics, Applied
Dangqi Fang
Summary: The study found that electron-phonon coupling leads to a reduction in the indirect bandgap of MgSiN2, with calculated bandgap showing good agreement with experimental results when considering bandgap renormalization. Additionally, the predicted phonon-assisted optical absorption spectra show a redshift in absorption onset with increasing temperature.
JOURNAL OF APPLIED PHYSICS
(2021)
Article
Engineering, Electrical & Electronic
Ruobing Wang, Zhenhui Yuan, Xin Chen, Sannian Song, Zhitang Song
Summary: Phase change memory (PCM) has gained attention as a potential alternative to dynamic random access memory (DRAM). Hf addition in Sb2Te has been studied, showing that it can significantly enhance the crystallization temperature and retention temperature, as well as reduce the grain size. The PCM cell based on Hf-0.04(Sb2Te)0.96 demonstrates reversible switching and good endurance, indicating its potential for novel applications.
JOURNAL OF MATERIALS SCIENCE-MATERIALS IN ELECTRONICS
(2022)
Article
Chemistry, Physical
Wei Li, Alexey V. Akimov
Summary: For simulations using the repetition approximation, the state transition time scales may strongly depend on the length of the repeated data, and the repetition approach could under-or overestimate the time scales by a factor of <= 7-8. This dependence is not directly related to the dispersion of energy gap and nonadiabatic coupling frequencies, but may be influenced by the magnitude of the nonadiabatic couplings.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Multidisciplinary Sciences
M. Tyunina, O. Pacherova, T. Kocourek, A. Dejneka
Summary: The study demonstrates that oxygen vacancies in ABO(3) perovskite oxides primarily result in strong anisotropic strain in epitaxial thin films, rather than weak isotropic expansion in bulk samples. This anisotropic chemical strain is explained by the preferential orientation of elastic dipoles of the vacancies, which have critical impacts on the synthesis and response functions of the films.
SCIENTIFIC REPORTS
(2021)
Article
Chemistry, Physical
Gang Zhang, Honggang Liu, Zhiyu He, Baojun Chen
Summary: In this study, a nonspin-Hamiltonian method combining density functional theory (DFT)-based geometric optimization is used to accurately obtain the hyperfine structure and clock transitions of rare-earth ion-doped crystals. The results demonstrate that this approach can predict the hyperfine structure and clock transitions of these crystals accurately, which is important for designing and searching for quantum memory materials with longer coherence time.
JOURNAL OF PHYSICAL CHEMISTRY C
(2022)
Article
Chemistry, Multidisciplinary
Flor Maria Briceno-Vargas, Mariana Quesadas-Rojas, Gumersindo Miron-Lopez, David Caceres-Castillo, Ruben M. Carballo, Gonzalo J. Mena-Rejon, Ramiro F. Quijano-Quinones
Summary: This study investigates the n -> pi* interactions in amides and thioamides systems models through the analysis of electron density topology. The results suggest that dispersion forces play a significant role in the strength of these interactions.
Article
Biochemistry & Molecular Biology
Qingping Xu, Matthew Biancalana, Joanna C. Grant, Hsiu-Ju Chiu, Lukasz Jaroszewski, Mark W. Knuth, Scott A. Lesley, Adam Godzik, Marc-Andre Elsliger, Ashley M. Deacon, Ian A. Wilson
Article
Biochemistry & Molecular Biology
Monica Rosas-Lemus, George Minasov, Ludmilla Shuvalova, Zdzislaw Wawrzak, Olga Kiryukhina, Nathan Mih, Lukasz Jaroszewski, Bernhard Palsson, Adam Godzik, Karla J. F. Satchell
Article
Biochemical Research Methods
Mayya Sedova, Lukasz Jaroszewski, Arghavan Alisoltani, Adam Godzik
Review
Biochemistry & Molecular Biology
Eduard Porta-Pardo, Alfonso Valencia, Adam Godzik
Article
Biochemistry & Molecular Biology
Zhanwen Li, Lukasz Jaroszewski, Mallika Iyer, Mayya Sedova, Adam Godzik
NUCLEIC ACIDS RESEARCH
(2020)
Article
Multidisciplinary Sciences
Mallika Iyer, Zhanwen Li, Lukasz Jaroszewski, Mayya Sedova, Adam Godzik
Article
Biochemistry & Molecular Biology
George Minasov, Matthew R. Lam, Monica Rosas-Lemus, Joanna Slawek, Magdalena Woinska, Ivan G. Shabalin, Ludmilla Shuvalova, Bernhard O. Palsson, Adam Godzik, Wladek Minor, Karla J. F. Satchell
Article
Biochemistry & Molecular Biology
Youngchang Kim, Robert Jedrzejczak, Natalia I. Maltseva, Mateusz Wilamowski, Michael Endres, Adam Godzik, Karolina Michalska, Andrzej Joachimiak
