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Isamu Kusaka - One of the best experts on this subject based on the ideXlab platform.
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Direct calculation of solid-vapor coexistence points by thermodynamic integration: application to single component and binary systems.
The Journal of chemical physics, 2006Co-Authors: Pankaj A. Apte, Isamu KusakaAbstract:We present a new thermodynamic integration method that directly connects the vapor and solid phases by a Reversible Path. The thermodynamic integration in the isothermal-isobaric ensemble yields the Gibbs free energy difference between the two phases, from which the sublimation temperature can be easily calculated. The method extends to the binary mixture without any modification to the integration Path simply by employing the isothermal-isobaric semigrand ensemble. The thermodynamic integration, in this case, yields the chemical potential difference between the solid and vapor phases for one of the components, from which the binary sublimation temperature can be calculated. The coexistence temperatures predicted by our method agree well with those in the literature for single component and binary Lennard-Jones systems.
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Evaluation of the translational free energy in a melting temperature calculation by simulation.
Physical Review E, 2006Co-Authors: Pankaj A. Apte, Isamu KusakaAbstract:: We present two methods suitable for controlling the translational degrees of freedom of a system when evaluating directly the free energy difference between the liquid and the solid phases by thermodynamic integration along a Reversible Path connecting these two phases. Such a constraint is crucial for an accurate prediction of the melting point by means of simulation. In one of the methods, the free energy difference was calculated by fixing one of the particles of the system at the center of the simulation box. In the second method, the free energy difference was calculated by constraining the center of mass of the system to a small region taken around the center of the simulation box. The correction to the free energy difference due to each constraint must be evaluated by a direct simulation. Both methods give consistent results when applied to a truncated and shifted Lennard-Jones system with cutoff radius of 2.5sigma. However, the fixed particle constraint method is found to be more efficient computationally.
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evaluation of the translational free energy in a melting temperature calculation by simulation
Physical Review E, 2006Co-Authors: Pankaj A. Apte, Isamu KusakaAbstract:We present two methods suitable for controlling the translational degrees of freedom of a system when evaluating directly the free energy difference between the liquid and the solid phases by thermodynamic integration along a Reversible Path connecting these two phases. Such a constraint is crucial for an accurate prediction of the melting point by means of simulation. In one of the methods, the free energy difference was calculated by fixing one of the particles of the system at the center of the simulation box. In the second method, the free energy difference was calculated by constraining the center of mass of the system to a small region taken around the center of the simulation box. The correction to the free energy difference due to each constraint must be evaluated by a direct simulation. Both methods give consistent results when applied to a truncated and shifted Lennard-Jones system with cutoff radius of $2.5\ensuremath{\sigma}$. However, the fixed particle constraint method is found to be more efficient computationally.
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Direct calculation of solid-liquid coexistence points of a binary mixture by thermodynamic integration.
The Journal of chemical physics, 2005Co-Authors: Pankaj A. Apte, Isamu KusakaAbstract:We present a new thermodynamic integration method that directly connects the liquid and the solid phases of a binary mixture by a Reversible Path. The states along the Path are simulated in the isothermal-isobaric semigrand canonical ensemble, in which temperature, pressure, the total number of particles, and the fugacity fractions of the components are held fixed. The thermodynamic integration yields the chemical-potential difference between the two phases for one of the components and this information is then used to locate the solid-liquid coexistence points. The melting temperatures predicted by our method agree well with those predicted by the Gibbs-Duhem integration for a truncated and shifted Lennard-Jones system with a cutoff radius of 2.5σ.
Pankaj A. Apte - One of the best experts on this subject based on the ideXlab platform.
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Efficient computation of free energy of crystal phases due to external potentials by error-biased Bennett acceptance ratio method
The Journal of chemical physics, 2010Co-Authors: Pankaj A. ApteAbstract:Free energy of crystal phases is commonly evaluated by thermodynamic integration (TDI) along a Reversible Path that involves an external potential. A persistent problem in this method is that a significant hysteresis is observed due to differences in the center of mass position of the crystal phase in the presence and absence of the external potential. To alleviate this hysteresis, a constraint on the translational degrees of freedom of the crystal phase is imposed along the Path and subsequently a correction term is added to the free energy to account for such a constraint. In this work, we propose a new methodology termed as error-biased Bennett Acceptance ratio (EBAR) method that effectively solves this problem without the need to impose any constraint. This method is simple to implement as it does not require any modification to the Path or to the simulation code. We show the applicability of this method in the computation of crystal-melt interfacial energy by cleaving wall method [J. Chem. Phys., 118, 7651 (2003)] and bulk crystal-melt free energy difference by constrained fluid $\lambda$-integration method [J. Chem. Phys., 120, 2122 (2004)] for a model potential of silicon.
