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Showing 1 to 11 of 11 for “"brownian dynamics simulation"”.
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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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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 simulation of soft matter with hydrodynamics: methods for constrained systems and shear processing of 2D materials
… of soft matter particles. We then discuss the simulation methodology and mobility tensor approximations used in this thesis along with some additional considerations. In Chapter 2 we study methods for simulating constrained Brownian systems. We compare the current state-of-the-art method for …
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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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DNA-colloid systems and micro-rheology
… efficient. Chapter 3 investigates the dynamics of ADNA coated colloids using Brownian Dynamics simulation and a theoretical model, also applying the algorithm developed in Chapter 2. A two-regime diffusivity is identified, in contrast to previous works, which simply found an increased …
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Coupling molecular conformation to polymer chemistry and composition via flow
… of polymer materials. The first project utilizes Brownian Dynamics simulation techniques to examine the behavior of diblock copolymers in equilibrium and flow conditions. In equilibrium the two blocks are found to behave primarily independently, with the end to end distance of the copolymer …
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Hydrodynamics and Diffusion of Membrane Proteins to Engineer Chemical Reactions in Synthetic Biomembrane Platforms
… consistent with experimental work. Afterwards, a Brownian dynamics simulation method is described which includes 2D hydrodynamic interactions relevant for transmembrane proteins. Finally, efforts to use SLBs to engineer enzymatic reactions in a defined sequence are described. The transfer of a …
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Motion of Janus and Patchy Particles Near Various Boundaries
… interface, which significantly affect the dynamics of colloidal particles. Many studies have focused on understanding the dynamics and principles underlying the motion of active colloidal particles near various boundaries, yet a number of questions in the field remain to be answered.</p> …
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Single polymer dynamics in semi-dilute solutions: linear and ring polymers
… been established to investigate molecular-level dynamics, thereby allowing direct access to polymer chain relaxation mechanisms and polymer non-linear response under a variety of flows. Despite recent progress in the field of single polymer dynamics, however, the vast majority of single molecule …
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On the theory of Brownian aggregation in colloidal dispersions
Brownian aggregation kinetics is a topic of interest for colloidal dispersions, macromolecular fluids, nanoparticle self-assembly, and biochemical reactions. The manipulation of colloidal dispersion stability by containing or promoting aggregation rates is manifest in several natural phenomena and …
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Translocation of a Semiflexible Polymer Through a Nanopore
… been developed. In this thesis, we explore the dynamics of driven translocation of a semiflexible polymer through a nanopore in two dimensions (2D) using Langevin dynamics (LD) simulation. By carrying out extensive simulation as a function of different parameters such as, driving force, length …