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 6 of 6 for “"Free Energy Simulations"”.
-
FEARCF: Graph-based software library for multidimensional free energy simulations
This thesis presents the efforts to adapt the Free Energy from Adaptive Reaction Coordinate Forces (FEARCF) method into the form of a software library, enabling it to be interfaced with other molecular dynamics (MD) software packages. There exist many methods to calculate the free energy of …
-
Computational studies of the self-cleavage mechanism in the glmS ribozyme
… mechanical (QM/MM) calculations, and free energy simulations were employed to study the cleavage mechanisms and explain experimental observations such as the thio effects and metal ion rescue effects. A concerted yet asynchronous cleavage mechanism with an active site guanine as the …
-
COMPUTATIONAL APPROACHES FOR PROTEIN FOLDING AND LIGAND BINDING: FROM THERMODYNAMICS TO KINETICS
… predictions of these mechanisms, molecular simulations must be able to estimate the binding affinity and rates of association and dissociation of a protein-ligand complex, or the populations and rates of exchange between distinct conformational states (i.e. folding and unfolding, binding and …
-
Computational studies of the structure, dynamics, and catalysis of the hepatitis delta virus ribozyme
… approaches. Classical molecular dynamics (MD) simulations and non-linear Poisson-Boltzmann (NLPB) calculations were utilized to study the metal binding characteristics of the reverse G•U wobble close to the active site of the ribozyme. These studies revealed that the reverse wobble creates a …
-
The design and development of GPU accelerated algorithms for ab initio integrals and integral derivatives illustrated on ab initio quantum and hybrid QM/MM dynamics
… Library (QSL) to perform the above calculations/simulations. In contrast to GPU packages developed from the ground up, the QSL is a library of routines aimed at accelerating legacy codes, such as GAMESS-UK, GAMESS-US and NWChem, used in electronic structure calculations. Algorithms are presented …
-
Ordering of Nanoparticles by Wrinkle-Assisted Self-Assembly : Controlling Plasmonic Coupling Effects
… Moreover, we performed Monte Carlo (MC) computer simulations in collaboration with the theoretical physics department (Prof. Dr. Matthias Schmidt and Dr. Andrea Fortini) at the Uni-versity of Bayreuth to assess the dominant driving forces during the assembly process. Be using MC, colloidal …