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Direct calculation of solid-vapor coexistence points by thermodynamic integration: application to single component and binary systems.
The Journal of chemical physics, 2006Co-Authors: Pankaj A. Apte, Isamu KusakaAbstract:We present a new thermodynamic integration method that directly connects the vapor and solid phases by a Reversible Path. The thermodynamic integration in the isothermal-isobaric ensemble yields the Gibbs free energy difference between the two phases, from which the sublimation temperature can be easily calculated. The method extends to the binary mixture without any modification to the integration Path simply by employing the isothermal-isobaric semigrand ensemble. The thermodynamic integration, in this case, yields the chemical potential difference between the solid and vapor phases for one of the components, from which the binary sublimation temperature can be calculated. The coexistence temperatures predicted by our method agree well with those in the literature for single component and binary Lennard-Jones systems.
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Evaluation of the translational free energy in a melting temperature calculation by simulation.
Physical Review E, 2006Co-Authors: Pankaj A. Apte, Isamu KusakaAbstract:: We present two methods suitable for controlling the translational degrees of freedom of a system when evaluating directly the free energy difference between the liquid and the solid phases by thermodynamic integration along a Reversible Path connecting these two phases. Such a constraint is crucial for an accurate prediction of the melting point by means of simulation. In one of the methods, the free energy difference was calculated by fixing one of the particles of the system at the center of the simulation box. In the second method, the free energy difference was calculated by constraining the center of mass of the system to a small region taken around the center of the simulation box. The correction to the free energy difference due to each constraint must be evaluated by a direct simulation. Both methods give consistent results when applied to a truncated and shifted Lennard-Jones system with cutoff radius of 2.5sigma. However, the fixed particle constraint method is found to be more efficient computationally.
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evaluation of the translational free energy in a melting temperature calculation by simulation
Physical Review E, 2006Co-Authors: Pankaj A. Apte, Isamu KusakaAbstract:We present two methods suitable for controlling the translational degrees of freedom of a system when evaluating directly the free energy difference between the liquid and the solid phases by thermodynamic integration along a Reversible Path connecting these two phases. Such a constraint is crucial for an accurate prediction of the melting point by means of simulation. In one of the methods, the free energy difference was calculated by fixing one of the particles of the system at the center of the simulation box. In the second method, the free energy difference was calculated by constraining the center of mass of the system to a small region taken around the center of the simulation box. The correction to the free energy difference due to each constraint must be evaluated by a direct simulation. Both methods give consistent results when applied to a truncated and shifted Lennard-Jones system with cutoff radius of $2.5\ensuremath{\sigma}$. However, the fixed particle constraint method is found to be more efficient computationally.
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Direct calculation of solid-liquid coexistence points of a binary mixture by thermodynamic integration.
The Journal of chemical physics, 2005Co-Authors: Pankaj A. Apte, Isamu KusakaAbstract:We present a new thermodynamic integration method that directly connects the liquid and the solid phases of a binary mixture by a Reversible Path. The states along the Path are simulated in the isothermal-isobaric semigrand canonical ensemble, in which temperature, pressure, the total number of particles, and the fugacity fractions of the components are held fixed. The thermodynamic integration yields the chemical-potential difference between the two phases for one of the components and this information is then used to locate the solid-liquid coexistence points. The melting temperatures predicted by our method agree well with those predicted by the Gibbs-Duhem integration for a truncated and shifted Lennard-Jones system with a cutoff radius of 2.5σ.
Pablo G Debenedetti - One of the best experts on this subject based on the ideXlab platform.
