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Results for “energy optimization”

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At least 145 records · Page 8Linked to original sources

PubMed1997

[Experimental and clinical studies for laser irradiation to the prostate].

BACKGROUND: The object of the study is to observe the influence of laser on the prostate tissue and to evaluate the efficiency as well as safety. METHODS: Ten canine prostates were irradiated by Nd:YAG laser with a lateral firing fiber. The lasing was carried out either spot or running irradiation on the free beam method. Laser energy was applied for 30, 40 and 60 seconds at 50 watts power output. On the basis of the animal experiments, clinical application was performed in patients with BPH. RESULTS: Immediately after the irradiation, the prostate became swollen by the edema. But the irradiated tissue became necrotic and sloughed resulting in a big cavity of the prostatic urethra by two weeks. The higher the energy density with spot irradiation, the larger the tissue effect as well as the risks. Therefore, it would be important to combine spot with running irradiation for optimal energy density. Clinically, subjective and objective improvements were noted significantly after treatment. CONCLUSION: Thus, the endoscopical laser prostatic therapy proved to be useful and safe from the present fundamental and clinical investigations.

Aged↗

PubMed2004

An ab initio theoretical prediction: an antiaromatic ring pi-dihydrogen bond accompanied by two secondary interactions in a "wheel with a pair of pedals" shaped complex FH . . . C4H4 . . . HF.

By the counterpoise-correlated potential energy surface method (interaction energy optimization), the structure of the pi H-bond complex FH cdots, three dots, centered FH . . . C4H4 . . . HF has been obtained at the second-order Møller-Plesset perturbation theory (MP2/aug-cc-pVDZ) level. Intermolecular interaction energy of the complex is calculated to be -7.8 kcal/mol at the coupled-cluster theory with single, double substitutions and perturbatively linked triple excitations CCSD (T)/aug-cc-pVDZ level. The optimized structure is a "wheel with a pair of pedals" shaped (1mid R:1) structure in which both HF molecules almost lie on either vertical line passing through the middle-point of the C[Double Bond]C bond on either side of the horizontal plane of the C4 ring for cyclobutadiene. In the structure, an antiaromatic ring pi-dihydrogen bond is found, in which the proton acceptor is antiaromatic 4 electron and 4 center pi bond and the donors are both acidic H atoms of HF molecules. In accompanying with the pi-dihydrogen bond, two secondary interactions are exposed. The first is a repulsive interaction between an H atom of HF and a near pair of H atoms of C4H4 ring. The second is the double pi-type H bond between two lone pairs on a F atom and a far pair of H atoms.

Journal Article↗

PubMed2002

Energy estimation in protein design.

The progress achieved by several groups in the field of computational protein design shows that successful design methods include two major features: efficient algorithms to deal with the combinatorial exploration of sequence space and optimal energy functions to rank sequences according to their fitness for the given fold.

Algorithms↗

PubMedDate not supplied

Noninvasive digital energy subtraction angiography with a channeling-radiation x-ray source.

Channeling radiation could provide a viable source for digital energy subtraction angiography (DESA). A signal to noise ratio (SNR) of 6.2 for a resolution of 0.5 mm x 0.5 mm could be achieved using a 6-mA 100-ms 20-MeV electron-beam pulse and a diamond channeling crystal as the x-ray source. This article investigates the choice of a DESA contrast agent and the parameters of a channeling-radiation x-ray source to develop a channeling-radiation DESA imaging system. The production of dual-energy peaks, the maximum available x-ray flux, the advantages of an area exposure, the necessity of a mosaic Bragg-crystal filter to reduce patient dose, the optimal energy separation of the peaks for a quasi-monochromatic x-ray source, and the reduction of the signal from bone are discussed, leading to estimated SNRs and image resolution for a channeling-radiation imaging system. The computer analysis developed to calculate the image quality is also discussed.

Angiography, Digital Subtraction↗

PubMed1993

The ability of the acoustic energy/stone burden ratio to predict gallstone clearance in biliary lithotripsy.

