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PubMedDate not supplied

Spectral tuning of photoactive yellow protein.

We report a theoretical study on the optical properties of a small, water-soluble photosensory receptor, photoactive yellow protein (PYP). A hierarchical ab initio molecular orbital calculation accurately evaluated the optical absorption maximum of the wild-type, as well as the lambda(max) values of 12 mutants. Electronic excitation of the chromophore directly affects the electronic state of nearby atoms in the protein environment. This effect is explicitly considered in the present study. Furthermore, the spectral tuning mechanism of PYP was investigated at the atomic level. The static disorder of a protein molecule is intimately related to the complex nature of its energy landscape. By using molecular dynamics simulation and quantum mechanical structure optimization, we obtained multiple minimum energy conformations of PYP. The statistical distribution of electronic excitation energies of these minima was compared with the hole-burning experiment (Masciangioli, T. [2000] Photochem. Photobiol. 72, 639), a direct observation of the distribution of excitation energies.

Amino Acid Substitution↗

PubMed1985

Optimal CT settings for bone evaluations.

In CT densitometry the precision, sensitivity and accuracy of the procedure are limited by photon noise, the degree of tissue differentiation and artefacts caused by the finite size of the x-ray beam, hardening of the x-rays and scattered radiation. These artefacts are highly dependent on the CT settings, such as x-ray spectrum and effective energy, intensity of photon flux and collimation of the beam. To monitor the progression of a disease or the efficacy of a therapy, longitudinal studies are necessary; thus the radiation dose per examination should be kept at a minimum. For bone evaluation of the peripheral skeleton it is shown that there is a narrow optimal energy range of 30-40 keV where a dose below 150 mu Sv is sufficient to detect a change of 1% in trabecular bone density at the 0.1 confidence level. Concomitantly accuracy might be better than 1% if adequate beam collimation is applied.

Absorptiometry, Photon↗

PubMed1977

The torsional potential for phosphate diesters. The effect of geometry optimization in CNDO and ab initio molecular orbital calculations.

CNDO and ab initio calculations on the dimethyl phosphate monoanion demonstrate that geometry optimization can dramatically alter the relative energies of the conformational isomers of the phosphate ester. Thus, with geometry optimization (particularly of the diester RO-P-OR bond angle) the energy differences between the gauche-gauche, gauche-trans, and trans-trans conformations is less than 1 kcal/mol rather than approximately 7 kcal/mol previously reported. A torsional energy map for the two ester torsional angles which includes ester bond angle optimization is presented. Ab initio (STO-3G level) and CNDO calculations confirm the strong coupling of the diester RO-P-OR bond angle to the torsional conformation.

Calorimetry↗

PubMed2003

Effects of varying dietary protein and energy levels on the production of lactating dairy cows.

Forty-five multiparous and 18 primiparous Holstein cows were fed three levels of crude protein (CP), each at three levels of neutral detergent fiber (NDF), to identify optimal dietary CP and energy. Cows were blocked by parity and days in milk into seven groups of nine and randomly assigned to an incomplete 9 x 9 Latin square trial with four, 4-wk periods. Diets were formulated from alfalfa and corn silages, high-moisture corn, soybean meal, minerals, and vitamins. Forage was 60% alfalfa and 40% corn silage on all diets; NDF contents of 36, 32, and 28% were obtained by feeding 75, 63, and 50% forage, respectively. Dietary CP contents of 15.1, 16.7, and 18.4% were obtained by replacing high-moisture corn with soybean meal. Production data were from the last 2 wk of each period. Spot fecal and urine samples were collected from 36 cows to estimate N excretion using fecal indigestible acid detergent fiber (ADF) and urinary creatinine as markers. There were no interactions (P > or = 0.08) between dietary CP and NDF for any trait; thus, effects of CP were not confounded by NDF or vice versa. Intake of DM and fat yield were lower on 15.1% CP than at higher CP. There were linear increases in milk urea and urinary N excretion and linear decreases in N efficiency with increasing CP. Increasing CP from 15.1 to 18.4% reduced milk N from 31 to 25% of dietary N, increased urinary N from 23 to 35% of dietary N, and reduced fecal N from 45 to 41% of dietary N. Decreasing NDF gave linear increases in BW gain, yield of milk, protein, true protein, lactose, and SNF, and milk/DM intake and milk N/N intake, and linear decreases in milk urea. However, fat yield was lower on 28% than 32% NDF. Reducing NDF from 36 to 28% increased purine derivative excretion by 19%, suggesting increased microbial protein. Increasing CP by adding soybean meal to diets fed cows averaging 34 kg/d of milk increased intake and fat yield but depressed N efficiency. Increasing dietary energy by reducing forage improved milk yield and efficiency and decreased excretion of environmentally labile urinary N.

