110 research outputs found
Not gate in a cis-trans photoisomerization model
We numerically study the implementation of a NOT gate by laser pulses in a
model molecular system presenting two electronic surfaces coupled by non
adiabatic interactions. The two states of the bit are the fundamental states of
the cis-trans isomers of the molecule. The gate is classical in the sense that
it involves a one-qubit flip so that the encoding of the outputs is based on
population analysis which does not take the phases into account. This gate can
also be viewed as a double photo-switch process with the property that the same
electric field controls the two isomerizations. As an example, we consider
one-dimensional cuts in a model of the retinal in rhodopsin already proposed in
the literature. The laser pulses are computed by the Multi Target Optimal
Control Theory with chirped pulses as trial fields. Very high fidelities are
obtained. We also examine the stability of the control when the system is
coupled to a bath of oscillators modelled by an Ohmic spectral density. The
bath correlation time scale being smaller than the pulse duration the dynamics
is carried out in the Markovian approximation.Comment: 29 pages, 7 figure
Performance of ab initio and density functional methods for conformational equilibria of CnH2n+2 alkane isomers (n=2-8)
Conformational energies of n-butane, n-pentane, and n-hexane have been
calculated at the CCSD(T) level and at or near the basis set limit.
Post-CCSD(T) contribution were considered and found to be unimportant. The data
thus obtained were used to assess the performance of a variety of density
functional methods. Double-hybrid functionals like B2GP-PLYP and B2K-PLYP,
especially with a small Grimme-type empirical dispersion correction, are
capable of rendering conformational energies of CCSD(T) quality. These were
then used as a `secondary standard' for a larger sample of alkanes, including
isopentane and the branched hexanes as well as key isomers of heptane and
octane. Popular DFT functionals like B3LYP, B3PW91, BLYP, PBE, and PBE0 tend to
overestimate conformer energies without dispersion correction, while the M06
family severely underestimates GG interaction energies. Grimme-type dispersion
corrections for these overcorrect and lead to qualitatively wrong conformer
orderings. All of these functionals also exhibit deficiencies in the conformer
geometries, particularly the backbone torsion angles. The PW6B95 and, to a
lesser extent, BMK functionals are relatively free of these deficiencies.
Performance of these methods is further investigated to derive conformer
ensemble corrections to the enthalpy function, , and the Gibbs
energy function, , of these alkanes. While
is only moderately sensitive to the level of theory, exhibits more pronounced sensitivity. Once again, double hybrids
acquit themselves very well.Comment: J. Phys. Chem. A, revised [Walter Thiel festschrift
Target highlights in CASP14 : Analysis of models by structure providers
Abstract The biological and functional significance of selected CASP14 targets are described by the authors of the structures. The authors highlight the most relevant features of the target proteins and discuss how well these features were reproduced in the respective submitted predictions. The overall ability to predict three-dimensional structures of proteins has improved remarkably in CASP14, and many difficult targets were modelled with impressive accuracy. For the first time in the history of CASP, the experimentalists not only highlighted that computational models can accurately reproduce the most critical structural features observed in their targets, but also envisaged that models could serve as a guidance for further studies of biologically-relevant properties of proteins. This article is protected by copyright. All rights reserved.Peer reviewe
Benchmark thermochemistry of the C_nH_{2n+2} alkane isomers (n=2--8) and performance of DFT and composite ab initio methods for dispersion-driven isomeric equilibria
The thermochemistry of linear and branched alkanes with up to eight carbons
has been reexamined by means of W4, W3.2lite and W1h theories. `Quasi-W4'
atomization energies have been obtained via isodesmic and hypohomodesmotic
reactions. Our best atomization energies at 0 K (in kcal/mol) are: 1220.04
n-butane, 1497.01 n-pentane, 1774.15 n-hexane, 2051.17 n-heptane, 2328.30
n-octane, 1221.73 isobutane, 1498.27 isopentane, 1501.01 neopentane, 1775.22
isohexane, 1774.61 3-methylpentane, 1775.67 diisopropyl, 1777.27 neohexane,
2052.43 isoheptane, 2054.41 neoheptane, 2330.67 isooctane, and 2330.81
hexamethylethane. Our best estimates for are: -30.00
n-butane, -34.84 n-pentane, -39.84 n-hexane, -44.74 n-heptane, -49.71 n-octane,
-32.01 isobutane, -36.49 isopentane, -39.69 neopentane, -41.42 isohexane,
-40.72 3-methylpentane, -42.08 diisopropyl, -43.77 neohexane, -46.43
isoheptane, -48.84 neoheptane, -53.29 isooctane, and -53.68 hexamethylethane.
