[The structure of working energy expenditure and optimal environmental temperature].
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Adult↗
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Results for “energy optimization”
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[Means of optimizing conversion of light energy in the primary stages of photosynthesis. I. The need for optimizing the structure of a photosynthetic unit and calculation of its efficiency].
It is shown, that the photosynthetic unit structure is to be strongly optimized in vivo to operate with a 90% quantum yield of primary charge separation in reaction centers, which means that a macroscopic photosynthetic unit is neither uniform nor isotropic. Some requirements for optimization of photosynthetic unit structure are determined. The modified probability matrix method to simulate the excitation energy transfer in photosynthesis is proposed. The method is adapted to excitation trapping time (but not to excitation jumps number) calculation. The calculations assume a Förster inductive resonance mechanism for energy transfer within light-harvesting antenna and pairwise dipolar interactions.
Light↗
Optimization of the low energy electron point source microscope: imaging of macromolecules.
Optimal conditions for low energy electron point source microscopy are investigated by the simulation and numerical reconstruction of holograms of phthalocyaninato polysiloxane, PcPS, a rod-like macromolecule. The effects of the electron energy, width of the electron beam and the detector size on the spatial resolution in the reconstructed images are modeled. We find that for electron energies around 200eV, with the specimen 0.1 microm from the source, a screen recording the image in a cone of at least 15 degrees half angle (7 cm lateral dimension at 10 cm from the source) with at least 512 x 512 pixel and 8-bit resolution will result in near atomic resolution.
Journal Article↗
Optimization of hemodynamic energy expenditure in the arterial system.
Experimental evaluations and comparisons of the passive and active biomechanical properties of isolated blood vessels from different species (dog, pig, calf, human), as well as the nature of different arterial pressure oscillations, reveal that: 1) Characteristic impedance of middle-size and large arteries changes with intraluminal mean pressure usually resulting in a U-shaped function with a minimum value around the normal physiological 100 mmHg pressure; 2) Similarly, pressure dependent adrenergic diameter responses (active strain) of different large arteries also exhibit parabolic shape with an extreme (maximum) value at 50-100 mmHg intraluminal pressure, suggesting that biomechanical characteristics of the vessel wall may define an optimum for hemodynamic operations; 3) Changes in the arterial smooth muscle tone shift the characteristic impedance curve along the pressure axis and alter the slopes of the parabola; 4) There are significant interactions between the fast 1st-order (pulsatile) and the slow 3rd-order arterial pressure wave components. These and some other characteristics of the circulatory system suggest the existence of an "extremal" forced oscillation blood pressure control mechanism in the body, optimizing the afterload of heart and the blood perfusion of systemic microvessels by minimizing the pulsatile energy expenditure at the physiological mean pressure operation level. A versatile mathematical model of this hypothetical mechanism was developed by us on an IBM PC using Pascal and 8086 Assembly languages. Simulation experiments show that such a physiological adaptive system could control arterial pressure effectively. The computer model is available on a PC disc.
Animals↗
True stabilization energies for the optimal planar hydrogen-bonded and stacked structures of guanine...cytosine, adenine...thymine, and their 9- and 1-methyl derivatives: complete basis set calculations at the MP2 and CCSD(T) levels and comparison with experiment.
Planar H-bonded and stacked structures of guanine...cytosine (G.C), adenine...thymine (A...T), 9-methylguanine...1-methylcytosine (mG...mC), and 9-methyladenine...1-methylthymine (mA...mT) were optimized at the RI-MP2 level using the TZVPP ([5s3p2d1f/3s2p1d]) basis set. Planar H-bonded structures of G...C, mG...mC, and A...T correspond to the Watson-Crick (WC) arrangement, in contrast to mA...mT for which the Hoogsteen (H) structure is found. Stabilization energies for all structures were determined as the sum of the complete basis set limit of MP2 energies and a (DeltaE(CCSD(T)) - DeltaE(MP2)) correction term evaluated with the cc-pVDZ(0.25,0.15) basis set. The complete basis set limit of MP2 energies was determined by two-point extrapolation using the aug-cc-pVXZ basis sets for X = D and T and X = T and Q. This procedure is required since the convergency of the MP2 interaction energy for the present complexes is rather slow, and it is thus important to include the extrapolation to the complete basis set limit. For the MP2/aug-cc-pVQZ level of theory, stabilization energies for all complexes studied are already very close to the complete basis set limit. The much cheaper D-->T extrapolation provided a complete basis set limit close (by less than 0.7 kcal/mol) to the more accurate T-->Q term, and the D-->T extrapolation can be recommended for evaluation of complete basis set limits of more extended complexes (e.g. larger motifs of DNA). The convergency of the (DeltaE(CCSD(T)) - DeltaE(MP2)) term is known to be faster than that of the MP2 or CCSD(T) correlation energy itself, and the cc-pVDZ(0.25,0.15) basis set provides reasonable values for planar H-bonded as well as stacked structures. Inclusion of the CCSD(T) correction is essential for obtaining reliable relative values for planar H-bonding and stacking interactions; neglecting the CCSD(T) correction results in very considerable errors between 2.5 and 3.4 kcal/mol. Final stabilization energies (kcal/mol) for the base pairs studied are very substantial (A...T WC, 15.4; mA...mT H, 16.3; A...T stacked, 11.6; mA...mT stacked, 13.1; G...C WC, 28.8; mG...mC WC, 28.5; G...C stacked, 16.9; mG...mC stacked, 18.0), much larger than published previously. On the basis of comparison with experimental data, we conclude that our values represent the lower boundary of the true stabilization energies. On the basis of error analysis, we expect the present H-bonding energies to be fairly close to the true values, while stacked energies are still expected to be about 10% too low. The stacking energy for the mG...mC pair is considerably lower than the respective H-bonding energy, but it is larger than the mA...mT H-bonding energy. This conclusion could significantly change the present view on the importance of specific H-bonding interactions and nonspecific stacking interactions in nature, for instance, in DNA. Present stabilization energies for H-bonding and stacking energies represent the most accurate and reliable values and can be considered as new reference data.
