Download or read book Coarse grained Simulations of the Self assembly of DNA linked Gold Nanoparticle Building Blocks written by Charles Armistead and published by . This book was released on 2016 with total page 260 pages. Available in PDF, EPUB and Kindle. Book excerpt: The self-assembly of nanoparticles (NPs) of varying shape, size, and composition for the purpose of constructing useful nanoassemblies with tailored properties remains challenging. Although progress has been made to design anisotropic building blocks that exhibit the required control for the precise placement of various NPs within a defined arrangement, there still exists obstacles in the technology to maximize the programmability in the self-assembly of NP building blocks. Currently, the self-assembly of nanostructures involves much experimental trial and error. Computational modeling is a possible approach that could be utilized to facilitate the purposeful design of the self-assembly of NP building blocks into a desired nanostructure. In this report, a coarse-grained model of NP building blocks based on an effective anisotropic mono-functionalization approach, which has shown the ability to construct six building block configurations, was used to simulate various nanoassemblies. The purpose of the study was to validate the model's ability to simulate the self-assembly of the NP building blocks into nanostructures previously produced experimentally. The model can be programmed to designate up to six oligonucleotides attached to the surface of a Au NP building block, with a modifiable length and nucleotide sequence. The model successfully simulated the self-assembly of Au NP building blocks into a number of previously produced nanostructures and demonstrated the ability to produce visualizations of self-assembly as well as calculate interparticle distances and angles to be used for the comparison with the previous experimental data for validation of the model. Also, the model was used to simulate nanoassemblies which had not been produced experimentally for its further validation. The simulations showed the capability of the model to use specific NP building blocks and self-assemble. The coarse-grained NP building block model shows promise as a tool to complement the purposeful experimental design of functional nanostructures.

Download or read book Molecular Dynamics Simulations of DNA functionalized Nanoparticle Building Blocks on GPUs written by Tyler Landon Fochtman and published by . This book was released on 2017 with total page 100 pages. Available in PDF, EPUB and Kindle. Book excerpt: This thesis discusses massively parallel molecular dynamics simulations of nBLOCKs using graphical processing units. nBLOCKs are nanoscale building blocks composed of gold nanoparticles functionalized with single-stranded DNA molecules. To explore greater simulation time scales we implement our nBLOCK computational model as an extension to the coarse grain molecular simulator oxDNA. oxDNA is parameterized to match the thermodynamics of DNA strand hybridization as well as the mechanics of single stranded DNA and double stranded DNA. In addition to an in-depth review of our implementation details we also provide results of the model validation and performance tests. These validation and performance tests are comprised of over a hundred separate simulations spanning in simulation length from one thousand to ten million times steps and with simulation sizes ranging from 16 to 27832 particles. Together these tests show the ability of our implementation to handle the full range of basic nBLOCK topologies in a diverse set of conditions. A selection of the utilities developed during the course of this thesis are also discussed. We provide descriptions of the scripting utilities which support nBLOCK assembly generation, simulation, and analysis.

Download or read book Linear DNA linked Nanoparticle Building Blocks nBLOCKs for Modular Self assembly of Nanostructures written by Jakob Thomas Hockman and published by . This book was released on 2017 with total page 116 pages. Available in PDF, EPUB and Kindle. Book excerpt: Controlling the shapes and sizes of nanomaterials often enables controlling their properties for certain applications. The most promising methods for controlling the shapes and sizes of nanostructures use base-pairing between complementary DNA strands to self-assemble nanostructures from DNA and nanoparticles. DNA Brick-based self-assembly is a particularly useful method for creating DNA nanostructures. It offers a large amount of control over the final shapes and sizes because it uses building blocks that are anisotropic and have predictable geometry. However, this control has not been extended to the self-assembly of nanostructures from nanoparticles. Applying DNA Brick based self-assembly to the self-assembly of nanostructures from nanoparticles would require DNA-linked nanoparticles that are anisotropic and have predictable geometry. To this end, Solidworks models were used to study the interactions between DNA Bricks so that detailed information could be gained about their mode of self-assembly. This information was used to generate Solidworks models of DNA-linked nanoparticle building blocks (nBLOCKs) that can be used for DNA Brick-based self-assembly. These nBLOCKs could be created by attaching a single 43 base pair (bp) long DNA strand to gold nanoparticles using the anisotropic monofunctionalization technique. However, accomplishing this feat would require improving the efficiency of the anisotropic monofunctionalization method first. Attempts to improve all three steps of the anisotropic monofunctionalization technique yielded mixed results. The efficiency of the first step, binding DNA to a solid support, was improved by implementing the photocleavable (PC) biotin – streptavidin interaction. UV-Vis absorbance spectroscopy revealed that the PC biotinylated DNA strands became bound to streptavidin-coated magnetic beads with nearly 100% efficiency. However, the second and third steps, binding gold nanoparticles (AuNPs) to DNA and cleaving DNA-linked AuNPs from the beads, still suffer from low yields. The efficiency of the second step was incrementally improved from 3% to 25% by tuning the reaction conditions. The third step was carried out at a maximum of 10% efficiency. The method was successfully used to generate nBLOCKs but the overall yield was less than 5%. Explanations of and possible solutions to the low-yield are suggested for future experiments.

