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作者： Pazderka, Tomáš Charles University of Prague

Title: Study of protein structure and dynamics by means of optical spectroscopy Author: Tomáš Pazderka Institute: Institute of Physics of Charles University Supervisor: RNDr. Vladimír Kopecký, Ph.D., Institute of Physics of Charles University Abstract: The aim of this thesis is to improve understanding of protein structure and dynamics and extend experimental setup and data processing for such stud- ies. We focus on the extension of experimental feasability of vibrational optical activity (VOA). We have demonstrated a usability of intensity calibration in the field of Raman optical activity. Advantages for measurements on multiple instru- ments and/or using different configurations have been shown. A new instrumental setup has been developed for microsampling measurements of vibrational circular dichroism spectra with a spatial resolution of 1 mm. Using this technique, spatial inhomogeneities in a sample of protein fibrils have been observed. Model com- pounds for amide nonplanarity have been investigated utilizing several methods of optical spectroscopy and key spectral features for determination of amide non- planarity and the absolute configuration have been identified. A comprehensive set of Raman spectra of proteinogenic amino acids has been measured. Sample concentration dependencies and consequent...

关键词： two-dimensional correlation spectroscopy peptides and proteins vibrational optical activity structure and dynamics

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Solution structure and dynamics of Xanthomonas albilineans Cas2 provide mechanistic insight on nuclease activity (vol 592, pg 147, 2018)

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FEBS LETTERS 2018年第4期592卷 655-655页

作者： Jeong, Migyeong Kim, Iktae Kim, Gowoon Ka, Donghyun Kim, Nak-Kyoon Bae, Euiyoung Ryu, Kyoung-Seok Suh, Jeong-Yong Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences Seoul National University Seoul Korea Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences Seoul National University Seoul Korea Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences Seoul National University Seoul Korea Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences Seoul National University Seoul Korea Advanced Analysis Center Korea Institute of Science and Technology Seoul Korea Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences Seoul National University Seoul Korea Protein Structure Research Team Korea Basic Science Institute Ochang Chungbuk Korea Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences Seoul National University Seoul Korea Institute for Biomedical Sciences Shinshu University Nagano Japan

Cas2 protein in the CRISPR-Cas system functions as a scaffold for the acquisition of foreign DNA fragments, and as a nuclease against DNA and RNA substrates. Crystal structures of Cas2 have shown catalytically inactive conformational states that do not explain the mechanism of Cas2 nuclease activity. Here, we report that Xanthomonas albilineans Cas2 (XaCas2) assumes an inactive conformation in solution. Residual dipolar couplings and NMR relaxation, however, provide direct evidence on conformational dynamics at the predicted hinge region. Furthermore, XaCas2 transiently associates with metal ions for nuclease activity via highly mobile Asp8. Taken together, the dual function of Cas2 can be explained by a dynamic equilibrium of conformational states that serve as a scaffold or as a nuclease on demand.

关键词： Cas2 nuclease activity structure and dynamics

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structure and dynamics of monohydroxy alcohols-Milestones towards their microscopic understanding, 100 years after Debye

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PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS 2014年第4期545卷 125-195页

作者： Boehmer, Roland Gainaru, Catalin Richert, Ranko Tech Univ Fac Phys D-44221 Dortmund Germany Arizona State Univ Dept Chem & Biochem Tempe AZ 85287 USA

In 1913 Debye devised a relaxation model for application to the dielectric properties of water and alcohols. These hydrogen-bonded liquids continue to be studied extensively because they are vital for biophysical processes, of fundamental importance as solvents in industrial processes, and in every-day use. Nevertheless, the way to a microscopic understanding of their properties has been beset with apparently conflicting observations and conceptual difficulties. Much of this remains true for water, but fortunately the situation for monohydroxy alcohols is different. Here, with the experimental progress witnessed in recent years and with the growing recognition of the importance of specific supramolecular structures, a coherent microscopic understanding of the structure and dynamics of these hydrogen-bonded liquids is within reach. (C) 2014 Elsevier B.V. All rights reserved.

