The Experts below are selected from a list of 24504 Experts worldwide ranked by ideXlab platform
Mitchell M. Rawlins - One of the best experts on this subject based on the ideXlab platform.
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physicochemical Thermodynamic Framework for the interpretation of peptide tandem mass spectra
Journal of Physical Chemistry C, 2010Co-Authors: William R. Cannon, Mitchell M. RawlinsAbstract:The interpretation of tandem mass spectra of peptides from collision-induced dissociation is discussed from the perspective of a multinomial data analysis problem and from the perspective of statistical mechanics. Both approaches use the same statistical likelihood function, but the free energy differs from the statistical likelihood by a term that additionally accounts for the size of the system. In addition, it is shown that the statistical likelihood is equivalent to the information theory entropy when scaled appropriately. The likelihood function provides a physically and chemically principled way to incorporate intensity information into the interpretation of tandem mass spectra. As a result, we demonstrate that incorporating the intensity information in this manner leads to an increased identification rate for database searches and allows for the simultaneous use of spectral libraries with standard database searching. The use of spectral libraries further increases the identification rate relative t...
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Physicochemical/Thermodynamic Framework for the Interpretation of Peptide Tandem Mass Spectra†
The Journal of Physical Chemistry C, 2009Co-Authors: William R. Cannon, Mitchell M. RawlinsAbstract:The interpretation of tandem mass spectra of peptides from collision-induced dissociation is discussed from the perspective of a multinomial data analysis problem and from the perspective of statistical mechanics. Both approaches use the same statistical likelihood function, but the free energy differs from the statistical likelihood by a term that additionally accounts for the size of the system. In addition, it is shown that the statistical likelihood is equivalent to the information theory entropy when scaled appropriately. The likelihood function provides a physically and chemically principled way to incorporate intensity information into the interpretation of tandem mass spectra. As a result, we demonstrate that incorporating the intensity information in this manner leads to an increased identification rate for database searches and allows for the simultaneous use of spectral libraries with standard database searching. The use of spectral libraries further increases the identification rate relative t...
William R. Cannon - One of the best experts on this subject based on the ideXlab platform.
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physicochemical Thermodynamic Framework for the interpretation of peptide tandem mass spectra
Journal of Physical Chemistry C, 2010Co-Authors: William R. Cannon, Mitchell M. RawlinsAbstract:The interpretation of tandem mass spectra of peptides from collision-induced dissociation is discussed from the perspective of a multinomial data analysis problem and from the perspective of statistical mechanics. Both approaches use the same statistical likelihood function, but the free energy differs from the statistical likelihood by a term that additionally accounts for the size of the system. In addition, it is shown that the statistical likelihood is equivalent to the information theory entropy when scaled appropriately. The likelihood function provides a physically and chemically principled way to incorporate intensity information into the interpretation of tandem mass spectra. As a result, we demonstrate that incorporating the intensity information in this manner leads to an increased identification rate for database searches and allows for the simultaneous use of spectral libraries with standard database searching. The use of spectral libraries further increases the identification rate relative t...
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Physicochemical/Thermodynamic Framework for the Interpretation of Peptide Tandem Mass Spectra†
The Journal of Physical Chemistry C, 2009Co-Authors: William R. Cannon, Mitchell M. RawlinsAbstract:The interpretation of tandem mass spectra of peptides from collision-induced dissociation is discussed from the perspective of a multinomial data analysis problem and from the perspective of statistical mechanics. Both approaches use the same statistical likelihood function, but the free energy differs from the statistical likelihood by a term that additionally accounts for the size of the system. In addition, it is shown that the statistical likelihood is equivalent to the information theory entropy when scaled appropriately. The likelihood function provides a physically and chemically principled way to incorporate intensity information into the interpretation of tandem mass spectra. As a result, we demonstrate that incorporating the intensity information in this manner leads to an increased identification rate for database searches and allows for the simultaneous use of spectral libraries with standard database searching. The use of spectral libraries further increases the identification rate relative t...
Kumbakonam R. Rajagopal - One of the best experts on this subject based on the ideXlab platform.
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A model for a solid undergoing rate-independent dissipative mechanical processes:
Mathematics and Mechanics of Solids, 2020Co-Authors: U. Saravanan, Kumbakonam R. Rajagopal, Roshan M Tom, Keshav BharadwajAbstract:A Thermodynamic Framework is proposed to capture the dissipative response of metals. In contrast to the conventional practice, a stressed reference configuration is assumed instead of a stress-free...
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Nonlinear Viscoelastic Model for Describing the Response of Asphalt Binders within the Context of a Gibbs-Potential–Based Thermodynamic Framework
Journal of Engineering Mechanics, 2015Co-Authors: S. P. Atul Narayan, Dallas N. Little, Kumbakonam R. RajagopalAbstract:Many researchers have asserted the importance of considering the nonlinearity of the mechanical behavior of asphalt binders for accurately estimating their performance under field conditions, and for comparing and ranking them accordingly. To do so, it is necessary to have a robust and reliable nonlinear viscoelastic theory and a model derived under its purview that can describe the mechanical response of asphalt binders reasonably well. The objective of this study is to develop such a model. A new Gibbs-potential-based Thermodynamic Framework is used for this purpose. The model developed in this paper is a generalization of the Oldroyd-B model. It is used successfully to describe results of several experiments from the literature concerning the nonlinear response of asphalt binders, including nonlinear creep-recovery and stress-relaxation behavior, thinning behavior, and the appearance of normal forces perpendicular to the plane of shear in simple shear tests.
