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 “"all-atom molecular dynamics"”.
-
Computational Studies of Polyetherimides: Beyond All-Atom Molecular Dynamics Simulations
… adhesive properties, and chemical stability. All-atom molecular dynamics (MD) simulation is a useful tool to study polymers, but the accessible length and time scales are limited. In this thesis, we explore several computational methods that go beyond all-atom MD simulations to investigate …
-
Parameterization of the Gay-Berne coarse-grained potential from atomistically detailed anisotropic free energy volumes
Simulating a system of 300,000+ atoms, such as an explicitly solvated protein using all atom molecular dynamics on the microsecond time-scale, would require an enormous amount of computing power and specialized software, even with which would still require months of computing time. However, if the …
-
Roles of cosolvents on protein stability
… from the delicate balance of forces involving atoms of the protein and the solvent. This balance can be perturbed by changing temperature, pressure, pH and by adding organic molecules known as cosolvents to the solution. Despite the wide use of cosolvents to perturb protein structures in the …
-
Systematic coarse-graining of ionic liquid
… force fields (CGFFs) for computationally efficient and accurate molecular simulation of imidazolium-based ionic liquids (ILs). To obtain CGFF parameters, we employ a systematic coarse-graining approach based on the relative entropy (RE) method to reproduce not only the structure but …
-
Development of Transferable Coarse-Grained Models of Amino Acids
… of those amino acids. In CG models, several atoms are represented together as a single pseudo-atom or "bead," which can allow the modeling of processes like self-assembly of biomolecules and biomaterials through reduction of degrees of freedom and corresponding increased computational speed. …
-
Conformational Dynamics of K-Ras and H-Ras Proteins: Is There Functional Specificity At The Catalytic Domain?
… on lobe II of Ras catalytic domain alters dynamics and leads to differential preference for different effectors or modulators. In this work, we used all atom molecular dynamics to analyze the dynamics in the catalytic domain of H-ras and K-ras. We have also analyzed the dynamics of a …
-
Computing Wall Thickness and Young's Modulus of Carbon Nanotubes with Atomistic Molecular Dynamics Simulations
… tubular structure of a layer or layers of carbon atoms. CNTs serve as a prototypical nanomaterial holding great promises for various basic and applied research applications in the fields of electrical, thermal, and structural materials owing to their superlative mechanical, thermal, electrical, …
-
Multiscale Simulations of Phosphatidylinositol Bisphosphate: Understanding Its Biological Role Through Physical Chemistry
… electronic structure calculations to all-atom molecular dynamics simulations of bilayers to characterize the biological role of PtdInsP2. Our results demonstrate that the different roles of PtdIns(4,5)P2 and PtdIns(3,5)P2 in vivo are not simply determined by their localization, but …
-
Voltage-Gating Mechanism in Potassium Channels
… potential across the cell membrane, and allow passage of K+ ions through their conduction pore. In excitable cells, an interplay of voltage-gated K+, Na +, and Ca2+ channels results in generation of electrical signals, known as action potential, that are propagated along the cell …
-
Voltage-Gating Mechanism in Potassium Channels
… potential across the cell membrane, and allow passage of K+ ions through their conduction pore. In excitable cells, an interplay of voltage-gated K+, Na+, and Ca2+ channels results in generation of electrical signals, known as action potential, that are propagated along the cell membrane. …
-
COMPUTATIONAL APPROACHES FOR PROTEIN FOLDING AND LIGAND BINDING: FROM THERMODYNAMICS TO KINETICS
… by drug applications, are both governed by biomolecular thermodynamics and kinetics. In order to make meaningful and efficient predictions of these mechanisms, molecular simulations must be able to estimate the binding affinity and rates of association and dissociation of a protein-ligand …
-
The Interaction of Cofilin with the Actin Filament
… for many cell functions. Since actin is found in all cells, understanding how actin-binding-proteins: ABPs) bind and how their regulating mechanisms work is not only important to the basics of cytoskeletal pathways, but also to understanding associated diseases and creating possible therapeutics …
-
Modeling Disorder in Proteins Yields Insights into the Evolution of Stability and Function
<p>The central dogma of molecular biology dictates that a DNA sequence codes for an RNA sequence, which in turn codes for a sequence of amino acids that comprises a protein. Proteins are responsible with performing myriad functions within living organisms and most proteins require a folded …
-
Coarse-grained Modeling of Protein Dynamics using Elastic Network Models
Dynamics is crucial for the functioning of biological macromolecules. Because of severe limitations in studying protein dynamics experimentally or with all-atom simulations, coarse-grained methods, especially elastic network models (ENMs), are frequently employed. In the last years, studies on …
-
Modeling and simulation of the equilibrium and nonequilibrium dynamics of DNA
… have been made to understand the underlying dynamics of the formation and dissipation of these structures by means of novel experiments. In these experiments, single molecules of DNA are subjected to forces and torques similar to the ones they would experience within the cell in order to …
-
Atomistic Investigation of Nucleosomal H3 Histone Tail in Unmodified and Epigenetically Modified States
… is a growing area of research that could potentially unlock the understanding of questions like how and why we develop certain diseases, how we age, how we inherit certain traits and even how our species evolves. Epi is a prefix meaning above, referring to chemical tags that sit above your …
-
Biomolecular transport at and through two-dimensional materials
… single molecule nanoscale manipulation and molecular detection. Graphene is one such 2D material whose single-atom thickness and high in-plane electrical conductivity enables potential nanopore sensing applications for controllable nanofluidics and nanopore sensing applications conducive …
-
Sequence and structural effects on molecular conductance of bioinspired peptoid oligomers
… studying how helical secondary structure affects molecular charge transport in peptoid oligomers. In Chapter 2, characterizations of electron charge transport in peptoid oligomers uses the scanning tunneling microscopy break-junction (STM-BJ) method build upon previous studies on the effect of …
-
Molecular modeling and simulation of bacterial chemosensory arrays
… to this ability, bacteria posses a universally conserved sensory apparatus, known as the chemosensory array, which involves the clustering of thousands of proteins into a highly cooperative signaling network. The present dissertation will present my work using techniques in computational …
-
Quantitative all-atom and coarse-grained molecular dynamics simulation studies of DNA
… molecule that encodes genetic information for all life on earth—DNA—is a polymer with unusual physical properties. The mechanical and electrostatic properties of DNA are utilized extensively by cells in the replication, regular maintenance, and expression of their genetic material. This can be …
Page 1 of 2