Statistical Physics of Water in Hydrophobic Nano-Confinement and at Proteins Interfaces
Water is commonly associated with life. This substance affects the living beings in countless aspects and length scales, ranging from molecular biology to climatology. Water exhibits a long series of anomalous behaviors. These anomalies can be rationalized as a consequence of a second critical point...
| Autor: | |
|---|---|
| Tipo de recurso: | tesis doctoral |
| Estado: | Versión publicada |
| Fecha de publicación: | 2013 |
| País: | España |
| Institución: | CBUC, CESCA |
| Repositorio: | TDR. Tesis Doctorales en Red |
| OAI Identifier: | oai:www.tdx.cat:10803/120095 |
| Acceso en línea: | http://hdl.handle.net/10803/120095 |
| Access Level: | acceso abierto |
| Palabra clave: | Aigua Agua Water Proteïnes Proteínas Proteins Hidrogen Hidrógeno Hydrogen Nanoconfinament Nanoconfinamiento Nano confinement Enllaç d'hidrogen Enlace de hidrógeno Hydrogen bond Ciències Experimentals i Matemàtiques 53 |
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España |
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| dc.title.none.fl_str_mv |
Statistical Physics of Water in Hydrophobic Nano-Confinement and at Proteins Interfaces |
| title |
Statistical Physics of Water in Hydrophobic Nano-Confinement and at Proteins Interfaces |
| spellingShingle |
Statistical Physics of Water in Hydrophobic Nano-Confinement and at Proteins Interfaces Bianco, Valentino Aigua Agua Water Proteïnes Proteínas Proteins Hidrogen Hidrógeno Hydrogen Nanoconfinament Nanoconfinamiento Nano confinement Enllaç d'hidrogen Enlace de hidrógeno Hydrogen bond Ciències Experimentals i Matemàtiques 53 |
| title_short |
Statistical Physics of Water in Hydrophobic Nano-Confinement and at Proteins Interfaces |
| title_full |
Statistical Physics of Water in Hydrophobic Nano-Confinement and at Proteins Interfaces |
| title_fullStr |
Statistical Physics of Water in Hydrophobic Nano-Confinement and at Proteins Interfaces |
| title_full_unstemmed |
Statistical Physics of Water in Hydrophobic Nano-Confinement and at Proteins Interfaces |
| title_sort |
Statistical Physics of Water in Hydrophobic Nano-Confinement and at Proteins Interfaces |
| dc.creator.none.fl_str_mv |
Bianco, Valentino |
| author |
Bianco, Valentino |
| author_facet |
Bianco, Valentino |
| author_role |
author |
| dc.contributor.none.fl_str_mv |
Franzese, Giancarlo Universitat de Barcelona. Departament de Física Fonamental |
| dc.subject.none.fl_str_mv |
Aigua Agua Water Proteïnes Proteínas Proteins Hidrogen Hidrógeno Hydrogen Nanoconfinament Nanoconfinamiento Nano confinement Enllaç d'hidrogen Enlace de hidrógeno Hydrogen bond Ciències Experimentals i Matemàtiques 53 |
| topic |
Aigua Agua Water Proteïnes Proteínas Proteins Hidrogen Hidrógeno Hydrogen Nanoconfinament Nanoconfinamiento Nano confinement Enllaç d'hidrogen Enlace de hidrógeno Hydrogen bond Ciències Experimentals i Matemàtiques 53 |
| description |
Water is commonly associated with life. This substance affects the living beings in countless aspects and length scales, ranging from molecular biology to climatology. Water exhibits a long series of anomalous behaviors. These anomalies can be rationalized as a consequence of a second critical point in the supercooled region of the liquid phase. Nevertheless, the large part of the phase diagram of supercooled water is to date experimentally inaccessible for the inevitable crystallization of the bulk liquid. Confinement of water in nano-structures is a possible way to prevent the crystallization of molecules. In this thesis we present a coarse-grain model to describe the physical behavior of water at hydrophobic interfaces. The essential feature of the model is the description of water-water interaction via directional and cooperative components of the hydrogen bond (HB). We explore the phase diagram of supercooled water nano-confined between hydrophobic walls. Our results, grounded in statistical physics methods and Monte Carlo simulations, show the presence of a line of first order phase transition in the temperature-pressure plane separating two liquid phases and ending in a liquid-liquid critical point (LLCP). The LLCP universality class approaches the one of the Ising model in two dimensions in the thermodynamic limit, while large deviations are observed for strong confinement. Below the LLCP we find the locus of maxima of correlation length (the Widom line) of the system. Near the LLCP we find a large increase of the thermodynamic response functions consistent with the anomalous behaviors of water. These predictions are confirmed by a percolation description of water molecules based on the definition of cluster of correlated degrees of freedom. Along the phase transition line and the Widom