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Simulation Studies Of The Mechanisms Of Interaction Between Carbon Nanotubes And Amino Acids
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Book Synopsis Simulation Studies of the Mechanisms of Interaction Between Carbon Nanotubes and Amino Acids by : George Bassem Botros Abadir
Download or read book Simulation Studies of the Mechanisms of Interaction Between Carbon Nanotubes and Amino Acids written by George Bassem Botros Abadir and published by . This book was released on 2010 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Molecular Dynamics Investigation of Single-walled Carbon Nanotubes with Soluble Proteins by : Aryan Vahedi-Faridi
Download or read book Molecular Dynamics Investigation of Single-walled Carbon Nanotubes with Soluble Proteins written by Aryan Vahedi-Faridi and published by . This book was released on 2015 with total page 332 pages. Available in PDF, EPUB and Kindle. Book excerpt: Many biotechnology applications rely on immobilization of macromolecules to inert surfaces or the detection of biological reactions on biosensor surfaces. Thus, due to their unique physical, chemical and electrical properties, carbon nanotubes have attracted a lot in interest in the scientific community. This study was aimed at elucidating mechanisms for potential interactions between proteins and single-walled carbon nanotubes (SWCNTs). Through use of atomistic molecular dynamics simulations, the non-bonded interactions of the well-characterized green fluorescent protein (GFP) and cellulose hydrolyzing enzyme cellobiohydrolase I (CEL7A) with a SWCNT of small diameter have been investigated. After 100 ns simulations, a residue-based method was applied to subsequent energy calculations in order to better characterize the mechanisms of adsorption between a SWCNT and each protein. For both simulations, it was observed that adsorption to SWCNT was preferred along flexible sections of turn and bend residues in between more recognizable secondary structure features. For GFP, residues adjacent to turn 2 of the protein's crystal structure were found to mediate interactions which maintained conformation of the protein when SWCNT was present. Altered dynamics of conserved residues in the chromophore region suggested that presence of SWCNT might impede fluorescent activity of the protein. For CEL7A, residues of the N-terminus were found to contribute to migration of the N-terminal end from a position adjacent to the enzyme to a position along the nanotube sidewall. This migration prevented equilibration of the enzyme within the simulation time frame, suggesting that cellulolytic activity of CEL7A could be compromised in the presence of SWCNT. Observation of the SWCNT preference for localization along flexible turn/bend residues of soluble proteins may serve to inform the design of protein-nanotube conjugates. The study has also established methods and procedures for simulating and modeling protein-SWCNT interactions. -- Abstract.
Author :Konstantinos I. Tserpes Publisher :Springer Science & Business Media ISBN 13 :3319012010 Total Pages :341 pages Book Rating :4.3/5 (19 download)
Book Synopsis Modeling of Carbon Nanotubes, Graphene and their Composites by : Konstantinos I. Tserpes
Download or read book Modeling of Carbon Nanotubes, Graphene and their Composites written by Konstantinos I. Tserpes and published by Springer Science & Business Media. This book was released on 2013-10-15 with total page 341 pages. Available in PDF, EPUB and Kindle. Book excerpt: A large part of the research currently being conducted in the fields of materials science and engineering mechanics is devoted to carbon nanotubes and their applications. In this process, modeling is a very attractive investigation tool due to the difficulties in manufacturing and testing of nanomaterials. Continuum modeling offers significant advantages over atomistic modeling. Furthermore, the lack of accuracy in continuum methods can be overtaken by incorporating input data either from experiments or atomistic methods. This book reviews the recent progress in continuum modeling of carbon nanotubes and their composites. The advantages and disadvantages of continuum methods over atomistic methods are comprehensively discussed. Numerical models, mainly based on the finite element method, as well as analytical models are presented in a comparative way starting from the simulation of isolated pristine and defected nanotubes and proceeding to nanotube-based composites. The ability of continuum methods to bridge different scales is emphasized. Recommendations for future research are given by focusing on what still continuum methods have to learn from the nano-scale. The scope of the book is to provide current knowledge aiming to support researchers entering the scientific area of carbon nanotubes to choose the appropriate modeling tool for accomplishing their study and place their efforts to further improve continuum methods.
