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 25 for “"Metadynamics"”.
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Determining the surface tension of gas-liquid interfaces through metadynamics
… is molecular dynamics (MD) with well-tempered metadynamics for a one component simulation of Lennard-Jones Ar. The system operates in the NP<sub>xx</sub>T ensemble with the simulation x-axis cell length L<sub>x</sub> as the chosen collective variable (CV). This allows the system to transition …
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Understanding long timescale phenomena in atomic systems from accelerated molecular simulation methods
… matter. The first method, all-atom Metadynamics, is a version of the popular advanced sampling method Metadynamics. By biasing over all atoms rather than collective variables, all-atom Metadynamics samples the potential energy landscape in all-atom dependent variable space. All-atom …
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Development of Free Energy Calculation Methods for the Study of Monosaccharides Conformation in Computer Simulations
… and methods exist, such as umbrella sampling or metadynamics, that allow to accelerate the sampling of different conformations by adding bias forces. In general, accelerated sampling methods are based on the choice of collective variables (CVs), which is of particular importance for the proper …
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Direct energy landscape sampling of the homogeneous nucleation and crystal growth of a model liquid
… this temporal limitation by using an improved metadynamics method based on the adaptive basin-climbing algorithm to directly sample the potential-energy landscape of a monotonic, model-liquid Argon system. The algorithm biases the system to evolve from a liquid-like structure towards an FCC …
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On the fidelity of translation
… to the other by the adenylate bound. Finally, metadynamics and fluorescence spectroscopy was used to study the binding of ATP to aaRS, a millisecond process essential for the aminoacylation. The calculated minimum free energy pathway suggested a two-step binding mechanism, which consists of a …
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Insight into G Protein-Coupled Receptors through Molecular Dynamics Simulations
… the (un)binding paths differences, and metadynamics (MetaD) enhances the number of the states explored. These techniques were employed in this PhD thesis to study G protein-coupled receptors (GPCRs),one of the largest families of proteins in the mammalian genome. In particular two …
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Motion in the solid state studied by NMR and extended time scale MD simulation
… simulations. To combat this deficiency, the metadynamics extended time scale technique has been implemented, allowing rare dynamic events to be observed in very short simulations, and the effects of complex correlated motions to be explored.
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Computational methods for transport properties
… to extract the real transition time from a metadynamics simulation, skipping in this way the timescale problem in computer 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 …
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The Role of CH–π Interactions in Protein-Carbohydrate Binding
… sites, I used CH–π distance features to bias metadynamics simulations of a curated set of protein–β-D-galactoside complexes. From these simulations, I found that while bound carbohydrates sample many CH–π stacking orientations, the hydrogen bonds in the protein binding site drive the optimal …
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From structural dynamics to drug repurposing: computational approaches in the context of precision medicine
… binding site. Furthermore, using Well-Tempered Metadynamics, we explored the binding and unbinding pathways of PD176252, revealing a path asymmetry where extracellu- lar loops 1 and 2 play a critical role in the ligand’s entry and exit. To address the therapeutic gap for CD38, a virtual …
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Mechanochemical Understanding of Metal-Coordinated Polymers Using Simulation and Experiment
… relaxation dynamics of the network. We use metadynamics simulations to show that the free energy landscape of metal-coordination bonds can be related to the macroscopic dynamic relaxation of these bonds in ideal polymer hydrogels as measured through experimental rheology. We then expand …
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Modelling and validation of bacterial O-antigen conformations: ring puckering in Shigella flexneri 7a and 7b O-antigens as a case study
… provide further insight, molecular dynamics and metadynamics simulations of a range of 3,4-disubstituted β-D-GlcNAc trisaccharides with two carbohydrate force fields (CHARMM36 and GLYCAM06) were performed. The simulations reveal that 3,4-α-linked β-D-GlcpNAc puckers to a similar extent as the S. …
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MARKOV STATE MODELS AND THEIR APPLICATIONS IN PROTEIN FOLDING SIMULATION, SMALL MOLECULE DESIGN, AND MEMBRANE PROTEIN MODELING
… cells. Multiple MD approaches, including metadynamics and free energy perturbation methods are used to describe the origins of selectivity for Na,K-ATPase.
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Molecular recognition, in- and out- of equilibrium, in the actions of bacterial multidrug efflux nanomachines
… of the experimental tripartite assembly using metadynamics simulations captures transition states for the process and provides insight into the inter-subunit allosteric pathways. The simulations identify critical residues in this intramolecular communication, leading to testable hypotheses for …
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Simulation informed design of stimuli responsive structures and higher-order assemblies in DNA nanotechnology
… inform nanostructure design, I have implemented metadynamics in a popular coarse-grained DNA molecular simulation package. I have demonstrated its application in predicting the energetic cost in bending a mechanically compliant DNA origami, and the relative conformer stability of Holliday …
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COMPUTATIONAL ENZYME ENGINEERING: FROM MOLECULAR MODELING TO MACHINE LEARNING
… substrate access was not limited, well-tempered metadynamics simulations revealed that catalytic inefficiency toward bulkier substrates arises from unfavorable conformational dynamics and misaligned reactive geometries. These findings emphasize the critical role of enzyme dynamics in determining …
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Understanding the Structure and Dynamics of Supramolecular Assemblies and Peptides in Solution
… a bias potential, by implementing it within metadynamics.
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Structure and Property of Polymers and Biopolymers from Molecular Dynamic Simulations
… substrate were determined using combined MD and Metadynamics (MTD) simulations. The research clearly demonstrate that the solvent plays a critical role in the cellulose hydrolysis reaction catalyzed by novel enzyme mimic polymeric catalysts PSSA and PIL. It is found that PSSA chain is likely to …
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A computational approach for identification and development of novel inhibitors targeting viral polymerases
… and unbinding of ligand from the binding site, Metadynamics) to explore, at microscopic level, the key pattern of interaction between protein and ligand, to understand the effect of mutations, to get an insight of the full docking and undocking path and to calculate binding energetics. 4
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MOLECULAR PHYSIOLOGY OF BLOOD-BRAIN BARRIER TIGHT JUNCTIONS
<p>The molecular interface of the blood-brain barrier (BBB) is a highly selective physiological barrier. The BBB shields the central nervous system (CNS) for harmful agents while also preventing lifesaving drugs from entering the CNS. With the prevalence of neurogenerative disease on the rise, …
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