Download or read book Mesoscale Chemistry written by National Research Council and published by National Academies Press. This book was released on 2015-08-06 with total page 229 pages. Available in PDF, EPUB and Kindle. Book excerpt: In the last few decades great strides have been made in chemistry at the nanoscale, where the atomic granularity of matter and the exact positions of individual atoms are key determinants of structure and dynamics. Less attention, however, has been paid to the mesoscale-it is at this scale, in the range extending from large molecules (10 nm) through viruses to eukaryotic cells (10 microns), where interesting ensemble effects and the functionality that is critical to macroscopic phenomenon begins to manifest itself and cannot be described by laws on the scale of atoms and molecules alone. To further explore how knowledge about mesoscale phenomena can impact chemical research and development activities and vice versa, the Chemical Sciences Roundtable of the National Research Council convened a workshop on mesoscale chemistry in November 2014. With a focus on the research on chemical phenomena at the mesoscale, participants examined the opportunities that utilizing those behaviors can have for developing new catalysts, adding new functionality to materials, and increasing our understanding of biological and interfacial systems. The workshop also highlighted some of the challenges for analysis and description of mesoscale structures. This report summarizes the presentations and discussion of the workshop.

Download or read book Comprehensive Nanoscience and Technology written by and published by Academic Press. This book was released on 2010-10-29 with total page 2785 pages. Available in PDF, EPUB and Kindle. Book excerpt: From the Introduction: Nanotechnology and its underpinning sciences are progressing with unprecedented rapidity. With technical advances in a variety of nanoscale fabrication and manipulation technologies, the whole topical area is maturing into a vibrant field that is generating new scientific research and a burgeoning range of commercial applications, with an annual market already at the trillion dollar threshold. The means of fabricating and controlling matter on the nanoscale afford striking and unprecedented opportunities to exploit a variety of exotic phenomena such as quantum, nanophotonic and nanoelectromechanical effects. Moreover, researchers are elucidating new perspectives on the electronic and optical properties of matter because of the way that nanoscale materials bridge the disparate theories describing molecules and bulk matter. Surface phenomena also gain a greatly increased significance; even the well-known link between chemical reactivity and surface-to-volume ratio becomes a major determinant of physical properties, when it operates over nanoscale dimensions. Against this background, this comprehensive work is designed to address the need for a dynamic, authoritative and readily accessible source of information, capturing the full breadth of the subject. Its six volumes, covering a broad spectrum of disciplines including material sciences, chemistry, physics and life sciences, have been written and edited by an outstanding team of international experts. Addressing an extensive, cross-disciplinary audience, each chapter aims to cover key developments in a scholarly, readable and critical style, providing an indispensible first point of entry to the literature for scientists and technologists from interdisciplinary fields. The work focuses on the major classes of nanomaterials in terms of their synthesis, structure and applications, reviewing nanomaterials and their respective technologies in well-structured and comprehensive articles with extensive cross-references. It has been a constant surprise and delight to have found, amongst the rapidly escalating number who work in nanoscience and technology, so many highly esteemed authors willing to contribute. Sharing our anticipation of a major addition to the literature, they have also captured the excitement of the field itself in each carefully crafted chapter. Along with our painstaking and meticulous volume editors, full credit for the success of this enterprise must go to these individuals, together with our thanks for (largely) adhering to the given deadlines. Lastly, we record our sincere thanks and appreciation for the skills and professionalism of the numerous Elsevier staff who have been involved in this project, notably Fiona Geraghty, Megan Palmer and Greg Harris, and especially Donna De Weerd-Wilson who has steered it through from its inception. We have greatly enjoyed working with them all, as we have with each other.