Book Synopsis Mechanical Behaviors of Carbon Nanotubes by : K.M. Liew
Download or read book Mechanical Behaviors of Carbon Nanotubes written by K.M. Liew and published by William Andrew. This book was released on 2016-12-25 with total page 463 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mechanical Behaviors of Carbon Nanotubes: Theoretical and Numerical Approaches presents various theoretical and numerical studies on mechanical behaviors of carbon nanotubes. The main theoretical aspects included in the book contain classical molecular dynamics simulation, atomistic-continuum theory, atomic finite element method, continuum plate, nonlocal continuum plate, and shell models. Detailed coverage is also given to structural and elastic properties, trace of large deformation, buckling and post-buckling behaviors, fracture, vibration characteristics, wave propagation, and the most promising engineering applications. This book not only illustrates the theoretical and numerical methods for analyzing the mechanical behavior of carbon nanotubes, but also contains computational results from experiments that have already taken place. Covers various theoretical and numerical studies, giving readers a greater understanding of the mechanical behavior of carbon nanotubes Includes multiscale methods that provide the advantages of atomistic and continuum approaches, helping readers solve complex, large-system engineering problems Allows engineers to create more efficient carbon nanotube structures and devices
Book Synopsis Multiscale Simulation Studies of Interactions of Carbon Nanotubes with Biopolymers and Lipid Bilayer by : Edita Sarukhanyan
Download or read book Multiscale Simulation Studies of Interactions of Carbon Nanotubes with Biopolymers and Lipid Bilayer written by Edita Sarukhanyan and published by . This book was released on 2013 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Carbon Nanotubes as Nanodelivery Systems by : Melvin Choon Giap Lim
Download or read book Carbon Nanotubes as Nanodelivery Systems written by Melvin Choon Giap Lim and published by Springer Science & Business Media. This book was released on 2013-05-18 with total page 68 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book showcases the application of carbon nanotubes as nanodelivery systems for copper atoms, using molecular dynamics simulations as a means of investigation. The nanodelivery system of the carbon nanotube presents the possible usage of the carbon structure in many areas in the future. This book is comprehensive and informative, and serves as a guide for any reader who wishes to perform a molecular dynamics simulation of his own and to conduct an analytical study of a molecular system.
Book Synopsis Foundations of Nanotechnology, Volume Three by : Saeedeh Rafiei
Download or read book Foundations of Nanotechnology, Volume Three written by Saeedeh Rafiei and published by CRC Press. This book was released on 2015-05-08 with total page 290 pages. Available in PDF, EPUB and Kindle. Book excerpt: In this research notes book, the modelling of mechanical properties of CNT/polymer nanocomposites is presented. The book begins with the structural and intrinsic mechanical properties of CNTs and then introduces computational methods that have been applied to polymer nanocomposites, covering from molecular scale (molecular dynamics, Monte Carlo), m
Book Synopsis Carbon Nanotube-Polymer Composites by : Dimitrios Tasis
Download or read book Carbon Nanotube-Polymer Composites written by Dimitrios Tasis and published by Royal Society of Chemistry. This book was released on 2015-11-09 with total page 293 pages. Available in PDF, EPUB and Kindle. Book excerpt: Chemically-modified carbon nanotubes (CNTs) exhibit a wide range of physical and chemical properties which makes them an attractive starting material for the preparation of super-strong and highly-conductive fibres and films. Much information is available across the primary literature, making it difficult to obtain an overall picture of the state-of-the-art. This volume brings together some of the leading researchers in the field from across the globe to present the potential these materials have, not only in developing and characterising novel materials but also the devices which can be fabricated from them. Topics featured in the book include Raman characterisation, industrial polymer materials, actuators and sensors and polymer reinforcement, with chapters prepared by highly-cited authors from across the globe. A valuable handbook for any academic or industrial laboratory, this book will appeal to newcomers to the field and established researchers alike.
