Dissertations / Theses: 'Brownian dynamics'

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Levitz, Pierre. "Intermittent brownian dynamics over strands." Universitätsbibliothek Leipzig, 2016. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-194192.

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Levitz, Pierre. "Intermittent brownian dynamics over strands." Diffusion fundamentals 6 (2007) 78, S. 1-2, 2007. https://ul.qucosa.de/id/qucosa%3A14258.

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Craig, Erin Michelle. "Models for Brownian and biomolecular motors /." Connect to title online (Scholars' Bank) Connect to title online (ProQuest), 2008. http://hdl.handle.net/1794/8565.

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Thesis (Ph. D.)--University of Oregon, 2008.
Typescript. Includes vita and abstract. Includes bibliographical references (leaves 164-171). Also available online in Scholars' Bank; and in ProQuest, free to University of Oregon users.

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Ansell, G. C. "A simulation of Brownian dynamics of colloidal dispersions." Thesis, University of Leeds, 1986. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.373523.

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Lappala, Anna. "Molecular dynamics simulations : from Brownian ratchets to polymers." Thesis, University of Cambridge, 2015. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.709251.

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Burmenko, Irina. "Brownian dynamics simulations of fine-scale molecular models." Thesis, Massachusetts Institute of Technology, 2005. http://hdl.handle.net/1721.1/32330.

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Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2005.
Includes bibliographical references (leaves 105-111).
One of the biggest challenges in non-Newtonian fluid mechanics is calculating the polymer contribution to the stress tensor, which is needed to calculate velocity and pressure fields as well as other quantities of interest. In the case of a Newtonian fluid, the stress tensor is linearly proportional to the velocity gradient and is given by the Newton's law of viscosity, but no such unique constitutive equation exists for non-Newtonian fluids. In order to predict accurately a polymer's rheological properties, it is important to have a good understanding of the molecular configurations in various flow situations. To obtain this information about molecular configurations and orientations, a micromechanical representation of a polymer molecule must be proposed. A micromechanical model may be fine scale, such as the Kramers chain model, which accurately predicts a real polymer's heological properties, but at the same time possesses too many degrees of freedom to be used in complex flow simulations, or it may be a coarse-grained model, such as the Hookean or the FENE dumbbell models, which can be used in complex flow analysis, but have too few degrees of freedom to adequately describe the rheology. The Adaptive Length Scale (ALS) model proposed by Ghosh et al. is only marginally more complicated than the FENE dumbbell model, yet it is able to capture the rapid stress growth in the start-up of uniaxial elongational flow, which is not predicted correctly by the simple dumbbell models. The ALS model is optimized in order to have its simulation time as close as possible to that of the FENE dumbbell.
(cont.) Subsequently, the ALS model is simulated in the start-up of the uniaxial elongational and shear flows as well as in steady extensional and shear flows, and the results are compared to those obtained with other competing rheological models such as the Kramers chain, FENE chain, and FENE dumbbell. While a 5-spring FENE chain predicts results that are in very good agreement with the Kramers chain, the required simulation time clearly makes it impossible to use this model in complex flow simulations. The ALS model agrees better with the Kramers chain than does the FENE dumbbell in the start-up of shear and elongational flows. However, the ALS model takes too long to achieve steady state, which is something that needs to be explored further before the model is used in complex flow calculations. Understanding of this phenomena may explain why the stress-birefringence hysteresis loop predicted by the ALS model is unexpectedly small. In general, if polymer stress is to be calculated using Brownian dynamics simulations, a large number of stochastic trajectories must be simulated in order to predict accurately the macroscopic quantities of interest, which makes the problem computationally expensive. However, recent technological advances as well as a new simulation algorithm called Brownian configuration fields make such problems much more tractable. The operation count in order to assess the feasibility of using the ALS model in complex flow situations yields very promising results if parallel computing is used to calculate polymer contribution to stress. In an attempt to capture polydispersity of real polymer solutions, the use of multi-mode models is explored.
(cont.) The model is fit to the linear viscoelastic spectrum to obtain relaxation times and individual modes' contributions to polymer viscosity. Then, data-fitting to the dimensionless extensional viscosity in the startup of the uniaxial elongational flow is performed for the ALS and the FENE dumbbell models to obtain the molecule's contour length, bmax. It is found that the results from the single-mode and the four-mode ALS models agree much better with the experimental data than do the corresponding single-mode and four-mode FENE dumbbell models. However, all four models resulted in a poor fit to the steady shear data, which may be explained by the fact that the zero-shear-rate viscosity obtained via a fit to the dynamic data by Rothstein and McKinley and used in present simulations, tends to be somewhat lower than the steady-state shear viscosity at very low shear rates, which may have caused a mismatch between the value of ... used in the simulation and the true ... of the polymer solution. As a motivation for using the ALS model in complex flow calculations, the results by Phillips, who simulated the closed-form version of the model in the benchmark 4:1:4 contraction- expansion problem are presented and compared to the experimental results by Rothstein and McKinley [49]. While the experimental observations show that there exists a large extra pres- sure drop, which increases monotonically with increasing De above the value observed for a Newtonian fluid subjected to the same flow conditions, the simulation results with a closed-form version of the FENE dumbbell model, called FENE-CR, exhibit the opposite trend.
(cont.) The ALS-C model, on the other hand, is able to predict the trend correctly. The use of the ALS-C model in another benchmark problem, namely the flow around an array of cylinders confined between two parallel plates, also shows very promising results, which are in much better agreement with experimental data by Liu as compared to the Oldroyd-B model. The simulation results for the ALS-C and the Oldroyd-B models are due to Joo, et al. [28] and Smith et al. [50], respectively. Overall, it is concluded that the ALS model is superior to the commonly used FENE dumb- bell model, although more work is needed to understand why it takes significantly longer than the FENE dumbbell to achieve steady state in uniaxial elongational flows, and why the stress birefringence hysteresis loop predicted by the ALS model is much smaller than that of the other rheological models.
by Irina Burmenko.
S.M.