The relationship between acoustic energy, stone burden, and stone clearance in biliary extracorporeal shock wave therapy (ESWL) is unclear. We hypothesized that there is a consistent relationship between these parameters that enables gallstone clearance to be predicted. Using a porcine model and various gallstone burdens, we performed biliary ESWL with varying energy levels and number of shock waves. The acoustic energy/stone burden ratio (AE/SB) was calculated that incorporated these variables. Stone clearance increased with higher energy settings and fewer stones present (p less than 0.005). The relationship between AE/SB ratio and stone clearance was logarithmic (r 2 = 0.82). The plateau of this curve showed optimal stone clearance at approximately 20 joules/g, beyond which point the benefit of further ESWL may not outweigh the risks. This relationship between AE/SB ratio and stone clearance may be able to predict the optimal energy required and probable outcome of biliary ESWL prior to the procedure.

Cholelithiasis↗

PubMed2002

11-cis-retinal protonated Schiff base: influence of the protein environment on the geometry of the rhodopsin chromophore.

Density functional theory (DFT) calculations based on the self-consistent-charge tight-binding approximation have been performed to study the influence of the protein pocket on the 3-dimensional structure of the 11-cis-retinal Schiff base (SB) chromophore. Starting with an effectively planar chromophore embedded in a protein pocket consisting of the 27 next-nearest amino acids, the relaxed chromophore geometry resulting from energy optimization and molecular dynamics (MD) simulations has yielded novel insights with respect to the following questions: (i) The conformation of the beta-ionone ring. The protein pocket tolerates both conformations, 6-s-cis and 6-s-trans, with a total energy difference of 0.7 kcal/mol in favor of the former. Of the two possible 6-s-cis conformations, the one with a negative twist angle (optimized value: -35 degrees ) is strongly favored, by 3.6 kcal/mol, relative to the one in which the dihedral is positive. (ii) Out-of-plane twist of the chromophore. The environment induces a nonplanar helical deformation of the chromophore, with the distortions concentrated in the central region of the chromophore, from C10 to C13. The dihedral angle between the planes formed by the bonds from C7 to C10 and from C13 to C15 is 42 degrees. (iii) The absolute configuration of the chromophore. The dihedral angle about the C12-C13 bond is +170 degrees from planar s-cis, which imparts a positive helicity on the chromophore, in agreement with earlier considerations based on theoretical and spectroscopic evidence.

Animals↗

PubMed1991

The effect of point mutations on energy profiles in a model of the nicotinic acetylcholine receptor (AChR) channel.

Energy profiles are calculated, using energy optimization computations, for a sodium cation in the AChR channel and four of its mutants, alpha E241D, beta E247Q, delta E255Q and alpha E241Q, using the model developed previously. The relative energy location of the calculated profiles confirms and specifies the role of each of the Glu residues found in the anionic ring at the bottom of the MII helices. The structural analysis of the results allows the understanding of the differences observed in the conductances for the wild-type and mutant alpha E241D, or for the mutants beta E247Q and delta E255Q in spite of the identity of the global charge of both channels in each couple. The striking correlation observed between the average relative energy location of the profiles and the conductance data appears to provide confirmation of the essential structural features adopted in the model, in particular the inclusion of the Glu(Gln in gamma)-Lys residues in the alpha-helical stretch of the MII helices and the overall location of the internal residues.

Amino Acid Sequence↗

PubMed2003

Low-temperature orientationally ordered structures of two-dimensional C60.

Orientationally ordered structures of two-dimensional (2D) C(60) at low temperature have been investigated theoretically and experimentally. Using total energy optimization with a phenomenological potential, we find the ground state is a close packed hexagonal lattice in which all the molecules have the same orientation. Several local minima of the potential energy surface are found to be associated with other 1 x 1 lattices as well as 2 x 2 lattices. The energies of the orientational domain boundaries of the 1x1 lattices are also computed, and two kinds of which yield negative values. A majority of these theoretical findings are confirmed by our low-temperature scanning tunneling microscopy study of a 2D C(60) array supported on a self-assembled monolayer.