Book Synopsis Computational Bioengineering by : Guigen Zhang
Download or read book Computational Bioengineering written by Guigen Zhang and published by CRC Press. This book was released on 2015-04-01 with total page 508 pages. Available in PDF, EPUB and Kindle. Book excerpt: Arguably the first book of its kind, Computational Bioengineering explores the power of multidisciplinary computer modeling in bioengineering. Written by experts, the book examines the interplay of multiple governing principles underlying common biomedical devices and problems, bolstered by case studies. It shows you how to take advantage of the la
Book Synopsis A Study of Peptide Affinity for Carbon Nanotubes Through Phage Display Experiments by : Caroline Kar Yan Lau
Download or read book A Study of Peptide Affinity for Carbon Nanotubes Through Phage Display Experiments written by Caroline Kar Yan Lau and published by . This book was released on 2004 with total page 60 pages. Available in PDF, EPUB and Kindle. Book excerpt: The use of biological molecules to facilitate the dispersal, separation and assembly of nanoscopic entities such as carbon nanotubes has received great attention and has been the focus of much current research activity. In this work we sought to identify peptide sequences with selective affinity for HiPco-produced SWNTs in order to gain some insight to the binding mechanisms and interactions. This was done using a phage display technique, in which a library of bacteriophages displaying greater than 109 different 12-amino acid long peptide sequences were exposed to carbon nanotubes. Non-specifically bound phages were successively washed off with increasingly stronger detergents until only tightly binding phages remained. It was observed that after six rounds of phage display tests, the percentage of sites of aromatic ring-containing amino acids increased while the percentage of sites of aliphatic amino acids decreased. Results were compared to previous phage display results on MWNTs. These results suggest that peptides are able to distinguish between different allotropes of carbon and that their highly specific binding mechanisms can be exploited in the future for use in precision placement of nanoscale components in devices such as electronic circuits and sensors.
Download or read book Carbon Nanotube Devices written by and published by John Wiley & Sons. This book was released on 2008-05-05 with total page 384 pages. Available in PDF, EPUB and Kindle. Book excerpt: Following on from the first AMN volume, this handy reference and textbook examines the topic of nanosystem design in further detail. It explains the physical and chemical basics behind the design and fabrication of nanodevices, covering all important, recent advances in the field, while introducing nanosystems to less experienced readers. The result is an important source for a fast, accurate overview of the state of the art of nanosystem realization, summarizing further important literature.
Book Synopsis Synthesis, Characterisation and Biological Activity of Functionalised Carbon Nanotubes by : Davide Pantarotto
Download or read book Synthesis, Characterisation and Biological Activity of Functionalised Carbon Nanotubes written by Davide Pantarotto and published by . This book was released on 2005 with total page 205 pages. Available in PDF, EPUB and Kindle. Book excerpt: Carbon nanotubes (CNT) consist of graphene sheets rolled-up into a tubular form. Since their discovery, they appeared immediately as an interesting material for technological applications, including for instance the fabrication of nanoelectronic components. Recently, CNT have also attracted much attention for their potential in biological applications. The main difficulty to integrate this material into biological systems derives from its complete lack of solubility in organic solvents and aqueous solutions. The ability to solubilise and separate individual CNT is still a great challenge. A very general way to achieve this is by organic functionalisation, which is a rapidly expanding field.In this thesis, I focused my interests on the synthesis and use of the first water soluble side-wall functionalised carbon nanotubes. I employed the 1,3-dipolar cicloaddition of azomethine ylides to carbon nanotubes. I have demonstrated that it is possible to further derivatise them by coupling single N-protected amino acids. This was the first step towards the preparation of covalently linked peptide-carbon nanotube conjugates. In this context, I have developed a powerful strategy for linking bioactive peptides to carbon nanotubes for immunological applications.Immobilisation of peptides to the external walls of carbon nanotubes may find interesting applications in diagnostics, vaccine and drug delivery or multipresentation of bioactive molecules.For this aim, peptides with immunological properties were selected for their coupling to the external surface of the CNT. The immunological reactivity and the peptide recognition were assessed by a peptide specific