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Mühle, Steffen [Verfasser]. "Nanoscale Brownian Dynamics of Semiflexible Biopolymers / Steffen Mühle." Göttingen : Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2020. http://d-nb.info/1214887090/34.

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Madraki, Fatemeh. "Shear Thickening in Non-Brownian Suspensions." Ohio University / OhioLINK, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1584354185678102.

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Sasai, Masaki, Masahiro Ueda, and Shin I. Nishimura. "Non-Brownian dynamics and strategy of amoeboid cell locomotion." American Physical Society, 2012. http://hdl.handle.net/2237/20623.

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Glaser, Jens, Masashi Degawa, Inka Lauter, Rudolf Merkel, and Klaus Kroy. "Tube geometry and brownian dynamics in semiflexible polymer networks." Universitätsbibliothek Leipzig, 2015. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-188856.

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Evensen, Tom Richard, Stine Nalum Naess, and Arnljot Elgsaeter. "Transport properties of nanoparticles studied by Brownian dynamics simulations." Universitätsbibliothek Leipzig, 2016. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-192972.

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Glaser, Jens, Masashi Degawa, Inka Lauter, Rudolf Merkel, and Klaus Kroy. "Tube geometry and brownian dynamics in semiflexible polymer networks." Diffusion fundamentals 11 (2009) 7, S. 1-2, 2009. https://ul.qucosa.de/id/qucosa%3A13927.

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Evensen, Tom Richard, Stine Nalum Naess, and Arnljot Elgsaeter. "Transport properties of nanoparticles studied by Brownian dynamics simulations." Diffusion fundamentals 7 (2007) 2, S. 1-2, 2007. https://ul.qucosa.de/id/qucosa%3A14158.

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Rashedi, Ahmadreza. "The design and flow dynamics of non brownian suspension." Thesis, Bordeaux, 2019. http://www.theses.fr/2019BORD0500.

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Les suspensions denses de particules non colloïdales présentent des caractéristiques originales. Dans un écoulement de cisaillement non homogène, on observe que les particules migrent des région de cisaillement élevé vers des régions de faible taux de cisaillement. Ce phénomène s'appelle migration induite par cisaillement (SIM). Le modèle de suspension (SBM) de Nott et Brady (1994) est une approche de la SIM où des flux diffusifs apparaissent naturellement à partir de gradients de contraintes de la phase particulaire. Cependant, il existe encore des débats sur la nature des contraintes particulaire dans les suspensions denses. Des expériences récentes montrent que le SBM échoue non seulement à prédire la distribution stationnaire des particules, mais aussi à rendre compte de sa cinétique. Nous avons conçu et construit une configuration originale pour revoir les modèles disponibles en effectuant des expériences bien résolues dans le temps et l'espace. Nous présentons nos résultats expérimentaux ainsi qu'une détermination préliminaires des paramètres du modèle tenant compte des inhomogénéités de fraction volumique et du taux de cisaillement
Dense suspensions of noncolloidal particles exhibit novel features. In a non-homogeneous shear flow, it is observed that particles migrate from the high shear rate region to the low shear rate region. This phenomenon is called Shear-Induced Migration (SIM). The Suspension Balance Model (SBM) of Nott and Brady (1994) has been taken as an approach to model SIM. Where the SIM is attributed to the diffusive fluxes that arise naturally from gradients in the particle phase stresses. However, there are still unanswered questions and an ongoing debate on the nature of particle stress in the dense suspensions. Recent experiments show that the SBM not only fails in predicting the steady-state distribution of particle phase in the flow of dense suspensions but also fails in predicting the kinetics of the SIM. In addition, recent theoretical works question the derivation of the SBM and the simple supposition of drag closures in inhomogeneous flows of dense suspensions. We have designed and built an original setup to revisit available drag closures via performing well-resolved experiments. We present our preliminary results of a drag closure taking into account inhomogeneities of the solid phase volume fraction and the shear rate

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Murrow, Matthew Alan. "Kinesin model for Brownian dynamics simulations of stepping efficiency." University of Akron / OhioLINK, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=akron156441669721832.