Adenine↗
Use of nonlinear programming to optimize performance response to energy density in broiler feed formulation.
A nonlinear programming optimization model was developed to maximize margin over feed cost in broiler feed formulation and is described in this paper. The model identifies the optimal feed mix that maximizes profit margin. Optimum metabolizable energy level and performance were found by using Excel Solver nonlinear programming. Data from an energy density study with broilers were fitted to quadratic equations to express weight gain, feed consumption, and the objective function income over feed cost in terms of energy density. Nutrient:energy ratio constraints were transformed into equivalent linear constraints. National Research Council nutrient requirements and feeding program were used for examining changes in variables. The nonlinear programming feed formulation method was used to illustrate the effects of changes in different variables on the optimum energy density, performance, and profitability and was compared with conventional linear programming. To demonstrate the capabilities of the model, I determined the impact of variation in prices. Prices for broiler, corn, fish meal, and soybean meal were increased and decreased by 25%. Formulations were identical in all other respects. Energy density, margin, and diet cost changed compared with conventional linear programming formulation. This study suggests that nonlinear programming can be more useful than conventional linear programming to optimize performance response to energy density in broiler feed formulation because an energy level does not need to be set.
Animal Feed↗
Optimal Er:YAG laser energy for preventing enamel demineralization.
OBJECTIVES: The purpose of this study was to identify the optimal laser energy range of Er:YAG laser irradiation for laser-induced caries prevention (LICP). METHODS: Twenty-one human non-carious molars were selected. The teeth were covered with nail varnish, except two 4 mm x 1 mm windows on both the buccal and lingual surfaces. The windows were randomly assigned to groups A, B, C and D, receiving no irradiation, 100, 200 and 300 mJ irradiation, respectively. The pulse width 10 pps (pulse per second) with a 1.0 mm spot size was used. After the laser treatment, each tooth was cut into two halves longitudinally. Then a two-day pH-cycling was performed, with an 18-hour demineralization followed by a 6-hour remineralization. Sections of 120 +/- 20 microm in thickness were obtained from each window. Lesion depth was measured using polarized light microscope coupled with an image analysis software. One-way ANOVA and post-hoc Tukey tests were used for evaluation of treatment effects. RESULTS: The laser treatments of 100 and 200 mJ have demonstrated significant protection of enamel demineralization (p = 0.01 and 0.001, respectively), but not the treatment with 300 mJ (p = 0.106). A smaller lesion depth was observed for the 200 mJ group (97.1 microm) than that of the 100 mJ group (105.6 microm). Compared with the control, a lesion reduction of 32.78 and 26.93% for the 200 mJ group and the 100 mJ group were obtained, respectively. CONCLUSION: Caries prevention may be achieved by using Er:YAG laser treatment if the optimal range of laser parameters for LICP can be employed.
Aluminum↗
Signal to noise ratio based filter optimization in triple energy window scatter correction.
