Download or read book Understanding Self assembly in Solution and at Interfaces Using All atom Molecular Dynamics Simulations and Enhanced Sampling Methods written by Arushi Prakash and published by . This book was released on 2018 with total page 234 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteins and biopolymers self-assemble to form nanostructures in solution or at interfaces. Notable examples include, the formation of plaque during Alzheimer’s disease, and the formation of protein-templates for biomineralization. Even though these assembly processes are well-studied, they remain poorly understood. The focus of this dissertation is to investigate early-stage assembly processes, including adsorption of particles on surfaces, and oligomer formation using classical molecular dynamics and enhanced sampling methods (like metadynamics and umbrella sampling). As these systems are explored, improved protocols for enhanced sampling of protein-adsorption simulations are developed to tackle the roles of ions in simulations, and to incorporate experimental data into the sampling using Bayesian inference. Further, a new sampling method is developed to make these enhanced sampling simulations more efficient.
Download or read book Self assembly at Solution solid Interfaces written by Henry D. Castillo and published by . This book was released on 2020 with total page 161 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular self-assembly at surfaces offers an efficient route to highly-ordered organic films that can be programmed for a variety of applications. However, the success of these materials depends on the ability to program intermolecular interactions that determine ordering at the surface. We study three systems: alkoxybenzonitriles (ABNs), tricarbazolo triazolophane macrocycles (tricarb), and triazolobenzene oligomers in flexible or macrocycle forms. For each model system, experiments employ a range of molecules in which aspects of molecular structure, especially symmetry and peripheral functionalization, are systematically varied to study the impact of intermolecular interactions on 2D supramolecular structure and to gain a deeper understanding of fundamental assembly mechanisms. The supramolecular assemblies are studied by scanning tunneling microscopy (STM) and molecular dynamic (MD) simulations at the solution/graphite interface. Variations in assembly conditions, including solvent, concentration, and temperature, also provide insight into assembly. ABNs exhibit competitive assembly with solvent that can be controlled with alkyl length. MD simulations on nanosecond timescales provide insight into ABN desorption, re-adsorption, and on-surface processes, and simulations reveal an asymmetry in desorption pathways. Triazolobenzene oligomers can be tuned between tight and loose packing of aromatic cores, the latter being separated by lamellar rows of alkanes. Flexible frameworks assemble more slowly compared to macrocycles due to a large conformational space, but self-assembly can be accelerated by co-solutes and STM perturbation. Tricarb exhibits polymorphism, and tricarb-tricarb hydrogen bonding can be controlled by varying the length and symmetry of peripheral alkanes into various structures including a high-density disordered packing. Variable solvent and peripheral group studies indicate that transitions from disordered to ordered structures involve a solution-mediated annealing pathway. MD simulations reveal solvent insertion between tricarb leading to disordered structures, but these can be sterically blocked by longer alkanes. The discoveries presented in this thesis provide insights into the dynamics and design rules of self-assembly.
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 Synthetic Biology written by Luc Brunsveld and published by Royal Society of Chemistry. This book was released on 2017-11-29 with total page 196 pages. Available in PDF, EPUB and Kindle. Book excerpt: Leading researchers draw on the recent literature in Synthetic Biology, from both dedicated journals and broader sources, making this an essential reference to any library supporting this research in this emerging field.