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Rashedi, Ahmadreza. "The Design and Flow Dynamics of Non-Brownian Suspensions." Ohio University / OhioLINK, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1598018383854045.

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Liu, Yanan. "Dynamics of flexible and Brownian filaments in viscous flow." Thesis, Sorbonne Paris Cité, 2018. http://www.theses.fr/2018USPCC196/document.

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La dynamique de filaments flexibles individuels en écoulement visqueux est une étape essentielle pour comprendre et contrôler la rhéologie de nombreux fluides complexes. Cette dynamique sous-tend également une multitude de processus biophysiques allant de la propulsion des micro-organismes aux écoulements intracellulaires. Cette thèse présente des expériences systématiques permettant d’étudier la dynamique de filaments flexibles browniens dans un écoulement visqueux. Nous avons choisi d’utiliser un biopolymère, l’actine, comme système modèle de filaments. Sa longueur typique varie de 1 à 100 μm, il est flexible à ces échelles avec une longueur de persistance de l’ordre de 20μm, à cause de ses petites dimensions, il est soumis aux forces Browniennes avec des fluctuations en flexion, et enfin il peut être marqué en fluorescence. Nous utilisons des dispositifs microfluidiques associés à des systèmes de contrôle d’écoulements, un microscope optique équipé́ avec une platine motorisée pour réaliser des expériences contrôlées permettant de suivre la dynamique des filaments d’actine dans un écoulement de cisaillement pur et dans un écoulement élongationnel. Pour les expériences en cisaillement pur, des simulations reproduisant les conditions expérimentales ont aussi été́ menées en utilisant la théorie des poutres inextensibles d’Euler-Bernoulli et la théorie non locale des corps élancés en présence de fluctuations Browniennes et sont en accord quantitatif avec les résultats expérimentaux. Nous montrons que la dynamique des filaments dans ce système est principalement régie par le nombre élasto-visqueux, nombre sans dimension comparant les forces de trainée visqueuses aux forces de flexion élastiques, les fluctuations thermiques ne jouant qu’un rôle secondaire. Nous présentons une caractérisation complète des différents modes de déformation subies par le filament pendant une rotation ainsi que des transitions entre les différents modes. Dans la géométrie élongationnelle, nous avons choisi un canal hyperbolique optimisé pour permettre de longs temps de résidence sous taux de déformation constant. Nous avons observé́ directement la suppression des fluctuations transverse dans la partie extensionnelle tandis que nous observons, dans la partie compressive la formation de structures hélocoïdales tridimensionnelles après le flambage du filament. Pour finir, ce manuscrit de thèse décrit des développements expérimentaux permettant de fabriquer des suspensions de filaments d’actine relativement monodisperse en taille ainsi que des résultats préliminaires sur des effets rhéofluidifiants. Au bilan, les résultats présentes dans ce manuscrit pose les premières pierres de travaux futurs en direction de l’étude de la dynamique de ces filaments dans des écoulements plus complexes comme des écoulements de Poiseuille ou oscillants. Ils permettent aussi d’envisager des études sur le lien entre déformations de particules et propriétés des suspensions diluées d’objets flexibles et Brownien, lien encore peu étudié du point de vue expérimental
The dynamics of individual flexible filament in a viscous flow is the key to deciphering the rheolog- ical behavior of many complex fluids and soft materials. It also underlies a wealth of biophysical processes from flagellar propulsion to intracellular streaming. This thesis presents systematic exper- iments to investigate the dynamics of flexible and Brownian filaments in viscous flows. Biopolymer actin has been chosen to be our experimental model filament: its typical length can be varied from 1 to 100 μm, it is flexible at these dimensions with a persistence length in the order of 20μm, it is Brow- nian due to its small diameter with bending fluctuations and it can be labelled by fluorescent dye. Microfluidic channels and flow control systems are combined to optical microscope with automated stage to carry out well-controlled experiments on the diverse dynamics of actin filaments in shear flow and pure straining flow. In shear flow, simulations matching the experimental conditions have also been performed using inextensible Euler-Bernoulli beam theory and non-local slender body hy- drodynamics in the presence of thermal fluctuations and agree quantitatively with the experimental results. We demonstrate that filament dynamics in this flow geometry is primarily governed by a dimension- less elasto-viscous number comparing viscous forces to elastic forces with thermal fluctuations only playing a secondary role. We present a complete characterization of the different modes of defor- mation undergone by the filament while rotating as well as of the transitions between these different modes. In pure straining flow, we opt to use an optimized hyperbolic channel to allow long resi- dence time at constant strain rate to be applied. We directly observe the suppression of transverse fluctuations in the extensional part of the hyperbolic channel while we observe, in the compressive part of the flow, the formation of three dimensional helical structures subsequent to the initial buck- ling of the filament. Finally, this thesis manuscript also reports on experimental developments to fabricate suspensions of actin filament with a narrow distribution of lengths and on preliminary re- sults on shear-thinning effects. All together the results presented here pave the way of future studies towards the understanding of filament dynamics in more complex flows, as Poiseuille flows or oscil- latory flows, as well as towards establishing the link between filament deformations and rheological response in dilute suspensions of flexible Brownian filaments, which remains nearly unexplored from an experimental point of view

