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Results for “energy optimization”

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PubMed1983

[Nutritional factors in the development of experimental renal failure].

Several experimental studies have shown that the development of glomerular sclerosis during aging in rats is related to nutritional factors: it is impeded by overall food restriction, as well as by reduction of the protein, carbohydrate or sodium intake. It is enhanced by high protein or high sodium diets. In remnant kidneys, lesions develop that are similar to those in aging kidneys and that seem to be influenced by the same factors. Through several experiments, we have shown that the rapidity of the deterioration of renal function after subtotal nephrectomy is closely related to the protein intake and that the length of survival can be reduced by a high protein diet or increased by a low protein diet. The influence of protein intake remains clearly apparent when the intake of all other nutrients, particularly minerals, and of calories is strictly controlled. Low protein diets supplemented with essential amino acids resulting in increased appetite are of little benefit for survival, suggesting that the calorie intake or growth-related factors may be of significance. Prolonged survival observed with phosphorus (P) deficient diets compared to low or normal P diets is mainly due to decreased appetite. The optimal supply of protein, energy, sodium and other nutrients should be determined according, not only to nutritional status, but also to effects on the renal parenchyma.

Aging↗

PubMed1996

Contact versus noncontact diode laser transscleral cyclophotocoagulation in cadaver eyes.

BACKGROUND AND OBJECTIVE: The optimal placement and laser energy levels of a new contact probe with a variable focus used for transscleral diode cyclophotocoagulation were compared with the diode laser noncontact technique. MATERIALS AND METHODS: Fresh cadaver eyes were evaluated by a modified posterior Miyake view using videotape, light microscopy, and scanning electron microscopy. RESULTS: The noncontact diode technique at maximum energy (1.2 J) and contact diode applications at similar energy levels failed to produce obvious gross tissue ciliary body change and mild alterations by histology. Consistent gross, histologic, and scanning electron microscopic damage was noted at 3.0 J or more with the contact probe placed at the surgical limbus and defocused 0.5 to 1.5 mm posteriorly. CONCLUSIONS: This study indicates that the Multilase contact diode laser causes transscleral ciliary body destruction in a cadaver eye model and may have potential clinical usefulness.

Cadaver↗

PubMed1985

Optimization of error-correction processes with respect to time. Comparison to free energy aspects.

Time aspects of selection processes with the possibility of error correction through proofreading branches are studied by mathematical modelling of the kinetics of the reaction network. The methods are similar to those previously developed for free energy aspects. The minimum time delay that is necessary for achieving a certain accuracy level can then be calculated. The main difference to previous results lies in the initial association-dissociation step. In the free energy picture, this shall be essentially equilibrated, but that would yield a too large time delay in the time picture. Characteristic features that are indicative for the optimization strategy of the cell are discussed.

Energy Metabolism↗

PubMed1998

Optimizing potentials for the inverse protein folding problem.

Inverse protein folding, which seeks to identify sequences that fold into a given structure, has been approached by threading candidate sequences onto the structure and scoring them with database-derived potentials. The sequences with the lowest energies are predicted to fold into that structure. It has been argued that the limited success of this type of approach is not due to the discrepancy between the scoring potential and the true potential but is rather due to the fact that sequences choose their lowest-energy structure rather than structures choosing the lowest-energy sequences. Here we develop a non-physical potential scheme optimized for the inverse folding problem. We maximize the average probability of success for a set of lattice proteins to obtain the optimal potential energy function, and show that the potential obtained by our method is more likely to produce successful predictions than the true potential.

Protein Folding↗

PubMed2003

Theoretical studies for structures and energetics of Rgn-N2O (Rg=He, Ne, Ar) clusters.

Minimum-energy structures of the Rg(2)-N(2)O (Rg=He, Ne, Ar) clusters have been determined with ab initio MP2 optimization, whereas the minimum-energy structures of the Rg(n)-N(2)O clusters with n = 3-7 have been obtained with the pairwise additive potentials. Interaction energies and nonadditive three-body effects of the Rg(2)-N(2)O ternary complex have been calculated using supermolecule method at MP4 and CCSD(T) levels. It was found from the calculations that there are two minima corresponding to one distorted tetrahedral structure and one planar structure for the ternary complex. The nonadditive three-body effects were found to be small for Rg(2)-N(2)O complexes. Our calculations also indicated that, for He(n)-N(2)O and Ne(n)-N(2)O clusters, the first six He and Ne atoms form the first solvation ring around the middle nitrogen of the N(2)O monomer, while for Ar(n)-N(2)O, the first five Ar atoms form the first solvation ring.

Journal Article↗

PubMed2006

Comparison of polynomial and neural fuzzy models as applied to the ethanolamine pulping of vine shoots.

The influence of operational variables in the pulping of vine shoots by use of ethanolamine [viz. temperature (155-185 degrees C), cooking time (30-90min) and ethanolamine concentration (50-70% v/v)] on the properties of the resulting pulp (viz. yield, kappa index, viscosity and drainability) was studied. A central composite factorial design was used in conjunction with the software BMDP and ANFIS Edit Matlab 6.5 to develop polynomial and fuzzy neural models that reproduced the experimental results of the dependent variables with errors less than 10%. Both types of models are therefore effective with a view to simulating the ethanolamine pulping process. Based on the proposed equations, the best choice is to use values of the operational valuables resulting in near-optimal pulp properties while saving energy and immobilized capital on industrial facilities by using lower temperatures and shorter processing times. One combination leading to near-optimal properties with reduced costs is using a temperature of 180 degrees C and an ethanolamine concentration of 60% for 60min, to obtain pulp with a viscosity of 6.13% lower than the maximum value (932.8ml/g) and a drainability of 5.49% lower than the maximum value (71 (o)SR).