Animals↗

PubMed2004

Phycobilisome rod mutants in Synechocystis sp. strain PCC6803.

The phycobilisome is a large pigment-protein assembly that harvests light energy for photosynthesis. This supramolecular complex is composed of two main structures: a core substructure and peripheral rods. Linker polypeptides assemble phycobiliproteins within these structures and optimize light absorption and energy transfer. Mutations have been constructed in three rod-linker-coding genes located in the cpc operon of Synechocystis sp. strain PCC6803. The cpcC1 gene encoding the 33 kDa linker is found to be epistatic to cpcC2 encoding the 30 kDa linker, indicating a specific role for each of these two linkers in rod growth. This corroborates studies on the sequential degradation of phycobilisomes upon nitrogen starvation. Three allelic mutants affecting cpcC2 revealed a polar effect of commonly used cassettes (aphI, aadA) on the operon steady-state transcripts and an effect of rod linker availability on the amount of phycocyanin incorporated in the phycobilisome. This led to the proposal that regulation of rod length could occur through processing of transcripts upstream of the cpcC2 gene.

Bacterial Proteins↗

PubMedDate not supplied

Changes in plasma somatomedin-C in response to ingestion of diets with variable protein and energy content.

We have attempted to determine the relative importance of dietary intake of protein and energy in restoring plasma immunoreactive somatomedin-C (Sm-C) concentrations after fasting. Ten healthy human volunteers were fasted for 5 days, then divided into two refeeding groups. One group (variable energy) was refed 1.0 g protein/kg ideal body weight, and in 9-day sequences, 11, 18 and 25 kcal of energy/kg. The other group (variable protein) was given 35 kcal energy/kg, and in 9-day sequences, 0.2, 0.4, and 1.0 g protein/kg. When subjects were refed the variable energy diets there was no significant increase in Sm-C at 11 kcal/kg (0.47 +/- 0.13 to 0.45 +/- 0.12 U/ml), suggesting that there is a threshold energy requirement below which optimal protein intake is not sufficient to raise the Sm-C. When subjects were refed 18 and 25 kcal/kg, it became apparent that the more energy added to the diet, the greater the absolute concentration of Sm-C attained (0.66 U/ml on 18 kcal/kg and 0.97 U/ml on 25 kcal/kg). Sm-C correlated with nitrogen balance (r = 0.58) during refeeding with the variable energy diets and was a good indicator of acute directional change in nitrogen balance. However, Sm-C was not a reliable indicator of nitrogen repletion, since it rose almost to control levels on the 25 kcal/kg diet while nitrogen balance remained slightly negative.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗

PubMed2005

Zero point energy of polyhedral water clusters.

Polyhedral water clusters (PWCs) are cage-like (H2O)n clusters where every O participates in exactly three H bonds. For a database of 83 PWCs, 8 < or = n < or = 20, geometry was optimized and zero point energy (ZPE) was calculated at the B3LYP/6-311++G** level. ZPE correlates negatively with electronic energy (E0): each increase of 1 kcal/mol in E0 corresponds to a decrease of about 0.11 kcal/mol in ZPE. For each n, a set of four connectivity parameters accounts for 98% or more of the variance in ZPE. Linear regression of ZPE against n and this set gives an RMS error of 0.13 kcal/mol. The contributions to ZPE from stretch modes only (ZPE(S)) and from torsional modes only (ZPE(T)) also correlate strongly with E0 and with each other.

