Article
Physics, Nuclear
Satyabrata Datta, Ambar Ghosal
Summary: The study proposes a model of neutrino mass matrix based on the type-II Seesaw mechanism and concept of badly broken symmetry, with the addition of an extra doublet and use of the Zee mechanism for neutrino mass generation. This modified model can accommodate all existing data by selecting suitable model parameters.
JOURNAL OF PHYSICS G-NUCLEAR AND PARTICLE PHYSICS
(2021)
Article
Chemistry, Organic
Ling Lin, Wang Jian, Li Jing, Li Yuxue, Lu Long
Summary: Homolytic cleavage is a common process in the pyrolysis of energetic molecules. This study investigated the pyrolysis pathways of 3-nitro-1,2,4-triazol-5-one (NTO) using density functional theory. The results showed that the best pathway involves the homolytic cleavage of the C-NO2 bond followed by radical recombination, leading to the formation of HNCO, N-2O, and CO. Further reactions between these small molecules result in the production of NO2, N-2, and CO2, consistent with experimental observations.
CHINESE JOURNAL OF ORGANIC CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
John P. Perdew, Adrienn Ruzsinszky, Jianwei Sun, Niraj K. Nepal, Aaron D. Kaplan
Summary: Strong correlations within a symmetry-unbroken ground-state wavefunction may manifest in approximate density functional theory as symmetry-broken spin densities or total densities, arising from soft modes of fluctuations such as spin-density or charge-density waves. An approximate density functional that breaks symmetry can be more revealing than an exact functional that does not, with examples including the stretched H-2 molecule, antiferromagnetic solids, and the static charge-density wave/Wigner crystal phase of a low-density jellium. Time-dependent density functional theory quantitatively shows that the static charge-density wave is a soft plasmon, with the frequency of a related density fluctuation dropping to zero.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Izumi Ishigami, Raymond G. Sierra, Zhen Su, Ariana Peck, Cong Wang, Frederic Poitevin, Stella Lisova, Brandon Hayes, Frank R. Moss, Sebastien Boutet, Robert E. Sublett, Chun Hong Yoon, Syun-Ru Yeh, Denis L. Rousseau
Summary: Cytochrome c oxidase (CcO) is a crucial enzyme in cellular respiration, and plays important roles in the oxidative and reductive phases. The research findings indicate that the active site of the O state in CcO, similar to the O-H state, is coordinated by a hydroxide ion and a water molecule. However, a key difference lies in the protonated form of the critical amino acid Y244, which distinguishes O from O-H. These structural characteristics provide valuable insights into the proton translocation mechanism of CcO.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Jake X. Shi, Nicodemo R. Ciccia, Subhajit Pal, Diane D. Kim, John N. Brunn, Carlos Lizandara-Pueyo, Martin Ernst, Alexander M. Haydl, Phillip B. Messersmith, Brett A. Helms, John F. Hartwig
Summary: In this study, strategies for derivatizing oxidized polyethylene with functional groups were described. The presence of ketones and alcohols in the polyethylene were controlled through different catalytic reactions. The introduction of esters and oximes onto the polymer improved its surface and bulk properties. The functionalized polymers were separated from plastic blends through selective dissolution, demonstrating the potential for novel approaches in polymer separation.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Review
Multidisciplinary Sciences
Yifeng Xiang, Qingjin Luo, Siqi Yang, Kaiyuan Zhang
Summary: The halo phenomenon in exotic nuclei has been a major focus in nuclear physics research since it was discovered in 1985. The covariant density functional theory has proven to be an effective tool in understanding the microscopic properties of halo nuclei. This theory has been successfully applied to study both spherical and deformed halo nuclei, and recently, a triaxial version of the theory has been developed and applied to investigate halos in triaxially deformed nuclei.
Article
Multidisciplinary Sciences
Chia-Shin Yang, Tzu-Ping Ko, Chao-Jung Chen, Mei-Hui Hou, Yu-Chuan Wang, Yeh Chen
Summary: The authors present the structural and functional characterization of bacterial CD-NTases that synthesize cyclic dipyrimidines for phage resistance. They reveal a motif dictating pyrimidine selection and propose a sequential pathway for synthesizing cyclic di-UMP. These findings provide important insights into bacterial defense mechanisms and cellular regulation.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Quan V. Vo, Nguyen Thi Hoa, Nguyen Minh Thong, Pham Cam Nam, Duong Tuan Quang, Nguyen Khoa Hien, Adam Mechler
Summary: Novel tetrahydrofuran lignans from Anogeissus rivularis show potential antioxidant effects and can be used for medicinal purposes in diseases associated with oxidative stress. A detailed analysis of their antioxidant activity in different media reveals that their hydroperoxyl radical trapping activity is higher in polar media compared to nonpolar media.
