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Biological Water: Static and Dynamic Properties of Water in Atomistic and Continuum Simulations of Polysaccharide Solutions and Gels
Biological Water: Static and Dynamic Properties of Water in Atomistic and Continuum Simulations of Polysaccharide Solutions and Gels
상세정보
- 자료유형
- 학위논문 서양
- 최종처리일시
- 20250211151448
- ISBN
- 9798382810010
- DDC
- 576
- 저자명
- Agles, Avery A.
- 서명/저자
- Biological Water: Static and Dynamic Properties of Water in Atomistic and Continuum Simulations of Polysaccharide Solutions and Gels
- 발행사항
- [Sl] : Princeton University, 2024
- 발행사항
- Ann Arbor : ProQuest Dissertations & Theses, 2024
- 형태사항
- 171 p
- 주기사항
- Source: Dissertations Abstracts International, Volume: 85-12, Section: B.
- 주기사항
- Advisor: Bourg, Ian C.
- 학위논문주기
- Thesis (Ph.D.)--Princeton University, 2024.
- 초록/해제
- 요약As the predominant mode of microbial life on Earth, biofilms are the hands by which microorganisms leave their mark on the world. The fingerprints of their existence can be found in the hierarchical structure of healthy soils, in the marine snow that processes organic matter in the ocean, and in the 1000‐fold increase in resistance to antibiotics they confer to their inhabitants. Investigations into the impact of divalent ions on the extracellular polymeric substance (EPS) comprising biofilms suggest that their macroscale properties might be informed by the molecular-scale architecture. To explore this relationship, we created large molecular dynamics (MD) simulations of a model EPS at a range of divalent/monovalent counterion ratios (0, 0.5, 1) and water contents (65 to 95 wt.%). In Chapter 2, we develop a methodology for the generation of equilibrated configurations of explicitly-hydrated EPS gels that utilizes an enhanced sampling technique developed by computational biologists. Measurements of the free energy and enthalpy of hydration show a large barrier to dehydration at water contents below 70 wt.% as well as a metastable regime at intermediate water contents that suggests an entropic driving force for dehydration. In chapter 3, we then use our equilibrated EPS configurations to investigate the structure and dynamics of water within these solutions and gels with particular attention paid to their consistency with continuum models of flow in porous media. These findings are the motivation for chapter 4, where we advance towards a numerical simulation capable of showcasing how ion diffusion in biofilms, and associated osmotic water fluxes, might play a role in the mesoscale structural heterogeneities observed by experimentalists. We conclude chapter 4 with a discussion of how to parameterize our numerical solver according to the findings of chapters 2 and 3.
- 일반주제명
- Microbiology
- 일반주제명
- Molecular biology
- 일반주제명
- Chemical engineering
- 키워드
- Biofilms
- 키워드
- Earth
- 기타저자
- Princeton University Chemical and Biological Engineering
- 기본자료저록
- Dissertations Abstracts International. 85-12B.
- 전자적 위치 및 접속
- 로그인 후 원문을 볼 수 있습니다.
MARC
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■020 ▼a9798382810010
■035 ▼a(MiAaPQ)AAI31296603
■040 ▼aMiAaPQ▼cMiAaPQ
■0820 ▼a576
■1001 ▼aAgles, Avery A.▼0(orcid)0000-0001-9443-3365
■24510▼aBiological Water: Static and Dynamic Properties of Water in Atomistic and Continuum Simulations of Polysaccharide Solutions and Gels
■260 ▼a[Sl]▼bPrinceton University▼c2024
■260 1▼aAnn Arbor▼bProQuest Dissertations & Theses▼c2024
■300 ▼a171 p
■500 ▼aSource: Dissertations Abstracts International, Volume: 85-12, Section: B.
■500 ▼aAdvisor: Bourg, Ian C.
■5021 ▼aThesis (Ph.D.)--Princeton University, 2024.
■520 ▼aAs the predominant mode of microbial life on Earth, biofilms are the hands by which microorganisms leave their mark on the world. The fingerprints of their existence can be found in the hierarchical structure of healthy soils, in the marine snow that processes organic matter in the ocean, and in the 1000‐fold increase in resistance to antibiotics they confer to their inhabitants. Investigations into the impact of divalent ions on the extracellular polymeric substance (EPS) comprising biofilms suggest that their macroscale properties might be informed by the molecular-scale architecture. To explore this relationship, we created large molecular dynamics (MD) simulations of a model EPS at a range of divalent/monovalent counterion ratios (0, 0.5, 1) and water contents (65 to 95 wt.%). In Chapter 2, we develop a methodology for the generation of equilibrated configurations of explicitly-hydrated EPS gels that utilizes an enhanced sampling technique developed by computational biologists. Measurements of the free energy and enthalpy of hydration show a large barrier to dehydration at water contents below 70 wt.% as well as a metastable regime at intermediate water contents that suggests an entropic driving force for dehydration. In chapter 3, we then use our equilibrated EPS configurations to investigate the structure and dynamics of water within these solutions and gels with particular attention paid to their consistency with continuum models of flow in porous media. These findings are the motivation for chapter 4, where we advance towards a numerical simulation capable of showcasing how ion diffusion in biofilms, and associated osmotic water fluxes, might play a role in the mesoscale structural heterogeneities observed by experimentalists. We conclude chapter 4 with a discussion of how to parameterize our numerical solver according to the findings of chapters 2 and 3.
■590 ▼aSchool code: 0181.
■650 4▼aMicrobiology
■650 4▼aMolecular biology
■650 4▼aChemical engineering
■653 ▼aBiofilms
■653 ▼aExtracellular polymeric substance
■653 ▼aMolecular dynamics
■653 ▼aEarth
■690 ▼a0410
■690 ▼a0542
■690 ▼a0307
■71020▼aPrinceton University▼bChemical and Biological Engineering.
■7730 ▼tDissertations Abstracts International▼g85-12B.
■790 ▼a0181
■791 ▼aPh.D.
■792 ▼a2024
■793 ▼aEnglish
■85640▼uhttp://www.riss.kr/pdu/ddodLink.do?id=T17161812▼nKERIS▼z이 자료의 원문은 한국교육학술정보원에서 제공합니다.