Algorithms↗

PubMed2002

Energy-based reconstruction of a protein backbone from its alpha-carbon trace by a Monte-Carlo method.

An automatic procedure is proposed for reconstruction of a protein backbone from its C(alpha)-trace; it is based on optimization of a simplified energy function of a peptide backbone, given its alpha-carbon trace. The energy is expressed as a sum of the energies of interaction between backbone peptide groups that are not neighbors in the sequence, the energies of local interactions within all amino acid residues, and a harmonic penalty function accounting for the conservation of standard bond angles. The energy of peptide group interactions is calculated using the assumption that each peptide group acts as a point dipole. For local interaction energy, use is made of a two-dimensional Fourier series expansion of the energies of model terminally blocked amino acid residues, calculated with the Empirical Conformational Energy Program for Peptides (ECEPP/3) force field in the angles lambda((1)) and lambda((2)) defining the rotation of peptide groups adjacent to a C(alpha) carbon atom about the corresponding C(alpha) em leader C(alpha) virtual-bond axes. To explore all possible rotations of peptide groups within a fixed C(alpha)-trace, a Monte Carlo search is carried out. The initial lambda angles are calculated by aligning the dipoles of the peptide groups that are close in space, subject to the condition of favorable local interactions. After the Monte Carlo search is accomplished with the simplified energy function, the energy of the structure is minimized with the ECEPP/3 force field, with imposition of distance constraints corresponding to the initial C(alpha)-trace geometry. The procedure was tested on model alpha-helices and beta-sheets, as well as on the crystal structure of the immunoglobulin binding protein (PDB code: 1IGD, an alpha/beta protein). In all cases, complete backbone geometry was reconstructed with a root-mean-square (rms) deviation of 0.5 A from the all-atom target structure.

Algorithms↗

PubMed2006

Cooperativity and the origins of rapid, single-exponential kinetics in protein folding.

The folding of naturally occurring, single-domain proteins is usually well described as a simple, single-exponential process lacking significant trapped states. Here we further explore the hypothesis that the smooth energy landscape this implies, and the rapid kinetics it engenders, arises due to the extraordinary thermodynamic cooperativity of protein folding. Studying Miyazawa-Jernigan lattice polymers, we find that, even under conditions where the folding energy landscape is relatively optimized (designed sequences folding at their temperature of maximum folding rate), the folding of protein-like heteropolymers is accelerated when their thermodynamic cooperativity is enhanced by enhancing the nonadditivity of their energy potentials. At lower temperatures, where kinetic traps presumably play a more significant role in defining folding rates, we observe still greater cooperativity-induced acceleration. Consistent with these observations, we find that the folding kinetics of our computational models more closely approximates single-exponential behavior as their cooperativity approaches optimal levels. These observations suggest that the rapid folding of naturally occurring proteins is, in part, a consequence of their remarkably cooperative folding.

Kinetics↗

PubMed2004

The parameterization and validation of generalized born models using the pairwise descreening approximation.

Generalized Born Surface Area (GBSA) models for water using the Pairwise Descreening Approximation (PDA) have been parameterized by two different methods. The first method, similar to that used in previously reported parameterizations, optimizes all parameters against the experimental free energies of hydration of organic molecules. The second method optimizes the PDA parameters to compensate only for systematic errors of the PDA. The best models are compared to Poisson-Boltzmann calculations and applied to the computation of potentials of mean force (PMFs) for the association of various molecules. PMFs present a more rigorous test of the ability of a solvation model to correctly reproduce the screening of intermolecular interactions by the solvent, than its accuracy at predicting free energies of hydration of small molecules. Models derived with the first method are sometimes shown to fail to compute accurate potentials of mean force because of large errors in the computation of Born radii, while no such difficulties are observed with the second method. Furthermore, accurate computation of the Born radii appears to be more important than good agreement with experimental free energies of solvation. We discuss the source of errors in the potentials of mean force and suggest means to reduce them. Our findings suggest that Generalized Born models that use the Pairwise Descreening Approximation and that are derived solely by unconstrained optimization of parameters against free energies of hydration should be applied to the modeling of intermolecular interactions with caution.

