Abstract

Design of biomimetic systems is an alternative method of finding biologically active molecules. Peptides incorporating tetrahydrofuran amino acids (TAA) adopt secondary folding patterns and thus mimic natural peptides. The preferred conformation of TAA derived linear and cyclized peptides depends on the stereochemistry of the tetrahydrofuran (THF) ring. Control of stereochemistry of THF ring in the structure of the linear tripeptide Boc-TAA-Leu-Val- OMe containing (2R,5S)-cis TAA, (2S,5R)-cis TAA, (2R,5R)-trans TAA and (2S,5S)-trans TAA is investigated using structural parameters and energetics data obtained from density functional theory (DFT) based calculations at B3LYP/6-31G(d,p) level of theory. We found that the conformations associated with -, -turn structures are stabilized by intramolecular hydrogen bonding interactions. Kinetic control of reactions leading to intra and inter molecular cyclization of tripeptide TAA-Gly-Gly containing (2S,5R)-cis TAA and (2S,5S)-trans TAA is studied at the same level of theory in gas phase.[1] We observe that kinetic control favors cyclodimerization instead of intramolecular cyclization.

Abstract

Cyclic peptides incorporating a 5 membered ring such as furan mimic naturally occurring cyclic peptides[1]. The preferred conformation of linear and cyclic tripeptides incorporating such sugar amino acids depends on the stereochemistry at the chiral center. Control of stereochemistry at C position of amino ethyl furan carboxylic acid (AEFC) unit in the linear and cyclic tripeptides is investigated using structural parameters and energetics data obtained from density functional theory (DFT) based calculations at B3LYP/6-31G(d,p) level of theory. We found that R-isomer of AEFC unit prefers to form bond with its S-isomer. Thermodynamic analysis revealed that linear tripeptide formed by two R-configured isomers of AEFC and one S-configured isomer of AEFC (RRS or RSR linear) is more stable than that formed by three R-configured isomers of AEFC (RRR linear). It is found that the cyclic tripeptide formed by two R-configured isomers of AEFC and one S-configured isomer of AEFC, i. e., cyclic RRS product is formed with high yield than that formed by three R-configured isomers of AEFC (RRR cyclic) though cyclic RRR trimer is more stable than cyclic RRS trimer. This is substantiated by kinetic control of reactions leading to cyclic tripeptides from linear tripeptides. Using NBO analysis stabilizing interactions in all the linear and cyclic tripeptides are identified. Molecular electrostatic potential (MESP) surfaces of cyclic tripeptides provide insights of intramolecular hydrogen bond interactions. The MESP mapped electron density surfaces have shown the charge distribution around the cyclic peptides.

Abstract

Quantum optimal control theory along with time dependent quantum dynamics is used to control the nuclear motion in the hydrogen bonds of adenine-thymine (A-T) DNA base pair [1]. Optimal infrared laser pulses are designed for selective excitations of (a) single N-H


O hydrogen bond and (b) both N-H


O and N-H


N bonds simultaneously. The conjuagte gradient method is employed to optimize the constructed eld dependent grand functional. Optimal laser elds are realized which give more than 99% population transfer to the preselected vibrational states. The mechanism of population transfer during the vibrational excitation process is investigated by projecting the laser driven nuclear wavefunction onto the vibrational states of the system.

Abstract

Conventionally optimal control theory [1, 2, 3] has been used in the theoretical design of laser pulses through the direct variation of the electric field of the laser pulse as a function of time. This often leads to designed laser pulses which contain a broad and seemingly arbitrary frequency structure that varies in time in a manner which may be difficult to realize experimentally. In contrast, in Genetic Algorithm (GA) approach, a few control parameters are used, which are actually available to the experimentalist. In this work, we investigate the possibility of using GA optimization methods in the theoretical design of laser pulses to bring about quantum state transitions in molecules. This allows us to select only a small limited number of parameters to vary and to choose these parameters so that they correspond to those available to the experimentalist. In this work, we apply our methods to the vibrational-rotational excitation of the HF molecule. We choose a small limited number of frequencies and vary only the associated electric field amplitudes and pulse envelopes. We show that laser pulses designed in this way can lead to very high transition probabilities. The mechanism of population transfer during the excitation process is investigated by projecting the laser driven nuclear wave function onto the eigenstates of the system. We have also investigated the possibility of photodissociation of HF molecule by climbing up the vibrational ladder using this genetic algorithm approach.

