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Molecular Dynamics Simulations to Study Drug Delivery Systems 分子动力学模拟研究药物输送系统
Pub Date : 2018-08-01 DOI: 10.5772/INTECHOPEN.75748
Juan M. R. Albano, E. Paula, M. Pickholz
Molecular dynamics simulation is a very powerful tool to understand biomolecular processes. In this chapter, we go over different applications of this methodology to drug delivery systems (DDS) carried out in the group. DDS—a formulation or a device that enables the introduction of a therapeutic substance in the body and improves its efficacy and safety by controlling the rate, time, and place of release of drugs—are an important component of drug development and therapeutics. Biocompatible nanoparticles are materials in the nanoscale that emerged as important players, improving efficacy of approved drugs, for example. The molecular understanding of the encapsulation process could be very helpful to guide the nanocarrier for a specific system. Here we discuss different applications of drug delivery carriers, such as liposomes, polymeric micelles, and polymersomes using atomistic and coarse grain (CG) molecular dynamics simulations.
分子动力学模拟是理解生物分子过程的有力工具。在本章中,我们将讨论该方法在小组中进行的药物输送系统(DDS)中的不同应用。dds是一种能够将治疗物质引入体内并通过控制药物释放的速度、时间和地点来提高其疗效和安全性的制剂或设备,是药物开发和治疗学的重要组成部分。生物相容性纳米粒子是在纳米尺度上发挥重要作用的材料,例如可以提高已批准药物的疗效。对包封过程的分子认识有助于指导特定体系的纳米载体的制备。在这里,我们讨论了药物传递载体的不同应用,如脂质体、聚合物胶束和聚合体,使用原子和粗粒(CG)分子动力学模拟。
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引用次数: 8
Introductory Chapter: Molecular Dynamics: Basic Tool of Nanotechnology Simulations for “Production 4.0” Revolution 导论章:分子动力学:纳米技术模拟“生产4.0”革命的基本工具
Pub Date : 2018-08-01 DOI: 10.5772/INTECHOPEN.79045
A. Vakhrushev
© 2016 The Author(s). Licensee InTech. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. I tr ct ry a ter: lec lar y a ics: asic T l of Nanotechnology Si ulations for “Production 4.0” Revolution
©2016作者。InTech被许可方的哲理。本章是在知识共享署名许可(http://creativecommons.org/licenses/by/3.0)的条款下发布的,该许可允许在任何媒体上不受限制地使用、分发和复制,只要原始作品被适当引用。我试着为“生产4.0”革命的纳米技术技术的基本原理提供一个更好的方法
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引用次数: 1
Atomic Mechanisms Governing Strength of Metallic Nanosized Crystals 控制金属纳米晶体强度的原子机制
Pub Date : 2018-08-01 DOI: 10.5772/INTECHOPEN.75159
S. Kotrechko, O. Ovsijannikov, I. Mikhailovskij, N. Stetsenko
Fundamentals of the atomic mechanisms governing the strength of nanosized metallic crystals are described. An attempt is made to explain on this basis the size and orientation effects, temperature dependence of strength and atomism of fracture of bcc crystals under triaxial uniform (hydrostatic) tension. A feature of the proposed material is that it com-bines the results of molecular dynamics simulation with the data of experimental research findings on failure of metallic nanosized crystals under the high-field mechanical loading. It is exhibited that local instability of the lattice is the main mechanism governing the strength of defect-free nanosized crystals (NSC). Based on the concept of local instability, an explanation is given of the nature of the size effect in NSC, as well as of the differences in its manifestation in nanocrystals with bcc and fcc lattices. The concept of the mechanism of thermal activation of local instability is outlined. This enables to explain the specific features of the temperature dependence of NSC. The results of experimental studies and molecular dynamics simulation of the failure of tungsten nanocrystals under hydrostatic tension are presented. The ideas about the atomism of the bcc-fcc transition in these conditions are articulated. as a result of electrochemical polishing. This means that formation of an atomically smooth surface of nanoneedles is one of the factors to reach the ultimate strength levels.
