Biomedical subjects

J D Doll

Publications and source records attributed to J D Doll.

8 recordsLinked to original sources

PubMed2005

Combining smart darting with parallel tempering using Eckart space: application to Lennard-Jones clusters.

The smart-darting algorithm is a Monte Carlo based simulation method used to overcome quasiergodicity problems associated with disconnected regions of configurations space separated by high energy barriers. As originally implemented, the smart-darting method works well for clusters at low temperatures with the angular momentum restricted to zero and where there are no transitions to permutational isomers. If the rotational motion of the clusters is unrestricted or if permutational isomerization becomes important, the acceptance probability of darting moves in the original implementation of the method becomes vanishingly small. In this work the smart-darting algorithm is combined with the parallel tempering method in a manner where both rotational motion and permutational isomerization events are important. To enable the combination of parallel tempering with smart darting so that the smart-darting moves have a reasonable acceptance probability, the original algorithm is modified by using a restricted space for the smart-darting moves. The restricted space uses a body-fixed coordinate system first introduced by Eckart, and moves in this Eckart space are coupled with local moves in the full 3N-dimensional space. The modified smart-darting method is applied to the calculation of the heat capacity of a seven-atom Lennard-Jones cluster. The smart-darting moves yield significant improvement in the statistical fluctuations of the calculated heat capacity in the region of temperatures where the system isomerizes. When the modified smart-darting algorithm is combined with parallel tempering, the statistical fluctuations of the heat capacity of a seven-atom Lennard-Jones cluster using the combined method are smaller than parallel tempering when used alone.

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PubMed2005

Pressure dependent study of the solid-solid phase change in 38-atom Lennard-Jones cluster.

Phase change phenomena in clusters are often modeled by augmenting physical interaction potentials with an external constraining potential to handle evaporation processes in finite temperature simulations. These external constraining potentials exert a pressure on the cluster. The influence of this constraining pressure on phase change phenomena in 38-atom Lennard-Jones clusters is investigated, and it is demonstrated that modest changes in the parameters of the constraining potential can lead to an order of magnitude change in the constraining pressure. At sufficiently high pressures the solid to solidlike phase change region in the 38-atom Lennard-Jones cluster is completely eliminated.

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PubMed2004

Broken-symmetry unrestricted hybrid density functional calculations on nickel dimer and nickel hydride.

In the present work we investigate the adequacy of broken-symmetry unrestricted density functional theory for constructing the potential energy curve of nickel dimer and nickel hydride, as a model for larger bare and hydrogenated nickel cluster calculations. We use three hybrid functionals: the popular B3LYP, Becke's newest optimized functional Becke98, and the simple FSLYP functional (50% Hartree-Fock and 50% Slater exchange and LYP gradient-corrected correlation functional) with two basis sets: all-electron (AE) Wachters+f basis set and Stuttgart RSC effective core potential (ECP) and basis set. We find that, overall, the best agreement with experiment, comparable to that of the high-level CASPT2, is obtained with B3LYP/AE, closely followed by Becke98/AE and Becke98/ECP. FSLYP/AE and B3LYP/ECP give slightly worse agreement with experiment, and FSLYP/ECP is the only method among the ones we studied that gives an unacceptably large error, underestimating the dissociation energy of Ni(2) by 28%, and being in the largest disagreement with the experiment and the other theoretical predictions. We also find that for Ni(2), the spin projection for the broken-symmetry unrestricted singlet states changes the ordering of the states, but the splittings are less than 10 meV. All our calculations predict a deltadelta-hole ground state for Ni(2) and delta-hole ground state for NiH. Upon spin projection of the singlet state of Ni(2), almost all of our calculations: Becke98 and FSLYP both AE and ECP and B3LYP/AE predict (1)(d(A)(x(2)-y(2)d(B)(x(2)-y(2)) or (1)(d(A)(xy) (d)(B)(xy)) ground state, which is a mixture of (1)Sigma(g) (+) and (1)Gamma(g). B3LYP/ECP predicts a (3)(d(A)(x(2)-y(2))d(B)(xy) (mixture of (3)Sigma(g) (-) and (3)Gamma(u)) ground state virtually degenerate with the (1)(d(A)(x(2)-y(2)d(B)(x)(2)-y(2)/(1)(d(A)(xy)D(B)(xy) state. The doublet delta-hole ground state of NiH predicted by all our calculations is in agreement with the experimentally predicted (2)Delta ground state. For Ni(2), all our results are consistent with the experimentally predicted ground state of 0(g) (+) (a mixture of (1)Sigma(g) (+) and (3)Sigma(g) (-)) or 0(u) (-) (a mixture of (1)Sigma(u) (-) and (3)Sigma(u) (+)).

