Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 20 of 68 for “"Brownian dynamics"”.
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Robust Biased Brownian Dynamics for Rate Constant Calculation
… probability problem, it is usually solved by Brownian dynamics simulations, which is also known as a random walk or path integral method, instead of solving the equivalent partial differential equation by a discretization method. In this thesis, a robust importance sampling algorithm for …
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Brownian dynamics simulations of fine-scale molecular models
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 …
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Fast algorithms for Brownian dynamics simulation with hydrodynamic interactions
In the Brownian dynamics simulation with hydrodynamic interactions, one needs to generate the total displacement vectors of Brownian particles consisting of two parts: a deterministic part which is proportional to the product of the Rotne-Prager-Yamakawa (RPY) tensor D [1, 2] and the given external …
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A Brownian Dynamics Analysis of Ion Movement in Membrane Channels
… this equation is presented. The technique called Brownian dynamics is then used to study ion transport through membrane channels. Four cases are considered: (1) no ion-ion interaction, no channel structure; (2) no ion-ion interaction, channel structure present; (3) ion-ion interaction, no channel …
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1-D Brownian Dynamics Simulation With Its Application in Study of Ion Channel
… algorithm, this process could be investigated by Brownian Dynamics simulation, which is a more straightforward and accurate method than traditional permeation theory. The basic assumption is that the motion of ion in the solution consists of a random collision with surrounding media and a …
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Brownian dynamics study of the self-assembly of ligated gold nanoparticles and other colloidal systems
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 …
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Efficient coarse-grained brownian dynamics simulations for dna and lipid bilayer membrane with hydrodynamic interactions
The coarse-grained molecular dynamics (CGMD) or Brownian dynamics (BD) simulation is a particle-based approach that has been applied to a wide range of biological problems that involve interactions with surrounding fluid molecules or the so-called hydrodynamic interactions (HIs). From simple …
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Conformation and Rheology of Semiflexible Macromolecules Using Non-Equilibrium Brownian Dynamics and Monte Carlo Simulations
Non-Equilibrium Brownian Dynamics Simulations (NEBD) and Configuration-Biased Monte Carlo (CBMC) methods are used to model the dynamics of semi-flexible macromolecules and polyelectrolytes undergoing shear and extensional flow. The mathematical model utilizes a discretized version of the …
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Brownian dynamics simulation of soft matter with hydrodynamics: methods for constrained systems and shear processing of 2D materials
… 2 we study methods for simulating constrained Brownian systems. We compare the current state-of-the-art method for these simulations, GMRES, to a different method called the projected conjugate gradient (PrCG) method. In particular, we compared PrCG and GMRES for rigid bodies, freely jointed …
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Computational modeling of biological molecule separation in nanofluidic devices
… In this Thesis, we focus on the development of Brownian Dynamics (BD) simulation tools for modeling the performance of nanofluidic devices for the separation of short, Ogston-regime, dsDNA molecules. The first part of this Thesis focuses on the development of Brownian Dynamics models to predict …
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Interplay of flow and microstructure in complex fluids: Semiflexible polymer solutions and emulsions
… An efficient algorithm is presented for Brownian dynamics simulations of semiflexible bead-rod chains with configuration-dependent anisotropic bead friction tensor. The algorithm for the dynamics and the stress generalizes an earlier one restricted to isotropic, configuration-independent …
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Direct imaging of single-walled carbon nanotubes reptational dynamics in packed-colloid porous media
Understanding Brownian dynamics of single-walled carbon nanotubes (SWCNTs) in complex porous media is key to understanding transport and mechanical properties in a variety of systems. Motion of semi-flexible filaments in gel-like porous media including polymer networks and cell cytoskeleton have …
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Modeling and simulation of micro/nano-rod distribution in micro channel flows
… particle. Initially, a systematic method using Brownian dynamics simulation of the rotational motion of nanorod was performed to obtain the average orientation distribution of a nanorod in various range of Peclet number and position from the confining wall. Subsequently, the results of the angle …
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Caracterização estrutural, dinâmica e reológica de suspensões coloidais via simulação molecular
… is necessary studiyng the particle aggregation dynamics to understanding the dynamic mechanisms of paraffins and asphaltenes precipitation. The goal of this work was the implementation of algorithms that calculate structural (Radial Distribution function (RDF) and Structure Factor), dynamical …
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Simulation Studies of Biological Ion Channels
… their structure to their functional properties. Brownian dynamics simulations are introduced, in which the motions of individual ions are simulated as they move through the channel and in baths attached to each end. The techniques for setting boundary conditions which maintain ion concentrations …
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Simulation Studies of Biological Ion Channels
… their structure to their functional properties. Brownian dynamics simulations are introduced, in which the motions of individual ions are simulated as they move through the channel and in baths attached to each end. The techniques for setting boundary conditions which maintain ion concentrations …
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From Spheres to Sheets: Colloidal Hydrodynamics, Thermodynamics, and Statistical Inference
… with high resolution by performing extensive Brownian dynamics simulations and experiments with mono- and polydisperse solutions of gold nanoparticles as well as single walled carbon nanotubes. We then extend the non-parametric Bayesian framework developed to infer the orientation probability …
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Dynamics and structures of linear and supercoiled DNAs
A normal mode theory is developed for the Brownian dynamics of weakly bending rods with preaveraged hydrodynamic interactions. An expression is given for the mean squared angular displacement $$ of the $m\sp{th}$ bond-vector around the instantaneous x-axis (perpendicular to the end-to-end vector …
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Computer Simulation of Biological Ion Channels
… These algorithms are then used to perform Brownian dynamics simulations on realistic models of biological ion channels. An iterative method of solution, in which the dielectric boundary is tiled with variable sized surface charge sectors, provides the flexibility to deal with arbitrarily …
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Computer Simulation of Biological Ion Channels
… These algorithms are then used to perform Brownian dynamics simulations on realistic models of biological ion channels. An iterative method of solution, in which the dielectric boundary is tiled with variable sized surface charge sectors, provides the flexibility to deal with arbitrarily …
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