Electronic spectra of guanine in the gas phase and in water were studied by quantum mechanical/molecular mechanical (QM/MM) methods. Geometries for the excited-state calculations were extracted from ground-state molecular dynamics (MD) simulations using the self-consistent-charge density functional tight binding (SCC-DFTB) method for the QM region and the TIP3P force field for the water environ...

Quality computational description of metalloproteins is a great challenge due to the vast span of time- and lengthscales characteristic of their existence. We present an efficient new method that allows for robust characterization of metalloproteins. It combines quantum mechanical (QM) description of the metal-containing active site, and extensive dynamics of the protein captured by discrete mo...

This paper studies numerical integration (or cubature) over the unit sphere S2 ⊂ R3 for functions in arbitrary Sobolev spaces Hs(S2), s > 1. We discuss sequences (Qm(n))n∈N of cubature rules, where (i) the rule Qm(n) uses m(n) points and is assumed to integrate exactly all (spherical) polynomials of degree ≤ n, and (ii) the sequence (Qm(n)) satisfies a certain local regularity property. This lo...

This work explores a new charge-dependent energy model consisting of van der Waals and polarization interactions between the quantum mechanical (QM) and molecular mechanical (MM) regions in a combined QMMM calculation. van der Waals interactions are commonly treated using empirical Lennard-Jones potentials, whose parameters are often chosen based on the QM atom type (e.g., based on hybridizatio...

Detailed molecular dynamics simulations of an acid-base reaction have been the subject of extensive investigations. Here we report the excited state proton transfer dynamics of pyranine (8-hydroxypyrene-1,3,6-trisulfonic acid, HPTS) in acetate buffer by time-resolved fluorescence (TF) and quantum mechanical/effective fragment potential molecular dynamics (QM/EFP-MD) simulations. High time resol...

Developing chemicals that inhibit checkpoint kinase 1 (Chk1) is a promising adjuvant therapeutic to improve the efficacy and selectivity of DNA-targeting agents. Reliable prediction of binding-free energy and binding affinity of Chk1 inhibitors can provide a guide for rational drug design. In this study, multiple docking strategies and Prime/Molecular Mechanics Generalized Born Surface Area (Pr...

In this paper, a framework for the classification of interorganizational business processes is presented. It focuses on workflow technology which is used to implement intercompany quality management (QM). The workflow management system (WMS) is embedded in an enterprise resource planning (ERP) system. The framework consists of six components: the business area(s) concerned, the relevant workflo...

c © 2009 by John von Neumann Institute for Computing Permission to make digital or hard copies of portions of this work for personal or classroom use is granted provided that the copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. To copy otherwise requires prior specific permission by the publisher ment...

c © 2007 by John von Neumann Institute for Computing Permission to make digital or hard copies of portions of this work for personal or classroom use is granted provided that the copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. To copy otherwise requires prior specific permission by the publisher ment...

Recently, from the deduction of result MIP* = RE in quantum computation, it was obtained that Quantum Field Theory (QFT) allows for different forms computation computers Mechanics (QM) does not allow. Thus, there must exist QFT representation Universe QM We explain a simple manner how by describing differences between and QM, obtain why future will require use QFT.