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Cakir, Rasit Grigolini Paolo. "Fractional Brownian motion and dynamic approach to complexity." [Denton, Tex.] : University of North Texas, 2007. http://digital.library.unt.edu/permalink/meta-dc-3992.

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Irfachsyad, Danial. "Mesoscopic simulation of polymers and colloids." Thesis, University of Southampton, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.252212.

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Streek, Martin Andreas. "Brownian dynamics simulation of migration of DNA in structured microchannels." [S.l. : s.n.], 2005. http://deposit.ddb.de/cgi-bin/dokserv?idn=973641908.

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Lodge, J. Felicity M. "Phase separation in model colloidal liquids by Brownian dynamics simulations." Thesis, University of Surrey, 1997. http://epubs.surrey.ac.uk/844592/.

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The technique of Brownian Dynamics simulation has been used to follow the evolution of model colloidal systems during phase separation in the liquid-vapour and solid-vapour regions of the phase diagram. Systems of monodisperse spherical particles interacting via LJ m:n type potentials were quenched in temperature from the one-phase region into the two phase region. Various structural and rheological properties were followed as the systems evolved, including the radial distribution functions, the small angle scattering peak of the structure factor, the interaction energy and the linear response rheology. The scaling behaviour of these quantities was found to be similar to that observed in light scattering experiments following the phase separation of colloidal systems. The aggregate structure could not be represented well by a single fractal dimension. Some evidence of fractal structure was found early in the phase separation, however the reversibility of the interactions allowed for a high degree of restructuring which led to a collapse of the initially tenuous structure into dense aggregates. The local structure was sensitive to the range of the interaction potential - as the potential became more short-ranged, increasing evidence of crystallisation of the denser phase was apparent from the form of g(f). Particles with 12:6 interactions formed structures displaying the rheological strength associated with an elastic gel. However restructuring was continual, resulting in a dense compact structure. The short-range 36:18 potential retained a tenuous gel-like structure and displayed an arrest of phase separation on long lengthscales. However, the particles did not have the interaction strength necessary to give significant rigidity to the system. This suggests that to form an arrested state with elastic gel-like rheology it would be necessary to have a more permanent form of interaction, in addition to the short-range reversible interactions used in this work.

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Endres, Derek. "Development and Demonstration of a General-Purpose Model for Brownian Motion." The Ohio State University, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=osu1307459444.

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Flöck, Dagmar. "Protein-protein docking and Brownian dynamics simulation of electron transfer proteins." [S.l. : s.n.], 2003. http://deposit.ddb.de/cgi-bin/dokserv?idn=969418736.

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Wittkowski, Raphael [Verfasser]. "Brownian dynamics of active and passive anisotropic colloidal particles / Raphael Wittkowski." Aachen : Shaker, 2012. http://d-nb.info/1066197733/34.

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Goko, Hiromichi. "One- and two-dimensional dynamics of Brownian motors and probability distributions." 京都大学 (Kyoto University), 2005. http://hdl.handle.net/2433/144387.

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Kyoto University (京都大学)
0048
新制・課程博士
博士(情報学)
甲第11958号
情博第182号
新制||情||40(附属図書館)
23747
UT51-2006-B137
京都大学大学院情報学研究科数理工学専攻
(主査)教授宗像豊哲, 教授岩井敏洋, 助教授五十嵐顕人
学位規則第4条第1項該当

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Carlsson, Tobias. "Brownian Dynamics Simulations of Macromolecules : Algorithm Development and Polymers under Confinement." Doctoral thesis, Uppsala universitet, Fysikalisk kemi, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-173435.

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In this thesis I have used computer simulations to study the structure and dynamics of grafted polymers during confinement. These systems are of importance for understanding e.g. colloidal stability and surface coatings. We have used Brownian dynamics simulations with the polymers modeled as discrete wormlike chains allowing for a variable persistence length as well as different non-bonded interactions. The size and shape of the chains are characterized by the radius of gyration and the degree of oblateness/prolateness, and the entanglement is followed by calculating the mean overcrossing number. Starting in the dilute regime with a single polymer mushroom we have investigated how the rate of compression and solvent quality effects the behaviour of a compressed chain. In the brush regime, we investigated how the surface coverage effects the behaviour during compression. For low coverages the chains have the possibilty to increase their lateral extension during confinement but in general, the chains have a low inter-entanglement, as they strive to keep their integrity during the confinement process. To go from a polymer brush to the construction of a connected network, we have developed a method to construct a closed network without using periodic boundary conditions by building the network on a sphere in R4. In this way we avoid the restrictions of periodicity at the cell boundaries. We finally also show how to develop the idea of using spherical boundary conditions, by presenting a novel algorithm for simulating diffusion on a spherical surface. The method is more stable and allows for larger time steps, compared to commonly used methods in computer simulations.