Download or read book Self Assembling Systems written by Li-Tang Yan and published by John Wiley & Sons. This book was released on 2016-10-06 with total page 384 pages. Available in PDF, EPUB and Kindle. Book excerpt: Provides comprehensive knowledge on concepts, theoretical methods and state-of-the-art computational techniques for the simulation of self-assembling systems Looks at the field of self-assembly from a theoretical perspective Highlights the importance of theoretical studies and tailored computer simulations to support the design of new self-assembling materials with useful properties Divided into three parts covering the basic principles of self-assembly, methodology, and emerging topics
Download or read book Self assembly Dynamics and Energetics at the Solution solid Interface written by Kirill Gurdumov and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: A comprehensive investigation on the formation dynamics and energetics of adlayer formation at the at the solution/solid interface has been performed using scanning tunneling microscopy (STM) with a custom solution flow cell design that offers new insight into the self-assembly process. Understanding the formation kinetics and thermodynamics of self-assembled monolayers (SAM) provides insight into the delicate balance of intermolecular forces on the molecular scale. We herein investigate the growth, dynamics, and stability of a model non-covalent self-assembler -- Co(II) octaethylporphyrin at the solution/solution interface on the HOPG and Au(111) surfaces. Real-time imaging of the nucleation and growth of the self-assembled layer was captured and studied by in-situ STM, and further explored using computational methods. A custom STM solution flow cell was designed and implemented to allow for in-situ monitoring of self-assembly at very low concentrations and with volatile solvents. Flow studies at low concentration provide insight into early-stage kinetics and structural formation of a SAM. It was found that the choice of organic solvent plays a dramatic role in the kinetics and structure of the SAM. These results, in turn, provide insight into the balance of the intermolecular forces driving the self-assembly. The role of the solvent was particularly strong in the case of 1,2,4-trichlorobenzene (TCB) on both HOPG and Au(111). Under TCB, a very stable rectangular structure is formed and stabilized by solvent-incorporation. A transition to a solvent free pseudo-hexagonal structure was only observed when extremely high concentrations of porphyrin were present in solution. Similarly, in the case of CoOEP adsorbed on Au(111) under toluene, a solvent-incorporated rectangular structure was observed that, like the TCB case, transitioned into a pseudo-hexagonal structure, but this transition occurred at much lower concentrations of porphyrin. Toluene co-adsorption was not observed on HOPG. When deposited from decane, a short-lived pseudo-rectangular structure was observed on Au(111) but not on HOPG. Only the pseudo-hexagonal structure was observed in the porphyrin adlayer when 1-phenyloctane were used as a solvent. On HOPG, mixed solvent competition was tested and gave further insight into the thermodynamic and kinetic roles that solvents play in self-assembly.
Download or read book Self Assembly written by John A. Pelesko and published by CRC Press. This book was released on 2007-05-21 with total page 332 pages. Available in PDF, EPUB and Kindle. Book excerpt: Hailed as one of the key areas of nanoscience likely to shape future scientific research, self-assembly offers the most promising route to true molecular nanotechnology. Focusing on this dynamic new field, Self Assembly: The Science of Things That Put Themselves Together explores nature's self-assembly of structures, the use of it to build engineer
Download or read book Systems Self Assembly written by and published by Elsevier. This book was released on 2011-09-22 with total page 369 pages. Available in PDF, EPUB and Kindle. Book excerpt: Systems Self-Assembly is the only book to showcase state-of-the-art self-assembly systems that arise from the computational, biological, chemical, physical and engineering disciplines. Written by world experts in each area, it provides a coherent, integrated view of both book practice examples and new trends with a clearly presented computational flavor. The unifying thread throughout the text is the computational nature of self-assembling systems. This book consists of 13 chapters dealing with a variety of topics such as the patterns of self-organised nanoparticle assemblies; biomimetic design of dynamic self-assembling systems; computing by self-assembly involving DNA molecules, polyominoes, and cells; evolutionary design of a model of self-assembling chemical structures; self-assembly as an engineering concept across size scales; and probabilistic analysis of self-assembled molecular networks. Other chapters focus on the programming language of dynamic self-assembly; self-assembled computer architectures; simulation of self-assembly processes using abstract reduction systems; computer aided search for optimal self-assembly systems; theoretical aspects of programmable self-assembly; emergent cooperativity in large-scale patterns; and automated self-assembling programming. Systems Self-Assembly is an ideal reference for scientists, researchers and post-graduate students; practitioners in industry, engineering and science; and managers, decision-makers and policy makers. The only book to showcases state-of-the-art self-assembly systems that arise from the computational, biological, chemical, physical and engineering disciplines Coherent, integrated view of both book practice examples and new trends with a clearly presented computational flavor Written by world experts in each area
Download or read book Self assembly at Ionic Liquid based Interfaces written by Denzil Frost and published by . This book was released on 2013 with total page 333 pages. Available in PDF, EPUB and Kindle. Book excerpt: Liquid-liquid interfaces serve as ideal 2-D templates on which solid particles can self-assemble into various structures. These self-assembly processes are important in fabrication of micron-sized devices and emulsion formulation. At oil/water interfaces, these structures can range from close-packed aggregates to ordered lattices. By incorporating an ionic liquid (IL) at the interface, new self-assembly phenomena emerge. ILs are ionic compounds that are liquid at room temperature (essentially molten salts at ambient conditions) that have remarkable properties such as negligible volatility and high chemical stability and can be optimized for nearly any application. The nature of IL-fluid interfaces has not yet been studied in depth. Consequently, the corresponding self-assembly phenomena have not yet been explored. We demonstrate how the unique molecular nature of ILs allows for new self-assembly phenomena to take place at their interfaces. These phenomena include droplet bridging (the self-assembly of both particles and emulsion droplets), spontaneous particle transport through the liquid-liquid interface, and various gelation behaviors. In droplet bridging, self-assembled monolayers of particles effectively "glue" emulsion droplets to one another, allowing the droplets to self-assembly into large networks. With particle transport, it is experimentally demonstrated the ILs overcome the strong adhesive nature of the liquid-liquid interface and extract solid particles from the bulk phase without the aid of external forces. These phenomena are quantified and corresponding mechanisms are proposed. The experimental investigations are supported by molecular dynamics (MD) simulations, which allow for a molecular view of the self-assembly process. In particular, we show that particle self-assembly depends primarily on the surface chemistry of the particles and the non-IL fluid at the interface. Free energy calculations show that the attractive forces between nanoparticles and the liquid-liquid interface are unusually long-ranged, due to capillary waves. Furthermore, IL cations can exhibit molecular ordering at the IL-oil interface, resulting in a slight residual charge at this interface. We also explore the transient IL-IL interface, revealing molecular interactions responsible for the unusually slow mixing dynamics between two ILs. This dissertation, therefore, contributes to both experimental and theoretical understanding of particle self-assembly at IL based interfaces.