line we recover a power law cluster distribution. At the LLCP the scaling of the percolation quantities agree with the Ising critical exponents. The density, energy and entropy fluctuations that are at the base of the anomalies of water and the existence of its LLCP have also consequences in the context of protein stability. General thermodynamic prediction asserts the existence of a close stability region (SR) in temperature-pressure plane for the native folded state of a protein. Experimental evidences support this theory showing hot-, cold- and pressure-denaturation. Water behavior at the protein interface is expected to be the driving force for the folding-unfolding process. To shed light on this mechanism we study the SR of a folded hydrophobic polymer solvated in the coarse-grain water. Tuning the water-water interaction at the interface and the density of the hydration shell we find an elliptic protein SR in the temperature-pressure plane, qualitatively consistent with available experimental data. Our work contributes to the ongoing debate about the role of hydration water in stabilizing the native protein state. We show here that the physics of water, and in particular its energy, density and entropy fluctuations are sufficient to rationalize the existence of a protein SR with respect to temperature and pressure. |
| publishDate |
2013 |
| dc.date.none.fl_str_mv |
2013 2013 2013 |
| dc.type.none.fl_str_mv |
info:eu-repo/semantics/doctoralThesis info:eu-repo/semantics/publishedVersion |
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doctoralThesis |
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publishedVersion |
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http://hdl.handle.net/10803/120095 |
| url |
http://hdl.handle.net/10803/120095 |
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Inglés |
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Inglés |
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info:eu-repo/semantics/openAccess |
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openAccess |
| dc.format.none.fl_str_mv |
130 p. application/pdf application/pdf |
| dc.publisher.none.fl_str_mv |
Universitat de Barcelona |
| publisher.none.fl_str_mv |
Universitat de Barcelona |
| dc.source.none.fl_str_mv |
TDX (Tesis Doctorals en Xarxa) reponame:TDR. Tesis Doctorales en Red instname:CBUC, CESCA |
| instname_str |
CBUC, CESCA |
| reponame_str |
TDR. Tesis Doctorales en Red |
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TDR. Tesis Doctorales en Red |
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| _version_ |
1869412114272092160 |
| spelling |
Statistical Physics of Water in Hydrophobic Nano-Confinement and at Proteins InterfacesBianco, ValentinoAiguaAguaWaterProteïnesProteínasProteinsHidrogenHidrógenoHydrogenNanoconfinamentNanoconfinamientoNano confinementEnllaç d'hidrogenEnlace de hidrógenoHydrogen bondCiències Experimentals i Matemàtiques53Water is commonly associated with life. This substance affects the living beings in countless aspects and length scales, ranging from molecular biology to climatology. Water exhibits a long series of anomalous behaviors. These anomalies can be rationalized as a consequence of a second critical point in the supercooled region of the liquid phase. Nevertheless, the large part of the phase diagram of supercooled water is to date experimentally inaccessible for the inevitable crystallization of the bulk liquid. Confinement of water in nano-structures is a possible way to prevent the crystallization of molecules. In this thesis we present a coarse-grain model to describe the physical behavior of water at hydrophobic interfaces. The essential feature of the model is the description of water-water interaction via directional and cooperative components of the hydrogen bond (HB). We explore the phase diagram of supercooled water nano-confined between hydrophobic walls. Our results, grounded in statistical physics methods and Monte Carlo simulations, show the presence of a line of first order phase transition in the temperature-pressure plane separating two liquid phases and ending in a liquid-liquid critical point (LLCP). The LLCP universality class approaches the one of the Ising model in two dimensions in the thermodynamic limit, while large deviations are observed for strong confinement. Below the LLCP we find the locus of maxima of correlation length (the Widom line) of the system. Near the LLCP we find a large increase of the thermodynamic response functions consistent with the anomalous behaviors of water. These predictions are confirmed by a percolation description of water molecules based on the definition of cluster of correlated degrees of freedom. Along the phase transition line and the Widom line we recover a