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Watanabe, Satoshi. "Brownian dynamics simulation and modeling of spontaneous ordering of mesoscale particles." 京都大学 (Kyoto University), 2005. http://hdl.handle.net/2433/144945.

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Song, Lu. "Dynamics and structures of linear and supercoiled DNAs /." Thesis, Connect to this title online; UW restricted, 1989. http://hdl.handle.net/1773/8615.

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Cakir, Rasit. "Fractional Brownian motion and dynamic approach to complexity." Thesis, University of North Texas, 2007. https://digital.library.unt.edu/ark:/67531/metadc3992/.

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The dynamic approach to fractional Brownian motion (FBM) establishes a link between non-Poisson renewal process with abrupt jumps resetting to zero the system's memory and correlated dynamic processes, whose individual trajectories keep a non-vanishing memory of their past time evolution. It is well known that the recrossing times of the origin by an ordinary 1D diffusion trajectory generates a distribution of time distances between two consecutive origin recrossing times with an inverse power law with index m=1.5. However, with theoretical and numerical arguments, it is proved that this is the special case of a more general condition, insofar as the recrossing times produced by the dynamic FBM generates process with m=2-H. Later, the model of ballistic deposition is studied, which is as a simple way to establish cooperation among the columns of a growing surface, to show that cooperation generates memory properties and, at same time, non-Poisson renewal events. Finally, the connection between trajectory and density memory is discussed, showing that the trajectory memory does not necessarily yields density memory, and density memory might be compatible with the existence of abrupt jumps resetting to zero the system's memory.

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Darricarrere, Gwenaël, Julien Dutour, and François Henn. "A microscopic flow model based on Brownian dynamics for simulating ionic diffusion in glasses: A microscopic flow model based on Brownian dynamics forsimulating ionic diffusion in glasses." Diffusion fundamentals 2 (2005) 15, S. 1-2, 2005. https://ul.qucosa.de/id/qucosa%3A14344.

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Nixon, Grant Ian. "A Brownian dynamics algorithm for the simulation of polymers in confined media." Thesis, University of Ottawa (Canada), 1994. http://hdl.handle.net/10393/9525.

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The techniques of electrophoresis have undergone rapid development in recent years. The problem of predicting and explaining results of electrophoretic experiments requires a well designed dynamical model that reproduces the proper dynamics under well-understood conditions. The challenge is to design a model which can predict complex dynamics in a variety of situations of interest and yet, be efficient enough to run on common workstations. We believe that we have been successful in achieving these goals. Our Brownian Dynamics model is sufficiently general for the investigation of a wide variety of problems (as we will demonstrate), moreover, it implements a simulation innovation, a dynamically self-regulating time increment which varies in accordance with the stresses in the system. This permits for reasonably long simulation times with good averaging statistics. After benchmarking the model with the well understood Rouse regime in isotropic and confined media, the model was applied to two case studies of particular interest: (i) electrophoretic collisions and stacking (chain pinning), and (ii), the onset of the entropic trapping regimes for low fields. We have found that, as far as simple isolated collisions are concerned, our model predicts a widening of electrophoretic molecular bands with an accompanying loss in spatial resolution. The onset of entropic regimes for low fields is demonstratedly counter-productive due to the wide variance of trapping times. Both these results are in accord with recent experimental observations. A more complete study is planned for a supercomputer to elaborate on these findings as well as to investigate kink-formations in pulsed-field gel electrophoresis (PFGE).

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Schnoering, Gabriel. "On the Brownian dynamics of a particle in a bistable optical trap." Thesis, Strasbourg, 2016. http://www.theses.fr/2016STRAF057/document.

