Jeffry D. Madura

Comparison of simple potential functions for simulating liquid water

Classical Monte Carlo simulations have been carried out for liquid water in the NPT ensemble at 25 °C and 1 atm using six of the simpler intermolecular potential functions for the water dimer: Bernal–Fowler (BF), SPC, ST2, TIPS2, TIP3P, and TIP4P. Comparisons are made with experimental thermodynamic and structural data including the recent neutron diffraction results of Thiessen and Narten. The computed densities and potential energies are in reasonable accord with experiment except for the original BF model, which yields an 18% overestimate of the density and poor structural results. The TIPS2 and TIP4P potentials yield oxygen–oxygen partial structure functions in good agreement with the neutron diffraction results. The accord with the experimental OH and HH partial structure functions is poorer; however, the computed results for these functions are similar for all the potential functions. Consequently, the discrepancy may be due to the correction terms needed in processing the neutron data or to an effect uniformly neglected in the computations. Comparisons are also made for self‐diffusion coefficients obtained from molecular dynamics simulations. Overall, the SPC, ST2, TIPS2, and TIP4P models give reasonable structural and thermodynamic descriptions of liquid water and they should be useful in simulations of aqueous solutions. The simplicity of the SPC, TIPS2, and TIP4P functions is also attractive from a computational standpoint.

Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew

A re-parameterization of the standard TIP4P water model for use with Ewald techniques is introduced, providing an overall global improvement in water properties relative to several popular nonpolarizable and polarizable water potentials. Using high precision simulations, and careful application of standard analytical corrections, we show that the new TIP4P-Ew potential has a density maximum at approximately 1 degrees C, and reproduces experimental bulk-densities and the enthalpy of vaporization, DeltaH(vap), from -37.5 to 127 degrees C at 1 atm with an absolute average error of less than 1%. Structural properties are in very good agreement with x-ray scattering intensities at temperatures between 0 and 77 degrees C and dynamical properties such as self-diffusion coefficient are in excellent agreement with experiment. The parameterization approach used can be easily generalized to rehabilitate any water force field using available experimental data over a range of thermodynamic points.

Temperature and size dependence for Monte Carlo simulations of TIP4P water

A series of Monte Carlo simulations has been carried out to characterize the temperature and size dependence of the results for liquid water using the TIP4P potential function. Five temperatures from -25 to 100°C and four system sizes from 64 to 512 molecules have been studied. Comparisons are made with experimental thermodynamic and structural data as well as results of prior simulations.

Atomic force microscopy and molecular modeling of protein and peptide binding to calcite

AbstractOyster shell protein and polyaspartate bound to calcite have been visualized at the atomic and molecular levels by atomic force microscopy. The identities of potential binding sites have been suggested from atomic force microscopy (AFM) images and have been evaluated by molecular modeling. Energies and conformations of binding to (110) and

Family 18 chitinase-oligosaccharide substrate interaction: subsite preference and anomer selectivity of Serratia marcescens chitinase A.

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Dopamine transporter comparative molecular modeling and binding site prediction using the LeuTAa leucine transporter as a template

prism faces, (001) basal calcium planes, and (104) cleavage planes are considered. The interaction with the basal plane is strongest and is essentially irreversible. Binding to

Diffusion-controlled enzymatic reactions

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