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.
Results
Showing 1 to 20 of 23 for “"Implicit solvent"”.
-
Finite element methods for implicit solvent models
… we develop finite element methods (FEMs) for implicit solvent models. Implicit models treat the solvent in biomolecular systems as bulk continuum and are thus computationally efficient. The Poisson-Boltzmann equation (PBE) is one important example. We design a FEM for the linear PBE by …
-
Improving of the accuracy and efficiency of implicit solvent models in Biomolecular Modeling
… modeling is an accurate description of the solvent (water). The challenge is to make this description computationally facile that is reasonably fast, simple, robust and easy to incorporate into existing software packages. The most rigorous procedure to model the effect of aqueous solvent is …
-
Lengthening the timescale reach of molecular dynamics
… elongation. Second, a generalized Born model of implicit solvent accelerates simulation through reduced computational expense as well as increased conformational sampling due to reduced viscosity of the implicit solvent. Finally, advanced computing technologies, such as graphics processing units, …
-
Efficient Biomolecular Computations Towards Applications in Drug Discovery
… in target biomolecules surrounded by water. The implicit solvent model – which treats solvent as a continuum with the dielectric and non-polar properties of water – offers a good balance between accuracy and speed. Simple and efficient, generalized Born (GB) model has become a widely used …
-
A novel algorithm for creating density dependent, coarse-grained models for the simulation of surfactant systems
… simulations of solvated molecules that treat the solvent explicitly are very computationally expensive, and as a result work has been done on modifying the potentials to treat solvent implicitly. Implicit solvation is well-known in Brownian Dynamics of dilute solutions, but offers promise to speed …
-
Stratification in Drying Particle Suspensions
… nanoparticle mixtures. I first use an explicit solvent model to investigate how the structure of the dry film depends on the evaporation rate of the solvent and the initial volume fractions of the nanoparticles. My simulation results show that the particle mixtures stratify according to their …
-
Molecular simulation of biomaterials and biomolecules at the solid-liquid interface
… While simple models involving reduced solvent representations and polymer flexibility have found some success in limited applications, robust performance for systems of varying size and composition can generally be expected only through accurate inclusion of these key details. Fully …
-
Random search conformational analysis of piperazine and piperadine analogs of GBR12909 : implicit aqueous solvation effects
… object of this work was to study the effect of solvent on the conformational potential energy surface (PES) of GBR12909 analogs. Local minima on the PES's were found by the Random Search algorithm using the Sybyl molecular modeling package from Tripos, Inc., and an implicit solvent model. Two …
-
Green fluorescent protein as a mechanical sensor
… candidate with many desirable characteristics. Implicit solvent molecular dynamics CHARMM simulations demonstrated details inaccessible by AFM and OT methods, such as the linkage dependency of fluorophore environment changes and the energy exchanges between protein components during protein …
-
Speeding up electrostatic computations for molecular dynamics
… is comparable to the industry standard explicit solvent particle mesh Ewald (PME), and is in general more accurate than the spherical cutoff method. And, unlike the PME, the DIA can be easily extended to implicit solvent GB models. 50 ns implicit solvent simulations for a representative set of …
-
Simulate Time-integrated Coarse-grained Molecular Dynamics with Geometric Machine Learning
… (1) single-chain coarse-grained polymers in implicit solvent; (2) multi-component Li-ion polymer electrolyte systems.
-
Structural analyses of the ribosome by hybrid approach
… protocol and second by the use of a so-called implicit solvent model. In pursuit of the needed methodological development we participated in the Cryo-EM Modeling Challenge 2010, competing with the MDFF method against other hybrid methods. Two aspects of ribosomal functions were investigated. …
-
Exploring the mechanism of interfacial self-assembly of colloidal quantum dot nanoparticles
… NPs. However, this is infeasible in an explicit-solvent setting with the typically available computing resources. To this end, a key contribution of this work is to develop an efficient (implicit-solvent) model that is not only able to reproduce experimentally exhibited behavior by NPs at …
-
Exploring Molecular Systems From Chemical Physics To Biochemistry Using Classical And Quantum Mechanics
… and products of guanine oxidation. Using implicit solvent modeling and accounting for relevant tautomers and protonation states present in aqueous solution, the trends in the calculated oxidation potentials were found to be in relatively good agreement with the trends in experimentally …
-
Investigating the effect of charge hydration asymmetry and incorporating it in continuum solvation framework
… is an accurate description of water as a solvent. The challenge is to make this description computationally facile -- reasonably fast, simple, robust and easy to incorporate into existing software packages, yet accurate. The most rigorous procedure to model the effect of aqueous solvent is …
-
Computational Modelling of Nanoscale Interactions for Nanophotonics and Biosensing
… section, we develop a model to investigate solvent effects on the polarizability of Ångstrom-sized amino acids. Molecular polarizability serves as a molecular fingerprint that is encoded in the biosensor signals. Our model builds on existing methods in density functional theory to calculate …
-
Interactions of environmentally-responsive nanoparticles with synthetic and biological membranes
… both a coarse-grained methodology and a novel implicit bilayer, implicit solvent model. I show that NPs with flexible ligands can fuse with lipid bilayers by "snorkeling" charged end groups out of the bilayer core and into solution. Several experimental studies confirm aspects of this fusion …
-
Ligand-based drug design : I. conformational studies of GBR 12909 analogs as cocaine antagonists; II. 3d-QSAR studies of salvinorin a analogs as kappa opioid agonists
… molecule were generated in the vacuum phase and implicit solvent (also known as continuum solvent) by random search conformational analysis using the molecular mechanics methods and the Tripos and MMFF94 force fields. These conformer populations were classified by relative energy, molecular …
-
Understanding the ATP hydrolysis mechanism in myosin using computer simulation techniques
… (QM/MM) reaction path simulations. To include solvent screening effects in the calculations, a new approximate method "Non-Uniform Charge Scaling" (NUCS) was developed which scales the partial atomic charges on the molecular mechanical atoms so as to optimally reproduce electrostatic …
Page 1 of 2