antibody using surface plasmon resonance and ELISA test.These experiments showed that the peptide linked to CNT retain its conformational characteristics for antibody recognition. Furthermore, biological studies performed in vivo demonstrated that CNT-peptide conjugates elicited high antibody titers. Significant pathogen neutralising capacity was observed for the antibodies induced by CNT-peptide conjugates. This highlights: 1) the potential of carbon nanotubes for vaccine delivery, and 2) the importance of antigen presentation in vivo for the induction of antibodies with the right specificity.Functionalised carbon nanotubes have been showed able to cross the cell membrane and to accumulate in the cytoplasm or reach the nucleus without being toxic for the cell up to 10 μM concentration. These findings highlight the potential use of peptide-carbon nanotube conjugates for diagnostic purposes and pave the way for their application in vaccine and drug delivery. Although the elucidation of the mechanism of entry requires further investigations, I excluded active ATP dependent endocytosis. This is because inhibitors of endosome-mediated translocation and decrease of the incubation temperature did not prevent cellular uptake of the different functionalised CNT. In addition, TEM images revealed the tubes crossing the cell membrane as nano-needles without any perturbation or disruption of the membrane.Cell viability after treatment with functionalised nanotubes has also been largely investigated. Highly soluble functionalised CNT in aqueous biological media exhibited notably reduced cellular toxicity in vitro. Cell viability was studied using flow cytometry.Following the synthesis of positively charged carbon nanotubes I investigate their interaction with plasmid DNA. The cationic-anionic interaction between CNT and DNA has been characterised by different techniques both qualitatively and quantitatively. TEM, photocorrelation spectroscopy, SPR and electrophoresis allowed to describe the stability of the CNT-DNA complexes. The condensation of genetic material onto the carbon nanotubes was then confirmed and biological test were performed. The excellent ability of the ammonium functionalised carbon nanotubes to enter cells and potentially reach their nuclei was exploited for the delivery of plasmid DNA. In vitro experiments showed a high level of gene expression when mammalian cells were transfected with DNA-CNT complexes. The following success obtained in in vivo treatment of mice, highlighted the possibility to use this system for gene delivery in gene therapy. Preliminary comparative gene expression data between functionalised CNT:DNA and commercially available lipid:DNA delivery systems showed that our first generation CNT-based gene delivery system is less efficient for in vitro transfection than the lipid:DNA system. However, there is a lot of room for further improvement of the carbon nanotube system for gene delivery.In conclusion, in this Thesis it was possible to develop and characterise a new chemical macromolecular architecture exploitable as new tool for molecular delivery, and molecular recognition. The further development of carbon nanotube chemistry, the optimisation of their interaction with biomolecules and their use in biomedical applications represent the future perspectives of this research.
Book Synopsis Modelling Interaction of DNA with Carbon Nanostructures by : Mansoor Hassan S. Alshehri
Download or read book Modelling Interaction of DNA with Carbon Nanostructures written by Mansoor Hassan S. Alshehri and published by . This book was released on 2014 with total page 142 pages. Available in PDF, EPUB and Kindle. Book excerpt: This thesis focuses on the development of mathematical models for the interaction between deoxyribonucleic acid molecules (DNA) and certain carbon nanostructures. We model such atomic interactions by adopting the 6-12 Lennard-Jones potential and the continuum approach. The latter assumes that a discrete atomic structure can be replaced with an average constant atomic surface density of atoms that is assumed to be smeared over each molecule, in our case a DNA molecule and a carbon nanostructure. First, we develop a mathematical model for the interaction between a deoxyribonucleic acid molecule and a carbon nanotube, and we examine the storage of DNA molecules in carbon nanotubes. Following earlier authors, the carbon nanotube is modelled as a right circular cylinder, while the helical structure of the DNA molecule is modelled as a continuously twisted ribbon. We next determine the binding energies between DNA molecules interacting with a graphene sheet, and finally, we determine the binding energies of a C60 fullerene interacting with a DNA molecule. Experiments in nanotechnology are often expensive and time consuming, and mathematical models and numerical simulations are necessary to complement the efforts of experimentalists and to confirm observed experimental outcomes. Despite recent improvements in the rapidity of numerical