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Showing 1 to 20 of 24 for “"Umbrella sampling"”.
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Development of a ReaxFF force field for glyphosate and investigation of its abiotic degradation pathways
… simulations of glyphosate degradation and the umbrella sampling method has been used to determine the free energy barriers opposing C-P and C-N bond dissociation. Approximately fifty carbon-phosphorus interaction parameters were fitted against a density functional theory (DFT) derived training …
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A parallel multidimensional weighted histogram analysis method
… biased distributions of samples from multiple Umbrella Sampling simulations to yield an estimate of the global unbiased distribution. The WHAM algorithm iterates two coupled, non-linear, equations, until convergence at an acceptable level of accuracy. The equations have quadratic time …
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Bridging molecular and systems scales in membrane biology
… steered molecular dynamics (SMD), coupled with umbrella sampling (US), and Alchemical Free-Energy Perturbation (Alchemical FEP) to study how the structural changes associated with point mutations affect mechanical aspects of conformational change in channels, such as hERG (Chapter 5), and the …
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Non-equilibrium Dynamics of Nanoscale Soft Matter Deformation
… Molecular dynamics simulations as well as umbrella sampling were employed. The behavior of the bilayers discussed in the work provides evidence that small defects on confining surfaces can promote nucleation of lipid tethers. Results the second part of this work indicate elastin-like …
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Aqueous systems from first-principles : structure, dynamics and electron-transfer reactions
… free-energy surfaces are then constructed from umbrella sampling on large ensembles of configurations. As a paradigmatic case study, the self-exchange reaction between ferrous and ferric ions in water is studied in detail. Since the solvent plays an central role in mediating the process, …
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Validation of the charge equilibration lipid force field for simulations of phospholipid membranes with an application to the study of the free energetics of methyl guanidinium permeation across a DPPC bilayer
… as it crosses a DPPC lipid bilayer. Combining umbrella sampling MD simulations with the Weighted Histogram Analysis Method (WHAM) for unbiasing probabilities, we compute a potential of mean force (PMF) for the reversible trans-fer of methyl guanidinium from bulk solution to bilayer center. …
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Atom-Based Computer Simulation Studies of Gas-to-Liquid Nucleation in Atmospherically Relevant Systems: Clarifying Discrepancies and Elucidating Mechanisms
… of aggregation-volume-bias Monte Carlo, umbrella sampling, and histogram reweighting), to investigate the homogeneous vapor-to-liquid nucleation of various nucleating systems. We found out that these systems could nucleate through a variety of unique non-ideal mechanisms. Alongside …
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Atomistic and Coarse-Grained Investigation of Membrane-Protein Interactions
… membranes subjectedto high tension. We performed umbrella sampling calculations to provide the first quantita-tive evidence that tension energetically promotes the insertion of a transmembrane helicaldomain of epsin. Next, we embarked on an ambitious journey to build a coarse-grainedMonte Carlo …
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Towards More Efficient Enhanced Sampling Methods To Study Phase Transitions
… To circumvent these difficulties, non-Boltzmann sampling methods such as the umbrella sampling and Wang-Landau sampling techniques, have been employed to study these phase transitions. </p> <p>Vapor-solid and liquid-solid phase transitions were studied using a combination of hybrid Monte Carlo …
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Development of Free Energy Calculation Methods for the Study of Monosaccharides Conformation in Computer Simulations
… energy calculations, 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 …
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Molecular insights on the solvent effect of methanol additive in glycine polymorph selection
… polymorph. Free energy calculations through the Umbrella Sampling method show an increased stability of the centrosymmetric dimer structure ([alpha]-glycine growth unit) in the presence of the methanol additive. Even though the dimer structure is more stable in water-methanol mixtures, a higher …
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Computational modeling of melanin aggregation
… mechanisms of stacking were investigated using umbrella sampling (US) and DFT calculations, revealing strong non-covalent stacking interactions between the eumelanin protomolecules. Both the free energy calculations and DFT revealed these strong stacking interactions. The electrostatic potential …
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Investigating Lipase Stability in Hydrophobic Solvent at Extreme Temperatures: A Molecular Dynamics Study of Candida Antarctica Lipase B in Polydimethylsiloxane
… and the extremely hydrophobic, non-polar PDMS. Umbrella sampling of CALB was then performed across a water-PDMS interfacial system. The free energy profile revealed a significant increase in the change in free energy from CALB solvated in water to CALB solvated in PDMS. The free energy profile …
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Electronic and solvent effects on monosaccharide conformations
… using the Potential of Mean Force (PMF), umbrella sampling and Weighted Histogram Analysis Methods (WHAM). The PMF calculations were performed in the canonical (NVT) ensemble in the gaseous and aqueous phase where each monosaccharide was modelled with Parameter Model 3 for Carbohydrates …
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Electronic and solvent effects on monosaccharide conformations
… using the Potential of Mean Force (PMF), umbrella sampling and Weighted Histogram Analysis Methods (WHAM). The PMF calculations were performed in the canonical (NVT) ensemble in the gaseous and aqueous phase where each monosaccharide was modelled with Parameter Model 3 for Carbohydrates …
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On the fidelity of translation
… by unbiased molecular dynamics simulations and umbrella sampling in ∆CP1 LeuRS, an ideal system for pre-transfer editing investigation. Our results suggested a surprisingly simple model for pre-transfer editing, which only requires a small rotation of A76 that makes space for a water molecule to …
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Collective dynamics in lattice models far from equilibrium
… same model under a fixed external field. We use umbrella sampling to compute the free-energy cost of a critical nucleus and use forward flux sampling for the direct estimation of nucleation rates. For moderate to strong disorder, our results indicate that the size of the nucleating cluster is not …
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A density functional theory study into the mechanism and reactivity in heterogeneous system
… advanced Molecular Dynamic (MD) approach, namely umbrella sampling. Both the hollow site and the top site are simulated for CO adsorption and desorption with free energy chemisorption energy obtained.<br/><br/>In chapter 6, the slow-growth (SG) approach and constrained molecular dynamics (CMD) are …
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Computational investigation of early events in plant growth signaling
… extracellular domains. Using a replica exchange umbrella sampling scheme together with alchemical free energy calculations and conventional molecular dynamics simulations, we examine the mechanisms through which brassinosteroid binding to the BRI1 extracellular domain induces association with the …
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Multiscale Modelling of Biomolecular Phase Behaviour
… strength of such transitions. Using atomistic umbrella sampling simulations I estimated the free energy of binding when 8-residue NUP-98 sequence replicas remain disordered as opposed to when they undergo folding into a beta-sheet, finding that folding can increase the binding free energy up to …
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