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metastable liquid liquid transition in a molecular model of water
Nature, 2014Co-Authors: Jeremy C Palmer, Fausto Martelli, Athanassios Z Panagiotopoulos, Pablo G DebenedettiAbstract:A stable crystal phase and two metastable liquid phases of the ST2 model of water exist at the same deeply supercooled condition, and the two liquids undergo a first-order liquid–liquid transition that meets stringent thermodynamic criteria. Water's anomalous physical properties become markedly enhanced upon supercooling below the freezing point and even seem to diverge towards infinity at around 228 K. Two papers in this issue use contrasting techniques to study this little-explored 'no-man's land' of water where extremely fast ice formation has prohibited measurements of the liquid state. Jonas Sellberg et al. use femtosecond X-ray laser pulses to measure bulk liquid water structure in droplets evaporatively cooled to 227 K. Even at this temperature some droplets remained liquid on a millisecond timescale. Pushing this technique further can shed light on controversial scenarios that aim to describe and explain the many anomalous properties of water. Jeremy Palmer et al. use six advanced computational methods to demonstrate the existence of two metastable liquid phases of ST2 water at the same deeply supercooled condition, undergoing a liquid–liquid transition that meets stringent thermodynamic criteria and could explain the behavior of water in this regime. Liquid water’s isothermal compressibility1 and isobaric heat capacity2, and the magnitude of its thermal expansion coefficient3, increase sharply on cooling below the equilibrium freezing point. Many experimental4,5,6,7,8, theoretical9,10,11 and computational12,13 studies have sought to understand the molecular origin and implications of this anomalous behaviour. Of the different theoretical scenarios9,14,15 put forward, one posits the existence of a first-order phase transition that involves two forms of liquid water and terminates at a critical point located at deeply supercooled conditions9,12. Some experimental evidence is consistent with this hypothesis4,16, but no definitive proof of a liquid–liquid transition in water has been obtained to date: rapid ice crystallization has so far prevented decisive measurements on deeply supercooled water, although this challenge has been overcome recently16. Computer simulations are therefore crucial for exploring water’s structure and behaviour in this regime, and have shown13,17,18,19,20,21 that some water models exhibit liquid–liquid transitions and others do not. However, recent work22,23 has argued that the liquid–liquid transition has been mistakenly interpreted, and is in fact a liquid–crystal transition in all atomistic models of water. Here we show, by studying the liquid–liquid transition in the ST2 model of water24 with the use of six advanced sampling methods to compute the free-energy surface, that two metastable liquid phases and a stable crystal phase exist at the same deeply supercooled thermodynamic condition, and that the transition between the two liquids satisfies the thermodynamic criteria of a first-order transition25. We follow the rearrangement of water’s coordination shell and topological ring structure along a thermodynamically Reversible Path from the low-density liquid to cubic ice26. We also show that the system fluctuates freely between the two liquid phases rather than crystallizing. These findings provide unambiguous evidence for a liquid–liquid transition in the ST2 model of water, and point to the separation of time scales between crystallization and relaxation as being crucial for enabling it.
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Metastable liquid–liquid transition in a molecular model of water
Nature, 2014Co-Authors: Jeremy C Palmer, Fausto Martelli, Athanassios Z Panagiotopoulos, Yang Liu, Roberto Car, Pablo G DebenedettiAbstract:Liquid water’s isothermal compressibility^ 1 and isobaric heat capacity^ 2 , and the magnitude of its thermal expansion coefficient^ 3 , increase sharply on cooling below the equilibrium freezing point. Many experimental^ 4 , 5 , 6 , 7 , 8 , theoretical^ 9 , 10 , 11 and computational^ 12 , 13 studies have sought to understand the molecular origin and implications of this anomalous behaviour. Of the different theoretical scenarios^ 9 , 14 , 15 put forward, one posits the existence of a first-order phase transition that involves two forms of liquid water and terminates at a critical point located at deeply supercooled conditions^ 9 , 12 . Some experimental evidence is consistent with this hypothesis^ 4 , 16 , but no definitive proof of a liquid–liquid transition in water has been obtained to date: rapid ice crystallization has so far prevented decisive measurements on deeply supercooled water, although this challenge has been overcome recently^ 16 . Computer simulations are therefore crucial for exploring water’s structure and behaviour in this regime, and have shown^ 13 , 17 , 18 , 19 , 20 , 21 that some water models exhibit liquid–liquid transitions and others do not. However, recent work^ 22 , 23 has argued that the liquid–liquid