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Cette thèse présente la réalisation d’un piège optique dans une configuration originale, le piston optique, où le contrôle sur la phase de l’interférence d’un faisceau incident avec sa réflexion sur un miroir permet de réaliser différents types d’expériences. Nous avons d’abord étudié les propriétés thermodynamiques d’une compression progressive du piston qui fait passer la dynamique de la particule piégée d’une région de stabilité vers une région de bistabilité mécanique. Dans le contexte de la résonance stochastique où une force extérieure périodique est appliquée sur cette dynamique bistable, une approche exploitant le facteur de Mandel ainsi qu’une analyse des délais entre les transitions d’états métastables se révèle efficace pour interpréter nos mesures dans différents régimes de forçage. Nous montrons également comment des nanoparticules métalliques peuvent être piégées aisément dans un tel piston optique et nous exploitons notre configuration pour mesurer de faibles effets de forces optiques. Enfin, nous piégeons des nano-objets chiraux uniques et nous montrons comment la configuration de notre piston permet de réaliser des expériences de reconnaissance chirale par polarimétrie différentielle
This thesis describes the experimental realization of an original optical trap, the optical piston, where controlling the phase of the interference of an incident beam with its reflection on a mirror allows achieving various experiments. We have first looked into the thermodynamics associated with a progressive compression of the piston leading the dynamics of a trapped particle from a region of stability to a region of mechanical bistability. In the context of stochastic resonance where a periodic external force is applied on this bistable dynamics, an approach exploiting the Mandel factor and a time-delay analysis on the hopping events between metastable states have proven efficient in interpreting the different results acquired in different regimes of drive. We have also shown how metallic nanoparticles can be trapped fairly easily in this kind of optical piston and we exploit our configuration to measure weak optical forces. Finally, we trap unique chiral nano-objects and we show how the configuration of our piston allows the realization of chiral recognition experiments by differential polarimetry

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Hu, Xin. "Simulations of single molecular dynamics in hydrodynamic and electrokinetic flows." Columbus, Ohio : Ohio State University, 2006. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1148579763.

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Haddadian, Esmael Jafari. "Brownian dynamics study of cytochrome f / Rieske interactions with cytochrome c₆ and plastocyanin." Connect to resource, 2005. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1123695434.

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Thesis (Ph. D.)--Ohio State University, 2005.
Title from first page of PDF file. Document formatted into pages; contains xxiii, 184 p.; also includes graphics (some col.). Includes bibliographical references (p. 169-184). Available online via OhioLINK's ETD Center

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Jafari, haddadian Esmael. "Brownian dynamics study of cytochrome f / Rieske interactions with cytochrome c6 and plastocyanin." The Ohio State University, 2005. http://rave.ohiolink.edu/etdc/view?acc_num=osu1123695434.

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Corry, Ben Alexander. "Simulation studies of biological ion channels." View thesis entry in Australian Digital Theses Program, 2002. http://thesis.anu.edu.au/public/adt-ANU20030423.162927/index.html.

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Beranek, Vaclav. "Dynamics of composite beads in optical tweezers and their application to study of HIV cell entry." Thesis, Georgia Institute of Technology, 2014. http://hdl.handle.net/1853/54024.

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In this thesis, we report a novel symmetry breaking system in single-beam optical trap. The breaking of symmetry is observed in Brownian dynamics of a linked pair of beads with substantially differing radii (500nm and 100nm). Such composite beads were originally conceived as a manipulation means to study of Brownian interactions between mesoscopic biological agents of the order of 100 – 200 nm (viruses or bacteria) with cell surfaces. During the initial testing of the composite bead system, we discovered that the system displayed thermally activated transitions and energetics of symmetry breaking. This thesis, while making a brief overview of the biological relevance of the composite bead system, focuses primarily on the analysis and experimentation that reveals the complex dynamics observed in the system. First, we theoretically analyze the origin of the observed symmetry breaking using electromagnetic theory under both Gaussian beam approximation and full Debye-type integral representation. The theory predicts that attachment of a small particle to a trapped microsphere results in creation of a bistable rotational potential with thermally activated transitions. The theoretical results are then verified using optical trapping experiments. We first quantify the top-down symmetry breaking based on measurement of the kinetic transition rates. The rotational potential is then explored using an experiment employing a novel algorithm to track rotational state of the composite bead. The results of the theory and experiments are compared with results of a Brownian dynamics simulation based on Smart Monte Carlo algorithm.

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Fritschi, Sebastian [Verfasser]. "Event-driven Brownian dynamics simulations of two-dimensional fluids far from equilibrium / Sebastian Fritschi." Konstanz : Bibliothek der Universität Konstanz, 2018. http://d-nb.info/1159880484/34.

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39

Darricarrere, Gwenaël, Julien Dutour, and François Henn. "A microscopic flow model based on Brownian dynamics for simulating ionic diffusion in glasses." Universitätsbibliothek Leipzig, 2016. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-195262.

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Pearson, Douglas C. "Brownian dynamics study of the interaction between Cytochrome F and Mobile Electron Transfer Proteins /." The Ohio State University, 1999. http://rave.ohiolink.edu/etdc/view?acc_num=osu1488193272066355.

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41

Khan, Siddique J. "Brownian dynamics study of the self-assembly of ligated gold nanoparticles and other colloidal systems." Diss., Kansas State University, 2012. http://hdl.handle.net/2097/13508.

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Doctor of Philosophy
Department of Physics
Amit Chakrabarti
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 Binder–Stauffer 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.

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42

Gomez-Solano, Juan Rubén. "Nonequilibrium fluctuations of a Brownian particle." Phd thesis, Ecole normale supérieure de lyon - ENS LYON, 2011. http://tel.archives-ouvertes.fr/tel-00680302.

