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.
Results
Showing 1 to 20 of 38 for “"coarse grained model"”.
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A simple coarse-grained model to predict infectious disease outbreak statistics and the consequences of glycolysis inhibition on cell junction mechanics
Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2025-03-28 without embargo terms
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Molecular dynamics simulations of EMIM − BF4 ionic liquid for electrospray thrusters
… the comparison of an all atom and a coarse grained model of EMIM − BF4 under the influence of an external electric field, and the process of fragmentation that occurs in the electrospray’s plume for dimer and trimer ionic species. In order to compare the all atom and the coarse …
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Theory of Slow Dynamics and Barrier Hopping in Colloidal Suspensions and Polymer Melts
… theory is extended to polymer melts based on a coarse-grained model in which the melt is treated as a liquid of segments. The barrier is predicted to be a function of a single parameter that is chemical structure, temperature and pressure dependent. Qualitative agreement with experiment is found …
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Graphics processing unit accelerated coarse-grained protein-protein docking
… unit (GPU) implementation of the Kim-Hummer coarse-grained model for protein docking simulations, using a Replica Exchange Monte-Carlo (REMC) method. Our highly parallel implementation vastly increases the size- and time scales accessible to molecular simulation. We describe in detail the …
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Multiscale Modelling of Biomolecular Phase Behaviour
… spatial scales. Simulations with a minimal coarse-grained model showed how enriching the structural ensemble of proteins in open, expanded conformations can promote their propensity to undergo liquid-liquid phase separation. This is because more expanded conformations favour inter-protein …
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Towards extending coarse-grained circuit-host modeling to complex environments
… Recent advances have shown that a mechanistic, coarse-grained approach can give fundamental insight into how synthetic circuits interact with their host cells, though how this model can be applied in complex environments remains an open question. In this thesis, I will discuss how an extension …
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Conformational Dynamics of the Nuclear Pore Complex Studied With Coarse-Grained Modelling and Polarized Light Microscopy
… of the nuclear pore complex (NPC) through coarse-grained modelling and polarized-total internal reflection fluorescence (pol-TIRF) microscopy. The NPC is a large (~120 MDa in humans) macromolecular assembly that controls the flow of molecules into and out of the nucleus. The NPC is a key …
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ON DEFORMATION STABILITY AND DUCTILE DAMAGE IN NANOTWINNED METALS
… kinetic relation is then adopted in developing a coarse grained model for probing the size-dependent stress-strain responses and microstructural instabilities in polycrystalline NT materials, without explicitly modeling twins. Finally, we investigate the role of twinning mediated microstructure …
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Theoretical and simulation tools for electron transfer and chain reactions in single walled carbon nanotubes
… of metallic/semiconducting nanotubes from a modelling perspective to gauge the phenomena from a molecular standpoint; (b) Develop a simple coarse-grained model that describes the characteristics of one-dimensional nanoenergetic materials and extracts the properties of the thermally propagated …
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Mechanical behavior and microstructure of self-assembling oligopeptide gels
… are also examined. Steered molecular dynamics modeling was used to characterize the mechanical interaction between filaments, and a coarse-grained model was developed to extend the system to ordinary time scales. A microindentation assay was developed and used to characterize the mechanical …
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Brownian dynamics simulations of fine-scale molecular models
… 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 …
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Modeling Hydrophobic Effects at different lengthscales
… areas be predicted in a simple way? A simple coarse-grained model of water/protein system, which is developed here shows the conditions for wet and dry hydrophobic protein cavities, and is able to reproduce all atom simulation results. The method should serve as an intermediate step between …
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Conformation of Transmembrane Segments of a Protein by a Coarse Grain Model
… of the protein hH<sub>V</sub>1 is studied by a coarse-grained model as a function of temperature where structural detail of a residue is ignored and its specificity is captured by its unique interaction. How residues of the protein hH<sub>v</sub>1 assemble or disperse as the temperature varies …
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Shaping of membranes by arc-like particles
… The shaping of membranes is investigated with coarse-grained modeling and Monte Carlo simulations. In the coarse-grained model, the membrane is described as a discretized elastic surface, and the particles as segmented arcs. Concave arc-like particles, i.e. particles interacting with the …
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The physics of cell-fate choice
… to the success of various systems biology models of cell-fate choice. Next, I present two models concerning noise in cell-fate choice--- a mechanical model of DNA supercoiling-mediated transcriptional noise and a coarse-grained model of noise in partitioning during cell division that can …
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Molecular Mechanisms of Protein Self-Assembly and Aggregation
… into amyloid structures using a native-centric coarse-grained model, and explain the results with a novel Markov state analysis from which we are able to extract structural, kinetic and thermodynamic information on elongation reactions. Finally, we probe the interactions of A$\beta_{42}$ …
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Computational methods for transport properties
… simulations, and we will finish with an ultra coarse grained model, that can be used to study the transport properties through a bacterial channel. Finally we will list the results obtained using the three aforementioned methods and we will summarise this thesis with the conclusions.
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Investigation of an immune algorithm and differential evolution to study folding of model proteins
… have been used to study the folding of model proteins, with the aim of accurately predicting the native state of a protein from its amino acid sequence. Through modelling, knowledge of the folding process can be obtained. In this thesis, two search techniques have been applied to a …
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Simulation Studies Of Self-assembly And Phase Diagram Of Amphiphilic Molecules
… computer simulation methods. The semi-realistic coarse-grained model, used extensively for simulation of polymers and surfactant molecules, is adopted in an off-lattice approach to study how the geometric structure of amphiphiles affects the aggregation properties. The results of simulations show …
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Nanomechanics of Glassy Polymers Under Confinement
… confinement has an effect are reasonable to model using computer simulations. This Thesis investigates the confinement of polymer glasses and polymer nanocomposites using molecular dynamics and Monte Carlo simulations. In Chapter 2, we use a coarse-grained model to investigate the effect of …
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