Article
Biochemistry & Molecular Biology
Mayya Sedova, Lukasz Jaroszewski, Mallika Iyer, Zhanwen Li, Adam Godzik
Summary: There is a significant gap between the number of proteins characterized only by their amino acid sequence and those with structurally characterized by direct experiment. To bridge this gap, homology-based inference and modeling are used to predict the structures of uncharacterized proteins. The use of different templates with distinct structural flexibility can provide more informative results depending on the research questions.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Houriiyah Tegally, Eduan Wilkinson, Marta Giovanetti, Arash Iranzadeh, Vagner Fonseca, Jennifer Giandhari, Deelan Doolabh, Sureshnee Pillay, Emmanuel James San, Nokukhanya Msomi, Koleka Mlisana, Anne von Gottberg, Sibongile Walaza, Mushal Allam, Arshad Ismail, Thabo Mohale, Allison J. Glass, Susan Engelbrecht, Gert Van Zyl, Wolfgang Preiser, Francesco Petruccione, Alex Sigal, Diana Hardie, Gert Marais, Nei-Yuan Hsiao, Stephen Korsman, Mary-Ann Davies, Lynn Tyers, Innocent Mudau, Denis York, Caroline Maslo, Dominique Goedhals, Shareef Abrahams, Oluwakemi Laguda-Akingba, Arghavan Alisoltani-Dehkordi, Adam Godzik, Constantinos Kurt Wibmer, Bryan Trevor Sewell, Jose Lourenco, Luiz Carlos Junior Alcantara, Sergei L. Kosakovsky Pond, Steven Weaver, Darren Martin, Richard J. Lessells, Jinal N. Bhiman, Carolyn Williamson, Tulio de Oliveira
Summary: The article describes a newly emerged lineage of SARS-CoV-2, 501Y.V2, characterized by eight mutations in the spike protein, which may result in increased transmissibility or immune escape. This lineage originated in South Africa and quickly became dominant in Eastern Cape, Western Cape, and KwaZuluNatal provinces within weeks.
Article
Biochemistry & Molecular Biology
Isuru Karunatillaka, Lukasz Jaroszewski, Adam Godzik
Summary: A study investigated a PETase enzyme from environmental samples and its distribution in other bacterial communities, identifying similar homologs in JGI metagenomic datasets through BLAST searches. By verifying the protein sequences and conducting phylogenetic analyses, it confirmed that these proteins are putative PETases, and docking analysis further confirmed their functional assignment.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Lukasz Jaroszewski, Mallika Iyer, Arghavan Alisoltani, Mayya Sedova, Adam Godzik
Summary: The mutation patterns in the SARS-CoV-2 virus genomes are closely linked to the structure and function of the proteins they encode, with highly mutated regions corresponding to more easily adaptable structural regions. Understanding these patterns is important for developing tools like antibodies, vaccines, and drugs to target conserved genomic regions due to natural selection.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Cell Biology
Xinru Qiu, Jiang Li, Jeff Bonenfant, Lukasz Jaroszewski, Aarti Mittal, Walter Klein, Adam Godzik, Meera G. Nair
Summary: This study uses single-cell analysis to examine short-term temporal changes in immune cell populations in sepsis patients, finding that platelet and erythroid precursor responses are drivers of fatal sepsis. It also identifies dynamic effects in individual cell subsets, showing that hypoxic stress plays a key role in immune and metabolic dysfunction. Additionally, the study supports CD52 as a prognostic biomarker and therapeutic target for sepsis.
JOURNAL OF LEUKOCYTE BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Abraham Takkouche, Xinru Qiu, Mayya Sedova, Lukasz Jaroszewski, Adam Godzik
Summary: Leucine Rich Repeat (LRR) domains, present in various proteins, play important roles in protein-protein interactions and ligand recognition. The least characterized class of LRR proteins, TpLRR-like LRRs, have unique structural features and sequence patterns. These proteins are involved in interactions between human pathogens and the host immune system. This study analyzed the relation of conserved residues, specific structural features, and functions of these proteins using experimental structures and AlphaFold models.
JOURNAL OF STRUCTURAL BIOLOGY
(2023)
Meeting Abstract
Rheumatology
Matthew Linnik, Adam Godzik, Lukasz Jaroszewski, Carl Ware, Andrew Vendel
ARTHRITIS & RHEUMATOLOGY
(2019)