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 26 for “"langevin dynamics"”.
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Bödeker's Effective Theory: From Langevin Dynamics to Dyson-Schwinger Equations
The dynamics of weakly coupled, non-abelian gauge fields at high temperature is non-perturbative if the characteristic momentum scale is of order |k| \sim g^2 T. Such a situation is typical for the processes of electroweak baryon number violation in the early Universe. Bödeker has derived an …
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Characterization of nanopores with internal cavities for DNA manipulation using Langevin dynamics simulations
… this geometry is studied using coarse-grained Langevin dynamics. The most striking result is that translocation time through the system is found to be minimal for polymers of medium length: both longer and shorter chains take longer to translocate. The length at which this occurs is named the …
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Biomolecular Folding Rates As Understood From Single-Reaction-Coordinate Langevin Dynamics And Kramers’ Theory
Langevin dynamics was used to model the folding and unfolding of simple, hairpin-like biomolecules whose ends are attached to laser-trapped beads, as occurs in optical tweezers experiments. The Langevin process was evolved numerically, using parameters motivated by real experimental systems. …
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Exploring Downhill Protein Folding Free Energy Landscapes
… temperature-jump kinetics measurements and Langevin dynamics simulations. A kinetic and thermodynamic survey of multiple WW domain mutants is performed in combination with a model to reveal the correlation between protein stability and downhill folding propensity. A designed histidine …
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Towards Enhanced Proposals for PINN-Based Neural Sampler Training
… a partially learned vector field with annealed Langevin dynamics. However, isolated modes and other pathological properties of the annealing path imply that such proposals achieve insufficient exploration and thereby lower performance post training. In this work we extend existing work and …
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Efficient Sampling Methods of, by, and for Stochastic Dynamical Systems
… of computational statistics and computational dynamics. Stochastic differential equations (SDEs) are used to model a variety of physical systems, and computing expectations over marginal distributions of SDEs is important for the analysis of such systems. In particular, quantifying the …
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Optimizing Irreversible Perturbations of the Unadjusted Langevin Algorithm
… Monte Carlo (MCMC) methods, and in particular Langevin dynamics, provide a powerful framework for this task by constructing stochastic processes that converge to the target distribution. However, practical implementations face two challenges: slow mixing when the target distribution is …
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Some Investigations Of Phase Transitions In Rod-Like Macro-Molecules And Fibrous Gels
… transitions are presented here.First, we conduct Langevin dynamics calculations on a chain of masses and bistable springs in a viscous fluid, and extract a temperature dependent kinetic relation by observing that the dissipation at a phase boundary can be estimated by performing an energy balance. …
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Statistical and Algorithmic Thresholds in Spin Glasses
… spin glasses and shows that lowtemperature Langevin dynamics finds the ground state in the topologically trivial regime; the latter result is new even in the single-species setting. Part II of this thesis concerns algorithms for optimization and sampling problems on spin glasses. Chapter 5 …
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Polymer translocation: a nonequilibrium process
3D Langevin dynamics simulations of the capture and translocation of polymers through a nanopore are conducted for several polymer lengths and two different Péclet values (that quantify the drift-diffusion balance of the system). By measuring the average conformation of the polymer and the average …
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Simulation and modelling to develop a nanopore-based device for ricin detection
… of ionic flow through the pore. Molecular dynamics simulations are an effective method of quantitatively and qualitatively studying key design features and mechanisms of current blockage. This work uses coarse-grained Langevin dynamics simulations to explore various aptamer-encoded nanopore …
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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 …
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Are Particle-Based Methods the Future of Sampling in Joint Energy Models? A Deep Dive into SVGD and SGLD
… comparing its performance to Stochastic Gradient Langevin Dynamics (SGLD). We incorporated a generative loss term with an entropy component to enhance diversity and a smoothing factor to mitigate numerical instability issues commonly associated with the energy function in energy-based models. …
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Computational modelling of the vortex state in high-temperature superconductors
… are represented as particles and we employ Langevin dynamics to study the statics and dynamics of the system.<br/><br/>We show that the long-range nature of the vortex-vortex interaction can result in numerical artefacts, and provide two techniques to overcome these problems: (i) using a …
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Study of 3D Genome Organisation in Budding Yeast by Heterogeneous Polymer Simulations
… of biophysical properties of chromatin on the dynamics and structure of chromosomes, I developed a 3D computational model of the nucleus of the yeast S. cerevisiae during interphase. In the model, each chromosome was a hetero-polymer informed by our bioinformatics analysis for heterogeneous …
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Near-Field Hydrodynamics of Optically Trapped Colloids in Simple and Complex Fluids
… results are further complemented by Molecular Dynamics simulations. I show that hydrodynamic interactions between two trapped colloids encode detailed information about the surrounding flow field and its modulation by nearby boundaries. A rapid cross-correlation analysis of particle …
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Computational Hardness in Random Optimization Problems from the Overlap Gap Property
… descent, approximate message passing, and Langevin dynamics run for bounded time. In particular, this includes the algorithms achieving ALG. We prove these results by extending the overlap gap property (OGP) framework of Gamarnik and Sudan to multi-OGPs, which consider forbidden …
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Modeling and Experimental Techniques to Demonstrate Nanomanipulation With Optical Tweezers
… key tools must first be developed. We implement Langevin dynamics simulations to model the interaction of nanoparticles with an optical trap. Physically accurate simulations provide a robust platform to test new methods to characterize and improve the performance of optical tweezers at the …
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Statistical Inference and Learning for Stochastic and Partial Differential Equations
… directly target the posterior distribution with Langevin dynamics for sampling, with parameter estimation via maximum marginal likelihood methods. Convergence rates are derived and validated in the linear case, and both preconditioning and warm-start techniques are explored and shown to improve …
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Computational modeling of intrinsic dissipation in nano-structure
… systems (NEMS). We, first, use molecular dynamics (MD) simulation and gain an understanding of the underlying loss mechanisms. Using insights from the MD simulation, a multi-scale method to model intrinsic damping is developed. The high frequency vibration in NEMS have important …
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