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A Thermodynamic Framework to model thixotropic materials
International Journal of Non-Linear Mechanics, 2013Co-Authors: Paulo R. De Souza Mendes, Kumbakonam R. Rajagopal, Roney L. ThompsonAbstract:Abstract Thixotropic materials are widely used in a variety of industrial applications. The constitutive relations to describe these materials are based on one-dimensional experiments in which the material is subjected to a shear motion and there is no unique methodology to obtain proper three-dimensional models. The path towards generalization to a three-dimensional Framework is invariably carried out in a ad hoc manner. Here we propose a three-dimensional model that stems from a general Thermodynamic Framework that has proved to be quite robust in the development of constitutive relations, namely the application of the second law of Thermodynamics together with the maximization of the entropy production. This leads to a constitutive equation that has the same form of a generalized Upper Convected Maxwell equation, if we require that changes of microstructure due to the deformation of each Maxwell element that comprises the model are reversible. Changes in microstructure are governed by a potential that is a measure of the difference between the current structure and the equilibrium structure associated with it. The equilibrium structure associated with the current structure is determined by the current value of stress, considered the main break up agent. We assume that the state of equilibrium would be achieved in a Motion With Constant Stress History, starting from the current stress state, until a steady state where the kinematics is not changing.
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A Thermodynamic Framework to develop rate-type models for fluids without instantaneous elasticity
Acta Mechanica, 2009Co-Authors: S. Karra, Kumbakonam R. RajagopalAbstract:In this paper, we apply the Thermodynamic Framework recently put into place by Rajagopal and co-workers, to develop rate-type models for viscoelastic fluids which do not possess instantaneous elasticity. To illustrate the capabilities of such models, we make a specific choice for the specific Helmholtz potential and the rate of dissipation and consider the creep and stress relaxation response associated with the model. Given specific forms for the Helmholtz potential and the rate of dissipation, the rate of dissipation is maximized with the constraint that the difference between the stress power and the rate of change of Helmholtz potential is equal to the rate of dissipation and any other constraint that may be applicable such as incompressibility. We show that the class of models that are developed exhibit fluid-like characteristics, when none of the material moduli that appear in the model are not zero, and are incapable of instantaneous elastic response. They also include Maxwell-like and Kelvin-Voigt-like viscoelastic materials (when certain material moduli take special values).
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Modelling Sand–Asphalt Mixtures Within a Thermodynamic Framework: Theory and Application to Torsion Experiments
International Journal of Pavement Engineering, 2009Co-Authors: Parag Ravindran, J.m. Krishnan, Eyad Masad, Kumbakonam R. RajagopalAbstract:Sand–asphalt mixtures are difficult to model, partly due to their composition and partly due to the complex interplay among their constituents. This work is concerned with the development of an anisotropic model to describe the nonlinear behaviour of sand–asphalt mixtures. A general Thermodynamic Framework is used, which allows for the material to have multiple natural configurations corresponding to its underlying structure. The evolution of the natural configuration takes place in a Thermodynamically consistent manner. The model developed is corroborated using experimental results published by Ravindran et al. (2007a,b) on torsion tests of sand–asphalt specimens over a range of conditions.
Donifan Barahona - One of the best experts on this subject based on the ideXlab platform.
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analysis of the effect of water activity on ice formation using a new Thermodynamic Framework
Atmospheric Chemistry and Physics, 2014Co-Authors: Donifan BarahonaAbstract:Abstract. In this work a new Thermodynamic Framework is developed and used to investigate the effect of water activity on the formation of ice within supercooled droplets. The new Framework is based on a novel concept where the interface is assumed to be made of liquid molecules "trapped" by the solid matrix. It also accounts for the change in the composition of the liquid phase upon nucleation. Using this Framework, new expressions are developed for the critical ice germ size and the nucleation work with explicit dependencies on temperature and water activity. However unlike previous approaches, the new model does not depend on the interfacial tension between liquid and ice. The Thermodynamic Framework is introduced within classical nucleation theory to study the effect of water activity on the ice nucleation rate. Comparison against experimental results shows that the new approach is able to reproduce the observed effect of water activity on the nucleation rate and the freezing temperature. It allows for the first time a phenomenological derivation of the constant shift in water activity between melting and nucleation. The new Framework offers a consistent Thermodynamic view of ice nucleation, simple enough to be applied in atmospheric models of cloud formation.