描述了控制纳米金属晶体强度的原子机制的基本原理。在此基础上,试图解释三轴均匀(静水)拉伸作用下bcc晶体的尺寸和取向效应、强度的温度依赖性和断裂的原子性。该材料的一个特点是将分子动力学模拟结果与金属纳米晶体在高场机械载荷下破坏的实验研究结果相结合。研究表明,晶格的局部不稳定性是控制无缺陷纳米晶体强度的主要机制。基于局部不稳定性的概念,解释了NSC中尺寸效应的性质,以及其在具有bcc和fcc晶格的纳米晶体中表现的差异。概述了局部失稳热活化机理的概念。这可以解释NSC的温度依赖性的具体特征。本文介绍了静水张力作用下钨纳米晶破坏的实验研究和分子动力学模拟结果。在这些条件下,阐述了bcc-fcc跃迁的原子论。作为电化学抛光的结果。这意味着纳米针原子光滑表面的形成是达到最终强度水平的因素之一。
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引用次数: 0
Modeling Soft Supramolecular Nanostructures by Molecular Simulations 用分子模拟方法模拟软超分子纳米结构
Pub Date : 2018-08-01 DOI: 10.5772/INTECHOPEN.74939
Tânia Cova, S. Nunes, B. F. Milne, A. Jorge, A. Pais
The design and assembly of soft supramolecular structures based on small building blocks are governed by non-covalent interactions, selective host-guest interactions, or a combination of different interaction types. There is a surprising number of studies supporting the use of computational models for mimicking supramolecular nanosystems and studying the underlying patterns of molecular recognition and binding, in multi-dimensional approaches. Based on physical properties and mathematical concepts, these models are able to provide rationales for the conformation, solvation and thermodynamic characterization of this type of systems. Molecular dynamics (MD), including free-energy calculations, yield a direct coupling between experimental and computational investigation. This chapter provides an overview of the available MD-based methods, including path-based and alchemical free-energy calculations. The theoretical background is briefly reviewed and practical instructions are introduced on the selection of methods and post-treatment procedures. Relevant examples in which non-covalent interactions dominate are presented.
基于小构建块的软超分子结构的设计和组装受非共价相互作用、选择性主客体相互作用或不同相互作用类型的组合的支配。有大量的研究支持使用计算模型来模拟超分子纳米系统,并在多维方法中研究分子识别和结合的潜在模式。基于物理性质和数学概念,这些模型能够为这类体系的构象、溶剂化和热力学表征提供理论依据。分子动力学(MD),包括自由能计算,产生了实验和计算研究之间的直接耦合。本章概述了可用的基于md的方法,包括基于路径和炼金术的自由能计算。简要回顾了理论背景,并介绍了方法选择和后处理程序的实践指导。提出了非共价相互作用占主导地位的相关例子。
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引用次数: 0
Effects of Voids in Tensile Single-Crystal Cu Nanobeams 拉伸单晶铜纳米梁中孔洞的影响
Pub Date : 2018-02-23 DOI: 10.5772/INTECHOPEN.74169
A. Ahadi, P. Hansson, S. Melin
Molecular dynamic simulations of defect nano-sized beams of single-crystal Cu, loaded in displacement controlled tension until rupture, have been performed. The defects are square-shaped, through-the-thickness voids of different sizes, placed centrally in the beams. Three different cross section sizes and two different crystallographic orientations are investigated. As expected, the sizes of the beam cross section and the void as well as the crystal orientation strongly influences both the elastic and the plastic behaviors of the beams. It was seen that the strain at plastic initiation increases with beam cross section size as well as with decreasing void size. It is further observed that the void deformed in different ways depending on cross section and void size. Sometimes void closure, leading to necking of the beam cross section followed by rupture occurred. In other cases the void elongated leading to that the two ligaments above and below the void ruptured independently. (Less)
对单晶铜缺陷纳米梁在位移控制张力下加载直至断裂的过程进行了分子动力学模拟。这些缺陷是方形的,大小不同的穿过厚度的空洞,放置在梁的中央。研究了三种不同的截面尺寸和两种不同的晶体取向。正如预期的那样,梁的横截面和空洞的大小以及晶体取向对梁的弹性和塑性行为都有很大的影响。塑性初始应变随梁截面尺寸的增大而增大,随空隙尺寸的减小而减小。进一步观察到,随着孔洞截面和孔洞尺寸的不同,孔洞的变形方式也不同。有时孔洞闭合,导致梁截面颈缩,随后发生断裂。在其他情况下,空洞拉长导致空洞上下的两个韧带独立破裂。(少)
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引用次数: 0
Tumor Spheres Quantification with Smoothed Euclidean Distance Transform. 基于光滑欧氏距离变换的肿瘤球定量。
Pub Date : 2018-01-01 Epub Date: 2018-07-06 DOI: 10.4172/2155-9937.1000143
Ismet Sahin, Yu Zhang, Florencia McAllister