NEW JOURNAL OF CHEMISTRY
(2023)
Article
Nanoscience & Nanotechnology
Songlin Li, Min Zhang, Youqiang Dong, Jie Gao, Pengfei Cheng, Hai Wang
Summary: This study used density functional theory calculations to investigate the sensing properties of P-doped Co3O4(111) surface towards volatile organic compounds (VOCs). The results showed that P doping can change the surface electronic distribution, enhance the charge transfer of formaldehyde, and increase the adsorption energy of other molecules, thus improving the sensing properties.
ACS APPLIED NANO MATERIALS
(2023)
Article
Energy & Fuels
Chunhua Zhang, Jiahui Shen, Ji Li, Mei Wan
Summary: By studying the inhibition mechanism of different chloride salts on the spontaneous combustion of coal, it was found that different chloride salts have different inhibitory effects at different stages, and magnesium chloride participates in the entire coal-oxygen reaction process.
Article
Computer Science, Interdisciplinary Applications
Hsuan Ming Yu, Amartya S. Banerjee
Summary: This study presents a real-space formulation and implementation of Kohn-Sham Density Functional Theory for twisted geometries, and applies it to the study of torsional deformations of nanotubes. The authors discuss different aspects of the computational method, including the governing equations, numerical implementation, convergence, accuracy, and efficiency properties. The technique is shown to be well suited for simulating quasi-one-dimensional structures and their deformations, and can provide valuable insights into the mechanical behavior and electronic properties of nanomaterials.
JOURNAL OF COMPUTATIONAL PHYSICS
(2022)
Article
Chemistry, Physical
Xingzhu Chen, Luigi Cavallo, Kuo-Wei Huang
Summary: In the past decade, density functional theory (DFT) calculations have been used to investigate the mechanism of electrochemical CO2 reduction reactions. However, the lack of understanding regarding CO2 chemisorption states, proton-coupled-electron-transfer (PCET) steps, and dynamic redox reactions of the electrode surface has limited the reliability of these simulations. This work proposes a descriptor, the energy difference between *COOH on neutral and extra-electron substrates, as a means to determine the selectivity of electrochemical CO2 reduction.
Article
Chemistry, Physical
Xiang Xu, Yang You, Xingyu Liu, Dafu Wei, Yong Guan, Anna Zheng
Summary: The study found that 0.1-0.5 wt% of multi-wall carbon nanotubes can prevent the auto-oxidation degradation of fluorosilicone rubber by scavenging alkyl radicals, showing antioxidant effect. Density functional theory calculations revealed that carbon nanotubes are an open-shell system capable of reacting with highly reactive radicals.
Article
Neurosciences
Shunshun Cui, Ping Jiang, Yan Cheng, Huanhuan Cai, Jiajia Zhu, Yongqiang Yu
Summary: Previous literature has shown that there are sex differences in behavioral inhibition and its neural substrates. This study aimed to investigate whether there are sex-dependent associations between behavioral inhibition and resting-state brain function, and how they are modulated by molecular mechanisms. The authors used resting-state functional MRI data to compute functional connectivity density (FCD) and examined its associations with behavioral inhibition ability in a large cohort of healthy young adults. They found a significant negative correlation between behavioral inhibition and FCD in the left superior parietal lobule in females but not in males. Further analyses revealed that the neural correlates of behavioral inhibition were associated with gene expression and neurotransmitter atlases, particularly those related to the cerebral cortex and the serotonergic system. These findings provide important insights into the molecular mechanisms underlying the female-specific neural substrates of behavioral inhibition, and shed light on the contribution of biological sex to variation in behavioral inhibition and its related disease risk.
