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331.
Bucher D Pierce LC McCammon JA Markwick PR 《Journal of chemical theory and computation》2011,7(4):890-897
We have implemented the accelerated molecular dynamics approach (Hamelberg, D.; Mongan, J.; McCammon, J. A. J. Chem. Phys. 2004, 120 (24), 11919) in the framework of ab initio MD (AIMD). Using three simple examples, we demonstrate that accelerated AIMD (A-AIMD) can be used to accelerate solvent relaxation in AIMD simulations and facilitate the detection of reaction coordinates: (i) We show, for one cyclohexane molecule in the gas phase, that the method can be used to accelerate the rate of the chair-to-chair interconversion by a factor of ~1 × 10(5), while allowing for the reconstruction of the correct canonical distribution of low-energy states; (ii) We then show, for a water box of 64 H(2)O molecules, that A-AIMD can also be used in the condensed phase to accelerate the sampling of water conformations, without affecting the structural properties of the solvent; and (iii) The method is then used to compute the potential of mean force (PMF) for the dissociation of Na-Cl in water, accelerating the convergence by a factor of ~3-4 compared to conventional AIMD simulations.(2) These results suggest that A-AIMD is a useful addition to existing methods for enhanced conformational and phase-space sampling in solution. While the method does not make the use of collective variables superfluous, it also does not require the user to define a set of collective variables that can capture all the low-energy minima on the potential energy surface. This property may prove very useful when dealing with highly complex multidimensional systems that require a quantum mechanical treatment. 相似文献
332.
The percent composition of blends of biodiesel and conventional diesel from a variety of retail sources were modeled and predicted using partial least squares (PLS) analysis applied to gas chromatography-total-ion-current mass spectrometry (GC-TIC), gas chromatography-mass spectrometry (GC-MS), comprehensive two-dimensional gas chromatography-total-ion-current mass spectrometry (GCxGC-TIC) and comprehensive two-dimensional gas chromatography-mass spectrometry (GCxGC-MS) separations of the blends. In all four cases, the PLS predictions for a test set of chromatograms were plotted versus the actual blend percent composition. The GC-TIC plot produced a best-fit line with slope = 0.773 and y-intercept = 2.89, and the average percent error of prediction was 12.0%. The GC-MS plot produced a best-fit line with slope = 0.864 and y-intercept = 1.72, and the average percent error of prediction was improved to 6.89%. The GCxGC-TIC plot produced a best-fit line with slope = 0.983 and y-intercept = 0.680, and the average percent error was slightly improved to 6.16%. The GCxGC-MS plot produced a best-fit line with slope = 0.980 and y-intercept = 0.620, and the average percent error was 6.12%. The GCxGC models performed best presumably due to the multidimensional advantage of higher dimensional instrumentation providing more chemical selectivity. All the PLS models used 3 latent variables. The chemical components that differentiate the blend percent compositions are reported. 相似文献
333.
N. M. Ercolani K. D. T-R. McLaughlin V. U. Pierce 《Communications in Mathematical Physics》2008,278(1):31-81
In this paper we derive analytic characterizations for and explicit evaluations of the coefficients of the matrix integral
genus expansion. The expansion itself arises from the large N asymptotic expansion of the logarithm of the partition function of N × N Hermitian random matrices. Its g
th
coefficient is a generating function for graphical enumeration on Riemann surfaces of genus g. The case that we particularly consider is for an underlying measure that differs from the Gaussian weight by a single monomial
term of degree 2ν. Our results are based on a hierarchy of recursively solvable differential equations, derived through a
novel continuum limit, whose solutions are the coefficients we want to characterize. These equations are interesting in their
own right in that their form is related to partitions of 2g + 1 and joint probability distributions for conditioned random walks.
K. D. T-R McLaughlin was supported in part by NSF grants DMS-0451495 and DMS-0200749, as well as a NATO Collaborative Linkage
Grant “Orthogonal Polynomials: Theory, Applications, and Generalizations” Ref no. PST.CLG.979738.
N. M. Ercolani and V. U. Pierce were supported in part by NSF grants DMS-0073087 and DMS-0412310. 相似文献