Journal Article↗

PubMed2003

On the electronic structures of the 1,3-diboracyclobutane-1,3-diyls and their valence isomers with a B2E2 skeleton (E=N, P, As).

The concept of through-space versus through-bond interactions on the stabilization of biradical structures with a singlet or triplet ground state is evaluated for the 1,3-diboracyclobutane-1,3-diyls and related congeners. Singlet biradicals are favored when the intermediate units E feature singlet character (PH(2) (+), AsH(2) (+)), while E fragments with triplet character (NH(2) (+)) induce small energy separations between the lowest singlet and triplet states. These considerations are supported by quantum chemical calculations with energy optimization at 1) MCSCF level plus MR-MP2 correction, 2) MR-MP2 level, and 3) two different types of density functional levels for the planar (D(2h)) geometries. The singlet-triplet energy separations in the planar compounds increase with increasing singlet stability of the corresponding E fragments. In addition to this newly developed principal features for singlet stabilization, which primarily occurs in bonded structures with higher main-group elements, the corresponding valence isomers with bicyclobutane, cyclobutene and cis-butadiene structures are investigated.

Journal Article↗

PubMed1981

Introduction of short-range restrictions in a protein-folding algorithm involving a long-range geometrical restriction and short-, medium-, and long-range interactions.

A protein-folding algorithm, based on short-range and geometrical long-range restrictions, is applied to bovine pancreatic trypsin inhibitor (BPTI). These restrictions are used to define a starting conformation, SI, by means of a space-filling model of the protein, whose energy is then minimized. The long-range restriction is the imposition of the native spatial geometric arrangement of the loops (SGAL) formed by the disulfide bonds. The short-range restrictions are applied as follows: the (varphi, psi) map of each residue is divided into six regions (corresponding to the right- and left-handed alpha-helical, extended, right- and left-handed bridge, and coil states) and the individual residues are placed in the states of the native structure [although not in conformations with the correct values of (varphi, psi)]. Minimization of the energy of SI leads to a structure, SF, with a root-mean-square deviation of 4.4 A from NI, a previously energy-optimized version of the x-ray structure. SF is closer to the native structure than is the structure RF, which was obtained previously by imposing only the correct SGAL as a restriction. The energy of SF is much lower than that of RF but still larger than the energy of NF (the energy-refined x-ray structure).

Journal Article↗

PubMed1987

Theoretical study of potential ion-channels formed by a bundle of alpha-helices: effect of the presence of polar residues along the channel inner wall.

In a channel-forming bundle of five alpha-helices of poly-L-alanine, the replacement of all the alanyl side-chains lining the inner wall by serines is shown, by energy optimization, to produce only small modifications of the packing. The stability of the bundle is larger than that of the pure alanyl package, owing to hydrogen bonding between serine hydroxyls and carbonyl oxygens. The energy profile for sodium as well as the water-channel interactions are favored by the presence of the OH groups and by the lability of the seryl side chains. The possible general significance of the results is suggested.

Energy Transfer↗

PubMed2005

Energy landscapes and solved protein-folding problems.

Energy-landscape theory has led to much progress in protein folding kinetics, protein structure prediction and protein design. Funnel landscapes describe protein folding and binding and explain how protein topology determines kinetics. Landscape-optimized energy functions based on bioinformatic input have been used to correctly predict low-resolution protein structures and also to design novel proteins automatically.

Computer Simulation↗

PubMed2004

Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy.

