Finite state logic machines can be realized by pump-probe spectroscopic experiments on an isolated molecule. The most elaborate setup, a Turing machine, can be programmed to carry out a specific computation. We argue that a molecule can be similarly programmed, and provide examples using two photon spectroscopies. The states of the molecule serve as the possible states of the head of the Turing machine and the physics of the problem determines the possible instructions of the program. The tape is written in an alphabet that allows the listing of the different pump and probe signals that are applied in a given experiment. Different experiments using the same set of molecular levels correspond to different tapes that can be read and processed by the same head and program. The analogy to a Turing machine is not a mechanical one and is not completely molecular because the tape is not part of the molecular,machine. We therefore also discuss molecular finite state machines, such as sequential devices, for which the tape is not part of the machine. Nonmolecular tapes allow for quite long input sequences with a rich alphabet (at the level of 7 bits) and laser pulse:shaping experiments provide concrete examples. Single molecule spectroscopies show that a single molecule can be repeatedly cycled through a logical operation. (C) 2001 American Institute of Physics.
The number and complexity of genes encoding nuclear lamina proteins has increased during metazoan evolution. Emerging evidence reveals that transcriptional repressors such as the retinoblastoma protein, and apoptotic regulators such as CED-4, have functional and dynamic interactions with the lamina. The discovery that mutations in nuclear lamina proteins cause heritable tissue-specific diseases, including Emery-Dreifuss muscular dystrophy, is prompting a fresh look at the nuclear lamina to devise models that can account for its diverse functions and dynamics, and to understand its enigmatic structure.
Anharmonic vibrational frequencies and intensities are calculated for 1:1 and 2:2 (HCl)(n)(NH(3))(n) and (HCl)(n-)(H(2)O)(n) complexes, employing the correlation-corrected vibrational self-consistent field method with ab initio potential surfaces at the MP2/TZP computational level. In this method, the anharmonic coupling between all vibrational modes is included, which is found to be important for the systems studied. For the 4:4 (HCL)(n)- (H(2)O)(n) complex, the vibrational spectra are calculated at the harmonic level, and anharmonic effects are estimated. Just as the (HCl)(n)(NH(3))(n) Structure switches from hydrogen-bonded to ionic for n = 2, the (HCl)(n)-(H(2)O)(n) switches to ionic structure for n = 4. For (HCl)(2)(H(2)O)2, the lowest energy structure corresponds to the hydrogen-bonded form. However, configurations of the ionic form are separated from this minimum by a barrier of less than an O-H stretching quantum. This suggests the possibility of experiments on ionization dynamics using infrared excitation of the hydrogen-bonded form. The strong cooperative effects on the hydrogen bonding, and concomitant transition to ionic bonding, makes an accurate estimate of the large anharmonicity crucial for understanding the infrared spectra of these systems. The anharmonicity is typically of the order of several hundred wavenumbers for the proton stretching motions involved in hydrogen or ionic bonding, and can also be quite large for the intramolecular modes. In addition, the large cooperative effects in the 2:2 and higher order (HCl)(n)(H(2)O)(n) Complexes may have interesting implications for solvation of hydrogen halides at ice surfaces.
Gbx2 homeobox genes are important for formation and function of the midbrain/hindbrain boundary, namely the isthmic organizer. Two Gbx2 genes were identified in Xenopus laevis, differing in 13 amino acids, including a change in the homeodomain. Xgbx2a is activated earlier during gastrulation and reaches higher levels of expression while Xgbx2b is expressed later, at lower levels and has an additional domain in the ventral blood islands. Their overexpression results in microcephalic embryos with shortened axes and defects in brain and notochord formation. Both genes encode functionally homologous proteins, which differ primarily in their temporal and spatial expression patterns.