Download or read book Enzymatic Ligation Creates Discrete Multi Nanoparticle Building Blocks for Self Assembly written by and published by . This book was released on 2008 with total page 23 pages. Available in PDF, EPUB and Kindle. Book excerpt: Enzymatic ligation of discrete nanoparticle?DNA conjugates creates nanoparticle dimer and trimer structures in which the nanoparticles are linked by single-stranded DNA, rather than double-stranded DNA as in previous experiments. Ligation is verified by agarose gel and small-angle X-ray scattering. This capability is utilized in two ways: first to create a new class of multiparticle building blocks for nanoscale self-assembly; second to develop a system which can amplify a population of discrete nanoparticle assemblies.

Download or read book Self Assembly written by Ramanathan Nagarajan and published by John Wiley & Sons. This book was released on 2018-12-03 with total page 368 pages. Available in PDF, EPUB and Kindle. Book excerpt: An introduction to the state-of-the-art of the diverse self-assembly systems Self-Assembly: From Surfactants to Nanoparticles provides an effective entry for new researchers into this exciting field while also giving the state of the art assessment of the diverse self-assembling systems for those already engaged in this research. Over the last twenty years, self-assembly has emerged as a distinct science/technology field, going well beyond the classical surfactant and block copolymer molecules, and encompassing much larger and complex molecular, biomolecular and nanoparticle systems. Within its ten chapters, each contributed by pioneers of the respective research topics, the book: Discusses the fundamental physical chemical principles that govern the formation and properties of self-assembled systems Describes important experimental techniques to characterize the properties of self-assembled systems, particularly the nature of molecular organization and structure at the nano, meso or micro scales. Provides the first exhaustive accounting of self-assembly derived from various kinds of biomolecules including peptides, DNA and proteins. Outlines methods of synthesis and functionalization of self-assembled nanoparticles and the further self-assembly of the nanoparticles into one, two or three dimensional materials. Explores numerous potential applications of self-assembled structures including nanomedicine applications of drug delivery, imaging, molecular diagnostics and theranostics, and design of materials to specification such as smart responsive materials and self-healing materials. Highlights the unifying as well as contrasting features of self-assembly, as we move from surfactant molecules to nanoparticles. Written for students and academic and industrial scientists and engineers, by pioneers of the research field, Self-Assembly: From Surfactants to Nanoparticles is a comprehensive resource on diverse self-assembly systems, that is simultaneously introductory as well as the state of the art.

Download or read book Self Assembly with DNA From Materials Design to Chromatin written by Joshua Paul Lequieu and published by . This book was released on 2017 with total page 180 pages. Available in PDF, EPUB and Kindle. Book excerpt: The ability to engineer the self-assembly of nano-scale objects to create highly ordered materials is of considerable scientific and practical interest. This new class of materials represents a powerful approach for engineering a next generation of devices, whose mechanical, optical, and electrical properties can be precisely tuned at the molecular scale. Though significant strides towards this goal have been achieved in recent years, the complexity achieved in engineered systems is still far surpassed by that achieved by nature. Precise self-assembly is achieved by nature through proteins and nucleic acids that fold into intricate, three-dimensional, and importantly, functional structures. A promising avenue towards improved engineered systems is to draw on discoveries from biophysics in order to inspire new approaches and paradigms for self-assembly and materials design. In this work, we explore the interplay between biophysics and engineering by exploring the self-assembly of DNA. Our discussion begins at the smallest length-scales of DNA, first by understanding the hybridization of DNA, and then at how hybridization can be used in materials to direct the self-assembly of gold nanoparticles. We report the first evidence of a tunable mechanical response in these assemblies, thereby suggesting the possibility of mechanical meta-materials constructed using DNA. Our discussion then proceeds to larger length scales, where we examine the biophysical processes that control the compaction of DNA into chromatin. Using a detailed molecular model, we explore the free energies and dynamics of smallest building block of chromatin, a protein-DNA complex called the nucleosome. Our results are in quantitative agreement with existing experimental measurements, and help to explain the molecular factors that dictate the first stages of DNA compaction into chromatin. Lastly, we present a multi-scale approach that can couple information across different length scales of chromatin in order to examine the folding of large regions DNA. By drawing on both the biophysics and engineering literature, the findings presented here suggest new approaches for materials design, and offer new paradigms for synthetic systems that seek to mimic the complexity achieved by nature.

