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 7 of 7 for “"Implicit Solvent Model"”.
-
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 …
-
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. …
-
Efficient Biomolecular Computations Towards Applications in Drug Discovery
Atomistic modeling and simulation methods facilitate biomedical research from many respects, including structure-based drug design. The ability of these methods to address biologically relevant problems is largely determined by the accuracy of the treatment of complex solvation effects in target …
-
Exploring the mechanism of interfacial self-assembly of colloidal quantum dot nanoparticles
… molecular simulation and a theoretical continuum model. I present the free-energy characteristics of the NPs as a function of their orientations and their vertical positions with respect to the interface. Meaningfully probing the self-assembly process at meso-scales requires simulation of O(10^3) …
-
Computational Modelling of Nanoscale Interactions for Nanophotonics and Biosensing
… computational methods in photonics and molecular modelling. In the first section, we investigate biosensor signals from the catalytic cycle of Adenylate Kinase (AdK); a large protein with more than 3000 atoms. We assume that the AdK molecule is situated in a region of high field intensity …
-
Interactions of environmentally-responsive nanoparticles with synthetic and biological membranes
… several biomolecular simulation techniques to model the interactions of amphiphilic, monolayer-protected NPs with lipid bilayers. This work is motivated by the recent experimental finding that certain gold NPs can penetrate into cells via an unexplained non-endocytic, non-disruptive mechanism. …
-
Optimal Point Charge Approximation: from 3-Atom Water Molecule to Million-Atom Chromatin Fiber
Atomistic modeling and simulation methods enable a modern molecular approach to bio-medical research. Issues addressed range from structure-function relationships to structure-based drug design. The ability of these methods to address biologically relevant problems is largely determined by their …