simulations, they can be more time consuming than the direct evaluation of an analytical expression arising from a mathematical model, because of the large numbers of atoms and force-field calculations that may be involved. Although a mathematical model will necessarily include many assumptions and approximations, nevertheless often the main physical parameters and optimal configurations can be accurately predicted. The model calculations presented here for ideal systems, represent average outcomes, and generally there is good agreement with any existing numerical results that are obtained from more intensive computational schemes. Here, we model the mechanics of the encapsulation of DNA molecules in carbon nanotubes to determine the optimal carbon nanotube that encloses the DNA molecule. The total interaction energy is calculated from the continuum approximation, where the atoms in each structure are assumed to be smeared over the surfaces of an ideal cylinder and a twisted ribbon, and the optimal carbon nanotube to enclose the DNA molecule is derived as the minimum energy configuration. Moreover, the binding energies between the DNA molecule adsorbing onto a graphene surface are derived by minimizing the binding energies to determine the preferred locations of the DNA molecules with respect to the graphene sheet. Finally, the binding of C60 to a DNA molecule is investigated, again by adopting the continuum approximation for modelling nanostructures. In summary, the original contribution of this thesis is the development of ideal mathematical models and new analytical formulae for the interaction energy between deoxyribonucleic acid molecules and various types of carbon nanostructures, including carbon nanotubes, graphite, and C60 fullerene. The interaction energies between the DNA molecules and the nanostructures are determined analytically from the mathematical models and thus can be readily evaluated using standard computer algebra packages such as MAPLE and MATLAB. Hence, the interaction mechanisms and equilibrium configurations for a wide variety of systems might be fully and quickly investigated.
Book Synopsis Recent Developments in Modeling and Applications of Carbon Nanotubes by : Q. Wang
Download or read book Recent Developments in Modeling and Applications of Carbon Nanotubes written by Q. Wang and published by . This book was released on 2009-01-01 with total page 201 pages. Available in PDF, EPUB and Kindle. Book excerpt: Carbon nanotubes are macromolecules of carbon in a periodic hexagonal arrangement with a cylindrical shell shape. Carbon nanotubes have been subjected to extensive research, with subsequent predictions of extremely high strength and exceptional electronic and thermal properties. They also hold substantial promise as fibers in composites and other devices for the development of superconductive devices for micro-electro-mechanical and nano-electro-mechanical system applications. It is expected that the material has great potential in biological, medical, energy storage, sensor, and other applications. It has been broadly recognized that atomic modeling of carbon nanotube is a powerful tool for analysis of carbon nanotube. Due to massive computations involved, the atomic modeling is limited to systems with a small number of molecules and atoms. On the other hand, attempts at applying continuum mechanics models to better investigate the analysis of carbon nanotube with large sizes have been initiated. However, continuum models are unable to adequately capture the atomic structures of carbon nanotube, and the applicability of the models needs to be justified. Recently, developments of multiscale methods have been proposed to the analysis of carbon nanotube. This book is dedicated to the publication of recent developments in modeling of carbon nanotube via atomic modeling, continuum modeling and multiscale methods for predictions of mechanical, electronic, and thermal properties of carbon nanotube. A wide range of fundamentally theoretical, computational topics on modeling and applications of carbon nanotube will be covered in the book. In addition, applications of carbon nanotubes as nano-devices in atomic and molecular transportations and bistable devices in switching or memory elements in signal processing and communications are also reported. It is with great pleasure that we present this book that covers a very wide and varied range of subject areas in modeling and applications of carbon nanotubes. The first chapter employs molecular dynamics simulations to show macroscopic flows of atomic and molecular hydrogen, helium, and a mixture of both gases both inside and outside a carbon nanotube. In particular, the simulations show a nanoseparation effect of the two gases. The new results in the chapter show the mass selectivity of the nanopumping effect can be used to develop a highly selective filter for various gases. The second chapter introduces a fine continuum model that is developed by virtue of the higher-order continuum