An extension of the vibrational self-consistent field (VSCF) method is developed for quantitative calculations of molecular vibrational spectroscopy in a crystalline solid environment. The approach is applicable to fields such as matrix-isolation spectroscopy and spectroscopy of molecular crystals. Advantages of the method are that extended solid vibrations and their coupling to intramolecular modes are incorporated, and that the treatment includes anharmonic effects, both due to the intrinsic property of individual modes and due to coupling between modes. Suitable boundary conditions are adopted in treating the solid environment. In applications, e.g., molecules in rare-gas crystals, hundreds of coupled molecular and matrix modes can be handled computationally. The method is applied to the vibrational matrix-shift of iodine in an argon matrix, and the calculated overtone frequencies are compared to experimental values obtained from both time-domain coherent Raman and frequency-domain Resonance Raman measurements. The physical origin of the shifts is interpreted in detail, and the properties of the iodine-argon interactions essential to obtain the correct sign and magnitude of the shift are elucidated. An I-2-Ar potential, based on anisotropic atom-atom interactions and fitted to ab initio calculations, gives the best agreement with experiment. The results show that the VSCF solid-state approach is a powerful tool for matrix spectroscopy. (C) 2001 American Institute of Physics.
Six industry experts comment on the future of information technology (IT) in the aftermath of the terrorist attacks of Sep 11, 2001. The experts are: David Dobrin, of WorldView; John McCarthy, with KPMG; MIT's Yosef Sheffi; Harvard business School professor Joseph Badaracco; David Foote, of Foote Partners; and Bruce Schneier, founder and CTO of Counterpane Internet Security.
Correlated sampling within the shifted contour auxiliary field Monte Carlo method, implemented using plane waves and pseudopotentials, allows computation of electronic forces on nuclei, potential energy differences, geometric and vibrotational spectroscopic constants. This is exemplified on the N2 molecule, where it is demonstrated that it is possible to accurately compute forces, dissociation energies, bond length parameters, and harmonic frequencies.
The shifted-contour auxiliary field Monte Carlo method applied within a plane waves and pseudopotential framework is shown capable of computing accurate molecular deformation barriers. The inversion barrier of water is used as a test case. A method of correlated sampling is extremely useful for deriving highly accurate barriers. The inversion barrier height is determined to be 1.37 eV with a statistical error bar of "0.01 eV. Recent high-level ab initio results are within the error bars. Several theoretical and methodological issues are discussed.
A numerical method is given for affecting nonlinear Schro¨dinger evolution on an initial wave function, applicable to a wide range of problems, such as time-dependent Hartree, Hartree-Fock, density-functional, and Gross-Pitaevskii theories. The method samples the evolving wave function at Chebyshev quadrature points of a given time interval. This achieves an optimal degree of representation. At these sampling points, an implicit equation, representing an integral Schro¨dinger equation, is given for the sampled wave function. Principles and application details are described, and several examples and demonstrations of the method and its numerical evaluation on the Gross-Pitaevskii equation for a Bose-Einstein condensate are shown.
A first-principles calculation of vibrational spectroscopy of HXeH, HXeCl, HXeBr, and HXeOH molecules is performed by combining ab initio codes with the vibrational self-consistent field (VSCF) method, and with its extension by perturbation theory (CC-VSCF). The MP2/CC-VSCF method is anharmonic, and it is able to reproduce the experimentally observed spectral features of HXeH, HXeCl, HXeBr, and HXeOH. The most intense bands of the HXeY molecules, the Xe-H stretching modes, are found to be highly anharmonic. In general, the other fundamental modes presented anharmonic effects to a lesser extent. New predictions of overtone and combination vibrations are made to help experimental investigations of these molecules. It is shown that vibrational spectroscopy calculations are reliable and useful for analyzing the spectral features of rare-gas-containing molecules. While the results of the MP2/CC-VSCF calculations are in much better agreement with experiments than the corresponding harmonic frequencies, substantial discrepancies remain. These are mostly due to the large electronic correlation effects in these systems, which are not sufficiently well presented at the MP2 level.