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This thesis describes an experimental study on fluctuations of a Brownian particle immersed in a fluid, confined by optical tweezers and subject to two different kinds of non-equilibrium conditions. We aim to gain a rather general understanding of the relation between spontaneous fluctuations, linear response and total entropy production for processes away from thermal equilibrium. The first part addresses the motion of a colloidal particle driven into a periodic non-equilibrium steady state by a nonconservative force and its response to an external perturbation. The dynamics of the system is analyzed in the context of several generalized fluctuation-dissipation relations derived from different theoretical approaches. We show that, when taking into account the role of currents due to the broken detailed balance, the theoretical relations are verified by the experimental data. The second part deals with fluctuations and response of a Brownian particle in two different aging baths relaxing towards thermal equilibrium: a Laponite colloidal glass and an aqueous gelatin solution. The experimental results show that heat fluxes from the particle to the bath during the relaxation process play the same role of steady state currents as a non-equilibrium correction of the fluctuation-dissipation theorem. Then, the present thesis provides evidence that the total entropy production constitutes a unifying concept which links the statistical properties of fluctuations and the linear response function for non-equilibrium systems either in stationary or non stationary states.

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Andrews, Casey Tyler. "Coarse grained potential functions for proteins derived from all-atom explicit-solvent molecular dynamics simulations." Diss., University of Iowa, 2014. https://ir.uiowa.edu/etd/1949.

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The use of computational simulation to study the dynamics and interactions of macromolecules has become an important tool in the field of biochemistry. A common method to perform these simulations is to use all-atom explicit-solvent molecular dynamics (MD). However, due to the limitations in computational power currently available, this method is not practical for simulating large-scale biomolecular systems on long timescales. An alternative is to perform implicit-solvent Brownian dynamics (BD) simulations using a coarse grained (CG) model that allows for increased computational efficiency. However, if simulations using the CG model are not realistic, then the gain in computational efficiency from using a CG model is not worthwhile. This thesis describes the derivation of a set of bonded and nonbonded CG potential functions for use in implicit-solvent BD simulations of proteins derived from all-atom explicit-solvent MD simulations of amino acids. To determine which force field and water model to use in the MD simulations, Chapter II describes 1 Μs all-atom explicit-solvent MD simulations of glycine, asparagine, phenylalanine, and valine solutions at 50, 100, 200 and 300 mg/ml concentrations performed using eight different force field and water model combinations. To evaluate the accuracy of the force fields at high solute concentrations, the density, viscosity, and dielectric increments of the four amino acids were calculated from the simulations and compared to experimental results. Additionally, the change in the strength of hydrophobic and electrostatic interactions with increasing solute concentration was calculated for each force field and water model combination. As a result of this study, the Amber ff99SB-ILDN force field and TIP4P-Ew explicit-solvent water model were chosen for all subsequent MD simulations. Chapter III describes the derivation of CG bonded potential functions from 1 Μs all-atom explicit-solvent MD simulations of each of the twenty amino acids, including a separate simulation for protonated histidine. The angle and dihedral probability distributions sampled during the MD simulations were used to optimize the bonded potential functions using the iterative Boltzmann inversion (IBI) method. Chapter IV describes the derivation of CG nonbonded potential functions from 1 Μs all-atom explicit-solvent MD simulations of every possible pairing of the amino acids (231 different systems). The radial distribution functions calculated from these MD simulations were used to optimize a set of nonbonded CG potential functions using the IBI method. The optimized set of bonded and nonbonded potential functions, which is termed COFFDROP (COarse-grained Force Field for Dynamic Representation Of Proteins), quantitatively reproduced all of the calculated MD distributions. To determine if COFFDROP would be useful for simulations of bimolecular systems, Chapter V describes the testing of the transferability of the force field. First, COFFDROP was used to simulate concentrated amino acid solutions. The clustering of the solutes in these simulations was directly compared with results from corresponding all-atom explicit-solvent MD simulations and found to be in excellent agreement. Next, BD simulations of 9.2 mM solutions of the small protein villin headpiece were performed. The proteins aggregated during these simulations, which is in agreement with results from MD simulation but in disagreement with experiment. After scaling the strength of COFFDROP's nonbonded potential functions by a factor of 0.8 and rerunning the BD simulations, the amount of aggregation was comparable to experimental observations. Based on these results, COFFDROP is likely to be applicable in CG BD simulations of large, highly concentrated, biomolecular systems.

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Anekal, Samartha Guha. "Stokesian dynamic simulations and analyses of interfacial and bulk colloidal fluids." Texas A&M University, 2003. http://hdl.handle.net/1969.1/4434.