These are in excellent agreement (typically better than 1 kJ/mol) with the
experimental heats of formation at 298 K obtained from the CCCBDB and/or NIST
Chemistry WebBook databases. However, at 0 K a large discrepancy between theory
and experiment (1.1 kcal/mol) is observed for only neopentane. This deviation
is mainly due to the erroneous heat content function for neopentane used in
calculating the 0 K CCCBDB value. The thermochemistry of these systems,
especially of the larger alkanes, is an extremely difficult test for density
functional methods. A posteriori corrections for dispersion are essential.
Particularly for the atomization energies, the B2GP-PLYP and B2K-PLYP
double-hybrids, and the PW6B95 hybrid-meta GGA clearly outperform other DFT
functionals.Comment: (J. Phys. Chem. A, in press
Undefined cellulase formulations hinder scientific reproducibility
In the shadow of a burgeoning biomass-to-fuels industry, biological conversion of lignocellulose to fermentable sugars in a cost-effective manner is key to the success of second-generation and advanced biofuel production. For the effective comparison of one cellulase preparation to another, cellulase assays are typically carried out with one or more engineered cellulase formulations or natural exoproteomes of known performance serving as positive controls. When these formulations have unknown composition, as is the case with several widely used commercial products, it becomes impossible to compare or reproduce work done today to work done in the future, where, for example, such preparations may not be available. Therefore, being a critical tenet of science publishing, experimental reproducibility is endangered by the continued use of these undisclosed products. We propose the introduction of standard procedures and materials to produce specific and reproducible cellulase formulations. These formulations are to serve as yardsticks to measure improvements and performance of new cellulase formulations
Local control of nonadiabatic photodissociation dynamics using Møller operators
peer reviewe
Vibrational computing: Simulation of a full adder by optimal control
Within the context of vibrational molecular quantum computing, we investigate the implementation of a full addition of two binary digits and a carry that provides the sum and the carry out. Four qubits are necessary and they are encoded into four different normal vibrational modes of a molecule. We choose the bromoacetyl chloride molecule because it possesses four bright infrared active modes. The ground and first excited states of each mode form the one-qubit computational basis set. Two approaches are proposed for the realization of the full addition. In the first one, we optimize a pulse that implements directly the entire addition by a single unitary transformation. In the second one, we decompose the full addition in elementary quantum gates, following a scheme proposed by Vedral [Phys. Rev. A 54, 147 (1996)]. Four elementary quantum gates are necessary, two two-qubit CNOT gates (controlled NOT) and two three-qubit TOFFOLI gates (controlled-controlled NOT). All the logic operations consist in one-qubit flip. The logic implementation is therefore quasiclassical and the readout is based on a population analysis of the vibrational modes that does not take the phases into account. The fields are optimized by the multitarget extension of the optimal control theory involving all the transformations among the 2(4) qubit states. A single cycle of addition without considering the preparation or the measure or copy of the result can be carried out in a very competitive time, on a picosecond time scale. (C) 2008 American Institute of Physics
Controlled full adder or subtractor by vibrational quantum computing
A controlled full addition or subtraction can be realized by a unitary transformation on a register of four qubits. The fourth qubit is then used as a control qubit to enforce the addition or the subtraction of two binary digits and a carry or a borrow. The transformation can be decomposed into six elementary gates. The network differs from the adder network of four elementary gates by including two new controlled-NOT gates. The scheme is general and its implementation using vibrational computing has the advantage that the single global transformation that connects the inputs to the outputs can be driven in one step by a single laser shot. This decreases the time of operation and allows for a better use of the optical resources and for an improvement of the fidelity. The laser pulses are optimized by optimal control theory
Computational investigation and experimental considerations for the classical implementation of a full adder on SO2 by optical pump-probe schemes
Following the scheme recently proposed by Remacle and Levine [Phys. Rev. A 73, 033820 (2006)], we investigate the concrete implementation of a classical full adder on two electronic states ((X) over tilde (1)A(1) and (C) over tilde B-1(2)) of the SO2 molecule by optical pump-probe laser pulses using intuitive and counterintuitive (stimulated Raman adiabatic passage) excitation schemes. The resources needed for providing the inputs and reading out are discussed, as well as the conditions for achieving robustness in both the intuitive and counterintuitive pump-dump sequences. The fidelity of the scheme is analyzed with respect to experimental noise and two kinds of perturbations: The coupling to the neighboring rovibrational states and a finite rotational temperature that leads to a mixture for the initial state. It is shown that the logic processing of a full addition cycle can be realistically experimentally implemented on a picosecond time scale while the readout takes a few nanoseconds. (c) 2008 American Institute of Physics
- …