Article
Engineering, Chemical
Solmaz Valizadeh, Leila Naji, Mohammad Karimi, Saeedeh Sarabadani Tafreshi, Bas Heijman, Nora H. de Leeuw
Summary: The study demonstrates that double-oxidized GO membranes exhibit higher water flux and antifouling properties compared to regular GO membranes, which show a significant decrease in separation performance over time.
CHEMICAL ENGINEERING RESEARCH & DESIGN
(2022)
Article
Chemistry, Physical
Zirui Zhang, Clarisse G. Ricci, Chao Fan, Li-Tien Cheng, Bo Li, J. Andrew McCammon
Summary: The hybrid approach combines the Monte Carlo method, a variational implicit-solvent model (VISM), and a binary level-set method for simulating biomolecular binding in an aqueous solvent. It estimates the solvation free energy for the biomolecular complex by minimizing the VISM free-energy functional, accurately predicting the electrostatic part of the solvation free energy by shifting the dielectric boundary. The new and fast binary level-set method allows for this functional minimization in each MC move.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Multidisciplinary Sciences
Terra Sztain, Thomas G. Bartholow, D. John Lee, Lorenzo Casalino, Andrew Mitchell, Megan A. Young, Jianing Wang, J. Andrew McCammon, Michael D. Burkart
Summary: Enzymes in metabolic pathways utilize a variety of regulatory mechanisms to maintain homeostasis, with carrier proteins playing an essential role in substrate shuttling. A unique communication mechanism between ACP and partner enzymes has been demonstrated, showing allosteric regulation dependent on fatty acid chain length. These findings provide insights into cargo communication by ACP and can potentially be used for engineering carrier protein-dependent pathways for specific products.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Chemistry, Physical
Surl-Hee Ahn, Sanbo Qin, Jason Z. Zhang, J. Andrew McCammon, Jin Zhang, Huan-Xiang Zhou
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Multidisciplinary
Terra Sztain, Surl-Hee Ahn, Anthony T. Bogetti, Lorenzo Casalino, Jory A. Goldsmith, Evan Seitz, Ryan S. McCool, Fiona L. Kearns, Francisco Acosta-Reyes, Suvrajit Maji, Ghoncheh Mashayekhi, J. Andrew McCammon, Abbas Ourmazd, Joachim Frank, Jason S. McLellan, Lillian T. Chong, Rommie E. Amaro
Summary: Through simulations, the study reveals the mechanism of spike protein receptor binding domain (RBD) opening in SARS-CoV-2 infection, highlighting the crucial role of N-glycan in facilitating RBD opening. This research represents a milestone in ensemble pathway simulations and provides a foundation for understanding the fundamental mechanisms of viral entry and infection.
Article
Multidisciplinary Sciences
Surl-Hee Ahn, Christian Seitz, D. Vinicius Wilian Cruzeiro, J. Andrew McCammon, W. Andreas Gotz
Summary: Cytochrome bd -type quinol oxidase is a crucial metalloenzyme for bacteria survival in low oxygen conditions, making it a promising drug target. This enzyme is present in various pathogenic bacteria like Mycobacterium tuberculosis, Vibrio cholerae, Pseudomonas aeruginosa, and Campylobacter jejuni. Parameters for Escherichia coli bd oxidase have been developed for molecular dynamics simulations, providing useful data for drug discovery and research.
Article
Chemistry, Physical
Surl-Hee Ahn, Anupam A. Ojha, Rommie E. Amaro, J. Andrew McCammon
Summary: Gaussian-accelerated molecular dynamics (GaMD) and weighted ensemble (WE) methods have their own advantages but also limitations, therefore combining these two methods can sample both the potential energy landscape and kinetic properties of a system more accurately and quickly.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Multidisciplinary Sciences
Varnavas D. Mouchlis, Daiki Hayashi, Alexis M. Vasquez, Jian Cao, J. Andrew McCammon, Edward A. Dennis
Summary: Lipoprotein-associated phospholipase A(2) (Lp-PLA(2)) associates with lipoproteins in human plasma and hydrolyzes oxidized phospholipids. The mechanism of enzyme-membrane association and substrate specificity were studied using lipidomics and mass spectrometry techniques.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Thomas G. Laughlin, Amar Deep, Amy M. Prichard, Christian Seitz, Yajie Gu, Eray Enustun, Sergey Suslov, Kanika Khanna, Erica A. Birkholz, Emily Armbruster, J. Andrew McCammon, Rommie E. Amaro, Joe Pogliano, Kevin D. Corbett, Elizabeth Villa
Summary: This study identifies a protein called ChmA as the main component of the bacteriophage nuclear shell. The structure and dynamics of the ChmA shell provide insights into its formation and functions.