Download or read book Free Energy Calculations written by Christophe Chipot and published by Springer Science & Business Media. This book was released on 2007-01-08 with total page 528 pages. Available in PDF, EPUB and Kindle. Book excerpt: Free energy constitutes the most important thermodynamic quantity to understand how chemical species recognize each other, associate or react. Examples of problems in which knowledge of the underlying free energy behaviour is required, include conformational equilibria and molecular association, partitioning between immiscible liquids, receptor-drug interaction, protein-protein and protein-DNA association, and protein stability. This volume sets out to present a coherent and comprehensive account of the concepts that underlie different approaches devised for the determination of free energies. The reader will gain the necessary insight into the theoretical and computational foundations of the subject and will be presented with relevant applications from molecular-level modelling and simulations of chemical and biological systems. Both formally accurate and approximate methods are covered using both classical and quantum mechanical descriptions. A central theme of the book is that the wide variety of free energy calculation techniques available today can be understood as different implementations of a few basic principles. The book is aimed at a broad readership of graduate students and researchers having a background in chemistry, physics, engineering and physical biology.
Download or read book Solvent Mediated Self assembly of Solids written by and published by . This book was released on 1997 with total page 23 pages. Available in PDF, EPUB and Kindle. Book excerpt: Solvent-mediated crystallization represents a robust approach to self-assembly of nanostructures and microstructures. In organic systems, the relative ease with which the structure of hydrogen- bonded molecules can be manipulated allows for generation of a wide variety of nanoscale crystal structures. In living organisms, control over the micron-to-millimeter form of inorganic crystals is achieved through introduction of bio-organic molecules. The purpose of this proposal is to understand the interplay between solution chemistry, molecular structure, surface chemistry, and the processes of nucleation and crystal growth in solvent-mediated systems, with the goal of developing the atomic and molecular basis of a solvent-mediated self-assembly technology. We will achieve this purpose by: (1) utilizing an atomic force microscopy (AFM) approach that provides in situ, real time imaging during growth from solutions, (2) by modifying kinetic Monte Carlo (KMC) models to include solution-surface kinetics, (3) by introducing quantum chemistry (QC) calculations of the potentials of the relevant chemical species and the near-surface structure of the solution, and (4) by utilizing molecular dynamics (MD) simulations to identify the minimum energy pathways to the solid state. Our work will focus on two systems chosen to address both the manometer and micron-to-millimeter length scales of assembly, the family of 2,5- diketopiperazines (X-DKPs) and the system of CaCO3 with amino acids. Using AFM, we will record the evolution of surface morphology, critical lengths, step speeds, and step-step interactions as a function of supersaturation and temperature. In the case of the X-DKPs, these measurements will be repeated as the molecular structure of the growth unit is varied. In the case of CaCO3, they will be performed as a function of solution chemistry including pH, ionic strength, and amino acid content. In addition, we will measure nucleation rates and orientations of CaCO3 on polyamino acid templates. From these measurements, we will extract fundamental growth parameters for input into KMC simulations whose predictions will in turn be compared to the experimental observations. The KMC simulations will incorporate atomic processes representing the minimum energy pathways as determined from the MD calculations. The interaction potentials of the relevant chemical species as well as the hydrated surface, including the electrochemical double layer, used in the MD simulations will be determined using coupled solutions to the Schrodinger and Poisson-Boltzmann equations which take account of electronic relaxation effects.
