Search results for "PERTURBATION"
showing 10 items of 811 documents
Toward the understanding of DNA fluorescence: The singlet excimer of cytosine
2006
By using the multiconfigurational second-order perturbation method CASPT2, including corrections for the basis set superposition error, the lowest-singlet excited state of the face-to-face π-stacked cytosine homodimer is revealed to be bound by about half an eV, being the source of an emissive feature consistent with the observed redshifted fluorescence. Gloria.Olaso@uv.es Daniel.Roca@uv.es Luis.Serrano@uv.es Manuela.Merchan@uv.es
On the absorbance changes in the photocycle of the photoactive yellow protein: A quantum-chemical analysis
2001
Spectral changes in the photocycle of the photoactive yellow protein (PYP) are investigated by using ab initio multiconfigurational second-order perturbation theory at the available structures experimentally determined. Using the dark ground-state crystal structure [Genick, U. K., Soltis, S. M., Kuhn, P., Canestrelli, I. L. & Getzoff, E. D. (1998) Nature (London) 392, 206–209], the ππ* transition to the lowest excited state is related to the typical blue-light absorption observed at 446 nm. The different nature of the second excited state ( n π*) is consistent with the alternative route detected at 395-nm excitation. The results suggest the low-temperature photoproduct PYP HL as the mo…
Peptide Bond Formation Mechanism Catalyzed by Ribosome
2015
In this paper we present a study of the peptide bond formation reaction catalyzed by ribosome. Different mechanistic proposals have been explored by means of Free Energy Perturbation methods within hybrid QM/MM potentials, where the chemical system has been described by the M06-2X functional and the environment by means of the AMBER force field. According to our results, the most favorable mechanism in the ribosome would proceed through an eight-membered ring transition state, involving a proton shuttle mechanism through the hydroxyl group of the sugar and a water molecule. This transition state is similar to that described for the reaction in solution (J. Am. Chem. Soc. 2013, 135, 8708–871…
On the theoretical determination of the electron affinity of ozone
1993
Multiconfigurational electron correlation methods have been analyzed in order to theoretically compute the electron affinity (EA) of ozone. The near-degeneracy correlation effects, which are so important in O3 and O 3 − , have been described using complete active space (CAS) SCF wave functions. Remaining dynamic correlation effects are computed using second-order perturbation theory (the CASPT2 method). The best calculated adiabatic value (including zero-point energy corrections), 2.19 eV, is about 0.09 eV larger than the experimental value. Comparative studies using size-consistent coupled pair functional approaches (CPF and ACPF) have also been performed. The harmonic frequencies in O 3 −…
Suitability ofMMGBSAfor the selection of correct ligand binding modes from docking results
2018
The estimation of the correct binding mode and affinity of a ligand into a target protein using computational methods is challenging. However, docking can introduce poses from which the correct binding mode could be identified using other methods. Here, we analyzed the reliability of binding energy estimation using the molecular mechanics-generalized Born surface area (MMGBSA) method without and with energy minimization to identify the likely ligand binding modes within docking results. MMGBSA workflow (a) outperformed docking in recognizing the correct binding modes of androgen receptor ligands and (b) improved the correlation coefficient of computational and experimental results of rescor…
Principal part of multi-parameter displacement functions
2012
This paper deals with a perturbation problem from a period annulus, for an analytic Hamiltonian system [J.-P. Françoise, Ergodic Theory Dynam. Systems 16 (1996), no. 1, 87–96 ; L. Gavrilov, Ann. Fac. Sci. Toulouse Math. (6) 14(2005), no. 4, 663–682. The authors consider the planar polynomial multi-parameter deformations and determine the coefficients in the expansion of the displacement function generated on a transversal section to the period annulus. Their first result gives a generalization to the Françoise algorithm for a one-parameter family, following [J.-P. Françoise and M. Pelletier, J. Dyn. Control Syst. 12 (2006), no. 3, 357–369. The second result expresses the principal terms in …
The multi-state CASPT2 method
1998
Abstract An extension of the multiconfigurational second-order perturbation approach CASPT2 is suggested, where several electronic states are coupled at second order via an effective-Hamiltonian approach. The method has been implemented into the MOLCAS-4 program system, where it will replace the single-state CASPT2 program. The accuracy of the method is illustrated through calculations of the ionic-neutral avoided crossing in the potential curves for LiF and of the valence-Rydberg mixing in the V-state of the ethylene molecule.
Superconvergent Perturbation Theory, KAM Theorem (Introduction)
2001
Here we are dealing with an especially fast converging perturbation series, which is of particular importance for the proof of the KAM theorem (cf. below).
KAM Techniques for Time Dependent Quantum Systems
1995
We consider a spin 1/2 in constant magnetic field perturbed by a quasiperiodic time dependent magnetic field. We discuss its stability properties in terms of the spectrum of the corresponding quasienergy operator. Since the spectrum of the unperturbed problem is dense, there appear small denominators in the perturbation theory, corresponding to resonances. They are treated with a technique developped by L.H. Eliasson, based on a KAM iteration.
Robust regulation with an H<inf>&#x221E;</inf> constrain for linear two-time scale systems
2010
In this paper, the problem of robust multi-objective control design with an H ∞ constrain is studied for a class of linear two-time scale systems. The design is based on a new modelling approach under the assumption of norm-boundedness of the fast dynamics. In this method, a portion of the fast dynamics is treated as a norm-bounded perturbation in the design by its maximum possible gain. In this view, the problem of robust multi-objective control design is performed only for the certain dynamics of the two-time scale system, whose order is less than that of the original system. One illustrative example is used to demonstrate the validity of the proposed approach.