Article
Biochemistry & Molecular Biology
Surl-Hee Ahn, Gary A. Huber, J. Andrew McCammon
Summary: Intrinsically disordered proteins (IDPs) have attracted significant attention due to their involvement in biological processes and diseases. Computational studies using Brownian dynamics (BD) simulations with a coarse-grained force field for proteins (COFFDROP) have been conducted to complement experimental work. The researchers found that IDPs' properties, such as hydrodynamic radii and entanglement indices, are influenced by salt concentration.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Joshua C. Corpuz, Ashay Patel, Tony D. Davis, Larissa M. Podust, J. Andrew McCammon, Michael D. Burkart
Summary: This study reveals the binding specificities between peptidyl carrier proteins (PCPs) and adenylation (A) domains in non-ribosomal peptide synthetases (NRPSs) using chemical biology approaches. The research also demonstrates the possibility of controlling PCP binding specificity through modifying interfacial interactions.
ACS CHEMICAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Yohei Takahashi, Krystal C. Bosmans, Po -Kai Hsu, Karnelia Paul, Christian Seitz, Chung-Yueh Yeh, Yuh-Shuh Wang, Dmitry Yarmolinsky, Maija Sierla, Triin Vahisalu, J. Andrew McCammon, Jaakko Kangasjaervi, Li Zhang, Hannes Kollist, Thien Trac, Julian I. Schroeder
Summary: The rise in atmospheric CO2 concentration affects stomatal closing in plants, impacting transpirational water loss, photosynthesis, and growth. This study identifies MPK4/12 and HT1 as the primary CO2 sensors in plants, located upstream of the CBC1 kinase. These findings are significant for understanding the plant response to CO2.
Article
Biochemistry & Molecular Biology
Jui-Hung Weng, Wen Ma, Jian Wu, Pallavi Kaila Sharma, Steve Silletti, J. Andrew McCammon, Susan Taylor
Summary: Mutations in LRRK2 increase the risk of Parkinson's disease, and its pathological functions are often associated with abnormal kinase activity. This study combines enhanced sampling simulations with HDX-MS to investigate the dynamic changes and allosteric communications within the C-terminal domains of LRRK2. It is found that different types of kinase inhibitors stabilize distinct kinase conformations and modulate the interdomain interactions between the kinase and GTPase domains.
ACS CHEMICAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Terra Sztain, Joshua C. Corpuz, Thomas G. Bartholow, Javier O. Sanlley Hernandez, Ziran Jiang, Desirae A. Mellor, Graham W. Heberlig, James J. La Clair, J. Andrew Mccammon, Michael D. Burkart
Summary: Carrier-protein-dependent metabolic pathways rely on protein-protein interactions to control enzyme reactivity and timing. Computational methods, such as the improved Rosetta score function, can be used to design customized pathways by optimizing protein-protein interactions. This method provides a promising platform for engineering carrier-protein-dependent pathways.
ACS CHEMICAL BIOLOGY
(2023)
Article
Physics, Applied
Marcus T. Hock, Abigail E. Teitgen, Kimberly J. McCabe, Sophia P. Hirakis, Gary A. Huber, Michael Regnier, Rommie E. Amaro, J. Andrew McCammon, Andrew D. McCulloch
Summary: dATP, a natural analog of ATP, has been shown to enhance cardiac function. In this study, computational modeling was used to investigate the mechanism by which dATP accelerates calcium re-uptake into the sarcoplasmic reticulum during cardiac relaxation. The results showed that dATP interacts with SERCA and increases calcium association rate constants, ultimately leading to accelerated calcium transient decay observed experimentally.
JOURNAL OF APPLIED PHYSICS
(2023)
Article
Chemistry, Physical
Christian Seitz, Ilker Deveci, J. Andrew McCammon
Summary: This study investigates how protein glycosylation and lateral crowding effects modulate the stability and dynamics of influenza neuraminidase. The results show that glycans stabilize the protein structure, while a crowded membrane environment encourages large-scale conformational changes.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)