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PubMed2004

Taming the rugged landscape: production, reordering, and stabilization of selected cluster inherent structures in the X13-nYn system.

We present studies of the potential energy landscape of selected binary Lennard-Jones 13 atom clusters. The effect of adding selected impurity atoms to a homogeneous cluster is explored. We analyze the energy landscapes of the studied systems using disconnectivity graphs. The required inherent structures and transition states for the construction of disconnectivity graphs are found by combination of conjugate gradient and eigenvector-following methods. We show that it is possible to controllably induce new structures as well as reorder and stabilize existing structures that are characteristic of higher-lying minima. Moreover, it is shown that the selected structures can have experimentally relevant lifetimes.

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PubMed2004

Phase changes in selected Lennard-Jones X13-nYn clusters.

Detailed studies of the thermodynamic properties of selected binary Lennard-Jones clusters of the type X13-nYn (where n=1, 2, 3) are presented. The total energy, heat capacity, and first derivative of the heat capacity as a function of temperature are calculated by using the classical and path integral Monte Carlo methods combined with the parallel tempering technique. A modification in the phase change phenomena from the presence of impurity atoms and quantum effects is investigated.

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PubMed2004

On the encapsulation of nickel clusters by molecular nitrogen.

The structures and energetic effects of molecular nitrogen adsorbates on nickel clusters are investigated using an extended Huckel model coupled with two models of the adsorbate-nickel interaction. The potential parameters for the adsorbates are chosen to mimic experimental information about the binding strength of nitrogen on both cluster and bulk surface phases of nickel. The first model potential is a simple Lennard-Jones interaction that leads to binding sites in holes defined by sets of near-neighbor nickel atoms. The second model potential has a simple three-body form that forces the model nitrogen adsorbates to bind directly to single nickel atoms. Significant rearrangement of the core nickel structures are found in both models. A disconnectivity graph analysis of the potential energy surfaces implies that the rearrangements arise from low transition state barriers and the small differences between available isomers in the nickel core.

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PubMed2003

Random series and discrete path integral methods: The Lévy-Ciesielski implementation.

We perform a thorough analysis of the relationship between discrete and series representation path integral methods, which are the main numerical techniques used in connection with the Feynman-Kaç formula. First, an interpretation of the so-called standard discrete path integral methods is derived by direct discretization of the Feynman-Kaç formula. Second, we consider a particular random series technique based upon the Lévy-Ciesielski representation of the Brownian bridge and analyze its main implementations, namely the primitive, the partial averaging, and the reweighted versions. It is shown that the n=2(k)-1 subsequence of each of these methods can also be interpreted as a discrete path integral method with appropriate short-time approximations. We therefore establish a direct connection between the discrete and the random series approaches. In the end, we give sharp estimates on the rates of convergence of the partial averaging and the reweighted Lévy-Ciesielski random series approach for sufficiently smooth potentials. The asymptotic rates of convergence are found to be O(1/n(2)), in agreement with the rates of convergence of the best standard discrete path integral techniques.

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PubMed1981

Nuclear magnetic resonance studies of cation transport across vesicle bilayer membranes.

We analyze an increasingly popular NMR method analogous to the black lipid membrane (BLM) isotopic tracer experiment for the study of mediated cation transport but involving the preparation of vesicles with an environment asymmetric in that paramagnetic metal ions are present only outside the vesicles. This asymmetry is manifest in the NMR spectrum as two distinct resonances for magnetic nuclei in outside and inside lipid headgroups. As mediated transport begins and for the paramagnetic metal ions enter the vesicles, the inner headgroup resonance line shifts and changes shape with a time course containing much information on the actual ion transport mechanism. Processes by which the ions enter the vesicles one or a few at a time (such as via a diffusive carrier) are easily distinguishable from those by which the ions enter in large bursts (such as by pore activation). The limiting case where intervesicular mediator exchange is slow relative to cation transport (the situation for integral membrane proteins) is treated analytically. Computer simulated curves indicate conditions necessary for certain changes in the line shape which are analogous to the "current jumps" observed in BLM conductance studies. The theory derived allows estimates of the average number of ions entering the first few bursts, how often the bursts occur, and how they depend on the concentration of the mediating species in the vesicular membrane. Preliminary experimental spectra illustrating some of the various possible line shape behaviors are presented.

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