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Journal of molecular imaging & dynamics最新文献

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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
Journal of molecular imaging & dynamics Pub Date : 2018-08-01 DOI: 10.5772/INTECHOPEN.75748
Juan M. R. Albano, E. Paula, M. Pickholz
{"title":"Molecular Dynamics Simulations to Study Drug Delivery Systems","authors":"Juan M. R. Albano, E. Paula, M. Pickholz","doi":"10.5772/INTECHOPEN.75748","DOIUrl":"https://doi.org/10.5772/INTECHOPEN.75748","url":null,"abstract":"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.","PeriodicalId":91553,"journal":{"name":"Journal of molecular imaging & dynamics","volume":"6 3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85114977","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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
Journal of molecular imaging & dynamics Pub Date : 2018-08-01 DOI: 10.5772/INTECHOPEN.79045
A. Vakhrushev
{"title":"Introductory Chapter: Molecular Dynamics: Basic Tool of Nanotechnology Simulations for “Production 4.0” Revolution","authors":"A. Vakhrushev","doi":"10.5772/INTECHOPEN.79045","DOIUrl":"https://doi.org/10.5772/INTECHOPEN.79045","url":null,"abstract":"© 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","PeriodicalId":91553,"journal":{"name":"Journal of molecular imaging & dynamics","volume":"48 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87932827","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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
Journal of molecular imaging & dynamics Pub Date : 2018-08-01 DOI: 10.5772/INTECHOPEN.75159
S. Kotrechko, O. Ovsijannikov, I. Mikhailovskij, N. Stetsenko
{"title":"Atomic Mechanisms Governing Strength of Metallic Nanosized Crystals","authors":"S. Kotrechko, O. Ovsijannikov, I. Mikhailovskij, N. Stetsenko","doi":"10.5772/INTECHOPEN.75159","DOIUrl":"https://doi.org/10.5772/INTECHOPEN.75159","url":null,"abstract":"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.","PeriodicalId":91553,"journal":{"name":"Journal of molecular imaging & dynamics","volume":"99 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88960759","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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
Journal of molecular imaging & dynamics Pub Date : 2018-08-01 DOI: 10.5772/INTECHOPEN.74939
Tânia Cova, S. Nunes, B. F. Milne, A. Jorge, A. Pais
{"title":"Modeling Soft Supramolecular Nanostructures by Molecular Simulations","authors":"Tânia Cova, S. Nunes, B. F. Milne, A. Jorge, A. Pais","doi":"10.5772/INTECHOPEN.74939","DOIUrl":"https://doi.org/10.5772/INTECHOPEN.74939","url":null,"abstract":"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.","PeriodicalId":91553,"journal":{"name":"Journal of molecular imaging & dynamics","volume":"23 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79077665","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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
Journal of molecular imaging & dynamics Pub Date : 2018-02-23 DOI: 10.5772/INTECHOPEN.74169
A. Ahadi, P. Hansson, S. Melin
{"title":"Effects of Voids in Tensile Single-Crystal Cu Nanobeams","authors":"A. Ahadi, P. Hansson, S. Melin","doi":"10.5772/INTECHOPEN.74169","DOIUrl":"https://doi.org/10.5772/INTECHOPEN.74169","url":null,"abstract":"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)","PeriodicalId":91553,"journal":{"name":"Journal of molecular imaging & dynamics","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-02-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89537899","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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。
Journal of molecular imaging & dynamics Pub Date : 2018-01-01 Epub Date: 2018-07-06 DOI: 10.4172/2155-9937.1000143
Ismet Sahin, Yu Zhang, Florencia McAllister
{"title":"Tumor Spheres Quantification with Smoothed Euclidean Distance Transform.","authors":"Ismet Sahin,&nbsp;Yu Zhang,&nbsp;Florencia McAllister","doi":"10.4172/2155-9937.1000143","DOIUrl":"https://doi.org/10.4172/2155-9937.1000143","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":91553,"journal":{"name":"Journal of molecular imaging & dynamics","volume":"8 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4172/2155-9937.1000143","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36628681","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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。
Journal of molecular imaging & dynamics 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
{"title":"Towards Real-time Metabolic Profiling of Cancer with Hyperpolarized Succinate.","authors":"Niki M Zacharias,&nbsp;Christopher R McCullough,&nbsp;Shawn Wagner,&nbsp;Napapon Sailasuta,&nbsp;Henry R Chan,&nbsp;Youngbok Lee,&nbsp;Jingzhe Hu,&nbsp;William H Perman,&nbsp;Cameron Henneberg,&nbsp;Brian D Ross,&nbsp;Pratip Bhattacharya","doi":"10.4172/2155-9937.1000123","DOIUrl":"https://doi.org/10.4172/2155-9937.1000123","url":null,"abstract":"<p><strong>Purpose: </strong>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.</p><p><strong>Procedures: </strong>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.</p><p><strong>Results: </strong>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 <sup>13</sup>C FISP imaging. We observed significant differences in uptake and conversion of both compounds in different cell types both <i>in vivo</i> and <i>in vitro</i>.</p><p><strong>Conclusion: </strong>With hyperpolarized DES and SUC, we are able to meet many of the requirements for a useable <i>in vivo</i> metabolic imaging compound - high polarization, relatively long T<sub>1</sub> 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.</p>","PeriodicalId":91553,"journal":{"name":"Journal of molecular imaging & dynamics","volume":"6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4172/2155-9937.1000123","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34382537","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 14
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