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You searched for subject:(Explicit Solvent Model). Showing records 1 – 3 of 3 total matches.

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George Mason University

1. Mishra, Pamela Haradhan. Unbinding of Abeta peptides from amyloid fibrils: explicit solvent molecular dynamics study .

Degree: 2009, George Mason University

We used all-atom molecular dynamics to investigate the unbinding of Alzheimer’s Abeta peptides from amyloid fibrils. The peptide unbinding is driven by temperature-induced structural fluctuations and is thought of as an elementary step in the molecular recycling occurring between fibrillized and soluble Abeta species. Several conclusions can be drawn from our data. Early unbinding stages can be observed on the 100 ns timescale, although complete dissociation is likely to occur on much longer timescale. The unbinding pathway starts with fraying of β-strands from Abeta fibril. We predict that most peptide-fibril interactions will be initially lost by the N-terminal of Abeta peptide. This unbinding scenario can be modified by the specific location of dissociating peptide on the fibril edge. Our simulations provide new molecular details on the process of amyloidogenesis linked to Alzheimer’s disease.

Subjects/Keywords: amyloid fibrils; Alzheimers; explicit solvent model; unbinding Abeta peptides

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6th Edition):

Mishra, P. H. (2009). Unbinding of Abeta peptides from amyloid fibrils: explicit solvent molecular dynamics study . (Thesis). George Mason University. Retrieved from http://hdl.handle.net/1920/3419

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16th Edition):

Mishra, Pamela Haradhan. “Unbinding of Abeta peptides from amyloid fibrils: explicit solvent molecular dynamics study .” 2009. Thesis, George Mason University. Accessed March 06, 2021. http://hdl.handle.net/1920/3419.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7th Edition):

Mishra, Pamela Haradhan. “Unbinding of Abeta peptides from amyloid fibrils: explicit solvent molecular dynamics study .” 2009. Web. 06 Mar 2021.

Vancouver:

Mishra PH. Unbinding of Abeta peptides from amyloid fibrils: explicit solvent molecular dynamics study . [Internet] [Thesis]. George Mason University; 2009. [cited 2021 Mar 06]. Available from: http://hdl.handle.net/1920/3419.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Mishra PH. Unbinding of Abeta peptides from amyloid fibrils: explicit solvent molecular dynamics study . [Thesis]. George Mason University; 2009. Available from: http://hdl.handle.net/1920/3419

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation


University of Waterloo

2. Amini, Kiana. Liquid Crystalline Polymer Brushes.

Degree: 2016, University of Waterloo

Liquid crystalline polymers are one of the best examples of successful interaction between sciences. This interdisciplinary area of study has benefited from popularity of polymers and uniqueness of liquid crystals. Liquid crystals are well-known for their applications in designing liquid crystalline displays (LCDs). Polymers, specifically polymer brushes, are attractive due to their ability in surface tailoring. The use of liquid crystalline polymer (LCP) brushes is of interest since they can lead to novel and enhanced methods for surface modification. One example of the potential application of LCP brushes is in designing alignment layers for LCDs. In order to design devices based on the LCP brush, it is necessary to understand the physical structure and behaviour of this system under different conditions. To accomplish such understanding, computational and theoretical study of the system can provide advantageous insights. This project uses the self-consistent field theory to investigate the phase behaviour of liquid-crystalline polymeric brushes immersed in solvent. The polymers are modelled as freely-jointed chain consisting of N rigid segments. The isotropic interactions between the polymer and the solvent are treated using the standard Flory-Huggins theory, while the anisotropic liquid-crystalline (LC) interactions between rigid segments are taken into account using the Maier-Saupe theory. For weak LC interactions, the brush exhibits the conventional parabolic-like profile, called conventional brush (CB), while for strong LC interactions, the polymers order near the substrate into a dense brush, which is called liquid crystalline (LC) brush. Free energy associated with each structure is calculated and the stable solutions are identified. It is shown that there is a first-order transition between the CB and LC phase. A phase diagram is created to show the effect of different system variables on the phase behaviour.

Subjects/Keywords: Liquid crystals; Polymer brushes; Self-consistent field theory; mean field theory; LCDs; Anderson-mixing; Simple-mixing method; Strong-stretching theory; Solvation model; Scalar order parameter; Implicit solvent; explicit solvent

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6th Edition):

Amini, K. (2016). Liquid Crystalline Polymer Brushes. (Thesis). University of Waterloo. Retrieved from http://hdl.handle.net/10012/10671

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16th Edition):

Amini, Kiana. “Liquid Crystalline Polymer Brushes.” 2016. Thesis, University of Waterloo. Accessed March 06, 2021. http://hdl.handle.net/10012/10671.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7th Edition):

Amini, Kiana. “Liquid Crystalline Polymer Brushes.” 2016. Web. 06 Mar 2021.