Download or read book Structural DNA Nanotechnology written by Nadrian C. Seeman and published by Cambridge University Press. This book was released on 2015 with total page 269 pages. Available in PDF, EPUB and Kindle. Book excerpt: Written by the founder of the field, this is a comprehensive and accessible introduction to structural DNA nanotechnology.

Download or read book Simulation of DNA Induced Self assembly of Nanoparticles written by and published by . This book was released on 2014 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Templated DNA directed Nanofabrication written by Cecilia Helena Lalander and published by . This book was released on 2010 with total page 162 pages. Available in PDF, EPUB and Kindle. Book excerpt: The main objective of this thesis was to develop a method to place individual building- blocks onto pre-ordinate positions on a templating nanopattern so that the building- blocks replicated the templating structures. The templating substrate was fabricated by a series of different processes conducted in the following sequence: electron-beam lithography, etching, chromium/gold evaporation and resist lift-off. The gold nanopatterns were functionalised with oligonucleotides (DNA) using thiol-gold chemistry and the building-blocks (DNA modified gold nanoparticles) were assembled onto the templating nanostructure by DNA-DNA interaction.The templating nanopattern consisted of gold features on a silicon substrate. A method to passivate the surrounding silicon surface was developed and the gold nanoparticles (AuNPs) hybridisation conditions were optimised. An assessment of the DNA-directed self-assembly of AuNPs was conducted. The hybridisation efficiency onto each adsorption site was 80% while the non-specific adsorption was 0.7%. Approximately 50% of all the six-dot lines had five AuNPs immobilised, while roughly 20% had six particles. The occurrence of defects could be repressed by modifying the geometry of the templating nanostructures.An additional objective was to develop a method to assemble AuNP structures into more complex structures that potentially could be used as building-blocks for additional self-assembly. For the nanostructures to be used as building-blocks they would have to be covalently interconnected (e.g. by cross-linking) prior to being released from the templating substrate, to ensure that their configuration remained intact upon release. Following the release, the templating substrate could be reused for additional AuNP self-assembly cycles.The release of the AuNPs and the reusability of DNA functionalised substrates was investigated on non-patterned substrates. It was found that AuNPs could be immobilised and released ten times without a statistically significant decrease in the number of particles immobilised per um2.A covalent cross-linking concept was developed and investigated for AuNPs im- mobilised onto non-patterned substrates. A clear difference in the release behaviour between AuNPs immobilised on substrates subjected to and not subjected to the cross- linking conditions was observed, which suggested that the cross-linking strategy was successful.When released AuNPs were recollected on capture substrates, no difference in the configuration of the released AuNPs was established between nanopatterns subject to and not subjected to the cross-linking conditions. It was found that the AuNPs were not stable at the temperatures required to drive the AuNPs release from the templating substrate and thus the temperature induced release of assembled nanostructures was not a viable option.Alternative systems, in which temperature is not used to drive the release of cross- linked nanostructures, could potentially circumvent the thermal instability of the particles. For example by using fuel-DNA to drive the desorption of cross-linked nanostructures, according to the work of Hazarika et al., or by using nanoprinting techniques to directly transfer the nanoparticle assemblies onto a capture substrate.

