Simulations of Single Molecular Dynamics in Hydrodynamic and Electrokinetic Flows PDF Download
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Author: Xin Hu
Publisher:
ISBN:
Category : Brownian movements
Languages : en
Pages : 180
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Book Description
Abstract: The dynamics of single DNA molecules in micro/nanofluidics has attracted a great deal of attention due to its importance in the biomedical applications such as DNA separation, gene mapping, and gene therapy. The conformation change of these single long chain molecules in different hydrodynamic flows (pure extensional and simple shear flows) was first observed with the fluorescence microscopy in experiments. The Brownian dynamics simulation was then carried out and it successfully explained the interesting phenomena in experimental observation. In this dissertation, two major flows (i.e., generated by either the hydrodynamic or electrokinetic forces) to control the DNA dynamics are thoroughly investigated. The main effort is concentrated on the electrokinetic micro-flows produced by different microfluidic patterns. The finite element method is used to simulate the electrokinetic flows and the solutions are used as inputs for the coarse-grained Brownian dynamics simulation, which can capture the dynamics of single DNA molecules. In the electrokinetic flows, the electroosmotic and electrophoretic interactions affect the flow patterns of charged particles. When the electrophoretic mobility of a charged particle is higher than the surface electroosmotic mobility, the flows in the microfluidic devices are essentially the electrophoresis-dominated extensional flows even with surface charge patterning. To avoid this limitation, a novel design of a five-cross microfluidic device is proposed based on simulations. This design can generate and maintain different particle flow patterns even when the electrophoretic mobility is much higher than the electroosmotic mobility. Different responses of single DNA molecules under various hydrodynamic and electrokinetic flows are also studied. The complicated DNA molecule is simplified as either a bead-spring or a bead-rod chain in the Brownian dynamics simulations. Different forces in the governing equation of a bead-spring or bead-rod chain are discussed thoroughly. Different time-marching schemes are used and compared in the simulation of the dynamics of single DNA molecules. The simulations of DNA dynamics in the hydrodynamic and electrokinetic flows agree well with the experiments and the previous simulation results.
Author: Xin Hu
Publisher:
ISBN:
Category : Brownian movements
Languages : en
Pages : 180
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Book Description
Abstract: The dynamics of single DNA molecules in micro/nanofluidics has attracted a great deal of attention due to its importance in the biomedical applications such as DNA separation, gene mapping, and gene therapy. The conformation change of these single long chain molecules in different hydrodynamic flows (pure extensional and simple shear flows) was first observed with the fluorescence microscopy in experiments. The Brownian dynamics simulation was then carried out and it successfully explained the interesting phenomena in experimental observation. In this dissertation, two major flows (i.e., generated by either the hydrodynamic or electrokinetic forces) to control the DNA dynamics are thoroughly investigated. The main effort is concentrated on the electrokinetic micro-flows produced by different microfluidic patterns. The finite element method is used to simulate the electrokinetic flows and the solutions are used as inputs for the coarse-grained Brownian dynamics simulation, which can capture the dynamics of single DNA molecules. In the electrokinetic flows, the electroosmotic and electrophoretic interactions affect the flow patterns of charged particles. When the electrophoretic mobility of a charged particle is higher than the surface electroosmotic mobility, the flows in the microfluidic devices are essentially the electrophoresis-dominated extensional flows even with surface charge patterning. To avoid this limitation, a novel design of a five-cross microfluidic device is proposed based on simulations. This design can generate and maintain different particle flow patterns even when the electrophoretic mobility is much higher than the electroosmotic mobility. Different responses of single DNA molecules under various hydrodynamic and electrokinetic flows are also studied. The complicated DNA molecule is simplified as either a bead-spring or a bead-rod chain in the Brownian dynamics simulations. Different forces in the governing equation of a bead-spring or bead-rod chain are discussed thoroughly. Different time-marching schemes are used and compared in the simulation of the dynamics of single DNA molecules. The simulations of DNA dynamics in the hydrodynamic and electrokinetic flows agree well with the experiments and the previous simulation results.
Author: George Karniadakis
Publisher: Springer Science & Business Media
ISBN: 0387286764
Category : Mathematics
Languages : en
Pages : 824
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Book Description
Subject area has witnessed explosive growth during the last decade and the technology is progressing at an astronomical rate. Previous edition was first to focus exclusively on flow physics within microdevices. It sold over 900 copies in North America since 11/01. New edition is 40 percent longer, with four new chapters on recent topics including Nanofluidics.
Author: Yun Kyung Shin
Publisher:
ISBN:
Category : Electrokinetics
Languages : en
Pages : 51
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Book Description
Abstract: The electrokinetic transport of a pure water system was investigated using continuum hydrodynamic theory. These studies are motivated by our recent numerical simulations of a non-electrolyte water system using non-equilibrium molecular dynamics (NEMD), in which we found an evidence of electric field-driven flow. To understand this observation, hydrodynamic equations that treat the rotational motion of molecules (i.e.''spin'') must be employed. The purpose of this thesis is to develop continuum theory that could explain electrokinetic flow in the absence of an electrolyte. In the bulk region, the local average polarization of the water is zero because of the random orientation of the water molecules. However, near the surface the water is anisotropic because of interactions with the walls. Application of an electric field produces a net torque density where the orientation of water molecules is anisotropic. The torque drives molecular spin which, through viscous coupling, eventually induces linear transport of the fluid. To understand the coupling between translational motion and internal rotational motion of water, we solved the hydrodynamic equations of motion for coupled linear and angular momentum. According to the analytical solution of these equations, the fluid velocity along the channel is related to the density of the torque component perpendicular to both the surface normal and the direction of flow, and a single combination of viscosity coefficients.