transition has been mistakenly interpreted, and is in fact a liquid–crystal transition in all atomistic models of water. Here we show, by studying the liquid–liquid transition in the ST2 model of water^ 24 with the use of six advanced sampling methods to compute the free-energy surface, that two metastable liquid phases and a stable crystal phase exist at the same deeply supercooled thermodynamic condition, and that the transition between the two liquids satisfies the thermodynamic criteria of a first-order transition^ 25 . We follow the rearrangement of water’s coordination shell and topological ring structure along a thermodynamically Reversible Path from the low-density liquid to cubic ice^ 26 . We also show that the system fluctuates freely between the two liquid phases rather than crystallizing. These findings provide unambiguous evidence for a liquid–liquid transition in the ST2 model of water, and point to the separation of time scales between crystallization and relaxation as being crucial for enabling it. A stable crystal phase and two metastable liquid phases of the ST2 model of water exist at the same deeply supercooled condition, and the two liquids undergo a first-order liquid–liquid transition that meets stringent thermodynamic criteria. Water's anomalous physical properties become markedly enhanced upon supercooling below the freezing point and even seem to diverge towards infinity at around 228 K. Two papers in this issue use contrasting techniques to study this little-explored 'no-man's land' of water where extremely fast ice formation has prohibited measurements of the liquid state. Jonas Sellberg et al . use femtosecond X-ray laser pulses to measure bulk liquid water structure in droplets evaporatively cooled to 227 K. Even at this temperature some droplets remained liquid on a millisecond timescale. Pushing this technique further can shed light on controversial scenarios that aim to describe and explain the many anomalous properties of water. Jeremy Palmer et al . use six advanced computational methods to demonstrate the existence of two metastable liquid phases of ST2 water at the same deeply supercooled condition, undergoing a liquid–liquid transition that meets stringent thermodynamic criteria and could explain the behavior of water in this regime.
Valeria Levi - One of the best experts on this subject based on the ideXlab platform.
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Reversible fast-dimerization of bovine serum albumin detected by fluorescence resonance energy transfer.
Biochimica et biophysica acta, 2002Co-Authors: Valeria Levi, F Luis González FlechaAbstract:Self-association of bovine serum albumin (BSA) was explored using fluorescence resonance energy transfer (FRET) between two populations of the protein labeled separately with either fluorescein-5'-isothiocyanate (FITC) or eosin-5'-isothiocyanate (EITC). The energy transfer reached the steady state after 5 s at 25 degrees C, indicating a fast exchange between oligomer subunits. The dependence of the energy transfer efficiency on the protein concentration and its reversion by unlabeled BSA demonstrate that association between BSA monomers occurs through a Reversible Path that involves specific interactions between the protein molecules. Because energy transfer took place even after blocking Cys 34 with iodoacetamide, this residue might not be involved in the Reversible self-association process. The number of subunits forming the oligomer and its dissociation constant were determined from measurements of energy transfer as a function of the donor-acceptor ratio and of the total protein concentration. Analysis of these data indicated that BSA is in a monomer-dimer equilibrium with a dissociation constant of 10 +/- 2 microM at 25 degrees C in 10 mM MOPS-K (pH 5.8).
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Reversible fast-dimerization of bovine serum albumin detected by fluorescence resonance energy transfer.
Biochimica et Biophysica Acta, 2002Co-Authors: Valeria Levi, F. Luis González FlechaAbstract:Abstract Self-association of bovine serum albumin (BSA) was explored using fluorescence resonance energy transfer (FRET) between two populations of the protein labeled separately with either fluorescein-5′-isothiocyanate (FITC) or eosin-5′-isothiocyanate (EITC). The energy transfer reached the steady state after 5 s at 25 °C, indicating a fast exchange between oligomer subunits. The dependence of the energy transfer efficiency on the protein concentration and its reversion by unlabeled BSA demonstrate that association between BSA monomers occurs through a Reversible Path that involves specific interactions between the protein molecules. Because energy transfer took place even after blocking Cys 34 with iodoacetamide, this residue might not be involved in the Reversible self-association process. The number of subunits forming the oligomer and its dissociation constant were determined from measurements of energy transfer as a function of the donor–acceptor ratio and of the total protein concentration. Analysis of these data indicated that BSA is in a monomer–dimer equilibrium with a dissociation constant of 10±2 μM at 25 °C in 10 mM MOPS-K (pH 5.8).
