在一维格子上随机抽取连接物排列的样本
Dibyajyoti Mohanta1, Albertas Dvirnas1, Tobias Ambjörnsson1
1Lund University, Computational Science for Health and Environment, Centre for Environmental and Climate Science, Lund, SE-223 62 Lund, Sweden.
Physical review. E
|February 20, 2025
概括
我们开发了一种新的计算方法来模拟分子如何与DNA结合. 这种方法有助于理解DNA条形码,并设计更好的光学DNA映射 (ODM) 实验.
科学领域:
- 计算生物学是一种计算生物学.
- 生物物理学的生物物理.
- 分子建模分子建模
背景情况:
- 在生物模板上精确模拟分子相互作用对于理解生物过程和设计实验至关重要.
- 现有的方法在处理任意的连接体类型,位置依赖性和合作性方面可能缺乏灵活性.
- 光学DNA映射 (ODM) 依赖于精确的配体结合,用于DNA条形码生成和分析.
研究的目的:
- 引入一个多功能计算框架,用于模拟在一维模板上的连接体排列.
- 为了能够从这些模拟安排中计算各种可观测值.
- 评估合成DNA条形码的质量,用于光学DNA映射实验.
主要方法:
- 基于转移矩阵的顺序采样方案用于生成随机连接物排列.
- 该方法容纳了任意数量的连接体类型,位置依赖的结合常数和合作性参数.
- 样本平均值用于计算生成的安排中的可观测值.
主要成果:
- 该框架成功模拟了多种类型 (网素,YOYO-1,乙基) 与DNA的竞争性结合.
- 该方法量化了合成生成的DNA条形码的质量,作为ODM中的联体度的函数.
- 提供的软件提供了与格子大小的计算时间的线性缩放.
结论:
- 开发的转移矩阵方法提供了一个灵活和高效的工具来模拟连接体-DNA相互作用.
- 这种计算方法有助于优化光学DNA映射和DNA条形码设计的实验条件.
- 公开可用的软件促进了计算生物物理学和分子识别方面的研究.
相关概念视频
Lattice Centering and Coordination Number
9.5K
The structure of a crystalline solid, whether a metal or not, is best described by considering its simplest repeating unit, which is referred to as its unit cell. The unit cell consists of lattice points that represent the locations of atoms or ions. The entire structure then consists of this unit cell repeating in three dimensions. The three different types of unit cells present in the cubic lattice are illustrated in Figure 1.
Types of Unit Cells
Imagine taking a large number of identical...
Types of Unit Cells
Imagine taking a large number of identical...
9.5K
Ligand Binding Sites
12.7K
Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
12.7K
Crystal Field Theory - Octahedral Complexes
26.1K
Crystal Field Theory
To explain the observed behavior of transition metal complexes (such as colors), a model involving electrostatic interactions between the electrons from the ligands and the electrons in the unhybridized d orbitals of the central metal atom has been developed. This electrostatic model is crystal field theory (CFT). It helps to understand, interpret, and predict the colors, magnetic behavior, and some structures of coordination compounds of transition metals.
CFT focuses on...
To explain the observed behavior of transition metal complexes (such as colors), a model involving electrostatic interactions between the electrons from the ligands and the electrons in the unhybridized d orbitals of the central metal atom has been developed. This electrostatic model is crystal field theory (CFT). It helps to understand, interpret, and predict the colors, magnetic behavior, and some structures of coordination compounds of transition metals.
CFT focuses on...
26.1K
Metallic Solids
18.2K
Metallic solids such as crystals of copper, aluminum, and iron are formed by metal atoms. The structure of metallic crystals is often described as a uniform distribution of atomic nuclei within a “sea” of delocalized electrons. The atoms within such a metallic solid are held together by a unique force known as metallic bonding that gives rise to many useful and varied bulk properties.
All metallic solids exhibit high thermal and electrical conductivity, metallic luster, and malleability....
All metallic solids exhibit high thermal and electrical conductivity, metallic luster, and malleability....
18.2K
Metal-Ligand Bonds
20.5K
The hemoglobin in the blood, the chlorophyll in green plants, vitamin B-12, and the catalyst used in the manufacture of polyethylene all contain coordination compounds. Ions of the metals, especially the transition metals, are likely to form complexes.
In these complexes, transition metals form coordinate covalent bonds, a kind of Lewis acid-base interaction in which both of the electrons in the bond are contributed by a donor (Lewis base) to an electron acceptor (Lewis acid). The Lewis acid in...
In these complexes, transition metals form coordinate covalent bonds, a kind of Lewis acid-base interaction in which both of the electrons in the bond are contributed by a donor (Lewis base) to an electron acceptor (Lewis acid). The Lewis acid in...
20.5K
The Equilibrium Binding Constant and Binding Strength
12.8K
The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:
12.8K