Author:
Publisher:
ISBN:
Category : Dissertations, Academic
Languages : en
Pages : 886
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Book Description
Author: Michel Mareschal
Publisher: Springer
ISBN:
Category : Science
Languages : en
Pages : 464
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Book Description
This volume contains the proceedings of a NATO Advanced Study Institute which was held in Alghero, Sardinia, in July 1991. The development of computers in the recent years has lead to the emergence of unconventional ideas aiming at solving old problems. Among these, the possibility of computing directly fluid flows from the trajectories of constituent particles has been much exploited in the last few years: lattice gases cellular automata and more generally Molecular Dynamics have been used to reproduce and study complex flows. Whether or not these methods may someday compete with more traditional approaches is a question which cannot be answered at the present time: it will depend on the new computer architectures as well as on the possibility to develop very simple models to reproduce the most complex phenomena taking place in the approach of fully developed turbulence or plastic flows. In any event, these molecular methods are already used, and sometimes in an applied engineering context, to study strong shock waves, chemistry induced shocks or motion of dislocations in plastic flows, that is in domains where a fully continuum description appears insufficient. The main topic of our Institute was the molecular simulations of fluid flows. The project to hold this Institute was made three years ago, in the summer of 1989 during a NATO workshop in Brussels on the same subject.
Author: Sean Matthew Ferree
Publisher:
ISBN:
Category :
Languages : en
Pages : 476
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Book Description
Author: Ryan Kelly
Publisher: BoD – Books on Demand
ISBN: 9535101064
Category : Science
Languages : en
Pages : 254
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Book Description
Advances in Microfluidics provides a current snapshot of the field of microfluidics as it relates to a variety of sub-disciplines. The chapters have been divided into three sections: Fluid Dynamics, Technology, and Applications, although a number of the chapters contain aspects that make them applicable to more than one section. It is hoped that this book will serve as a useful resource for recent entrants to the field as well as for established practitioners.
Author: Frank Boehm
Publisher: CRC Press
ISBN: 1439863237
Category : Medical
Languages : en
Pages : 746
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Book Description
Nanomedical Device and Systems Design: Challenges, Possibilities, Visions serves as a preliminary guide toward the inspiration of specific investigative pathways that may lead to meaningful discourse and significant advances in nanomedicine/nanotechnology. This volume considers the potential of future innovations that will involve nanomedical devic
Author: Wei Zhu
Publisher:
ISBN:
Category : Electrolytes
Languages : en
Pages :
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Book Description
Abstract: Electroosmotic flow is studied by non-equilibrium molecular-dynamics simulations in a model system chosen to facilitate comparison with existing continuum theories. The model system consists of spherical ions and solvent, with stationary, uniformly charged walls that make a channel with a height of 20 particle diameters. We find that hydrodynamic theory adequately describes simple pressure-driven flow (Poiseuille flow) in this model. However, when combined with Poisson-Boltzmann theory to describe electroosmotic flow, the continuum theory fails in important situations. The failure is traced to the exclusion of ions near the channel walls resulting from reduced solvation of the ions in that region. When Poisson-Boltzmann theory is adjusted to account for the exclusion of ions near the walls, agreement with hydrodynamic theory is restored. Monte Carlo simulation using an all-atom potential model is applied to evaluate two crystal structures of low density methyl chloride monolayer that have been proposed based on diffraction experiments. The equilibrium configuration proposed by Morishige, Tajima, Kittaka, Clarke and Thomas was found to be lower in energy than an alternative structure proposed by Shirazi and Knorr. The first-order melting transition of the monolayer crystal was found to occur between 85K and 90K, in qualitative agreement with experiments. However, the melting point from simulations is lower than the experimental melting point of 120K. After melting, short-range order within the methyl chloride fluid phase was found.
Author: David P. Landau
Publisher: Springer Science & Business Media
ISBN: 3642555225
Category : Science
Languages : en
Pages : 225
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Book Description
Over fifteen years ago, because of the tremendous increase in the power and utility of computer simulations, The University of Georgia formed the first institutional unit devoted to the use of simulations in research and teach ing: The Center for Simulational Physics. As the international simulations community expanded further, we sensed a need for a meeting place for both experienced simulators and neophytes to discuss new techniques and recent results in an environment which promoted lively discussion. As a consequence, the Center for Simulational Physics established an annual workshop on Re cent Developments in Computer Simulation Studies in Condensed Matter Physics. This year's workshop was the fifteenth in this series, and the con tinued interest shown by the scientific community demonstrates quite clearly the useful purpose that these meetings have served. The latest workshop was held at The University of Georgia, March 11-15, 2002, and these proceedings provide a "status report" on a number of important topics. This volume is published with the goal of timely dissemination of the material to a wider audience. We wish to offer a special thanks to IBM Corporation and to the National Science Foundation for partial support of this year's workshop. This volume contains both invited papers and contributed presentations on problems in both classical and quantum condensed matter physics. We hope that each reader will benefit from specialized results as well as profit from exposure to new algorithms, methods of analysis, and conceptual devel opments. Athens, GA, USA D. P.