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Understanding dynamics of colloidal dispersions is important for several applications ranging from coatings such as paints to growing colloidal crystals for photonic bandgap materials. The research outlined in this dissertation describes the use of Monte Carlo and Stokesian Dynamic simulations to model colloidal dispersions, and the development of theoretical expressions to quantify and predict dynamics of colloidal dispersions. The emphasis is on accurately modeling conservative, Brownian, and hydrodynamic forces to model dynamics of colloidal dispersions. In addition, we develop theoretical expressions for quantifying self-diffusion in colloids interacting via different particle-particle and particle-wall potentials. Specifically, we have used simulations to quantitatively explain the observation of anomalous attraction between like-charged colloids, develop a new criterion for percolation in attractive colloidal fluids, and validate the use of analytical expressions for quantifying diffusion in interfacial colloidal fluids. The results of this work contribute to understanding dynamics in interfacial and bulk colloidal fluids.

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45

Mousavi, Sayed Iman. "Mesoscale modeling of biological fluids: from micro-swimmers to intracellular transport." Digital WPI, 2019. https://digitalcommons.wpi.edu/etd-dissertations/585.

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After more than a century, there are no analytical solutions for the Navier-Stokes equations to describe complex fluid behavior, and we often resort to different computational methods to find solutions under specific conditions. In particular, to address many biological questions, we need to use techniques which are accurate at the mesoscale regime and computationally efficient, since atomistic simulations are still incredibly computationally costly, and continuum methods based on Navier-Stokes present challenges with complicated moving boundaries, in the presence of fluctuations. Here, we use a novel particle-based coarse-grained method, known as MPCD, to study ciliated swimmers. Using experimentally measured beating patterns, we show how we recapitulate the emergence of metachronal waves (MCW) on planar surfaces, and present new results on curved surfaces. To quantitatively study these waves, we also analyzed their effect on beating intervals, energy fluctuations, and fluid motion. We then extended our model to realistic cellular geometries, using experimentally obtained Basal Bodies locations.\par In the second part of our study, we focused on the intracellular fluid motion, neglecting hydrodynamic interactions. We developed the Digital Confocal Microscopy Suite (DCMS) that can run on multiple platforms using GPUs and can input realistic cell shapes and optical properties of the confocal microscope. It has this ability to simulate both (Fluorescence Recovery After Photobleaching) FRAP and Fluorescence Correlation Spectroscopy (FCS) experiments, as well as the capability to model photo-switching of fluorophores, acquisition photo-bleaching, and reaction-diffusion systems. With this platform, in collaboration with the Vidali Lab, we were able to elucidate the role of boundaries in interpreting FRAP experiments in \textit{moss} and estimate the binding rates of myosin XI.

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46

Cho, Jae Kyu. "The dynamics and phase behavior of suspensions of stimuli-responsive colloids." Diss., Atlanta, Ga. : Georgia Institute of Technology, 2009. http://hdl.handle.net/1853/31682.

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Thesis (Ph.D)--Chemical Engineering, Georgia Institute of Technology, 2010.
Committee Chair: Victor Breedveld; Committee Member: Eric W. Weeks; Committee Member: Hang Lu; Committee Member: J. Carson Meredith; Committee Member: L. Andrew Lyon. Part of the SMARTech Electronic Thesis and Dissertation Collection.

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47

Smith, Stephen. "Stochastic reaction-diffusion models in biology." Thesis, University of Edinburgh, 2018. http://hdl.handle.net/1842/33142.

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Every cell contains several millions of diffusing and reacting biological molecules. The interactions between these molecules ultimately manifest themselves in all aspects of life, from the smallest bacterium to the largest whale. One of the greatest open scientific challenges is to understand how the microscopic chemistry determines the macroscopic biology. Key to this challenge is the development of mathematical and computational models of biochemistry with molecule-level detail, but which are sufficiently coarse to enable the study of large systems at the cell or organism scale. Two such models are in common usage: the reaction-diffusion master equation, and Brownian dynamics. These models are utterly different in both their history and in their approaches to chemical reactions and diffusion, but they both seek to address the same reaction-diffusion question. Here we make an in-depth study into the physical validity of these models under various biological conditions, determining when they can reliably be used. Taking each model in turn, we propose modifications to the models to better model the realities of the cellular environment, and to enable more efficient computational implementations. We use the models to make predictions about how and why cells behave the way they do, from mechanisms of self-organisation to noise reduction. We conclude that both models are extremely powerful tools for clarifying the details of the mysterious relationship between chemistry and biology.

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Sasai, Masaki, Tomoki P. Terada, and Mitsunori Takano. "Unidirectional Brownian motion observed in an in silico single molecule experiment of an actomyosin motor." National Academy of Sciences, 2010. http://hdl.handle.net/2237/20619.

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Paudyal, Nabina. "Brownian Dynamics Simulation Of A Five-site Model for a Motor Protein on a Bead-Spring Substrate." University of Akron / OhioLINK, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=akron1415390064.

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Kollmann, Markus. "Dynamics and microstructure of interacting Brownian particle systems : electrokinetic effects, (quasi)-two-dimensional systems and sphere caging /." [S.l. : s.n.], 2001. http://www.bsz-bw.de/cgi-bin/xvms.cgi?SWB9674490.

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Dissertations / Theses on the topic 'Brownian dynamics'

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