Triple energy window (TEW) scatter correction estimates the contribution of scattered photons to the acquisition data by acquiring additional data through two narrow energy windows placed adjoined to the main (photopeak) energy window. The contribution is estimated by linear interpolation and then subtracted. Noise amplification is reduced by filtering both the photopeak scintigram and the scatter estimate. We have studied the filter settings of each filter using a physical phantom filled with a 201Tl-solution resulting in count densities comparable to clinical studies. The performance of order-8 Butterworth filters at different cut-off frequencies (CoFs) were compared based on signal to noise ratios (SNRs). The highest SNRs were obtained when the noisy scatter information was strongly filtered with the CoF less than or equal to 0.07 cycles/pixel (cpp). The best CoF for the filter of the photopeak image is object size dependent; smaller objects require a higher CoF. For objects with a size near the SPECT spatial resolution (approximately 15 mm) the optimal CoF is equal to 0.18 cpp. For larger objects (31.8 mm) the highest SNR was obtained with a CoF equal to 0.13 cpp. A CoF equal to 0.16 cpp is a good compromise for all objects with a diameter equal to the spatial resolution or larger. These results depend on the initial signal to noise ratio of the acquisition data and so on the count density.
Image Processing, Computer-Assisted↗
Modification and optimization of the united-residue (UNRES) potential energy function for canonical simulations. I. Temperature dependence of the effective energy function and tests of the optimization method with single training proteins.
We report the modification and parametrization of the united-residue (UNRES) force field for energy-based protein structure prediction and protein folding simulations. We tested the approach on three training proteins separately: 1E0L (beta), 1GAB (alpha), and 1E0G (alpha + beta). Heretofore, the UNRES force field had been designed and parametrized to locate native-like structures of proteins as global minima of their effective potential energy surfaces, which largely neglected the conformational entropy because decoys composed of only lowest-energy conformations were used to optimize the force field. Recently, we developed a mesoscopic dynamics procedure for UNRES and applied it with success to simulate protein folding pathways. However, the force field turned out to be largely biased toward -helical structures in canonical simulations because the conformational entropy had been neglected in the parametrization. We applied the hierarchical optimization method, developed in our earlier work, to optimize the force field; in this method, the conformational space of a training protein is divided into levels, each corresponding to a certain degree of native-likeness. The levels are ordered according to increasing native-likeness; level 0 corresponds to structures with no native-like elements, and the highest level corresponds to the fully native-like structures. The aim of optimization is to achieve the order of the free energies of levels, decreasing as their native-likeness increases. The procedure is iterative, and decoys of the training protein(s) generated with the energy function parameters of the preceding iteration are used to optimize the force field in a current iteration. We applied the multiplexing replica-exchange molecular dynamics (MREMD) method, recently implemented in UNRES, to generate decoys; with this modification, conformational entropy is taken into account. Moreover, we optimized the free-energy gaps between levels at temperatures corresponding to a predominance of folded or unfolded structures, as well as to structures at the putative folding-transition temperature, changing the sign of the gaps at the transition temperature. This enabled us to obtain force fields characterized by a single peak in the heat capacity at the transition temperature. Furthermore, we introduced temperature dependence to the UNRES force field; this is consistent with the fact that it is a free-energy and not a potential energy function. beta
Biophysics↗
Optimal estimates of free energies from multistate nonequilibrium work data.
We derive the optimal estimates of the free energies of an arbitrary number of thermodynamic states from nonequilibrium work measurements; the work data are collected from forward and reverse switching processes and obey a fluctuation theorem. The maximum likelihood formulation properly reweights all pathways contributing to a free energy difference and is directly applicable to simulations and experiments. We demonstrate dramatic gains in efficiency by combining the analysis with parallel tempering simulations for alchemical mutations of model amino acids.
Amino Acids↗
Self-consistently optimized statistical mechanical energy functions for sequence structure alignment.
A quantitative form of the principle of minimal frustration is used to obtain from a database analysis statistical mechanical energy functions and gap parameters for aligning sequences to three-dimensional structures. The analysis that partially takes into account correlations in the energy landscape improves upon the previous approximations of Goldstein et al. (1994, 1995) (Goldstein R, Luthey-Schulten Z, Wolynes P, 1994, Proceedings of the 27th Hawaii International Conference on System Sciences. Los Alamitos, California: IEEE Computer Society Press. pp 306-315; Goldstein R, Luthey-Schulten Z, Wolynes P, 1995, In: Elber R, ed. New developments in theoretical studies of proteins. Singapore: World Scientific). The energy function allows for ordering of alignments based on the compatibility of a sequence to be in a given structure (i.e., lowest energy) and therefore removes the necessity of using percent identity or similarity as scoring parameters. The alignments produced by the energy function on distant homologues with low percent identity (less than 21%) are generally better than those generated with evolutionary information. The lowest energy alignment generated with the energy function for sequences containing prosite signatures but unknown structures is a structure containing the same prosite signature, providing a check on the robustness of the algorithm. Finally, the energy function can make use of known experimental evidence as constraints within the alignment algorithm to aid in finding the correct structural alignment.