Vancouver:

Amini K. Liquid Crystalline Polymer Brushes. [Internet] [Thesis]. University of Waterloo; 2016. [cited 2021 Mar 06]. Available from: http://hdl.handle.net/10012/10671.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Amini K. Liquid Crystalline Polymer Brushes. [Thesis]. University of Waterloo; 2016. Available from: http://hdl.handle.net/10012/10671

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

3. Izadi, Saeed. Optimal Point Charge Approximation: from 3-Atom Water Molecule to Million-Atom Chromatin Fiber.

Degree: PhD, Engineering Mechanics, 2016, Virginia Tech

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 accurate treatment of electrostatic interactions in the target biomolecular structure. In practical molecular simulations, the electrostatic charge density of molecules is approximated by an arrangement of fractional "point charges" throughout the molecule. While chemically intuitive and straightforward in technical implementation, models based exclusively on atom-centered charge placement, a major workhorse of the biomolecular simulations, do not necessarily provide a sufficiently detailed description of the molecular electrostatic potentials for small systems, and can become prohibitively expensive for large systems with thousands to millions of atoms. In this work, we propose a rigorous and generally applicable approach, Optimal Point Charge Approximation (OPCA), for approximating electrostatic charge distributions of biomolecules with a small number of point charges to best represent the underlying electrostatic potential, regardless of the distance to the charge distribution. OPCA places a given number of point charges so that the lowest order multipole moments of the reference charge distribution are optimally reproduced. We provide a general framework for calculating OPCAs to any order, and introduce closed-form analytical expressions for the 1-charge, 2-charge and 3-charge OPCA. We demonstrate the advantage of OPCA by applying it to a wide range of biomolecules of varied sizes. We use the concept of OPCA to develop a different, novel approach of constructing accurate and simple point charge water models. The proposed approach permits a virtually exhaustive search for optimal model parameters in the sub-space most relevant to electrostatic properties of the water molecule in liquid phase. A novel rigid 4-point Optimal Point Charge (OPC) water model constructed based on the new approach is substantially more accurate than commonly used models in terms of bulk water properties, and delivers critical accuracy improvement in practical atomistic simulations, such as RNA simulations, protein folding, protein-ligand binding and small molecule hydration. We also apply our new approach to construct a 3-point version of the Optimal Point Charge water model, referred to as OPC3. OPCA can be employed to represent large charge distributions with only a few point charges. We use this capability of OPCA to develop a multi-scale, yet fully atomistic, generalized Born approach (GB-HCPO) that can deliver up to 2 orders of magnitude speedup compared to the reference MD simulation. As a practical demonstration, we exploit the new multi-scale approach to gain insight into the structure of million-atom 30-nm chromatin fiber. Our results suggest important structural details consistent with experiment: the linker DNA fills the core region and… Advisors/Committee Members: Onufriev, Alexey V. (committeechair), Davalos, Rafael V. (committee member), Bevan, David R. (committee member), Ross, Shane D. (committee member), Staples, Anne E. (committee member).

Subjects/Keywords: Molecular Modeling; Explicit Solvent Model; Force Field; Implicit Solvent Model; Point Charge Approximation; Multipole Moments; Electrostatics; Water Models; Multi-scale Models

…x28;2TRX) and Ubiquitin (1UBQ) using the reference explicit-solvent simulations… …extensively throughout this document. Explicit Solvent: Solvent models that treat the solvent… …have the average properties of the real solvent. Generalized Born model(GB): A… …37 Left. The most general configuration for a three point charge water model consistent… …4-point OPC water model. . . . . 40 The quality score distribution of test water models… 

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6th Edition):

Izadi, S. (2016). Optimal Point Charge Approximation: from 3-Atom Water Molecule to Million-Atom Chromatin Fiber. (Doctoral Dissertation). Virginia Tech. Retrieved from http://hdl.handle.net/10919/81539

Chicago Manual of Style (16th Edition):

Izadi, Saeed. “Optimal Point Charge Approximation: from 3-Atom Water Molecule to Million-Atom Chromatin Fiber.” 2016. Doctoral Dissertation, Virginia Tech. Accessed March 06, 2021. http://hdl.handle.net/10919/81539.

MLA Handbook (7th Edition):

Izadi, Saeed. “Optimal Point Charge Approximation: from 3-Atom Water Molecule to Million-Atom Chromatin Fiber.” 2016. Web. 06 Mar 2021.

Vancouver:

Izadi S. Optimal Point Charge Approximation: from 3-Atom Water Molecule to Million-Atom Chromatin Fiber. [Internet] [Doctoral dissertation]. Virginia Tech; 2016. [cited 2021 Mar 06]. Available from: http://hdl.handle.net/10919/81539.

Council of Science Editors:

Izadi S. Optimal Point Charge Approximation: from 3-Atom Water Molecule to Million-Atom Chromatin Fiber. [Doctoral Dissertation]. Virginia Tech; 2016. Available from: http://hdl.handle.net/10919/81539

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