Journal Article↗

PubMed2006

Single-shot dual-energy subtraction mammography with electronic spectrum splitting: feasibility.

We present a single-shot dual-energy subtraction mammography technique using an energy sensitive photon counting detector. An electronic threshold near the middle of the X-ray spectrum discriminates between high- and low-energy photons, and allows the simultaneous acquisition of high- and low-energy images which can be combined to suppress anatomical clutter. By setting the electronic threshold close to 33.2 keV (the k-edge of iodine) the system is optimized for dual-energy contrast-enhanced imaging of breast tumors. This method eliminates the need for separate exposures which might otherwise lead to motion artifacts. The method is illustrated in phantom images.

Artificial Intelligence↗

PubMed2006

Optimization of nano-emulsion preparation by low-energy methods in an ionic surfactant system.

The low-energy emulsification method Emulsion Inversion Point (EIP) was used to prepare O/W nano-emulsions in the W/potassium oleate-oleic acid-C(12)E(10)/hexadecane ionic system. This method had not practically been used in ionic systems up to now. The resulting droplet sizes, much smaller than those obtained with the high-energy emulsification methods, depend on the composition (formulation variables) and preparation variables (addition and mixing rate). Phase diagrams, rheology measurements, and experimental designs applied to nano-emulsion droplet sizes obtained were combined to study the formation of these nano-emulsions. To obtain small droplet sizes, it is necessary to cross a direct cubic liquid crystal phase along the emulsification path, and it is also crucial to remain in this phase long enough to incorporate all of the oil into the liquid crystal. When nano-emulsion forms, the oil is already intimately mixed with all of the components, and it only has to be redistributed. Results show that the smaller droplet sizes are obtained when the liquid crystal zone is wide and extends to high water content, because in this case, during the emulsification process, the system remains long enough in the liquid crystal phase to allow the incorporation of all of the oil. Around the optimal formulation variables, the liquid crystal zone crossed during emulsification is wide enough to incorporate all of the oil whatever mixing or stirring rate is used, and then the resulting droplet size is independent of preparation variables. However, when the composition is far from this optimum, the liquid crystal zone becomes narrower and the mixing of components controls the nano-emulsion formation. High agitation rates and/or low addition rates are required to ensure the dissolution of all of the oil into this phase.

Journal Article↗

PubMed2006

Ab initio potential energy surface and predicted microwave spectra for Ar--OCS dimer and structures of Arn--OCS (n = 2-14) clusters.

An ab initio potential energy surface for the Ar--OCS dimer was calculated using the coupled-cluster singles and doubles with noniterative inclusion of connected triples [CCSD(T)] with a large basis set containing bond functions. The interaction energies were obtained by the supermolecular approach with the full counterpoise correction for the basis set superposition error. The CCSD(T) potential was found to have two minima corresponding to the T-shaped and the collinear Ar--SCO structures. The two-dimensional discrete variable representation method was employed to calculate the rovibrational energy levels for five isotopomers Ar--OCS, Ar--OC34S, Ar--O13CS, Ar--18OCS, and Ar--17OCS. The calculated pure rotational transition frequencies for the vibrational ground state of the five isotopomers are in good agreement with the observed values. The corresponding microwave spectra show that the b-type transitions (Delta Ka = +/-1) are significantly stronger than the a-type transitions (Delta Ka = 0). Minimum-energy structures of the Ar2--OCS trimer were been determined with MP2 optimization, whereas the minimum-energy structures of the Arn--OCS clusters with n = 3-14 were obtained with the pairwise additive potentials. It was found that there are two minima corresponding to one distorted tetrahedral structure and one planar structure for the ternary complex. The 14 nearest neighbor Ar atoms form the first solvation shell around the OCS molecule.