Tumor sphere quantification plays an important role in cancer research and drugs screening. Even though the number and size of tumor spheres can be found manually, this process is time-consuming, prone to making errors, and may not be viable when the number of images is very large. This manuscript presents a method for automated quantification of spheres with a novel segmentation technique. The segmentation method relies on initial watershed algorithm which detects the minima of the distance transform and finds a tumor sphere for each minimum. Due to the irregular edges of tumor spheres, the distance transform matrix has often more number of minima than the true number of spheres. This leads to the over segmentation problem. The proposed approach uses the smoothed form of the distance transform to effectively eliminate superfluous minima and then seeds the watershed algorithm with the remaining minima. The proposed method was validated over pancreatic tumor spheres images achieving high efficiency for tumor spheres quantification.

肿瘤球定量在肿瘤研究和药物筛选中起着重要作用。尽管可以手动找到肿瘤球的数量和大小,但这个过程耗时,容易出错,并且当图像数量非常大时可能不可行。本文提出了一种新的球体分割技术的自动定量方法。该分割方法依赖于初始分水岭算法,该算法检测距离变换的最小值,并为每个最小值找到一个肿瘤球。由于肿瘤球的边缘不规则,距离变换矩阵的最小值数往往大于真实球数。这就导致了过度分割问题。该方法利用距离变换的平滑形式有效地去除多余的最小值,然后用剩余的最小值播种分水岭算法。该方法在胰腺肿瘤球图像上进行了验证,具有较高的定量效率。
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引用次数: 0
Towards Real-time Metabolic Profiling of Cancer with Hyperpolarized Succinate. 利用超极化琥珀酸盐实现癌症的实时代谢分析。
Pub Date : 2016-06-01 Epub Date: 2016-01-11 DOI: 10.4172/2155-9937.1000123
Niki M Zacharias, Christopher R McCullough, Shawn Wagner, Napapon Sailasuta, Henry R Chan, Youngbok Lee, Jingzhe Hu, William H Perman, Cameron Henneberg, Brian D Ross, Pratip Bhattacharya

Purpose: The energy-yielding mitochondrial Krebs cycle has been shown in many cancers and other diseases to be inhibited or mutated. In most cells, the Krebs cycle with oxidative phosphorylation generates approximately 90% of the adenosine triphosphate in the cell. We designed and hyperpolarized carbon-13 labeled succinate (SUC) and its derivative diethyl succinate (DES) to interrogate the Krebs cycle in real-time in cancer animal models.

Procedures: Using Parahydrogen Induced Polarization (PHIP), we generated hyperpolarized SUC and DES by hydrogenating their respective fumarate precursors. DES and SUC metabolism was studied in five cancer allograft animal models: breast (4T1), Renal Cell Carcinoma (RENCA), colon (CT26), lymphoma NSO, and lymphoma A20.

Results: The extent of hyperpolarization was 8 ± 2% for SUC and 2.1 ± 0.6% for DES. The metabolism of DES and SUC in the Krebs cycle could be followed in animals 5 s after tail vein injection. The biodistribution of the compounds was observed using 13C FISP imaging. We observed significant differences in uptake and conversion of both compounds in different cell types both in vivo and in vitro.

Conclusion: With hyperpolarized DES and SUC, we are able to meet many of the requirements for a useable in vivo metabolic imaging compound - high polarization, relatively long T1 values, low toxicity and high water solubility. However, succinate and its derivative DES are metabolized robustly by RENCA but not by the other cancer models. Our results underscore the heterogeneity of cancer cells and the role cellular uptake plays in hyperpolarized metabolic spectroscopy.

目的:产能线粒体克雷布斯循环在许多癌症和其他疾病中被抑制或突变。在大多数细胞中,氧化磷酸化的克雷布斯循环产生细胞中大约90%的三磷酸腺苷。我们设计并超极化了碳-13标记琥珀酸盐(SUC)及其衍生物琥珀酸二乙酯(DES),在癌症动物模型中实时检测克雷布斯循环。方法:利用对氢诱导极化(PHIP),我们通过加氢各自的富马酸前体生成超极化的SUC和DES。在乳腺癌(4T1)、肾癌(RENCA)、结肠癌(CT26)、淋巴瘤NSO和淋巴瘤A20五种异体肿瘤移植动物模型中研究DES和SUC的代谢。结果:动物尾静脉注射后5 s内可观察到DES和SUC在Krebs循环中的代谢情况,分别为超极化程度(8±2%)和超极化程度(2.1±0.6%)。用13C FISP显像观察化合物的生物分布。我们观察到两种化合物在体内和体外不同细胞类型中摄取和转化的显著差异。结论:利用超极化DES和超极化SUC,我们能够满足高极化、较长的T1值、低毒性和高水溶性等对一种可用的体内代谢成像化合物的要求。然而,琥珀酸盐及其衍生物DES可以被RENCA代谢,而不被其他癌症模型代谢。我们的研究结果强调了癌细胞的异质性和细胞摄取在超极化代谢光谱中的作用。
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引用次数: 14
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Journal of molecular imaging & dynamics
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