Any theory of nucleation requires two elements: first, a way to calculating properties of clusters such as their structure and free energies, and second, a dynamical description of fluctuations. Classical density functional theory has long been recognized to have the potential to provide the first element. cDFT has been used to determine the structure and energy of critical clusters for, first, nucleation of liquid droplets from a vapor and, later, that of crystallization. The second element necessary to describe nucleation is a description of fluctuations. A natural framework for this is fluctuating hydrodynamics that is now a widely used tool applied to a range of subjects such as mode coupling theory, glass transition, and nucleation, and its foundations in more fundamental statistical mechanics have been established. The basic quantities used in the theory are the spatially varying local densities of each species as well as the velocity and temperature fields. For large particles, such as colloids or macromolecules, in a bath of smaller particles (e.g., water), an approximate effective description of the large molecules can be derived in which the effect of the smaller molecules is modeled as a combination of friction and a stochastic force. In the present work, we focus on nucleation of protein crystals and clusters. Specific information on nucleation kinetics of protein molecules is not abundant, probably because the value of the nucleation stage was not realized by the protein crystallization community until recently. Protein crystal nucleation is a crucial problem in biological crystallography and other areas of science, technology and medicine; in particular: the in vivo nucleation process in the liquid{liquid region is also interesting for detection and understanding at the molecular level of illnesses related to protein aggregation. Protein molecules will be useful in the future for fundamental studies on nucleation because of their large size, which will permit visualization of the growth of crystals at the very beginning, when indirect information inferred from scattering studies is not very accurate. Recent studies have demonstrated that protein crystal nuclei form within crucial precursors: protein-dense liquid clusters are regions of high protein concentration. They have been recently observed in solutions of several proteins. The typical cluster size varies from several tens to several hundreds of nanometers.

EXPERIMENTAL CHARACTERIZATION OF LYSOZYME NUCLEATION THROUGH CONFOCAL DYNAMIC LIGHTSCATTERING / F. Simonetto ; Tutor: M.A.C.Potenza. - : . Dipartimento di Fisica Aldo Pontremoli, 2021 Mar 22. ((33. ciclo, Anno Accademico 2020.

EXPERIMENTAL CHARACTERIZATION OF LYSOZYME NUCLEATION THROUGH CONFOCAL DYNAMIC LIGHTSCATTERING

F. Simonetto
2021

Abstract

Any theory of nucleation requires two elements: first, a way to calculating properties of clusters such as their structure and free energies, and second, a dynamical description of fluctuations. Classical density functional theory has long been recognized to have the potential to provide the first element. cDFT has been used to determine the structure and energy of critical clusters for, first, nucleation of liquid droplets from a vapor and, later, that of crystallization. The second element necessary to describe nucleation is a description of fluctuations. A natural framework for this is fluctuating hydrodynamics that is now a widely used tool applied to a range of subjects such as mode coupling theory, glass transition, and nucleation, and its foundations in more fundamental statistical mechanics have been established. The basic quantities used in the theory are the spatially varying local densities of each species as well as the velocity and temperature fields. For large particles, such as colloids or macromolecules, in a bath of smaller particles (e.g., water), an approximate effective description of the large molecules can be derived in which the effect of the smaller molecules is modeled as a combination of friction and a stochastic force. In the present work, we focus on nucleation of protein crystals and clusters. Specific information on nucleation kinetics of protein molecules is not abundant, probably because the value of the nucleation stage was not realized by the protein crystallization community until recently. Protein crystal nucleation is a crucial problem in biological crystallography and other areas of science, technology and medicine; in particular: the in vivo nucleation process in the liquid{liquid region is also interesting for detection and understanding at the molecular level of illnesses related to protein aggregation. Protein molecules will be useful in the future for fundamental studies on nucleation because of their large size, which will permit visualization of the growth of crystals at the very beginning, when indirect information inferred from scattering studies is not very accurate. Recent studies have demonstrated that protein crystal nuclei form within crucial precursors: protein-dense liquid clusters are regions of high protein concentration. They have been recently observed in solutions of several proteins. The typical cluster size varies from several tens to several hundreds of nanometers.
POTENZA, MARCO ALBERTO CARLO
PARIS, MATTEO
Settore FIS/03 - Fisica della Materia
EXPERIMENTAL CHARACTERIZATION OF LYSOZYME NUCLEATION THROUGH CONFOCAL DYNAMIC LIGHTSCATTERING / F. Simonetto ; Tutor: M.A.C.Potenza. - : . Dipartimento di Fisica Aldo Pontremoli, 2021 Mar 22. ((33. ciclo, Anno Accademico 2020.
Doctoral Thesis
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/2434/819472
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