Journal Article↗

PubMed2004

Calculation of exchange-correlation potentials with auxiliary function densities.

The use of Hermite Gaussian auxiliary function densities from the variational fitting of the Coulomb potential for the calculation of exchange-correlation potentials is discussed. The basic working equations for the energy and gradient calculation are derived. The accuracy of this approximation for optimized structure parameters and bond energies are analyzed. It is shown that the quality of the approximation can be systematically improved by enlarging the auxiliary function set. Average errors of 0.5 kcal/mol are obtained with auxiliary function sets including f and g functions. The timings for a series of alkenes demonstrate a substantial performance improvement.

Journal Article↗

PubMed2003

Phase transition and landscape statistics of the number partitioning problem.

The phase transition in the number partitioning problem (NPP), i.e., the transition from a region in the space of control parameters in which almost all instances have many solutions to a region in which almost all instances have no solution, is investigated by examining the energy landscape of this classic optimization problem. This is achieved by coding the information about the minimum energy paths connecting pairs of minima into a tree structure, termed a barrier tree, the leaves and internal nodes of which represent, respectively, the minima and the lowest energy saddles connecting those minima. Here we apply several measures of shape (balance and symmetry) as well as of branch lengths (barrier heights) to the barrier trees that result from the landscape of the NPP, aiming at identifying traces of the easy-hard transition. We find that it is not possible to tell the easy regime from the hard one by visual inspection of the trees or by measuring the barrier heights. Only the difficulty measure, given by the maximum value of the ratio between the barrier height and the energy surplus of local minima, succeeded in detecting traces of the phase transition in the tree. In addition, we show that the barrier trees associated with the NPP are very similar to random trees, contrasting dramatically with trees associated with the p spin-glass and random energy models. We also examine critically a recent conjecture on the equivalence between the NPP and a truncated random energy model.

Journal Article↗

PubMed2004

Energy medicine.

Energy medicine is becoming more frequently used in supporting patients to attain optimal health. The concept of energy medicine as a holistic practice is introduced and its relationship to physical medicine is discussed. In addition, descriptions of energy systems and modalities that are commonly used are also offered.

Complementary Therapies↗

PubMed1988

Transcutaneous bilirubinometry. Effect of irradiation on the skin bilirubin index.

We studied the relation between irradiation and the percent decrease of skin and serum bilirubin during phototherapy. There was a significant positive correlation between the percent decrease of transcutaneous bilirubinometry readings at the sites exposed directly to light (chest) and irradiation (r = 0.593, p less than 0.001, n = 32). A significant positive correlation was also found between the percent decrease of serum bilirubin concentration and irradiation (r = 0.587, p less than 0.001, n = 32), and the percent decrease of skin bilirubin at exposed sites (chest) and the percent decrease of serum bilirubin concentration (r = 0.481, p less than 0.001, n = 32). Thus, light energy quantitatively affects skin and serum bilirubin. In order to determine the optimal effective wavelength and irradiation energy for phototherapy, it is necessary to examine skin bilirubin kinetics in detail during phototherapy.

Bilirubin↗

PubMed2003

A global energy function for the alignment of serially acquired slices.

An accurate, computationally efficient, and fully automated algorithm for the alignment of two-dimensional (2-D) serially acquired sections forming a three-dimensional (3-D) volume is presented. The approach relies on the optimization of a global energy function, based on the object shape, measuring the similarity between a slice and its neighborhood in the 3-D volume. Slice similarity is computed using the distance transform measure in both directions. No particular direction is privileged in the method avoiding global offsets, biases in the estimation and error propagation. The method was evaluated on real images [medical, biological, and other computerized tomography (CT) scanned 3-D data] and the experimental results demonstrated its accuracy as reconstuction errors are less than one degree in rotation and less than one pixel in translation.

Algorithms↗