theory. Moreover, a mesh-free computational framework is developed to implement the numerical simulation of single- walled carbon nanotubes. The rationality of the higher-order continuum model and the efficiency of mesh-free method are illustrated and discussed in the chapter. The study on the mechanics of buckled single-walled and multiwalled carbon nanotubes, carbon nanotube bundles and coupling effect between adjacent carbon nanotubes is reported in chapter three. Simple expressions of the buckle wavelength, amplitude and critical strain for buckling are given analytically, which show good agreement with experiments. Chapter 4 investigate the applicability of elastic shell model in analysis of graphene and carbon nanotubes. The author reports that the elasticity of graphene should be modeled as a shell composed of 2-dimensional (2D) isotropic materials with proper parameters rather than conventional 3D materials based on calculations by density functional theory. In addition, the elasticity of single-walled carbon nanotube with relative large radius can also be modeled as a shell composed of 2D isotropic materials, whereas the elasticity of single-walled carbon nanotubes with relative small radius should be modeled as a more complicated shell with seven elastic constants rather than the orthotropic thin shell. Mechanical integrity of carbon nanotubes is summarized in chapter 5. Young s modulus for the resistance to the infinitesimal deformation and ultimate strength to the finite deformation are tabled, which have been obtained by experiments, molecular dynamics simulations, and ab-initio calculations. Also the recent continuous modeling of carbon nanotubes is sorted out in tracing its advancement in the chapter. Chapter 6 presents an overview of studies on the wave propagation and the vibrational properties in carbon nanotubes by computational modeling and simulation. The models include the atomic-based continuum model, the Euler-beam model, the Timoshenko beam model, and the three-dimensional elastic shell model. Chapter seven reports the investigations of torsional buckling of both single-walled and double-walled carbon nanotubes. In the study of doubled-walled carbon nanotubes via molecular dynamics, a newly revealed buckling mode with one or three thin local rims on the outer tube is discovered while the inner tube shows a helically aligned buckling mode in three dimensions. The distinct buckling modes of the two tubes imply the inapplicability of continuum mechanics modeling in which it is postulated that the buckling modes of the constituent tubes have the same shape. The mechanical properties of single walled carbon nanotubes under both tensile and torsion are investigated using classical molecular dynamics simulations in chapter 8, based on reactive empirical bond-order potential. Based on the predicted mechanical properties, it is predicted that nanotubes may represent new candidates for novel porous, flexible and high strength and tough materials, e.g. ideal as scaffolds in the regenerative medicine. Bistable devices have been widely used as switching or memory elements in signal processing and communications. The bistablity is generally realized electrically or optically. Due to their small size and unique mechanical properties, carbon nanotubes have been proposed to form bistable devices mechanically. The chapter 9 reviews the recent advances of mechanical bistable devices of carbon nanotubes. In the final chapter, the authors have discussed a theoretical model based on kinetic concept of fracture of solids and molecular mechanics simulations for studying the time-dependent behavior of single-walled carbon nanotubes. The major advantage of this model is that the problem of real-time molecular level simulation is circumvented. Compared with recently published data on creep rupture of SWCNT ropes, it is seen that the predictions by the present model is quite reasonable, thus setting up a framework for modeling the time-dependent behavior of carbon nanotubes and their composites. We would like to extend our sincere thanks to the authors for their contributions, especially their precious time and efforts invested in the book. We also would like to thank Transworld Research Network Publishers for the opportunity to publish the book to address very important and challenging issues. The support and love from our families are deeply appreciated.
Book Synopsis Molecular Dynamics and Machine Learning in Drug Discovery by : Sergio Decherchi
Download or read book Molecular Dynamics and Machine Learning in Drug Discovery written by Sergio Decherchi and published by Frontiers Media SA. This book was released on 2021-06-08 with total page 119 pages. Available in PDF, EPUB and Kindle. Book excerpt: Dr. Sergio Decherchi and Dr. Andrea Cavalli are co-founders of BiKi Technologies s.r.l. - a company that commercializes a Molecular Dynamics-based software suite for drug discovery. All other Topic Editors declare no competing interests with regards to the Research Topic subject.
