A geometric recognition algorithm was developed to identify molecular surface complementarity. It is based on a purely geometric approach and takes advantage of techniques applied in the field ofpattern recognition. The algorithm involves an automated procedure including (i) a digital representation of the molecules (derived from atomic coordinates) by three-dimensional discrete functions that distinguishes between the surface and the interior; (ii) the calculation, using Fourier transformation, of a correlation function that assesses the degree of molecular surface overlap and penetration upon relative shifts of the molecules in three dimensions; and (iii) a scan of the relative orientations of the molecules in three dimensions. The algorithm provides a list of correlation values indicating the extent of geometric match between the surfaces of the molecules; each of these values is associated with six numbers describing the relative position (translation and rotation) of the molecules. The procedure is thus equivalent to a six-dimensional search but much faster by design, and the computation time is only moderately dependent on molecular size. The procedure was tested and validated by using five known complexes for which the correct relative position of the molecules in the respective adducts was successfully predicted. The molecular pairs were deoxyhemoglobin and methemoglobin, tRNA synthetase-tyrosinyl adenylate, aspartic proteinase-peptide inhibitor, and trypsin-trypsin inhibitor. A more realistic test was performed with the last two pairs by using the structures of uncomplexed aspartic proteinase and trypsin inhibitor, respectively. The results are indicative of the extent of conformational changes in the molecules tolerated by the algorithm.The association of proteins with their ligands involves intricate inter-and intramolecular interactions, solvation effects, and conformational changes. In view of such complexity, a comprehensive and efficient approach for predicting the formation of protein-ligand complexes from the structure of their free components is not yet available. However, with some assumptions, such predictions become feasible, and several attempts based on energy minimization have been partially successful (1-6). Another simplifying approach that could alleviate some of these difficulties is based on geometric considerations.The three-dimensional (3D) structures of most protein complexes reveal a close geometric match between those parts of the respective surfaces of the protein and the ligand that are in contact. Indeed, the shape and other physical characteristics of the surfaces largely determine the nature of the specific molecular interactions in the complex. Furthermore, in many cases the 3D structure of the components in the complex closely resembles that of the molecules in their free, native state. Geometric matching thus seems to play an important role in determining the structure of a complex.Several investigators have exploited a geometric approach to find shape complement...

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[aps,prl,twocolumn,showpacs,groupaddress]We experimentally demonstrate two-photon absorption (TPA) with broadband down-converted light (squeezed vacuum). Although incoherent and exhibiting the statistics of a thermal noise, broadband downconverted light can induce TPA with the same sharp temporal behavior as femtosecond pulses, while exhibiting the high spectral resolution of the narrowband pump laser. Using pulse-shaping methods, we coherently control TPA in Rubidium, demonstrating spectral and temporal resolutions that are 3-5 orders of magnitude below the actual bandwidth and temporal duration of the light itself. Such properties can be exploited in various applications such as spread-spectrum optical communications, tomography and nonlinear microscopy.

Geometric frustration, the inability of an ordered system to find a unique ground state plays a key role in a wide range of systems. We present a new experimental approach to observe large-scale geometric frustration with 1500 negatively coupled lasers arranged in a kagome lattice. We show how dissipation drives the lasers into a phase-locked state that directly maps to the classical XY spin Hamiltonian ground state. In our system, frustration is manifested by the lack of long range phase ordering. Finally, we show how next-nearest-neighbor coupling removes frustration and restores order.

We experimentally demonstrate shaping of the two-photon wave function of entangled-photon pairs, utilizing coherent pulse-shaping techniques. By performing spectral-phase manipulations we tailor the second-order correlation function of the photons exactly like a coherent ultrashort pulse. To observe the shaping we perform sum-frequency generation with an ultrahigh flux of entangled photons. At the appropriate conditions, sum-frequency generation performs as a coincidence detector with an ultrashort response time (approximately 100 fs), enabling a direct observation of the two-photon wave function. This property also enables us to demonstrate background-free, high-visibility two-photon interference oscillations.