Download or read book Molecular Self assembly at Interfaces written by Christopher Min-Far Yip and published by . This book was released on 1996 with total page 576 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Molecular Engineering of Peptide inorganic Interfaces written by Tyler Dean Jorgenson and published by . This book was released on 2020 with total page 151 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bio-inorganic interfaces, in which biomolecules intimately contact inorganic materials, have become the centerpiece for advanced technologies in medicine, catalysis, and electronics. Considering the convolutional complexity of interfaces involving environmental conditions and biomolecular and inorganic surface intricacies, it is of utmost importance to obtain a fundamental understanding of molecular conformations, interactions, and hybrid interfacial properties. Based on such basic understanding, it becomes feasible to engineer molecules with the tailored ability to spontaneously build-up, via self-assembly, a bio-inorganic interface with desired device relevant properties. It has been recognized in this Thesis that solid-binding peptides are suited perfectly for this molecular engineering task due to their vast sequence space, labile conformational nature, and reliance on soft intermolecular interactions that can be fine-tuned through environmental controls, and ability to form long-range ordered structures. Here, solid-binding peptides designed to bind and assemble on graphite surfaces are interrogated using scanning probe microscopy techniques and molecular dynamics simulations to explore and control their self-assembly pathway. Thermal selection of peptide conformations is shown to direct the long-range ordering of peptides at graphite surfaces. Through energetic analysis of peptide-graphite interactions, using a technique dubbed Intrinsic Friction Analysis, the molecular implications of thermal conformational selection are elucidated and used to rationally design a peptide with tailored binding energy and assembly structure. The impacts of these thermally selected conformations on electron transport across the bio-inorganic interface are interrogated via scanning tunneling spectroscopy and metadynamics, revealing control over device relevant properties. Peptide-substrate recognition is explored using atomic resolution microscopy to understand peptide miscibility and nucleation in binary assemblies. Finally, the role of lateral confinement on self-assembly is explored, revealing unexpected peptide adsorption and assembly phenomena enabling tailored self-assembly at various length scales. From these fundamental insights, novel bio-inorganic devices can be rationally designed for targeted technological applications.
Download or read book Fuzziness written by Monika Fuxreiter and published by Springer Science & Business Media. This book was released on 2012-03-07 with total page 210 pages. Available in PDF, EPUB and Kindle. Book excerpt: Detailed characterization of fuzzy interactions will be of central importance for understanding the diverse biological functions of intrinsically disordered proteins in complex eukaryotic signaling networks. In this volume, Peter Tompa and Monika Fuxreiter have assembled a series of papers that address the issue of fuzziness in molecular interactions. These papers provide a broad overview of the phenomenon of fuzziness and provide compelling examples of the central role played by fuzzy interactions in regulation of cellular signaling processes and in viral infectivity. These contributions summarize the current state of knowledge in this new field and will undoubtedly stimulate future research that will further advance our understanding of fuzziness and its role in biomolecular interactions.
Download or read book Improved Conformational Sampling Methods for Molecular Dynamics Simulations written by Asim Okur and published by . This book was released on 2007 with total page 366 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Molecular Dynamics Simulations of Self assembly and Its Implications on Optical Properties written by Johannes Träg and published by . This book was released on 2021 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Coarse Graining of Condensed Phase and Biomolecular Systems written by Gregory A. Voth and published by CRC Press. This book was released on 2008-09-22 with total page 492 pages. Available in PDF, EPUB and Kindle. Book excerpt: Exploring recent developments in the field, Coarse-Graining of Condensed Phase and Biomolecular Systems examines systematic ways of constructing coarse-grained representations for complex systems. It explains how this approach can be used in the simulation and modeling of condensed phase and biomolecular systems. Assembling some of the most influential, world-renowned researchers in the field, this book covers the latest developments in the coarse-grained molecular dynamics simulation and modeling of condensed phase and biomolecular systems. Each chapter focuses on specific examples of evolving coarse-graining methodologies and presents results for a variety of complex systems. The contributors discuss the minimalist, inversion, and multiscale approaches to coarse-graining, along with the emerging challenges of coarse-graining. They also connect atomic-level information with new coarse-grained representations of complex systems, such as lipid bilayers, proteins, peptides, and DNA.