Book Synopsis Physical Properties Of Carbon Nanotubes by : G Dresselhaus
Download or read book Physical Properties Of Carbon Nanotubes written by G Dresselhaus and published by World Scientific. This book was released on 1998-07-22 with total page 273 pages. Available in PDF, EPUB and Kindle. Book excerpt: This is an introductory textbook for graduate students and researchers from various fields of science who wish to learn about carbon nanotubes. The field is still at an early stage, and progress continues at a rapid rate. This book focuses on the basic principles behind the physical properties and gives the background necessary to understand the recent developments. Some useful computational source codes which generate coordinates for carbon nanotubes are also included in the appendix.
Book Synopsis Realistic Simulation of Slow Processes in Semiconductors and Bio-materials by : Naveen Gupta
Download or read book Realistic Simulation of Slow Processes in Semiconductors and Bio-materials written by Naveen Gupta and published by . This book was released on 2007 with total page 142 pages. Available in PDF, EPUB and Kindle. Book excerpt: Abstract: In the past, the vast majority of studies in the field of materials science have been experimental in nature. With the recent developments in the field of computational materials science, which include faster computer speed, more reliable interatomic potentials and the increased ability of quantum mechanical calculations to handle moderately big systems, computational materials science has been increasingly sought as an aid for research in the field of materials science and allows looking at materials in ways not possible with experiments. Computational modeling of materials allows to design novel materials by virtually predicting their stability and properties, model the evolution of a materials system with time on different scales and evaluate and interpret experimental characterization data. In this work we will touch upon the latter two aspects for two different classes of materials. semiconductors and biomaterials, where the modeling challenge is the time scale. Although atomic-level detail is necessary to understand the formation of the final structures, the system evolution time is much longer than the typical atomic time scale which is given by the time period of the characteristic thermal vibrations and which dictates the maximum time that can be covered by atomic-level simulations. Thus, straightforward molecular dynamics simulation techniques cannot he applied. We will begin with a brief survey of different computational techniques that we use in our study. Next, we look at the problem of arsenic segregation in ion implanted silicon. Generally, arsenic segregation to the Si/SiO2 interface is attributed to binding of arsenic to point defects, which are also made responsible for the dopant deactivation. For even higher concentrations, ordering of the arsenic atoms and eventually precipitation of the SiAs phase can be expected. The plan of action for simulating the segregation process is to find from ab-initio calculations the equilibrium structures and energies of a Si-As system of a given composition and feed these data as input parameters into a continuum model, which is developed by our collaborators at the Fraunhofer Institute of Integrated Systems and Device Technology (IISB) in Erlangen, Germany. In our part of the work, we use ab-initio modeling to study the feasibility of arsenic layer formation and formation of the SiAs phrase in silicon. Starting from a purely substitutional arrangement of arsenic, we move on to arsenic layers and SiAs precipitates. We find that the energetically most favorable configurations are most stable in the neutral charge state. Charged state calculations suggest that at high enough concentrations of arsenic, atoms resulting in a non-silicon neighborhood make arsenic electrically inactive even without the explicit presence of point defects and hence result in dopant dose loss. Recent continuum modeling results from our collaboration based on our data confirm our results and seem to suggest that precipitation, which has not been considered in previous work, is indeed an important part of the deactivation process. Finally, we study the interaction of amino acids (which are the building blocks for proteins in the human body) with carbon nanotubes. DNA-wrapped carbon nanotubes have been recently suggested as a sensor material for application in living cells. In our study with small parts of proteins, we found that after sufficiently long time of molecular dynamics simulation, the protein coils around the in carbon nanotube. We find that the oxygen atoms in the amino acid chains bind to the carbon nanotube. Subsequently we applied Fourier filtering techniques to the molecular dynamics trajectories of these systems to separate the motion of the system corresponding to different time scales and be able to explain the wrapping-mechanisms step by step and to understand the role of the stiffness/floppiness of the different parts of the protein in this process. For that, we worked on optimzing the Fourier filtering technique by studying the effect of different cutoff frequencies on the filtered trajectory of atoms. We then give a qualitative idea about the rigidity of the amino acid chains and the groups present on it from the animation of the original and filtered trajectory for the system and discuss the wrapping process in detail.