关键词： Monohydroxy alcohols structure and dynamics Review

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Study of dynamics and structure in sodium silicate glasses. Molecular dynamics simulation

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JOURNAL OF NON-CRYSTALLINE SOLIDS 2022年 581卷 121398-121398页

作者： San, L. T. Yen, N., V Thao, N. T. Hung, P. K. Noritake, Fumiya Duy Tan Univ Inst Theoret & Appl Res Hanoi 100000 Vietnam Duy Tan Univ Fac Nat Sci Da Nang 550000 Vietnam Hanoi Natl Univ Educ Fac Phys Hanoi Vietnam Hanoi Univ Sci & Technol Inst Engn Phys Hanoi Vietnam Univ Yamanashi Grad Fac Interdisciplinary Res Kofu Yamanashi Japan

We conduct molecular dynamics simulations to study dynamics and structure of sodium silicate glasses through Voronoi polyhedron and diffusion path consisting of Ox-polyhedrons connected via XY-lines. The result shows that Six-polyhedrons and the number of Ox-polyhedrons do not contain Na. Most of NBFx-polyhedrons contain 1, 2 or not Na, where BO, NBF is the O bonded with 2 and 1 or not Si, respectively. Average volume per polyhedron increases in order: Six-polyhedron-* BOx-polyhedron-* NBFx-polyhedron. Na atoms are concentrated in NBFxpolyhedrons and frequently move through them leading to very fast diffusivity of Na in comparison with Si and O. The simulation shows that the number of neighbors around NBFx-polyhedron is larger than that around BOxpolyhedron. Major Na atoms move over BN-and NN-lines connecting with NBFx-polyhedrons. Moreover, Na atoms displace through the preferential diffusion path comprising mainly of NBFx-polyhedrons. The correlation effect is significant for sodium diffusion.

关键词： sodium-silicate Voronoi polyhedron structure and dynamics correlation effect preferential diffusion path

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Unveiling the Performance of SCAN Functional for Studying the Hydrated Ion in Solution: A Hybrid Forces Molecular dynamics Study of La³⁺ Hydration

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INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 2024年第21期124卷

作者： Prasetyo, Niko Univ Gadjah Mada Fac Math & Nat Sci Dept Chem Yogyakarta Indonesia

SCAN/molecular mechanics molecular dynamics (SCAN/MM MD) simulations have been employed to investigate the structural and dynamical properties of La3+ in aqueous solution. These simulations revealed the presence of two distinct hydration shells, with the first shell exhibiting a La-O bond distance of 2.56 & Aring;. The water molecules in this initial hydration shell displayed a mean residence time (MRT) of 208 ps, suggesting a less rigid structure. Five successful ligand exchange events occurred within a simulation duration of 100 ps. The stretching frequency of La-O was found to be 331 cm(-1), with a force constant of 92 N/m. Notably, the data obtained from the SCAN/MM MD simulation demonstrated good agreement with experimental findings.

关键词： La3+ molecular dynamics QM/MM SCAN functional structure and dynamics

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Study of Diffusion in Sodium Silicate Glass Using Molecular dynamics Simulation

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SILICON 2024年第15期16卷 5571-5581页

作者： Nhan, N. T. Lien, P. T. Kien, P. H. San, L. T. Hung, P. K. Hanoi Univ Sci & Technol Fac Engn Phys Hanoi Vietnam Hanoi Natl Univ Educ Fac Phys Hanoi Vietnam Thai Nguyen Univ Univ Educ Thai Nguyen Vietnam

Using molecular dynamics simulation on sodium silicate glass we have investigated the sodium motion through Voronoi Si and O polyhedrons. The result shows that Na atoms are almost not present in Si polyhedrons, and sodium number density in non-bridging oxygen and free oxygen polyhedrons is larger by 2.5 - 10.5 times than in bridging oxygen polyhedrons. The volume of space occupied by non-bridging oxygen and free oxygen polyhedrons varies from 25 to 66% of total volume of system. The simulation reveals that Na atoms move frequently along non-bridging oxygen and free oxygen polyhedrons and rarely along bridging oxygen polyhedrons. Moreover, they often leave and comeback to starting polyhedron. Such movement is responsible for decreasing the correlation factor F. The system contains unconnected sodium mobile regions which consists of polyhedrons connected with each other by preferential moving paths. With decreasing SiO2 content the system possesses long diffusion pathways. We have established the expression for sodium diffusion constant D via the rate of hops xi, average square distance per visiting polyhedron d2\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${d}<^>{2}$$\end{document} and factor F. We find that as the temperature or SiO2 content changes, the variation of F is significantly larger either than xi or d2\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${d}<^>{2}$$\end{document}. Moreover, the dependence of D on F is found linear.

