Biomedical subjects

Xueyu Song

Publications and source records attributed to Xueyu Song.

8 recordsLinked to original sources

PubMed2006

Crystal-melt interfacial free energies of hard-dumbbell systems.

The crystal-melt interfacial free energies of different crystal orientations and crystal forms for the hard-dumbbell systems have been calculated directly using a multistep thermodynamic perturbation method via nonequilibrium work measurements with a cleaving procedure. We found that for the plastic crystal phase, the interfacial free energies decrease as the reduced bond length L* increases and the anisotropy is very weak as in isotropic systems. On the other hand, for the orientationally ordered crystal phase, the interfacial free energies become more than three times larger and the anisotropy is about 13%. These results may have significant implications for our understanding on the nucleation kinetics in molecular systems and the search of optimal conditions of protein crystallization.

Journal Article↗

PubMed2006

Dynamic solvation in imidazolium-based ionic liquids on short time scales.

Steady-state and time-resolved Stokes shift data for the probe coumarin 153 in two imidazoles, six imidazolium-based ionic liquids, and several other solvents are presented. These results are consistent with our original suggestion (J. Phys. Chem. B 2004, 108, 10245-10255) that initial solvation is dominated by the organic moiety of the ionic liquid, and they show that for the imidazole-based liquids initial solvation is in all cases very rapid. Solvation by methylimidazole and butylimidazole is complete in 100 ps, and all of the imidazolium ionic liquids demonstrate similarly rapid initial solvation. Owing to the importance of determining the amount of initial solvation that is missed in a given experiment with finite time resolution, we discuss a method of estimating the intramolecular contribution to the reorganization energy. This method yields 2068 cm(-1) and is compared with an alternative method.

Journal Article↗

PubMed2006

Fundamental-measure density functional theory study of the crystal-melt interface of the hard sphere system.

Two versions of the fundamental measure density functionals together with a new interfacial density profile parametrization were used to study the hard-sphere crystal-melt interface in the framework of the fundamental measure density functional theory. The equilibrium interfacial density profiles and interfacial free energies were found as a result of minimization of grand canonical potential of system with respect to parameters of density profile. We found that the average interfacial free energy is about 0.78, which is in reasonable agreement with simulation results.

Journal Article↗

PubMed2006

Calculations of crystal-melt interfacial free energies by nonequilibrium work measurements.

We developed a multistep thermodynamic perturbation method to compute the interfacial free energies by nonequilibrium work measurements with cleaving potential procedure. Using this method, we calculated the interfacial free energies of different crystal orientations for the Lennard-Jones system. Our results are in good agreement with the results by thermodynamic integration method. Compared with thermodynamic integration method, the multistep thermodynamic perturbation method is more efficient. For each stage of the cleaving process, only a few thermodynamic perturbation steps are needed, and there is no requirement on the reversibility of the path.

Journal Article↗

PubMed2005

Anisotropic interfacial free energies of the hard-sphere crystal-melt interfaces.

We present a reliable method to define the interfacial particles for determining the crystal-melt interface position, which is the key step for the crystal-melt interfacial free energy calculations using capillary wave approach. Using this method, we have calculated the free energies gamma of the fcc crystal-melt interfaces for the hard-sphere system as a function of crystal orientations by examining the height fluctuations of the interface using Monte Carlo simulations. We find that the average interfacial free energy gamma(0) = 0.62 +/- 0.02k(B)T/sigma(2) and the anisotropy of the interfacial free energies are weak, gamma(100) = 0.64 +/- 0.02, gamma(110) = 0.62 +/- 0.02, gamma(111) = 0.61 +/- 0.02k(B)T/sigma(2). The results are in good agreement with previous simulation results based on the calculations of the reversible work required to create the interfaces (Davidchack and Laird, Phys. Rev. Lett. 2000, 85, 4571). In addition, our results indicate gamma(100) > gamma(110) > gamma(111) for the hard-sphere system, similar to the results of the Lennard-Jones system.

Journal Article↗

PubMed2004

Calculations of free energies in liquid and solid phases: fundamental measure density-functional approach.

In this paper, a theoretical description of the free energies and correlation functions of hard-sphere (HS) liquid and solid phases is developed using fundamental measure density-functional theory. Within the framework of Weeks-Chandler-Andersen perturbation theory, free energies of liquid and solid phases with many interaction potentials can be obtained from these characteristics of the HS system within a single theoretical description. An application to the Lennard-Jones system yields liquid-solid coexistence results in good agreement with the ones from simulations.

Journal Article↗

PubMed2004

The van der Waals interaction between protein molecules in an electrolyte solution.

In this report we present a general formulation to calculate the van der Waals interaction between two protein molecules in an electrolyte solution using boundary element method of solving linearized Poisson-Boltzmann equation. Our formulation is based upon an inhomogeneous dielectric model of proteins at the residue level. Our results for bovine pancreatic trypsin inhibitor at various relative orientations indicate that the anisotropy of the interaction can be tens of kBT.

Binding Sites↗

PubMed2002

Role of anisotropic interactions in protein crystallization.

We have studied a simple model colloidal fluid to assess the role of anisotropic interactions in crystallization process when the interaction potential is short ranged compared with the size of the molecule, which is the case for the effective interaction between protein molecules in aqueous solutions. Using Monte Carlo simulations we have calculated the phase diagrams of soft dumbbell systems with different anisotropic interactions. It is shown that the anisotropic interactions change the phase behavior not only quantitatively but also qualitatively. By exploiting the anisotropic interactions in the crystallization process additional avenues for the search of optimal crystallization conditions are discussed.

Anisotropy↗