Unlike other methods for docking ligands to the rigid 3D structure of a known protein receptor, Glide approximates a complete systematic search of the conformational, orientational, and positional space of the docked ligand. In this search, an initial rough positioning and scoring phase that dramatically narrows the search space is followed by torsionally flexible energy optimization on an OPLS-AA nonbonded potential grid for a few hundred surviving candidate poses. The very best candidates are further refined via a Monte Carlo sampling of pose conformation; in some cases, this is crucial to obtaining an accurate docked pose. Selection of the best docked pose uses a model energy function that combines empirical and force-field-based terms. Docking accuracy is assessed by redocking ligands from 282 cocrystallized PDB complexes starting from conformationally optimized ligand geometries that bear no memory of the correctly docked pose. Errors in geometry for the top-ranked pose are less than 1 A in nearly half of the cases and are greater than 2 A in only about one-third of them. Comparisons to published data on rms deviations show that Glide is nearly twice as accurate as GOLD and more than twice as accurate as FlexX for ligands having up to 20 rotatable bonds. Glide is also found to be more accurate than the recently described Surflex method.

Binding Sites↗

PubMed2005

Stability and characterization of perphenazine aerosols generated using the capillary aerosol generator.

Perphenazine (a potent antiemetic) was aerosolized using capillary aerosol generator to generate respirable condensation aerosols from drug in propylene glycol (PG) solutions, by pumping the liquids through a heated capillary tube. The study characterized the stability of perphenazine during and following aerosol generation. The stability-indicating HPLC method (C-8 column with a mobile phase of 52% 0.01 M pH 3.0 acetate buffer+48% acetonitrile) also enabled the study of perphenazine stability in solution under acidic, basic, oxidizing and photolysing conditions. An LC-MS (ESI+) method was used to characterize the degradation products. Perphenazine was found to be stable in acidic and basic conditions, while perphenazine sulfoxide was the major product formed in dilute peroxide solutions. Two photo-degradation products were formed in PG that were tentatively identified by LC-MS; one of these was synthesized and confirmed to be 2-[4-(3-phenothiazin-10-yl-propyl)-piperazino]-ethanol. Both photolysis products showed that aromatic dechlorination had occurred and one appeared to also result from interaction with the solvent. Within an aerosolization energy window of 84-95 J, fine particle aerosols were generated from perphenazine PG formulations with no significant degradation. Small amounts of degradation products were produced in all samples during aerosolization at elevated (non-optimal) energies. These were largely consistent with those seen to result from oxidation and photolysis in solution, showing that oxidation and dehalogenation appeared to be the main degradation pathways followed when the CAG system was overheated.

Aerosols↗

PubMed1996

Refinement of 3D models of horseradish peroxidase isoenzyme C: predictions of 2D NMR assignments and substrate binding sites.

In this study, two alternative three-dimensional (3D) models of horseradish peroxidase (HRP-C)-differing mainly in the structure of a long untemplated insertion-were refined, systematically assessed, and used to make predictions that can both guide and be tested by future experimental studies. A key first step in the model-building process was a procedure for multiple sequence alignment based on structurally conserved regions and key conserved residues, including those side chains providing ligands to the two Ca2+ binding sites. The model refinements reported here include (1) optimization of side-chain conformations; (3) addition of structural waters using a template-independent procedure; (2) structural refinement of the untemplated 34 amino acid insertion located between the F and G helices, using both energy criteria and NMR data; (4) unconstrained energy optimization of the refined models. Using these procedures, two refined structures of HRP-C were obtained, differing mainly in the conformation of this long insertion. The presence of residues in this insertion that could potentially interact with bound substrates suggests a functional role that may be related to the general ability of class III peroxidases to form stable 1:1 complexes with a variety of substrates. The structural validity of the models was systematically assessed by a variety of criteria. Most notably, the ProsaII z scores and Profiles 3D scores of the two HRP-C models indicated that they are significantly better than would be obtained by simple amino acid replacement, using any of the known structures as a template. These two 3D HRP-C models, were then used to predict candidate residues for the assignment of NOESY cross-peaks previously noted in 2D-NMR studies. Specifically, the residues known as Ile X, Phe A, Phe B, aliphatic residue Q, and Ile T. Candidate substrate binding sites were also identified and compared with experimentally based predictions. This work is timely because new X-ray structures are anticipated that will facilitate the validation of these procedures.