power law cluster distribution. At the LLCP the scaling of the percolation quantities agree with the Ising critical exponents. The density, energy and entropy fluctuations that are at the base of the anomalies of water and the existence of its LLCP have also consequences in the context of protein stability. General thermodynamic prediction asserts the existence of a close stability region (SR) in temperature-pressure plane for the native folded state of a protein. Experimental evidences support this theory showing hot-, cold- and pressure-denaturation. Water behavior at the protein interface is expected to be the driving force for the folding-unfolding process. To shed light on this mechanism we study the SR of a folded hydrophobic polymer solvated in the coarse-grain water. Tuning the water-water interaction at the interface and the density of the hydration shell we find an elliptic protein SR in the temperature-pressure plane, qualitatively consistent with available experimental data. Our work contributes to the ongoing debate about the role of hydration water in stabilizing the native protein state. We show here that the physics of water, and in particular its energy, density and entropy fluctuations are sufficient to rationalize the existence of a protein SR with respect to temperature and pressure.El agua es, probablemente, el líquido más importante para la vida. Afecta el clima y la morfología de la Tierra, es fundamental en muchas tecnologías y desarrolla un papel fundamental en los procesos biológicos. A pesar de su importancia y abundancia su comportamiento sigue siendo difícil de entender respecto a los fluidos simples, del tipo argón (el agua tiene más de sesenta anomalías). En esta tesis proponemos un modelo de grano-grueso capaz de captar algunas características microscópicas de la interacción agua-agua en una interfaz hidrofóbica. Hemos analizado el diagrama de fases por baja temperatura de una mono-capa de agua confinada entre paredes paralelas hidrófobas encontrando un punto crítico líquido-líquido en la región sobre-enfriada, al final de una línea de transición de primer orden entre dos fases líquidas. El punto critico pertenece a la clase de universalidad Ising en dos dimensiones sólo por tamaño de las paredes muy grandes. Sorprendentemente, aumentando el confinamiento, la clase de universalidad desvía hacia la de Ising en tres dimensiones. Presentamos una descripción geométrica de la región de moléculas correladas en la monocapa sobreenfriada. Nuestros resultados enseñan que la línea de transición líquido-líquido y la línea Widom (su continuación analítica) se caracterizan por una línea de percolación, donde la distribución de los clúster decae según ley de potencia. Esta línea marca la región donde las fluctuaciones de puentes de hidrógeno se extienden por toda la red. Finalmente hemos estudiado cómo la red de puentes de hidrógeno puede estabilizar el estado nativo de una proteína, en función de la variación de la interacción agua-agua en la interfaz hidrofóbica y del aumento de densidad del agua interfacial al aumentar la presión. El modelo muestra que la proteína se desnaturaliza a alta y baja temperatura, y a alta y a baja presión, reproduciendo las características de desnaturalización observadas en los experimentos. La región de estabilidad de la proteína, tiene una forma elíptica de acuerdo con la teoría.Universitat de BarcelonaFranzese, GiancarloUniversitat de Barcelona. Departament de Física Fonamental201320132013info:eu-repo/semantics/doctoralThesisinfo:eu-repo/semantics/publishedVersion130 p.application/pdfapplication/pdfhttp://hdl.handle.net/10803/120095TDX (Tesis Doctorals en Xarxa)reponame:TDR. Tesis Doctorales en Redinstname:CBUC, CESCAInglésADVERTIMENT. L'accés als continguts d'aquesta tesi doctoral i la seva utilització ha de respectar els drets de la persona autora. Pot ser utilitzada per a consulta o estudi personal, així com en activitats o materials d'investigació i docència en els termes establerts a l'art. 32 del Text Refós de la Llei de Propietat Intel·lectual (RDL 1/1996). Per altres utilitzacions es requereix l'autorització prèvia i expressa de la persona autora. En qualsevol cas, en la utilització dels seus continguts caldrà indicar de forma clara el nom i cognoms de la persona autora i el títol de la tesi doctoral. No s'autoritza la seva reproducció o altres formes d'explotació efectuades amb finalitats de lucre ni la seva comunicació pública des d'un lloc aliè al servei TDX. Tampoc s'autoritza la presentació del seu contingut en una finestra o marc aliè a TDX (framing). Aquesta reserva de drets afecta tant als continguts de la tesi com als seus resums i índexs.info:eu-repo/semantics/openAccessoai:www.tdx.cat:10803/1200952026-06-14T12:46:07Z |
| score |
15,300724 |