Understanding β-Hairpin Formation by Molecular Dynamics Simulations of Unfolding

AbstractWe have studied the mechanism of formation of a 16-residue β-hairpin from the protein GB1 using molecular dynamics simulations in an aqueous environment. The analysis of unfolding trajectories at high temperatures suggests a refolding pathway consisting of several transient intermediates. The changes in the interaction energies of residues are related with the structural changes during the unfolding of the hairpin. The electrostatic energies of the residues in the turn region are found to be responsible for the transition between the folded state and the hydrophobic core state. The van der Waals interaction energies of the residues in the hydrophobic core reflect the behavior of the radius of gyration of the core region. We have examined the opposing influences of the protein-protein (PP) energy, which favors the native state, and the protein-solvent (PS) energy, which favors unfolding, in the formation of the β-hairpin structure. It is found that the behavior of the electrostatic components of PP and PS energies reflects the structural changes associated with the loss of backbone hydrogen bonding. Relative changes in the PP and PS van der Waals interactions are related with the disruption of the hydrophobic core of a protein. The results of the simulations support the hydrophobic collapse mechanism of β-hairpin folding

Two-qubit quantum gates with minimal pulse sequences

Working with trapped atoms at close distance to each other, we show that one can implement entangling gates based on non-independent qubits using a single pulse per qubit, or a single structured pulse. The optimal parameters depend on approximate solutions of Diophantine equations, causing the fidelity to never be exactly perfect, even under ideal conditions, although the errors can be made arbitrarily smaller at the cost of stronger fields. We fully characterize the mechanism by which the gates operate, and show that the main source of error in realistic implementations comes from fluctuations in the peak intensity, which especially damages the fidelity of the gates that use stronger fields. Working with two-pulse sequences, instead of one, enables the use of a plethora of mechanisms and a broad range of optimal parameters to choose from, to achieve high-fidelity gates.Comment: 10 pages, 7 figure

ChimerDB—a knowledgebase for fusion sequences

Chromosome translocation and gene fusion are frequent events in the human genome and are often the cause of many types of tumor. ChimerDB is the database of fusion sequences encompassing bioinformatics analysis of mRNA and expressed sequence tag (EST) sequences in the GenBank, manual collection of literature data and integration with other known database such as OMIM. Our bioinformatics analysis identifies the fusion transcripts that have non-overlapping alignments at multiple genomic loci. Fusion events at exon–exon borders are selected to filter out the cloning artifacts in cDNA library preparation. The result is classified into two groups—genuine chromosome translocation and fusion between neighboring genes owing to intergenic splicing. We also integrated manually collected literature and OMIM data for chromosome translocation as an aid to assess the validity of each fusion event. The database is available at for human, mouse and rat genomes

Ultrafast coherent control of giant oscillating molecular dipoles in the presence of static electric fields

The following article appeared in Journal of Chemical Physic 139.8 (2013): 084306 and may be found at http://scitation.aip.org/content/aip/journal/jcp/139/8/10.1063/1.4818878We propose a scheme to generate electric dipole moments in homonuclear molecular cations by creating, with an ultrashort pump pulse, a quantum superposition of vibrational states on electronic states strongly perturbed by very strong static electric fields. By field-induced molecular stabilization, the dipoles can reach values as large as 50 Debyes and oscillate on a time-scale comparable to that of the slow vibrational motion. We show that both the electric field and the pump pulse parameters can be used to control the amplitude and period of the oscillation, while preventing the molecule from ionizing or dissociatingThis work was supported by the NRF grant funded by the Korean government (2007-0056343 and 2012M3C1A6035358), the Basic Science Research program funded by MEST (2010-0005143), the Advanced Grant of the European Research Council XCHEM 290853, the European grant MC-RG ATTOTREND, the European COST Actions CM0702 (CUSPFEL) and CM1204 (XLIC), the European ITN CORINF, the MICINN Project Nos. CTQ2012-36184, FIS2010-15127, and CSD 2007-00010 (Spain), and the ERA-Chemistry project PIM2010EEC-0075

Full parallax integral 3d display and image processing techniques

Purpose – Full parallax integral 3D display is one of the promising future displays that provide different perspectives according to viewing direction. In this paper, the authors review the recent integral 3D display and image processing techniques for improving the performance, such as viewing resolution, viewing angle, etc. Design/methodology/approach – Firstly, to improve the viewing resolution of 3D images in the integral imaging display with lenslet array, the authors present 3D integral imaging display with focused mode using the time-multiplexed display. Compared with the original integral imaging with focused mode, the authors use the electrical masks and the corresponding elemental image set. In this system, the authors can generate the resolution-improved 3D images with the n×n pixels from each lenslet by using n×n time-multiplexed display. Secondly, a new image processing technique related to the elemental image generation for 3D scenes is presented. With the information provided by the Kinect device, the array of elemental images for an integral imaging display is generated. Findings – From their first work, the authors improved the resolution of 3D images by using the time-multiplexing technique through the demonstration of the 24 inch integral imaging system. Authors’ method can be applied to a practical application. Next, the proposed method with the Kinect device can gain a competitive advantage over other methods for the capture of integral images of big 3D scenes. The main advantage of fusing the Kinect and the integral imaging concepts is the acquisition speed, and the small amount of handled data. Originality / Value – In this paper, the authors review their recent methods related to integral 3D display and image processing technique

Full-parallax 3D display from stereo-hybrid 3D camera system

In this paper, we propose an innovative approach for the production of the microimages ready to display onto an integral-imaging monitor. Our main contribution is using a stereo-hybrid 3D camera system, which is used for picking up a 3D data pair and composing a denser point cloud. However, there is an intrinsic difficulty in the fact that hybrid sensors have dissimilarities and therefore should be equalized. Handled data facilitate to generating an integral image after projecting computationally the information through a virtual pinhole array. We illustrate this procedure with some imaging experiments that provide microimages with enhanced quality. After projection of such microimages onto the integral-imaging monitor, 3D images are produced with great parallax and viewing angle