Amino Acid Sequence↗

PubMed2006

Theory and characteristics of transition radiation emitted by low-energy storage-ring synchrotrons for use in X-ray lithography.

Existing theory is developed further for description of transition radiation (TR) emitted by low-energy storage-ring synchrotrons. It takes into account the fact that the dielectric constant of the TR target material is a complex function, introduces an expression for the number of passes of an injected electron through the target, and accounts more precisely for the absorption of TR. It is shown that the consideration of the complexity of the dielectric constant results in notable changes of the TR spectrum for emitted photons with energies close to the ionization energies of the target material. Since such TR is used mostly for performing X-ray lithography (XRL), the sensitivity of the photoresist used in XRL is formulated. Maximization of this resist sensitivity can be used for designing optimum targets for XRL. Study of the transmission of TR through a commonly used XRL mask, and its partial absorption in a common photoresist, illustrates that TR emission with E = [490, 1860] eV is most useful for performing such XRL, while E approximately equal to 1 keV is best. It is shown that, for a particular target material, a target consisting of only one foil emits the most TR energy. Optimization of an Al target, based on maximization of the resist sensitivity, indicates that a target containing one Al foil with a thickness of about 200 nm would be best for performing XRL by our low-energy storage-ring synchrotron MIRRORCLE-20SX.

Computer Simulation↗

PubMed2007

Experimental spectral measurements of heavy K-edge filtered beams for x-ray computed mammotomography.

A dual modality computed mammotomography (CmT) and single photon emission computed tomography (SPECT) system for dedicated 3D breast imaging is in development. Using heavy K-edge filtration, the CmT component narrows the energy spectrum of the cone-shaped x-ray beam incident on the patient's pendant, uncompressed breast. This quasi-monochromatic beam is expected to improve discrimination of tissue with similar attenuation coefficients while restraining absorbed dose to below that of dual view mammography. Previous simulation studies showed the optimal energy that maximizes dose efficiency for a 50/50% adipose/glandular breast is between 30 and 40 keV. This study experimentally validates these results using pre-breast and post-breast spectral measurements made under tungsten tube voltages between 40 and 100 kVp using filter materials with K-edge values ranging from 15 to 70 keV. Different filter material thicknesses are used, approximately equivalent to the 200th and 500th attenuating value layer (VL) thickness. Cerium (K = 40.4 keV) filtered post-breast spectra for 8-18 cm breasts are measured for a range of breast compositions. Figures of merit include mean beam energy, spectral full-width at tenth-maximum, beam hardening and dose for the range of breast sizes. Measurements corroborate simulation results, indicating that for a given dose, a 200th VL of cerium filtration may have optimal performance in the dedicated mammotomography paradigm.

Biophysical Phenomena↗

PubMed2004

Identification of protein-protein interaction sites from docking energy landscapes.

Protein recognition is one of the most challenging and intriguing problems in structural biology. Despite all the available structural, sequence and biophysical information about protein-protein complexes, the physico-chemical patterns, if any, that make a protein surface likely to be involved in protein-protein interactions, remain elusive. Here, we apply protein docking simulations and analysis of the interaction energy landscapes to identify protein-protein interaction sites. The new protocol for global docking based on multi-start global energy optimization of an all-atom model of the ligand, with detailed receptor potentials and atomic solvation parameters optimized in a training set of 24 complexes, explores the conformational space around the whole receptor without restrictions. The ensembles of the rigid-body docking solutions generated by the simulations were subsequently used to project the docking energy landscapes onto the protein surfaces. We found that highly populated low-energy regions consistently corresponded to actual binding sites. The procedure was validated on a test set of 21 known protein-protein complexes not used in the training set. As much as 81% of the predicted high-propensity patch residues were located correctly in the native interfaces. This approach can guide the design of mutations on the surfaces of proteins, provide geometrical details of a possible interaction, and help to annotate protein surfaces in structural proteomics.

Binding Sites↗