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 30 for “"coarse-grained molecular dynamics"”.
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Coarse-Grained Molecular Dynamics Simulations of Macromolecular Complexes
"Molecular dynamics simulations provide critical insights into molecular mechanisms underlying cellular processes. Most such processes, however, remain out of reach, due to large system sizes and long time scales involved. This thesis describes molecular dynamics simulations of large macromolecular …
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Accelerator-based look-up table for coarse-grained molecular dynamics computations
Molecular Dynamics (MD) is a simulation technique widely used by computational chemists and biologists to simulate and observe the physical properties of a system of particles or molecules. The method provides invaluable three-dimensional structural and transport property data for macromolecules …
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Simulate Time-integrated Coarse-grained Molecular Dynamics with Geometric Machine Learning
Molecular dynamics (MD) simulation is the workhorse of various scientific domains but is limited by high computational cost. Learning-based force fields have made major progress in accelerating ab-initio MD simulation but are still not fast enough for many real-world applications that require …
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Engineering the future of Hybrid Materials with Coarse-Grained Molecular Dynamics
… and designing these complex materials is coarse-grained (CG) molecular dynamics (MD) which allows researchers to capture molecular-level interactions while efficiently modeling larger, structurally diverse systems over longer timescales, bridging the gap between atomic-level insights and …
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Quantitative all-atom and coarse-grained molecular dynamics simulation studies of DNA
… fast to observe underlying DNA and DNA–protein dynamics. Acting on length and timescales that complement single-molecule experiments, molecular dynamics simulations provide a high-resolution glimpse into the mechanics of a biomolecular world. Here, several simulation studies are presented, each …
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GPU-Optimized Hybrid Neighbor/Cell List Algorithm for Coarse-Grained Molecular Dynamics Simulations
Molecular Dynamics (MD) simulations provide a molecular-resolution picture of
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All-atom and Coarse-grained Molecular Dynamics Modeling of Various Polymeric and Composite Materials
This dissertation leverages molecular dynamics (MD) simulations to reveal the structure-property relationship of various polymeric and composite materials, including polyacrylonitrile-poly(methyl methacrylate) (PAN-b-PMMA) copolymers, polyetherimide (PEI)-graphene composites, and epoxy network …
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Application of All-Atom and Coarse-Grained Molecular Dynamics Simulations to Long Timescale Structural Transitions of Proteins
… but very rarely both at the same time. Molecular dynamics (MD) simulations, in contrast, offer data on the motion of biomolecules with very high spatial and temporal resolution, and allow easy manipulation of the biomolecules and their environment to test the effects of perturbations …
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Selective transport of the nuclear pore complex studied through all-atom and coarse-grained molecular dynamics simulations
… the NPC’s selective transport. In this thesis, molecular dynamics has been used to model and study a representative volume of the FG-nup-filled central pore. One FG-nup was divided into 25 segments, each containing 100 amino acids. The 25 segments were then tethered onto a planar surface to …
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Efficient modeling of DNA translocations and ionic currents using coarse-grained molecular dynamics simulation and finite-element modeling
Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2022-11-11 without embargo terms
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Efficient modeling of DNA translocations and ionic currents using coarse-grained molecular dynamics simulation and finite-element modeling
Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2022-11-11 without embargo terms
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Structure, Dynamics and Rheology of Polymer Solutions from Coarse-Grained Molecular Dynamics: Effects of Polymer Concentration, Solvent Quality and Geometric Confinement
… flow-microstructure interactions in macromolecular fluids is of great</p> <p>importance in the design and optimization of ubiquitous polymer processing operations.</p> <p>Further, such interactions are routinely encountered in separation of biopolymer mixtures</p> <p>using gel …
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Dynamics Of Orientable Particulate Suspensions: Continuum Simulations Of ‘Living’ Fluids And Meso-Scale Simulations Of Anisotropic Particle Suspensions
… the living cells is probed by Fluid Particle Dynamics (FPD). In the second part, Coarse-Grained Molecular Dynamics (CGMD) simulation is applied to investigate the relation between microstructure of the suspension, such as orientation distribution function, particle moments to its rheological …
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Depletion induced bundling of rod-like colloids and simulations of triple helix bundles
We ran molecular dynamics simulations of rod-like colloids acting under depletion forces. In these simulations, we found bundling of the rods above a given strength of the depletion force. We then analyzed the bundle formation process and how the shape and flexibility of the rods could effect …
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Learning to Model Atoms Across Scales
… methods such as density functional theory and molecular dynamics simulation can offer an unparalleled spatiotemporal resolution for observing microscopic mechanisms and predicting macroscopic phenomena. However, many natural processes are extremely complex, requiring highly accurate modeling of …
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Dimensionality reduction and multiscale modeling for the understanding of protein folding and hierarchical self-assembly
… and assembled conformations. First, I employ molecular dynamics and nonlinear dimensionality reduction to study a family of antimicrobial peptides with different side chain lengths and demonstrate a critical side chain length that determines backbone secondary structure in solution. Second, I …
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Investigation into obstacles to the implementation of the directed-self assembly of block copolymers
… reasons for high LER, LWR, and defects using coarse-grained molecular dynamics and expands the library of BCP materials by synthesizing two new BCPs. Chapter 3 uses simulations to investigate the effect pinning stripe position, density multiplication, and defect order on the relative free …
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MOLECULAR DYNAMICS STUDY ON THE STRUCTURE, DYNAMICS AND STRESS RESPONSE OF DILUTE MICELLAR SYSTEMS IN UNIAXIAL EXTENSIONAL DEFORMATION
… pertinent to self-assembly and micellar dynamics. To this end, this work aims to utilise coarse-grained molecular dynamics simulations to investigate the dynamics and structural response of various infinitely dilute micellar solutions under the influence of uniaxial extensional flow.</p> …
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Topology and geometry-based methods for quantifying the complexity of protein structures
… combination with available experimental data and molecular simulations to analyze the topological complexity of tau proteins. These proteins are involved in a class of neurodegenerative diseases, called tauopathies. The methods developed in this dissertation are general and applicable to other …
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Structure, Assembly, and Maturation of High -Density Lipoproteins
… of arteriosclerosis. Little is known about the molecular level structure of these HDL particles or the mechanism by which they assemble from lipid-free proteins into discoidal protein-lipid particles and then into spherical particles. This thesis presents molecular dynamics simulations with …
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