| dc.identifier.uri | http://hdl.handle.net/11401/76639 | |
| dc.description.sponsorship | This work is sponsored by the Stony Brook University Graduate School in compliance with the requirements for completion of degree. | en_US |
| dc.format | Monograph | |
| dc.format.medium | Electronic Resource | en_US |
| dc.language.iso | en_US | |
| dc.publisher | The Graduate School, Stony Brook University: Stony Brook, NY. | |
| dc.type | Dissertation | |
| dcterms.abstract | Liquid water is a complex material with many anomalous properties. Three of these anomalies are an abnormally high dielectric constant, an abnormally high boiling point, and a solid phase which is less dense than the liquid phase. Each of these anomalies is known to have been critically important in the development of life on Earth. All of water's special properties can be linked to water's unique ability to form hydrogen bonds. Water's hydrogen bonds form a transient network. Understanding the average structure of this network and how it changes through the phase diagram remains the focus of intense research. In this thesis we focus on understanding dielectric and infrared measurements, which measure the absorption and refraction of electromagnetic waves at different frequencies. Computer simulation is a necessary tool for correctly interpreting these measurements in terms of the microscopic dynamics of molecules. In the first part of this thesis we compare three classes of water molecule model that are used in molecular dynamics simulation – rigid, flexible, and polarizable. We show how the inclusion of polarization is necessary to capture how water's properties change with pressure and temperature. This finding is relevant to biophysical simulation. In the next part, we conduct a detailed study of water's dielectric properties to discover vibrational modes that propagate through the hydrogen bond network. Parts of the absorption spectrum of water are due to electromagnetic waves coupling to these modes. Previously, vibrational motions in water were thought to be confined to small clusters of perhaps five molecules. Our work upends this view by arguing that dynamics occur on the hydrogen bond network, resulting in modes that can propagate surprisingly long distances of up to two nanometers. These modes bear many similarities to optical phonon modes in ice. We show how the LO-TO splitting of these modes provides a new window into the structure of the hydrogen bond network. In the final part of this thesis we turn to the problems one encounters when trying to simulate water from ``first principles'', ie. from the laws of quantum mechanics. The primary technique that physicists use to approximate the quantum mechanics of electrons, density functional theory, does not work well for water, and much work is being done to understand how to fix this problem. A usual assumption in first principles simulation is that only electrons need to be treated quantum mechanically. We argue that both electrons and nuclei need to be treated quantum mechanically and we present a new code to do this. The custom code presented in this thesis implements a novel algorithm which greatly speeds up the calculation of nuclear quantum effects with only minor losses in accuracy. We hope that others will start using our technique to advance first principles simulation. Accurate first principles simulation of water is important for understanding and developing solar water splitting catalysts and batteries. First principles simulations are also being increasingly used to understand proteins and drug molecules, and this trend will continue with Moore's law. | |
| dcterms.abstract | Liquid water is a complex material with many anomalous properties. Three of these anomalies are an abnormally high dielectric constant, an abnormally high boiling point, and a solid phase which is less dense than the liquid phase. Each of these anomalies is known to have been critically important in the development of life on Earth. All of water's special properties can be linked to water's unique ability to form hydrogen bonds. Water's hydrogen bonds form a transient network. Understanding the average structure of this network and how it changes through the phase diagram remains the focus of intense research. In this thesis we focus on understanding dielectric and infrared measurements, which measure the absorption and refraction of electromagnetic waves at different frequencies. Computer simulation is a necessary tool for correctly interpreting these measurements in terms of the microscopic dynamics of molecules. In the first part of this thesis we compare three classes of water molecule model that are used in molecular dynamics simulation – rigid, flexible, and polarizable. We show how the inclusion of polarization is necessary to capture how water's properties change with pressure and temperature. This finding is relevant to biophysical simulation. In the next part, we conduct a detailed study of water's dielectric properties to discover vibrational modes that propagate through the hydrogen bond network. Parts of the absorption spectrum of water are due to electromagnetic waves coupling to these modes. Previously, vibrational motions in water were thought to be confined to small clusters of perhaps five molecules. Our work upends this view by arguing that dynamics occur on the hydrogen bond network, resulting in modes that can propagate surprisingly long distances of up to two nanometers. These modes bear many similarities to optical phonon modes in ice. We show how the LO-TO splitting of these modes provides a new window into the structure of the hydrogen bond network. In the final part of this thesis we turn to the problems one encounters when trying to simulate water from ``first principles'', ie. from the laws of quantum mechanics. The primary technique that physicists use to approximate the quantum mechanics of electrons, density functional theory, does not work well for water, and much work is being done to understand how to fix this problem. A usual assumption in first principles simulation is that only electrons need to be treated quantum mechanically. We argue that both electrons and nuclei need to be treated quantum mechanically and we present a new code to do this. The custom code presented in this thesis implements a novel algorithm which greatly speeds up the calculation of nuclear quantum effects with only minor losses in accuracy. We hope that others will start using our technique to advance first principles simulation. Accurate first principles simulation of water is important for understanding and developing solar water splitting catalysts and batteries. First principles simulations are also being increasingly used to understand proteins and drug molecules, and this trend will continue with Moore's law. | |
| dcterms.available | 2017-09-20T16:50:51Z | |
| dcterms.contributor | Allen, Philip B | en_US |
| dcterms.contributor | Fernandez-Serra, Marivi | en_US |
| dcterms.contributor | Dawber, Matthew | en_US |
| dcterms.contributor | Calder, Alan C | en_US |
| dcterms.contributor | Reuter, Matthew. | en_US |
| dcterms.creator | Elton, Daniel C. | |
| dcterms.dateAccepted | 2017-09-20T16:50:51Z | |
| dcterms.dateSubmitted | 2017-09-20T16:50:51Z | |
| dcterms.description | Department of Physics | en_US |
| dcterms.extent | 317 pg. | en_US |
| dcterms.format | Monograph | |
| dcterms.format | Application/PDF | en_US |
| dcterms.identifier | http://hdl.handle.net/11401/76639 | |
| dcterms.issued | 2016-12-01 | |
| dcterms.language | en_US | |
| dcterms.provenance | Made available in DSpace on 2017-09-20T16:50:51Z (GMT). No. of bitstreams: 1
Elton_grad.sunysb_0771E_13076.pdf: 11259671 bytes, checksum: e567f820793b2f9b881f81a841f1d09f (MD5)
Previous issue date: 1 | en |
| dcterms.publisher | The Graduate School, Stony Brook University: Stony Brook, NY. | |
| dcterms.subject | Density functional theory, dielectric properties, molecular dynamics, path integral molecular dynamics, simulation, water | |
| dcterms.subject | Condensed matter physics -- Molecular physics -- Physics | |
| dcterms.title | Understanding the Dielectric Properties of Water | |
| dcterms.type | Dissertation | |