Download or read book Bottom up Construction of Complex Metal Nanoparticle Structures with DNA as a Chaperone written by Xin Luo and published by . This book was released on 2022 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: "Nanoscale metal structures has been an essential topic in modern nanotechnology due to their wide range of applications in catalysis, sensing, diagnosis, medicine and optics. Plasmonic metal nanostructures have attracted particular attention, as their light-focusing property can be efficiently tuned by changing their spatial structure. Traditionally, top-down lithography approaches have been the main tool to implement precise metal nanostructure designs, which, however, has shown drawbacks such as low throughput, high cost and low resolution when reaching the sub-5 nm scale. Over the past two decades, the field of DNA nanotechnology has enabled the fabrication of increasingly complex one-, two- and three-dimensional nanostructures with unprecedented specificity, programmability, and sub-nanometer precision. These DNA structures have been demonstrated to be an ideal chaperone for the bottom-up self-assembly of metal nanostructures, pushing the boundaries of plasmonic nanophotonics design and fabrication. This thesis targets a few challenges in constructing complex metal nanostructures with DNA as a template. First, to access hierarchical assembly in 3D, nanoparticles must be functionalized with anisotropic valency-controlled DNA strands. We developed a simple one-step method to encode 3D DNA strand patterns to gold nanoparticles with a controlled number of unique DNA strands in a predesigned spatial arrangement, through encapsulating the gold nanoparticle into a predesigned DNA minimal nanocage. The encapsulated gold nanoparticle, as a building block, inherits the 3D anisotropic molecular information from the DNA nanocage with enhanced structural stability, which allows its hierarchical self-assembly into complex metal architectures. Second, we developed an Assemble, Grow and Lift-Off (AGLO) strategy to construct robust standalone gold nanostructures with pre-designed customizable shapes in solution, using only a simple 2D DNA origami sheet as a transient template. AuNP seeds were assembled on DNA origami template in a predesigned shape, grown to merge into robust gold structures, and lifted-off to regenerate and recycle the DNA origami template. Finally, we discovered a Contact-dependent Localized Electrochemical Ripening (CLER) mechanism with DNA-templated metal growth, which, for the first time, systematically explains the heterogenous silver deposition phenomenon. The mechanism can be manipulated to synthesize deterministic asymmetric metal structures with core-shell NPs of pre-designed arrangements in a one-pot system, which demonstrates promising applications in surface-enhanced Raman spectroscopy. Overall, the work presented in this thesis not only pushes DNA-templated metal structures forward by demonstrating practical strategies to increase the 3D metal structure complexity and robustness, but also offers valuable fundamental insights in metal growth mechanisms. This knowledge provides guidelines for the future design and construction of DNA-templated metal structures. More importantly, the new mechanisms discovered contribute to the fundamental understanding of the metal nanoparticle synthesis process"--

Download or read book National Conference on Electrical Drives 3 written by and published by . This book was released on 1982 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book DNA Directed Self assembly of Plasmonic Nanoparticles written by Suchetan Pal and published by . This book was released on 2012 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Deoxyribonucleic acid (DNA), a biopolymer well known for its role in preserving genetic information in biology, is now drawing great deal of interest from material scientists. Ease of synthesis, predictable molecular recognition via Watson-Crick base pairing, vast numbers of available chemical modifications, and intrinsic nanoscale size makes DNA a suitable material for the construction of a plethora of nanostructures that can be used as scaffold to organize functional molecules with nanometer precision. This dissertation focuses on DNA-directed organization of metallic nanoparticles into well-defined, discrete structures and using them to study photonic interaction between fluorophore and metal particle. Presented here are a series of studies toward this goal. First, a novel and robust strategy of DNA functionalized silver nanoparticles (AgNPs) was developed and DNA functionalized AgNPs were employed for the organization of discrete well-defined dimeric and trimeric structures using a DNA triangular origami scaffold. Assembly of 1:1 silver nanoparticle and gold nanoparticle heterodimer has also been demonstrated using the same approach. Next, the triangular origami structures were used to co-assemble gold nanoparticles (AuNPs) and fluorophores to study the distance dependent and nanogap dependencies of the photonic interactions between them. These interactions were found to be consistent with the full electrodynamic simulations. Further, a gold nanorod (AuNR), an anisotropic nanoparticle was assembled into well-defined dimeric structures with predefined inter-rod angles. These dimeric structures exhibited unique optical properties compared to single AuNR that was consistent with the theoretical calculations. Fabrication of otherwise difficult to achieve 1:1 AuNP- AuNR hetero dimer, where the AuNP can be selectively placed at the end-on or side-on positions of anisotropic AuNR has also been shown. Finally, a click chemistry based approach was developed to organize sugar modified DNA on a particular arm of a DNA origami triangle and used them for site-selective immobilization of small AgNPs.