Avinash Chandra - One of the best experts on this subject based on the ideXlab platform.
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a computational study of excess properties for mw potential model of water in supercooled region
Physica A-statistical Mechanics and Its Applications, 2020Co-Authors: Arvind K. Gautam, Avinash ChandraAbstract:Abstract In this work, we studied the liquid–crystal transition of water using monatomic potential model (mW) (Molinero and Moore, 2009). To simulate water, the NPT-MC simulation were performed and obtained the average properties as potential energy ( 〈 ϕ ′ 〉 ) and density ( 〈 ρ 〉 ) at various temperatures which are in the very good agreement (i.e. 〈 ϕ ′ 〉 = − 1 . 766 and 〈 ρ 〉 = 0 . 448 at 202 K) with the literature values (Hujo et al., 2011). The free energy difference between the two liquid phases of water was computed by thermodynamic integration along with a Reversible Path at zero pressure and various temperatures. The recently developed thermodynamic integration (TDI) method was used to computed the excess Gibbs free energy of high density liquid (HDL) phase with respect to the crystalline phase at different temperatures in the supercooled region of mW-water model (Molinero and Moore, 2009). Based on the slope of excess Gibbs free energy with respect to temperature the excess entropy of the high density liquid (HDL) phase was obtained, which shows an anomalous behavior at or near the liquid–liquid transition temperature of T l l = 202 K (Molinero and Moore, 2009). The excess entropy of the liquid phase in the supercooled mW water shows a sharp decline at or near the liquid–liquid phase transition temperature ( T l l ) . The excess entropy of the HDL phase decreases as the temperature decreases to 197 K and increases at 192 K. Our results are in good agreement with the previous observation of a anomalous dependency of the density on temperature in MD simulations starting in the HDL phase at a temperature just above T l l (Moore and Molinero, 2009).
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a computational study of liquid solid interfacial free energy γ for sw ge potential model
Physica A-statistical Mechanics and Its Applications, 2018Co-Authors: Arvind K. Gautam, Avinash ChandraAbstract:Abstract In this work, the melting temperature and liquid–solid interfacial free energy for germanium has been computed by using Stillinger–Weber (SW) potential model. The tetrahedral parameter value of SW potential model was used as 19.5 for numerical simulations. The NVT-MC simulations were performed to compute interfacial free energy with 2235 and 2048 particles for liquid and solid respectively. Initially, the free energy difference between two liquid phase of germanium has been computed by thermodynamic integration method along a Reversible Path at zero pressure and different temperature values. The melting temperature for SW potential model of germanium is obtained as T m ≈ 1360 K . Further, the cleaving wall method was used to compute the liquid–solid interfacial free energy for high density liquid to low density liquid phase transition with SW-Ge potential model. This liquid–solid interfacial free energy has been computed below the melting temperature or at liquid–liquid transition temperature as T l l = 1312 K . This computational study has been performed for understanding the phase behavior and crystal growth of SW-Ge potential model at or near the transition temperature. The results shown here are consistent with the experimental and computational literature values of interfacial free energy for germanium.
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A computational study of liquid–solid interfacial free energy (γ) for SW-Ge potential model
Physica A: Statistical Mechanics and its Applications, 2018Co-Authors: Arvind K. Gautam, Avinash ChandraAbstract:Abstract In this work, the melting temperature and liquid–solid interfacial free energy for germanium has been computed by using Stillinger–Weber (SW) potential model. The tetrahedral parameter value of SW potential model was used as 19.5 for numerical simulations. The NVT-MC simulations were performed to compute interfacial free energy with 2235 and 2048 particles for liquid and solid respectively. Initially, the free energy difference between two liquid phase of germanium has been computed by thermodynamic integration method along a Reversible Path at zero pressure and different temperature values. The melting temperature for SW potential model of germanium is obtained as T m ≈ 1360 K . Further, the cleaving wall method was used to compute the liquid–solid interfacial free energy for high density liquid to low density liquid phase transition with SW-Ge potential model. This liquid–solid interfacial free energy has been computed below the melting temperature or at liquid–liquid transition temperature as T l l = 1312 K . This computational study has been performed for understanding the phase behavior and crystal growth of SW-Ge potential model at or near the transition temperature. The results shown here are consistent with the experimental and computational literature values of interfacial free energy for germanium.