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 17 of 17 for “"Replica Exchange"”.
-
Graphics processing unit accelerated coarse-grained protein-protein docking
… model for protein docking simulations, using a Replica Exchange Monte-Carlo (REMC) method. Our highly parallel implementation vastly increases the size- and time scales accessible to molecular simulation. We describe in detail the complex process of migrating the algorithm to a GPU as well as …
-
Theoretical Approaches to the Characterization of Water, Aqueous Interfaces, and Improved Sampling of Protein Conformational Changes
… for improving eciency of a sampling technique, Replica Exchange, by reducing the number of replicas. The improved method is called Replica Exchange with Driven Scaling (REDS2).</p>
-
Advances in Computational Solvation Thermodynamics
… each simulation; 3) Validation of Hamiltonian replica exchange, a technique which swaps λ values between two otherwise independent simulations. Taken together, these techniques promise to increase the accuracy and precision of free energy, entropy and enthalpy calculations. Improved …
-
Size-dependent mechanical properties of beta-structures in protein materials
… enhances toughness of the material. Based on replica-exchange MD simulations, the first representative atomistic model for spider silk is proposed. The computational, bottom-up approach predicts a multi-phase material with beta-sheet nanocrystals dispersed within semi-amorphous domains, where …
-
Prediction of Microstructural and Conformational Evolutions through Application of Steepest-Entropy-Ascent Quantum Thermodynamics
… define the degeneracy. However, the use of the Replica Exchange Wang Landau (REWL) algorithm has alleviated these challenges. The REWL algorithm is a non-Markovian MC method capable of estimating the density of the state of any discretely described system. Employing the derived discrete energy …
-
Computational approaches for drug design at the Protein-Protein interface
… force feld are then further developed to perform replica-exchange alchemical free energy calculations using the Bennett Acceptance Ratio non-biased estimator. These simulations are in general shown to be very accurate and show promise in generating hypotheses for novel high-affnity oligoamide …
-
Towards improved simulations of self-organising molecular materials
… final result chapter of this thesis, Hamiltonian replica exchange simulations are performed employing soft-core replicas for a Gay-Berne system. The simulation results show an order of magnitude increase in equilibration speed of the ordered phase when compared to conventional simulations of a …
-
Accurate Docking is Achieved by Decoupling Systematic Sampling from Scoring
… differential scanning calorimetry: DSC), and replica-exchange molecular dynamics: REMD). FSD-1's broad melting transition, similar to that of a helix-to-coil transition, was observed in CD, DSC, and REMD experiments. The N-terminal -hairpin was found to be flexible. FSD-1's apparent melting …
-
Modeling the self-assembly of functionalized fullerenes on solid surfaces using Monte Carlo simulations
… use Monte Carlo simulations in conjunction with replica exchange and force field biasing methods. For clusters adsorbed to smooth model surfaces, we determine free energy landscapes and demonstrate their utility for rationalizing and predicting self-assembly.</p>
-
Roles of cosolvents on protein stability
… molecular dynamics simulations of peptides and replica exchange molecular dynamics simulations (REMD) of the Trp-cage miniprotein are performed. Most previous studies have focused on the effect of this osmolyte on protein backbone. Our results are consistent with these studies as we show that …
-
Computational investigation of early events in plant growth signaling
… the BRI1 and BAK1 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 …
-
Dissecting the Architectural Properties of Chromatin and the Influence of the H1 Linker Histone on Chromatin Regulation
In this research, I used an existing coarse-grained chromatin model from the Collepardo Lab to study the binding of the H1 linker histone to chromatin and delve into the intrinsic properties of chromatin that regulate its architecture. The primary aim is to decipher the factors modulating chromatin …
-
Folding and aggregation of amyloid peptides
… In the present work extensive, fully atomistic replica exchange molecular dynamics simulations were performed to study the preaggregated, monomer states and early aggregation intermediates (dimers, trimers) of Aβ(25-35) and Aβ(10-35)-NH2 in aqueous solution. The folding and aggregation of …
-
Towards more robust and efficient methods for the calculation of Protein-Ligand binding affinities
… developed enhanced sampling technique REST (Replica Exchange with Solute Tempering) into normal FEP to solve the sampling problem in brute force FEP calculation. The computational cost of this method is comparable with normal FEP, and it can be very easily generalized to more complicated …
-
Sequence-structure correlations in the MaSp1 protein of N. clavipes dragline silk
… obtained using an in silico approach based on replica exchange molecular dynamics (REMD) and explicit water molecular dynamics. In particular, the atomistic simulations discussed in this parametric study explore the effects of the poly-alanine length of the N. clavipes MaSpi peptide sequence, …