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 27 for “"Coarse-grained models"”.
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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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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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Multiscale coarse-grained models for biological phase separation: Development and applications
… In this thesis, we present three multiscale coarse-grained models with amino acid resolution aimed at studying phase separation of proteins. The Mpipi model balances the dominant role of π–π and hybrid cation–π/π–π interactions with the rest of the interactions, while keeping R–based …
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Multilevel Monte Carlo simulation of soft matter using coarse-grained models
… in such situations, one often relies on a coarse-grained description that integrates out microscopic degrees of freedom, yielding a model that is composed of mesoscopic particles with effective interactions. In most cases, this coarse-graining procedure is not exact, resulting in a biased …
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Transferable Coarse-Grained Models: From Hydrocarbons to Polymers, and Backmapped by Machine Learning
Coarse-grained (CG) molecular dynamics (MD) simulations have seen a wide range of applications from biomolecules, polymers to graphene and metals. In CG MD simulations, atomistic groups are represented by beads, which reduces the degrees of freedom in the systems and allows larger timesteps. Thus, …
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A novel algorithm for creating density dependent, coarse-grained models for the simulation of surfactant systems
… solvent potentials within a more general coarse-graining framework. While a pairwise potential between solute sites is relatively simple and ubiquitous, an additional parameterization based on the local solute concentration has the possibility to increase the accuracy of the simulations …
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Coarse-grained models for prediction, uncertainty quantification, and extreme event statistics of turbulent flows in engineering and geophysical settings using physics-consistent data-driven closures
… data- driven closures that will provide accurate coarse-grained evolution equations? Can we formulate the corresponding physics-constrained closures for the quantification of uncertainty? Can high-order statistics and statistics of extreme events be computed from data-augmented coarse-scale or …
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Rheology of concentrated protein solutions and attractive colloidal dispersions
… dispersions due to inter-particle attractions. Coarse-grained models of protein solutions and colloidal dispersions are developed.
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Modelling the evolution of biological complexity with a two-dimensional lattice self-assembly process
… any all-encompassing model is unrealistic. Coarse-grained models, despite not faithfully capturing every detail of the original system, have massive potential to assist understanding complex phenomenon. A principal actor in self-assembly is the binding interactions between subunits, and so …
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Mesoscopic Distinct Element Method for Multiscale Modeling of Carbon Nanotubes
… of atomistic modeling and the lack of mesoscale models, mesoscopic simulation methods for CNT systems are missing. My work focuses on deriving ultra-coarse-grained models based on mesoscopic dintinct element method (mDEM). Our mDEM model is informed by atomistic data obtained with molecular …
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Coarse-graining and data mining approaches to the prediction of structures and their dynamics
… approaches to this problem is the systematic coarse-graining of less relevant degrees of freedom in order to obtain Hamiltonians that span larger length and time scale. Attempts to do this in the static regime (i.e. zero temperature) have already been developed, as well as thermodynamical …
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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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Adsorption of Dendritic Fluorocarbon End-Capped Poly(Ethylene Oxide) at an Air-Water Interface – A Synthetic, Analytical and Computational Study
… but we model the poly(ethylene oxide) using coarse-grained models. The advantage of coarse-graining (CG) is that it allows us to simulate much longer chains and much higher surface concentrations allowing direct predictions for the neutron reflectivity based on the calculated distribution …
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Multilevel frameworks for studying protein energy landscapes
… this problem, mechanical force fields and coarse-grained models have been developed to reduce the number of interaction sites. While advances like AlphaFold have improved native structure prediction, understanding thermodynamic stability and folding pathways remains a major challenge. This …
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An interdisciplinary study of the mechanical and dynamic properties of α-solenoid repeat proteins
… they are flexible, dynamic and elastic. Using coarse-grained models, I discuss how intrinsic flexibility may arise in repeat proteins and how it could be crucial for the biological function of two systems: PR65, the scaffold protein of the protein phosphatase 2A, and Rap proteins, which are …
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Physical interpretation of coarse-grained bead-spring models of complex fluids
… At the same time, simulations of highly coarse-grained particle-based models, such as lattice chain Monte Carlo and bead-spring simulations, have emerged as a promising alternative. The application of these methods, however, has been hampered by a lack of clear physical interpretation of …
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A computational study of DNA four-way junctions and their significance to DNA nanotechnology
… are used to inform finite-element method coarse-grained models for the ground-state structure determination and equilibrium Brownian Dynamics of large-scale DNA origamis. Together, this thesis presents a set of guidelines for the rational design of nanodevices comprising arrays of …
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A Simulation Approach to Thermodynamics in Interfacial Phenomena
… particles. Furthermore, a scheme for developing coarse-grained models of polymers with specific chemistry in contact with the solid surface is presented and quantitatively evaluated. These models are necessary to address the larger length scales required for study of polymer-particle mixtures. …
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Molecular Docking With Haptic Guidance and Path Planning
… to reduce this computational cost is to use more coarse-grained models that approximate molecular docking. Coarse-grained molecular docking prediction is generally performed first by sampling ligand states using a rigid body model or a partial flexibility model to reduce computation, then by …
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Energy Landscapes of Hybrid Potentials Based on NMR Data
… alongside explicit or implicit membranes, and coarse-grained models. Based on this novel approach, the protein E of the SARS-CoV-2 virus was in- vestigated. Our conformational dynamics study revealed the predicted structure for the open-state of the E viroporin in the absence of experimental …
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