Download or read book Self assembly of DNA in Simulation written by Michael West and published by . This book was released on 2004 with total page 136 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Brownian Dynamics Study of the Self assembly of Ligated Gold Nanoparticles and Other Colloidal Systems written by Siddique J. Khan and published by . This book was released on 2012 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: We carry out Brownian Dynamics Simulations to study the self-assembly of ligated gold nanoparticles for various ligand chain lengths. First, we develop a phenomenological model for an effective nanoparticle-nanoparticle pair potential by treating the ligands as flexible polymer chains. Besides van der Waals interactions, we incorporate both the free energy of mixing and elastic contributions from compression of the ligands in our effective pair potentials. The separation of the nanoparticles at the potential minimum compares well with experimental results of gold nanoparticle superlattice constants for various ligand lengths. Next, we use the calculated pair potentials as input to Brownian dynamics simulations for studying the formation of nanoparticle assembly in three dimensions. For dodecanethiol ligated nanoparticles in toluene, our model gives a relatively shallower well depth and the clusters formed after a temperature quench are compact in morphology. Simulation results for the kinetics of cluster growth in this case are compared with phase separations in binary mixtures. For decanethiol ligated nanoparticles, the model well depth is found to be deeper, and simulations show hybrid, fractal-like morphology for the clusters. Cluster morphology in this case shows a compact structure at short length scales and a fractal structure at large length scales. Growth kinetics for this deeper potential depth is compared with the diffusion-limited cluster-cluster aggregation (DLCA) model. We also did simulation studies of nanoparticle supercluster (NPSC) nucleation from a temperature quenched system. Induction periods are observed with times that yield a reasonable supercluster interfacial tension via classical nucleation theory (CNT). However, only the largest pre-nucleating clusters are dense and the cluster size can occasionally range greater than the critical size in the pre-nucleation regime until a cluster with low enough energy occurs, then nucleation ensues. Late in the nucleation process the clusters display a crystalline structure that is a random mix of fcc and hcp lattices and indistinguishable from a randomized icosahedra structure. Next, we present results from detailed three-dimensional Brownian dynamics simulations of the self-assembly process in quenched short-range attractive colloids. Clusters obtained in the simulations range from dense faceted crystals to fractal aggregates which show ramified morphology on large length scales but close-packed crystalline morphology on short length scales. For low volume fractions of the colloids, the morphology and crystal structure of a nucleating cluster are studied at various times after the quench. As the volume fraction of the colloids is increased, growth of clusters is controlled by cluster diffusion and cluster-cluster interactions. For shallower quenches and low volume fractions, clusters are compact and the growth-law exponent agrees well with BinderStauffer predictions and with recent experimental results. As the volume fraction is increased, clusters do not completely coalesce when they meet each other and the kinetics crosses over to diffusion-limited cluster-cluster aggregation (DLCA) limit. For deeper quenches, clusters are fractals even at low volume fractions and the growth kinetics asymptotically reaches the irreversible DLCA case.

Download or read book Self Assembly of Nanostructures and Patchy Nanoparticles written by Shafigh Mehraeen and published by BoD – Books on Demand. This book was released on 2020-11-04 with total page 102 pages. Available in PDF, EPUB and Kindle. Book excerpt: Top-down approaches are currently the main contributor of fabricating microelectronic devices. However, the prohibitive cost of numerous technological steps in these approaches is the main obstacle to further progress. Furthermore, a large number of applications necessitate fabrication of complex and ultra-small devices that cannot be made using these approaches. New approaches based on natural self-assembly of matter need to be developed to allow for fabrication of micro and nanoelectronic devices. Self-assembly of nanostructures is a dynamic field, which explores physics of these structures and new ways to fabricate them. However, the major problem is how to control the properties of the nanostructures resulting from low dimensionality. This book presents recent advances made to address this problem, and fabricate nanostructures using self-assembly.