Abstract

We provide theoretical insights for the observed preference of cyclodimerization over intramolecular cyclization reactions in tetrahydrofuran amino acid using high level DFT quantum chemical methods, in the gas phase as well as in continuum solvent medium. Thermodynamic results obtained from Hessian calculations indicate the higher stability of intermolecularly cyclized dimer over intramolecularly cyclized monomer. NBO and AIM analysis also support the existence of additional stabilizing hydrogen bond interactions in intermolecularly cyclized products. Further justification for the presence of stabilizing interactions in intermolecularly cyclized products comes from the molecular electrostatic potentials and electron density surfaces.

Abstract

Time dependent quantum dynamics and optimal control theory are used for selective vibrational excitation of the N6-H (amino N-H) bond in free adenine and in the adenine-thymine (A-T) base pair. For the N6-H bond in free adenine we have used a one dimensional model while for the hydrogen bond, N6-H (A)...O4(T), present in the A-T base pair, a two mathematical dimensional model is employed. The conjugate gradient method is used for the optimization of the field dependent cost functional. Optimal laser fields are obtained for selective population transfer in both the model systems, which give virtually 100% excitation probability to preselected vibrational levels. The effect of the optimized laser field on the other hydrogen bond, N1(A)...H- N3(T), present in A-T base pair is also investigated.

Abstract

xDNA constitutes a novel class of size expanded synthetic nucleic acids in which one of the bases of the base pairs is larger than the natural DNA bases. These expanded bases are called x-bases. In this paper, we investigate the hydrogen bonding characteristics and relevant molecular properties of model complexes (xAT)Aun, (xTA)Aun, (xGC)Aun, and (xCG)Aun (n = 4, 6, 8) consisting of xDNA base pairs and gold clusters, in order to study the nature of gold-xDNA binding. We offer detailed characterization of their different aspects, viz., structural, electronic and spectroscopic, effect of gold cluster size, aromaticity, and planarity using quantum mechanics based density functional theory (DFT). Significant charge transfer is seen between the gold clusters and x-base pairs. Gold complexation is found to affect the interbase hydrogen bonding in these complexes. In addition to anchor bonds, XHAu type of hydrogen bonding interactions are also found to contribute to the gold-base pair binding in these complexes.

Abstract

In this paper, we present the design and construction of a simple andinexpensive 3D display made up of polygonal elements. We use aper-pixel transformation of image and depth to produce accuratepicture and depth map on an arbitrary planar display facet fromany viewpoint. Though the facets are rendered independently, theimage and depth for rays from the eye-point through the facet pixelsis produced by our method. Thus, there are no artifacts on a facet orat facet boundaries. Our method can be extended to any polygonaldisplay surface as demonstrated using synthetic setups. We alsoshow a real display constructed using off-the-shelf LCD panels andcomputers. The display uses a simple calibration procedure and canbe setup in minutes. Frame-sequential and anaglyphic stereo modescan be supported for any eye-orientation and at high resolutions.

Abstract

Many vision problems map to the minimization of an energyfunction over a discrete MRF. Fast performance is needed if the energyminimization is one step in a control loop. In this paper, we presentthe incrementalα-expansion algorithm for high-performance multilabelMRF optimization on the GPU. Our algorithm utilizes the gridstruc-ture of the MRFs for good parallelism on the GPU. We improve the basicpush-relabel implementation of graph cuts using the atomicoperationsof the GPU and by processing blocks stochastically. We also reuse theflow using reparametrization of the graph from cycle to cycleand itera-tion to iteration for fast performance. We show results on various visionproblems on standard datasets. Our approach takes 950 milliseconds onthe GPU for stereo correspondence on Tsukuba image with 16 labelscompared to 5.4 seconds on the CPU.

Abstract

Graphics Processor Units are used for many general purpose pro-cessing due to high compute power available on them. Regular,data-parallel algorithms map well to the SIMD architecture of cur-rent GPU. Irregular algorithms on discrete structures like graphs areharder to map to them. Efficient data-mapping primitives can playcrucial role in mapping such algorithms onto the GPU. In this paper,we present a minimum spanning tree algorithm on Nvidia GPUsunder CUDA, as a recursive formulation of Bor ̊uvka’s approach forundirected graphs. We implement it using scalable primitives suchas scan, segmented scan and split. The irregular steps of superver-tex formation and recursive graph construction are mapped to prim-itives like split to categories involving vertex ids and edge weights.We obtain30to50times speedup over the CPU implementationon most graphs and3to10times speedup over our previous GPUimplementation. We construct the minimum spanning tree on a5million node and30million edge graph in under1second on onequarter of the Tesla S1070GPU.