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相关概念视频

Nuclear Overhauser Enhancement (NOE)01:07

Nuclear Overhauser Enhancement (NOE)

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Irradiation of a spin-active nucleus causes an increase or decrease in the signal intensity of neighboring nuclei that are not necessarily chemically bonded or involved in J-coupling.  This phenomenon, called the Nuclear Overhauser Enhancement (NOE), results from through-space interactions between the nuclear spins. The NOE effect decreases with increasing internuclear distance and is generally not observed beyond 4 angstroms. In NOE, dipole-dipole interactions between neighboring...
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Nucleic Acid Structure01:25

Nucleic Acid Structure

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The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA...
6.2K
Molecular Models02:00

Molecular Models

38.5K
Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
38.5K
Electron Microscope Tomography and Single-particle Reconstruction01:07

Electron Microscope Tomography and Single-particle Reconstruction

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Transmission electron microscopy (TEM) can be used to determine the 3D structure of biological samples with the help of techniques such as electron microscope tomography and single-particle reconstruction. While single-particle reconstruction can examine macromolecules and macromolecular complexes in vitro conditions only, tomography permits the study of cell components or small cells in vivo.
Electron Tomography
Electron tomography can be performed either in TEM or STEM (scanning transmission...
2.4K
Nuclear Magnetic Resonance (NMR): Overview01:07

Nuclear Magnetic Resonance (NMR): Overview

2.5K
Nuclear magnetic resonance (NMR) is a phenomenon exhibited by certain nuclei that can absorb characteristic radio frequency radiation under certain conditions. NMR has been extensively applied in molecular spectroscopy and medical diagnostic imaging. In both these applications, the molecule or subject under study is placed in a magnetic field and irradiated with radio frequency energy.
NMR spectroscopy generates a spectrum where the characteristic absorption frequencies of the sample are...
2.5K
Atomic Nuclei: Nuclear Relaxation Processes01:23

Atomic Nuclei: Nuclear Relaxation Processes

660
In the absence of an external magnetic field, nuclear spin states are degenerate and randomly oriented. When a magnetic field is applied, the spins begin to precess and orient themselves along (lower energy) or against (higher energy) the direction of the field. At equilibrium, a slight excess population of spins exists in the lower energy state. Because the direction of the magnetic field is fixed as the z-axis,  the precessing magnetic moments are randomly oriented around the z-axis.
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相关实验视频

Updated: Jul 12, 2025

Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures
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Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures

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OpenNucleome用于高分辨率的核结构和动态建模.

Zhuohan Lao1, Kartik Kamat1, Zhongling Jiang1

  • 1Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.

bioRxiv : the preprint server for biology
|October 31, 2023
PubMed
概括

OpenNucleome是一个新的开源软件,用于模拟人类核,帮助理解基因组的组织和功能. 它揭示了基因组"固定点"如何保持固定,支持基因组功能的核分区模型.

科学领域:

  • 细胞生物学 细胞生物学
  • 计算生物学 计算生物学
  • 基因组学就是基因组学.

背景情况:

  • 人类核的结构对于细胞功能和基因调节至关重要.
  • 先进的实验技术和计算建模为核组织提供了洞察力.
  • 缺乏标准化的建模工具阻碍了核研究.

研究的目的:

  • 介绍OpenNucleome,这是一个开源软件,用于人类核的GPU加速分子动力学模拟.
  • 为核架构提供准确建模和动态模拟的工具.
  • 研究基因组"固定点"背后的机制及其在基因组功能中的作用.

主要方法:

  • 开发了OpenNucleome,这是一个用于GPU加速分子动力学模拟的开源软件.
  • 使用基于粒子的染色体表示,分辨率为100KB.
  • 模拟核膜,核细胞和斑点,用于全面的核模拟.

主要成果:

  • 产生了人类核架构的精确结构模型.
  • 模拟了诸如凝聚物形成和融合之类的动态过程.
  • 发现了"固定点"的机制 弹性基因组位置在核体附近定.
  • 提供了支持基因组功能核区划模型的证据.

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Analyzing and Building Nucleic Acid Structures with 3DNA
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Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy
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相关实验视频

Last Updated: Jul 12, 2025

Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures
10:10

Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures

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Analyzing and Building Nucleic Acid Structures with 3DNA
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Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy
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Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy

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结论:

  • OpenNucleome 允许对核组织进行详细的机械探索.
  • 该软件有助于解释核生物学实验数据.
  • 这些发现支持核区划模型,通过定位置解释基因组功能.