关键词： Sodium-silicate Molecular dynamics simulation Voronoi polyhedron structure and dynamics Correlation effect

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High-resolution 2D solid-state NMR provides insights into nontuberculous mycobacteria

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SOLID STATE NUCLEAR MAGNETIC RESONANCE 2024年 134卷 101970页

作者： Byeon, Chang-Hyeock Hansen, Kasper Holst DePas, William Akbey, Uemit Univ Pittsburgh Sch Med Dept Struct Biol Pittsburgh PA 98195 USA Univ Pittsburgh Sch Med Dept Pediat Pittsburgh PA 15261 USA

We present a high-resolution magic-angle spinning (MAS) solid-state NMR (ssNMR) study to characterize nontuberculous mycobacteria (NTM). We studied two different NTM strains, Mycobacterium smegmatis, a model, non-pathogenic strain, and Mycobacterium abscessus, an emerging and important human pathogen. Hydrated NTM samples were studied at natural abundance without isotope-labelling, as whole-cells versus cell envelope isolates, and native versus fixed sample preparations. We utilized 1D(13)C and 2D H-1-C-13 ssNMR spectra and peak deconvolution to identify NTM cell-wall chemical sites. More than similar to 100 distinct C-13 signals were identified in the ssNMR spectra. We provide tentative assignments for similar to 30 polysaccharides by using well resolved H-1/C-13 chemical shifts from the 2D INEPT-based H-1-C-13 ssNMR spectrum. The signals originating from both the flexible and rigid fractions of the whole-cell bacteria samples were selectively analyzed by utilizing either CP or INEPT based C-13 ssNMR spectra. CP buildup curves provide insights into the dynamical similarity of the cell-wall components for NTM strains. Signals from peptidoglycan, arabinogalactan and mycolic acid were identified. The majority of the C-13 signals were not affected by fixation of the whole cell samples. The isolated cell envelope NMR spectrum overlap with the whole-cell spectrum to a large extent, where the latter has more signals. As an orthogonal way of characterizing these bacteria, electron microscopy (EM) was used to provide spatial information. ssNMR and EM data suggest that the M. abscessus cell-wall is composed of a smaller peptidoglycan layer which is more flexible compared to M. smegmatis, which may be related to its higher pathogenicity. Here in this work, we used high-resolution 2D ssNMR first time to characterize NTM strains and identify chemical sites. These results will aid the development of structure-based approaches to combat NTM infections.

关键词： Bacterial cell-wall Whole-cell MAS NMR spectroscopy Antimicrobial resistance Nontuberculous mycobacteria (NTM) cell envelope M. smegmatis M. abscessus structure and dynamics

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Solid-state NMR spectroscopy at ultrahigh resolution for structural and dynamical studies of MOFs

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Magnetic Resonance Letters 2023年第2期3卷 175-186,I0005页

作者： Qing Wang Min Peng Cong-Cong Liang Jing Tan Sophia Zhang Yue-Biao Zhang Haiming Liu School of Physical Science and Technology ShanghaiTech UniversityShanghai201210China Maling Middle School SuqianJiangsu223800China Washington University in St.Louis St.LouisMO63130USA

To characterize the structure and dynamics of metal--organic frameworks(MOFs)indepth at the molecular level,it is necessary to pursue high-resolution solid-state magic angle spinning(MAS)nuclear magnetic resonance(NMR)*** resolution is usually affected by the quality of materials and various experimental conditions,of which magic angle(MA)accuracy is a crucial *** current industrial criteria for MA calibration based on the common standard of KBr were found insufficient in guaranteeing optimal resolution MAS NMR for highly ordered *** drive towards higher-resolution MAS NMR spectroscopy,we propose_a calibration protocol for more accurate MA with a higher-precision criterion based on 79Br MAS NMR of KBr,where the linewidth ratio of the fifth-order spinning sideband to the central band of KBr should be less than *** a result,ultrahigh-resolution 13C cross-polarization(CP)MAS NMR of MOF-5 is achieved with minimal linewidths as low as 4 Hz,and therefore MOF-5 can be used as a new standard convenient for verifying MA accuracy and also optimizing 13c CP *** high-precision MA under variable temperature(VT)was found challenging on certain commercial MAS NMR probes,as was systematically investigated by VT NMR using KBr and ***,ultrahigh-resolution MAS NMR spectroscopy with stable MA under VT is employed to reveal fine structures and linker dynamics of a series of Zn-based MOFs with highly regulated *** ultrahigh-resolution NMR methodcan be generally applied to study a broad range of MOFs and other materials.

