Theoretical Studies of Dielectric Solvation Dynamics

Using a dynamical Gaussian model of solvation, we have developed a phenomenological theory of solvation dynamics. This theory is applied to compute the solvation dynamics correlation function for solutes in various solvents from timedependent Stokes shift experiments and to compute the peak shift as a function of population period from three-pulse photon-echo experiments. Employing a quantum chemical estimate of the solute\u27s charge distribution, the Pdchards-Lee estimate of its van der Waals surface, and the measured frequency dependent dielectric constant of the pure solvent, we found the calculated results agree closely with those determined by experiments

An Inhomogeneous Model of Protein Dielectric Properties: Intrinsic Polarizabilities of Amino Acids

A simple inhomogeneous model of proteindielectric properties is discussed. A protein in solution is modeled as a collection of polarizable dipoles in a cavity embedded inside a dielectric medium. The intrinsic polarizabilities of 20 amino acids are assumed to be portable to all proteins in nature. A reasonable set of these polarizability values has been obtained by comparing dielectricfluctuations from molecular dynamics simulations with model calculations. The results are consistent within a data set of three small proteins

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

Calculations of the Second Virial Coefficients of Protein Solutions with an Extended Fast Multipole Method

The osmotic second virial coefficients B2 are directly related to the solubility of protein molecules in electrolyte solutions and can be useful to narrow down the search parameter space of protein crystallization conditions. Using a residue level model of protein-protein interaction in electrolyte solutions B2 of bovine pancreatic trypsin inhibitor and lysozyme in various solution conditions such as salt concentration, pH and temperature are calculated using an extended fast multipole method in combination with the boundary element formulation. Overall, the calculated B2 are well correlated with the experimental observations for various solution conditions. In combination with our previous work on the binding affinity calculations it is reasonable to expect that our residue level model can be used as a reliable model to describe protein-protein interaction in solutions

Perturbation theory of solid-liquid interfacial free energies of bcc metals

A perturbation theory is used to calculate bcc solid-liquid interfacial free energies of metallic systems with embedded-atom model potentials. As a reference system for bcc crystals we used a single-occupancy cell, hard-sphere bcc system. Good agreements between the perturbation theory results and the corresponding results from simulations are found. The strategy to extract hard-sphere bcc solid-liquid interfacial free energies may have broader applications for other crystal lattices

Accurate Method to Calculate Liquid and Solid Free Energies for Embedded Atom Potentials

Using a perturbation theory with a hard-sphere reference system we have directly calculated free energies of fluid and solid phases of aluminum with an embedded atom model potential. Unlike other approaches such as thermodynamic integration, we do not require any simulations. Moreover, the free energies of the two different phases are calculated in a single approach, unlike approximations like the quasi-harmonic solid approach. The calculated free energies are with an average relative error 0.55% of the simulation values and the resulting melting temperature is within 5% of the simulation value

The Anisotropic Free Energy of the Lennard-Jones Crystal-Melt Interface

We have calculated the free energy of the crystal-melt interface for the Lennard-Jones system as a function of crystal orientation, near zero pressure, by examining the roughness of the interface using molecular dynamic simulations. The anisotropy is weak, but can be accurately resolved using this approach due to the sensitivity of the fluctuations on the anisotropy. We find that the anisotropy can be described well using two parameters, based upon a low-order expansion satisfying cubic symmetry. The results are in good agreement with previous calculations of the free energies, based upon simulations used to calculate the reversible work required to create the interfaces. The weak anisotropy is also in reasonable agreement: The work here and the work of Davidchack and Laird [R. L. Davidchack and B. B. Laird, J. Chem. Phys. 118, 7651 (2003)] both predict γ100\u3eγ110\u3eγ111. The only discrepancy is that we find a smaller value for the difference γ100−γ111 by an amount larger than the combined error bars

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

The Melting Lines of Model Systems Calculated from Coexistence Simulations

We have performed large-scale molecular dynamics simulations of coexisting solid and liquid phases using 4ε(σ/r)n interactions for n=9 and n=12, and for Lennard-Jones systems, in order to calculate the equilibrium melting curve. The coexisting systems evolve rapidly toward the melting temperature. The P–Tmelting curves agree well with previous calculations, as do the other bulk phase properties. The melting curve for the Lennard-Jones system, evaluated using various truncations of the potential, converges rapidly as a function of the potential cutoff, indicating that long-range corrections to the free energies of the solid and liquid phases very nearly cancel. This approach provides an alternative to traditional methods of calculating melting curves

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