Data Interpretation, Statistical↗
Optimal low-energy laser irradiation causes temporal G2/M arrest on rat calvarial osteoblasts.
Low-energy laser irradiation (LELI) accelerates wound healing and is thought to accelerate bone formation. However, the mechanism of laser healing is not clear. To clarify the biological mechanism of LELI healing, we investigated the effects of LELI on rat osteoblasts in vitro. Osteoblastic cells from 3-day-old Wistar rat calvaria were irradiated using a low-energy gallium-aluminum-arsenide (Ga-Al-As) diode laser. Bone formation, osteoblast differentiation, and cell proliferation were evaluated by von Kossa staining, reverse-transcription polymerase chain reaction, alkaline phosphatase (ALP) staining, 5-bromo-2'-deoxyuridine (BrdU) uptake, and fluorescence-activated cell sorter (FACS) analysis. At 21 days after LELI, the greatest bone formation was observed with irradiation energy of 3.75 J/cm2 and the first week after seeding. LELI (3.75 J/cm2) induced an increased number of cells at day 3. LELI-stimulated differentiation in osteoblastic cells was demonstrated by the increases of Runx2 expression and ALP-positive colonies. By contrast, at 1 day after laser irradiation, the number of cells in the irradiation group was significantly lower than that in the control group. BrdU uptake indicated lower proliferation 12 and 24 hours after irradiation compared with the control. Furthermore, FACS data demonstrated a higher proportion of cells in the G2/M phase of the cell cycle 12 hours after irradiation compared with the control. G2/M arrest was confirmed by the appearance of G2/M arrest marker 14-3-3-sigma or phospho-p53. These results demonstrate that LELI induces not only acceleration of bone formation but also initial G2/M arrest, which may cause wound healing like tissue repair.
Alkaline Phosphatase↗
Theoretical study of the spin trapping of hydroxyl radical by cyclic nitrones: a density functional theory approach.
The hydroxyl radical (*OH) is an important mediator of biological oxidative stress, and this has stimulated interest in its detection. 5,5-Dimethyl-1-pyrroline N-oxide (DMPO) and its alkoxycarbonyl and alkoxyphosphoryl analogues have been employed as spin traps for electron paramagnetic resonance (EPR) spectroscopic radical detection. Energies of optimized geometries of nitrones and their corresponding *OH adducts were calculated using density functional theory (DFT) at the B3LYP/6-31+G//B3LYP/6-31G level. Calculations predict that the trans adduct formation is favored in alkoxycarbonyl nitrones, while cis adducts with intramolecular H-bonding is favored for alkoxyphosphoryl nitrones. Addition of *OH to a phosphoryl-substituted nitrone is more exoergic than the carbonylated nitrones. Charge and spin densities on the nitrone spin traps were correlated with their rates of addition with *OH, and results show that the charge density on the nitronyl C, the site of *OH addition, is more positive in phosphorylated nitrones compared to DMPO and the alkoxycarbonyl nitrones. The dihedral angle between the beta-H and nitroxyl O bonds is smaller in phosphorylated nitrones, and that aspect appears to account for the longer half-lives of the spin adducts compared to those in DMPO and alkoxycarbonyl nitrones. Structures of nitrones with trifluoromethyl-, trifluoromethylcarbonyl-, methylsulfonyl-, trifluoromethylsulfonyl-, amido-, spiropentyl-, and spiroester substituents were optimized and their energies compared. Amido and spiroester nitrones were predicted to be the most suitable nitrones for spin trapping of *OH due to the similarity of their thermodynamic and electronic properties to those of alkoxyphosphoryl nitrones. Moreover, dimethoxyphosphoryl substitution at C-5 was found to be the most efficient substitution site for spin trapping of *OH, and their spin adducts are predicted to be the most stable of all of the isomeric forms.
Cyclic N-Oxides↗
Potential quasi-energy and energetically optimal size in living organisms.
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Animals↗
Global optimization and the energy landscapes of Dzugutov clusters.
The global minima of clusters bound by a Dzugutov potential form non-compact polytetrahedral clusters mainly composed of interpenetrating and face-sharing 13-atom icosahedra. As the size increases, these icosahedral units first form linear arrays, then two-dimensional rings, then three-dimensional networks. Characterization of the energy landscapes of these clusters shows that they are particularly rough and generally exhibit a multiple-funnel topography. These results provide new insights into the structure and dynamics of bulk supercooled Dzugutov liquids and the form of the bulk phase diagram.
Journal Article↗
Thermodynamic optimization of biological energy conversions.
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Adenosine Triphosphate↗
Cooling-rate dependence for the spin-glass ground-state energy: Implications for optimization by simulated annealing.
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Journal Article↗
[Energy optimum and optimal body size in animals].
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Animals↗