关键词： Solid-state NMR Ultrahigh resolution MOFs structure and dynamics Magic angle calibration

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Accumulative coarse-graining of simple structural descriptors enables accurately predicting the dynamics of metallic liquids

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MATERIALS TODAY PHYSICS 2024年 40卷

作者： You, Jiang Wang, Cheng Wang, Qi Zha, Min Jia, Hai -Long Wang, Jian Wang, Hui -Yuan Jilin Univ State Key Lab Automot Simulat & Control Changchun Peoples R China Jilin Univ Key Lab Automobile Mat Minist Educ Nanling Campus5988 Renmin St Changchun 130025 Peoples R China Jilin Univ Sch Mat Sci & Engn Nanling Campus5988 Renmin St Changchun 130025 Peoples R China Sci & Technol Surface Phys & Chem Lab POB 9-35 Jiangyou 621908 Sichuan Peoples R China Hebei Univ Technol Sch Mat Sci & Engn State Key Lab Reliabil & Intelligence Elect Equipm Tianjin 300130 Peoples R China Univ Nebraska Lincoln Dept Mech & Mat Engn Lincoln NE 68583 USA

The typical dynamic mode of liquids is often marked by a long-time alpha relaxation which is accompanied by heterogeneous dynamics. However, the explicit structural origin of the alpha relaxation is ongoing debated. Recent advances in graph neural networks (GNN) have shown promise in this area, with an intuitive approach that can be simplified as an iterative coarse-graining (CG) to update atomic features based on neighboring atoms. Here, we propose a new CG strategy called accumulative CG, which aggregates the spherically averaged and deviated features to generate a robust representation of atomic arrangement over a broad range. This can enhance the direct visibility of the center atom among all its surrounding atoms, as opposed to being limited to its nearestneighbors and relying on iterative message passing to indirectly observe further neighbors. Starting with two descriptors (local energy and volume), the augmented features derived from accumulative CG along with machine learning (ML) can accurately predict the atomic-level dynamics of multi-component liquids, as indicated by the inverse of alpha-relaxation time. We performed atomistic simulations of multi-component Al-Fe-(Si, Y) liquids with a set of deep-learning interatomic potentials to demonstrate the feasibility of the accumulative CG approach. By injecting physical inspirations from liquid dynamics theories into data-driven ML model, we interpret the structural origin of dynamic heterogeneity, particularly the bimodal behavior of Si atoms in Al-Fe-Si liquids.

关键词： Metallic liquids structure and dynamics Deep learning potential Molecular dynamics simulation

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Modeling the solid/liquid interfacial properties of methylimidazole confined in hydrophobic silica nanopores

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CHEMICAL ENGINEERING SCIENCE 2021年 231卷 116333-116333页

作者： Zheng, Weizhong Sun, Weizhen Zhao, Ling Qian, Feng East China Univ Sci & Technol Sch Chem Engn State Key Lab Chem Engn Shanghai 200237 Peoples R China XinJiang Univ Sch Chem & Chem Engn Urumqi 830046 Peoples R China East China Univ Sci & Technol Minist Educ Key Lab Adv Control & Optimizat Chem Proc Shanghai 200237 Peoples R China

Many chemical processes proceed in confined environments of silica nanopore, in which the confined reactants or guest adsorbates show drastically different properties from the bulk system. Therefore, the solid/liquid interfacial structure and dynamics of 1-methylimidazole (MeIm) confined in the hydrophobic silica nanopore passivated by methoxysilane groups (-Si(Me)(3)) were investigated using molecular dynamics (MD) simulations. The mass density of the confined MeIm is layering and poresize independent, while the negligible layering structure for charge density is observed. The smaller pore size gives rise to a significantly slower reorientation dynamics and translational diffusion of MeIm. In 2.8 nm pore, the parallel diffusion coefficient of MeIm is nearly 10 times larger than the perpendicular one, and their difference becomes smaller with the increase in pore size. Hopefully the insights from this work are helpful to a better understanding of the effects of hydrophobic silica pore on the confined behaviors of liquids. (C) 2020 Elsevier Ltd. All rights reserved.

关键词： Hydrophobic silica pore Confinement effect Solid-liquid interface structure and dynamics Molecular dynamics simulation

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