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Analysis of the effect of water activity on ice formation using a new Thermodynamic Framework
Atmospheric Chemistry and Physics Discussions, 2014Co-Authors: Donifan BarahonaAbstract:Abstract. In this work a new Thermodynamic Framework is developed and used to investigate the effect of water activity on the formation of ice within supercooled droplets. The new Framework is based on a novel concept where the interface is assumed to be made of liquid molecules "trapped" by the solid matrix. Using this concept new expressions are developed for the critical ice germ size and the nucleation work, with explicit dependencies on temperature and water activity. However unlike previous approaches, the new model does not depend on the interfacial tension between liquid and ice. Comparison against experimental results shows that the new theory is able to reproduce the observed effect of water activity on nucleation rate and freezing temperature. It allows for the first time a phenomenological derivation of the constant shift in water activity between melting and nucleation. The new Framework offers a consistent Thermodynamic view of ice nucleation, simple enough to be applied in atmospheric models of cloud formation.
K R Rajagopal - One of the best experts on this subject based on the ideXlab platform.
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nonlinear viscoelastic model for describing the response of asphalt binders within the context of a gibbs potential based Thermodynamic Framework
Journal of Engineering Mechanics-asce, 2015Co-Authors: S Atul P Narayan, Dallas N. Little, K R RajagopalAbstract:Many researchers have asserted the importance of considering the nonlinearity of the mechanical behavior of asphalt binders for accurately estimating their performance under field conditions, and for comparing and ranking them accordingly. To do so, it is necessary to have a robust and reliable nonlinear viscoelastic theory and a model derived under its purview that can describe the mechanical response of asphalt binders reasonably well. The objective of this study is to develop such a model. A new Gibbs-potential-based Thermodynamic Framework is used for this purpose. The model developed in this paper is a generalization of the Oldroyd-B model. It is used successfully to describe results of several experiments from the literature concerning the nonlinear response of asphalt binders, including nonlinear creep-recovery and stress-relaxation behavior, thinning behavior, and the appearance of normal forces perpendicular to the plane of shear in simple shear tests.
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A Thermodynamic Framework to develop rate-type models for fluids without instantaneous elasticity
Acta Mechanica, 2009Co-Authors: S. Karra, K R RajagopalAbstract:In this paper, we apply the Thermodynamic Framework recently put into place by Rajagopal and co-workers, to develop rate-type models for viscoelastic fluids which do not possess instantaneous elasticity. To illustrate the capabilities of such models we make a specific choice for the specific Helmholtz potential and the rate of dissipation and consider the creep and stress relaxation response associated with the model. Given specific forms for the Helmholtz potential and the rate of dissipation, the rate of dissipation is maximized with the constraint that the difference between the stress power and the rate of change of Helmholtz potential is equal to the rate of dissipation and any other constraint that may be applicable such as incompressibility. We show that the model that is developed exhibits fluid-like characteristics and is incapable of instantaneous elastic response. It also includes Maxwell-like and Kelvin-Voigt-like viscoelastic materials (when certain material moduli take special values).Comment: 18 pages, 5 figure
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modelling sand asphalt mixtures within a Thermodynamic Framework theory and application to torsion experiments
International Journal of Pavement Engineering, 2009Co-Authors: Parag Ravindran, J.m. Krishnan, Eyad Masad, K R RajagopalAbstract:Sand–asphalt mixtures are difficult to model, partly due to their composition and partly due to the complex interplay among their constituents. This work is concerned with the development of an anisotropic model to describe the nonlinear behaviour of sand–asphalt mixtures. A general Thermodynamic Framework is used, which allows for the material to have multiple natural configurations corresponding to its underlying structure. The evolution of the natural configuration takes place in a Thermodynamically consistent manner. The model developed is corroborated using experimental results published by Ravindran et al. (2007a,b) on torsion tests of sand–asphalt specimens over a range of conditions.
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Thermodynamic Framework for the constitutive modeling of asphalt concrete theory and applications
Journal of Materials in Civil Engineering, 2004Co-Authors: Murali J Krishnan, K R RajagopalAbstract:The response of an asphalt concrete pavement to external loading depends on its internal structure. Using a recent Framework that associates different natural (stress-free) configurations with distinct internal structures of the body, asphalt concrete is modeled. The authors assumed asphalt concrete to be a mixture of aggregate matrix and asphalt mortar matrix with evolving natural configurations. The evolution of the natural configuration is determined using a Thermodynamic criterion, namely, the maximization of the rate of dissipation. Appropriate choices for the Helmholtz potential, the rate of dissipation and the other Thermodynamic criteria are assumed to describe how energy is stored and the manner of the rate of dissipation. As an example, a specific form for the Helmholtz potential and the rate of dissipation function that leads to a generalized "upper convected Burgers's model" were chosen, its linearized version being the viscoelastic model that is usually used for modeling asphalt concrete. This model is just one example of how a class of Thermodynamically consistent models can be generated to describe the nonlinear behavior of materials such as asphalt concrete. The uniaxial compressive and tensile creep of asphalt concrete for 2 different types of specimens and test methods are modeled. Details are provided of the numerical scheme used to solve the initial value problem, and the experimental data of Monismith and Secor (1962) is compared with predictions of the model.
