Biomedical subjects

Thomas F Miller

Publications and source records attributed to Thomas F Miller.

6 recordsLinked to original sources

PubMed2006

Quantum simulation of a hydrated noradrenaline analog with the torsional path integral method.

An extended version of the torsional path integral Monte Carlo (TPIMC) method is presented and shown to be useful for studying the conformation of flexible molecules in solvated clusters. The new technique is applied to the hydrated clusters of the 2-amino-1-phenyl-ethanol (APE) molecule. APE + nH2O clusters with n = 0-4 are studied at 100 and 300 K using both classical and quantum simulations. Only at the lower temperature is the hydration number n found to impact the conformational distribution of the APE molecule. This is shown to be a result of the temperature-dependent balance between the internal energy and entropy contributions to the relative conformer free energies. Furthermore, at 100 K, large quantum effects are observed in the calculated conformer populations. A particularly large quantum shift of 30% of the total population is calculated for the APE + 2H2O cluster, which is explained in terms of the relative zero point energy of the lowest-energy hydrated structures for this cluster. Finally, qualitative agreement is found between the reported calculations and recent spectroscopy experiments on the hydrated clusters of APE, including an entropically driven preference for the formation of AG-type hydrated structures and the formation of a water "droplet" in the APE + 4H2O cluster.

Models, Molecular↗

PubMed2005

Quantum diffusion in liquid water from ring polymer molecular dynamics.

We have used the ring polymer molecular-dynamics method to study the translational and orientational motions in an extended simple point charge model of liquid water under ambient conditions. We find, in agreement with previous studies, that quantum-mechanical effects increase the self-diffusion coefficient D and decrease the relaxation times around the principal axes of the water molecule by a factor of around 1.5. These results are consistent with a simple Stokes-Einstein picture of the molecular motion and suggest that the main effect of the quantum fluctuations is to decrease the viscosity of the liquid by about a third. We then go on to consider the system-size scaling of the calculated self-diffusion coefficient and show that an appropriate extrapolation to the limit of infinite system size increases D by a further factor of around 1.3 over the value obtained from a simulation of a system containing 216 water molecules. These findings are discussed in light of the widespread use of classical molecular-dynamics simulations of this sort of size to model the dynamics of aqueous systems.

Journal Article↗

PubMed2005

Collision-induced conformational changes in glycine.

We present quantum dynamical calculations on the conformational changes of glycine in collisions with the He, Ne, and Ar rare-gas atoms. For two conformer interconversion processes (III-->I and IV-->I), we find that the probability of interconversion is dependent on several factors, including the energy of the collision, the angle at which the colliding atom approaches the glycine molecule, and the strength of the glycine-atom interaction. Furthermore, we show that attractive interactions between the colliding atom and the glycine molecule catalyze conformer interconversion at low collision energies. In previous infrared spectroscopy studies of glycine trapped in rare-gas matrices and helium clusters, conformer III has been consistently observed, but conformer IV has yet to be conclusively detected. Because of the calculated thermodynamic stability of conformer IV, its elusiveness has been attributed to the IV-->I conformer interconversion process. However, our calculations present little indication that IV-->I interconversion occurs more readily than III-->I interconversion. Although we cannot determine whether conformer IV interconverts during experimental Ne- and Ar-matrix depositions, our evidence suggests that the conformer should be present in helium droplets. Anharmonic vibrational frequency calculations illustrate that previous efforts to detect conformer IV may have been hindered by the overlap of its IR-absorption bands with those of other conformers. We propose that the redshifted symmetric -CH(2) stretch of conformer IV provides a means for its conclusive experimental detection.

Journal Article↗

PubMed2005

Quantum diffusion in liquid para-hydrogen from ring-polymer molecular dynamics.

We have used the ring-polymer molecular dynamics method to calculate approximate Kubo-transformed velocity autocorrelation functions and self-diffusion coefficients for low-pressure liquid para-hydrogen at temperatures of 25 and 14 K. The resulting diffusion coefficients are shown to be consistent with experimental shear viscosities and the established finite-size relation D(L) approximately = D(infinity)-2.837k(B)T6pietaL, where k(B) is the Boltzmann constant, T the absolute temperature, eta the shear viscosity, and L the length of the (cubic) simulation cell. The diffusion coefficients D(L) obtained in simulations with finite system sizes are therefore too small. However, the extrapolation to infinite system size corrects this deficiency and leads to excellent agreement with experimental results. This both demonstrates the influence of system-size effects on quantum mechanical diffusion coefficients and provides further evidence that ring-polymer molecular dynamics is an accurate as well as practical way of including quantum effects in condensed phase molecular dynamics.

Journal Article↗

PubMed2005

Comment on "A centroid molecular dynamics study of liquid para hydrogen and ortho deuterium" [J. Chem. Phys. 121, 6412 (2004)].

We show that the two phase points considered in the recent simulations of liquid para hydrogen by Hone and Voth lie in the liquid-vapor coexistence region of a purely classical molecular dynamics simulation. By contrast, their phase point for ortho deuterium was in the one-phase liquid region for both classical and quantum simulations. These observations are used to account for their report that quantum mechanical effects enhance the diffusion in liquid para hydrogen and decrease it in ortho deuterium.(c) 2005 American Institute of Physics.

Comment↗

PubMed2004

Army ants algorithm for rare event sampling of delocalized nonadiabatic transitions by trajectory surface hopping and the estimation of sampling errors by the bootstrap method.

The most widely used algorithm for Monte Carlo sampling of electronic transitions in trajectory surface hopping (TSH) calculations is the so-called anteater algorithm, which is inefficient for sampling low-probability nonadiabatic events. We present a new sampling scheme (called the army ants algorithm) for carrying out TSH calculations that is applicable to systems with any strength of coupling. The army ants algorithm is a form of rare event sampling whose efficiency is controlled by an input parameter. By choosing a suitable value of the input parameter the army ants algorithm can be reduced to the anteater algorithm (which is efficient for strongly coupled cases), and by optimizing the parameter the army ants algorithm may be efficiently applied to systems with low-probability events. To demonstrate the efficiency of the army ants algorithm, we performed atom-diatom scattering calculations on a model system involving weakly coupled electronic states. Fully converged quantum mechanical calculations were performed, and the probabilities for nonadiabatic reaction and nonreactive deexcitation (quenching) were found to be on the order of 10(-8). For such low-probability events the anteater sampling scheme requires a large number of trajectories ( approximately 10(10)) to obtain good statistics and converged semiclassical results. In contrast by using the new army ants algorithm converged results were obtained by running 10(5) trajectories. Furthermore, the results were found to be in excellent agreement with the quantum mechanical results. Sampling errors were estimated using the bootstrap method, which is validated for use with the army ants algorithm.

Journal Article↗