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 465 for “"Coarse-grained"”.
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Systematic development of coarse-grained polymer models
The coupling between polymer models and experiments has improved our understanding of polymer behavior both in terms of rheology and dynamics of single molecules. Developing these polymer models is challenging because of the wide range of time and length scales. Mechanical models of polymers have …
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Coarse-grained models of biomolecule dynamics and allostery
… of biological molecules. We employ a set of coarse-grained models to investigate the mechanism of transmission of allosteric signal via spatial fluctuations. Our models are coarser than those in computational techniques established in molecular biology, but allow for both the identification …
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Coarse-Grained Molecular Dynamics Simulations of Macromolecular Complexes
… relevant time scales, using a simplified, or ""coarse-grained"" description. The method developed for this purpose, called shape-based coarse-graining, is applied to a number of systems. Simulations of several viruses, including the first all-atom simulation of a complete virus, reveal how …
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A coarse grained transport model for nanofluidic systems
… time scale, increased the interest in efficient coarse-grained (CG) models. Although many existing CG models for various fluids are able to capture structure and dynamics of the bulk fluid accurately, these models are not suited to describe transport phenomena involving explicit walls in …
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Development of a multiscale coarse-grained chromatin model
… In this thesis, we develop a multiscale coarse-grained chromatin model, which integrates all-atom representations of proteins, DNA, and nucleosomes; a chemically specific coarse-grained model of kb scale chromatin; and a minimal model of sub-Mb scale chromatin. A key feature of this model …
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Atomistic and Coarse-Grained Investigation of Membrane-Protein Interactions
… we embarked on an ambitious journey to build a coarse-grainedMonte Carlo computational framework to simulate membrane-protein interactions at themesoscale. This framework utilizes building blocks such as body, bonded and non-bondedcomponents and discretized differential geometry operators …
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Fine and coarse-grained parallelisation techniques for complex systems
… therefore lack scalability.<br/><br/>A number of coarse- and fine-grained optimisation techniques have been developed, using portable standards (MPI and OpenCL), to produce scalable solutions to help overcome these issues. A leading ABM framework (FLAMEGPU) is compared with the more direct …
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On Extracting Coarse -Grained Function Parallelism From C Programs
We built an in-lining based prototype of the memory data-flow analysis system on top of the IMPACT compiler infrastructure. We applied the prototype to analyze the memory data-flow of several MediaBench programs. The experiment results showed that while the prototype performed reasonably well for …
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Coarse-grained modeling of the metabolism of Saccharomyces cerevisiae
Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2023-09-01 without embargo terms
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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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Understanding Chromatin Organization and Dynamics with Coarse-Grained Modeling
… of chromatin and biomolecular condensates, coarse-grained (CG) modeling is essential to achieve the biologically relevant timescales. We have developed CG models and toolkits to facilitate modeling chromatin and related proteins. We have also applied CG protein and DNA models to study …
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Development of Transferable Coarse-Grained Models of Amino Acids
… this study was to develop accurate transferable coarse-grained (CG) models of those amino acids. In CG models, several atoms are represented together as a single pseudo-atom or "bead," which can allow the modeling of processes like self-assembly of biomolecules and biomaterials through reduction …
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Coarse-grained Modeling of Protein Dynamics using Elastic Network Models
… experimentally or with all-atom simulations, coarse-grained methods, especially elastic network models (ENMs), are frequently employed. In the last years, studies on various proteins showed that ENMs reliably reproduce experimental data, despite the simplified protein representation and the …
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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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Multi-Level Coarse-Grained Modelling on DNA Functionalised Building Blocks
… strategy to demonstrate new horizons of coarse-grained simulation systems. From the detailed oxDNA molecular dynamics simulation of mimicking the most detailed behaviours of an individual DNA nanoparticle, to a second-level coarse-grained system with thousands of repeated units of …
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Taphonomic studies of fossil preservation in coarse-grained siliciclastic environments
… The rarity of similar fossils and textures in coarse-grained siliciclastic strata of the later Phanerozoic suggests that a taphonomic window facilitated this mode of fossil preservation. However, environmental and biological factors that promoted fossilization remain unclear. To experimentally …
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A coarse-grained variable-complexity MDO paradigm for HSCT design
… disciplines. A master-slave paradigm manages a coarse grained parallelism of the analysis and optimization codes required by the disciplines showing reasonable speedups and efficiencies on an Intel Paragon
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Coarse-grained simulations to predict structure and properties of polymer nanocomposites
… this contribution, we develop (1) an equilibrium coarse-graining method to predict nanoparticle dispersion in a polymer melt, (2) a dynamic coarse-graining method to predict rheological properties of polymer-nanoparticle melt mixtures, and (3) a numerical approach that includes interfacial layer …
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Forecasting the Transport and Fate of Pharmaceuticals in Coarse Grained Aquifers
… likely to impact specific compound behavior in coarse grained hydrogeologic settings. This research is a key component of an ongoing international effort to examine the fate and transport of a select group of pharmaceuticals identified as being persistent in groundwater. Laboratory and field …
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Forecasting the Transport and Fate of Pharmaceuticals in Coarse Grained Aquifers
… likely to impact specific compound behavior in coarse grained hydrogeologic settings. This research is a key component of an ongoing international effort to examine the fate and transport of a select group of pharmaceuticals identified as being persistent in groundwater. Laboratory and field …
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