Conservation of Natural Resources↗

PubMed1998

Penicillin biosynthesis: energy requirement for tripeptide precursor formation by delta-(L-alpha-aminoadipyl)-L-cysteinyl-D-valine synthetase from Acremonium chrysogenum.

In nonribosomal peptide formation by multifunctional enzymes, peptide synthetases catalyze the activation and directed condensation of amino acids. The peptide synthetase involved in penicillin biosynthesis (ACV synthetase) forms the tripeptide delta-(L-alpha-aminoadipyl)-L-cysteinyl-D-valine from the respective L-amino acids and ATP. So far, the energy requirements for the nonribosomal process have not been clearly established. For ACV synthetase we show that ATP consumption depends on the reaction conditions employed. By simultaneously estimating peptide and AMP production by employing fluorescence detection and UV spectroscopy, respectively, we have determined the energy consumption with high accuracy. Under unfavorable reaction conditions more than 20 mol of ATP are consumed/mol of tripeptide formed, while optimal conditions permit the expected energy requirement of one ATP for each carboxyl group activation, corresponding to three ATP for tripeptide formation. The third ATP is required for the activation of L-valine to maintain the valyl-thioester stage for epimerization and peptide bond formation, and this high-energy bond is sacrificed by hydrolytic removal of the product. No extra energy is required for the directed transport in peptide elongation. Additional energy consumed has been traced to hydrolytic loss of activated intermediates, as has been shown by the analysis of incomplete reaction mixtures.

Acremonium↗

PubMed2006

Structural and electronic properties of Si(n), Si(n)-, and PSi(n-1) clusters (2 < or = n < or = 13): Theoretical investigation based on ab initio molecular orbital theory.

The geometric and electronic structures of Si(n), Si(n)-, and PSi(n-1) clusters (2 < or = n < or = 13) have been investigated using the ab initio molecular orbital theory formalism. The hybrid exchange-correlation energy functional (B3LYP) and a standard split-valence basis set with polarization functions (6-31+G(d)) were employed to optimize geometrical configurations. The total energies of the lowest energy isomers thus obtained were recalculated at the MP2/aug-cc-pVTZ level of theory. Unlike positively charged clusters, which showed similar structural behavior as that of neutral clusters [Nigam et al., J. Chem. Phys. 121, 7756 (2004)], significant geometrical changes were observed between Si(n) and Si(n)- clusters for n = 6, 8, 11, and 13. However, the geometries of P substituted silicon clusters show similar growth as that of negatively charged Si(n) clusters with small local distortions. The relative stability as a function of cluster size has been verified based on their binding energies, second difference in energy (Delta2 E), and fragmentation behavior. In general, the average binding energy of Si(n)- clusters is found to be higher than that of Si(n) clusters. For isoelectronic PSi(n-1) clusters, it is found that although for small clusters (n < 4) substitution of P atom improves the binding energy of Si(n) clusters, for larger clusters (n > or = 4) the effect is opposite. The fragmentation behavior of these clusters reveals that while small clusters prefer to evaporate monomer, the larger ones dissociate into two stable clusters of smaller size. The adiabatic electron affinities of Si(n) clusters and vertical detachment energies of Si(n)- clusters were calculated and compared with available experimental results. Finally, a good agreement between experimental and our theoretical results suggests good prediction of the lowest energy isomeric structures for all clusters calculated in the present study.

Journal Article↗

PubMed2005

Considerations and approaches in determining the protein and energy composition of preterm infant formulas.

Optimal early nutritional support is considered a crucial issue in the care of the preterm infant, particularly of those with very low- or extremely low-brithweight. Unfortunately, this goal is seldom satisfactorily attained. Several conditions such as hypoxia, acidosis, patent ductus arteriosus, drug therapy, reduced intestinal motility may interfere with an adequate nutritional delivery in the early neonatal period. Moreover, there is still concern about metabolic and intestinal tolerance of the currently suggested intakes and a lack of uniformity in the nutritional program among different NICUs. Finally, the vast majority of the available preterm formulas are not fully adequate to the real nutritional needs of these infants. Inadequate protein content and inappropriate protein energy ratio of most preterm formulas represent a matter of major concern, since there is a strict relationship between formula composition and the quantity and quality of weight gain. As a consequence there is a need of at least two milk formulas for different preterm infants: one for LBW and VLBW infants, the other for preterm infants weighing >1500 g.

Energy Intake↗

PubMed2004

Closing loop base pairs in RNA loop-loop complexes: structural behavior, interaction energy and solvation analysis through molecular dynamics simulations.

Nanosecond molecular dynamics using the Ewald summation method have been performed to elucidate the structural and energetic role of the closing base pair in loop-loop RNA duplexes neutralized by Mg2+ counterions in aqueous phases. Mismatches GA, CU and Watson-Crick GC base pairs have been considered for closing the loop of an RNA in complementary interaction with HIV-1 TAR. The simulations reveal that the mismatch GA base, mediated by a water molecule, leads to a complex that presents the best compromise between flexibility and energetic contributions. The mismatch CU base pair, in spite of the presence of an inserted water molecule, is too short to achieve a tight interaction at the closing-loop junction and seems to force TAR to reorganize upon binding. An energetic analysis has allowed us to quantify the strength of the interactions of the closing and the loop-loop pairs throughout the simulations. Although the water-mediated GA closing base pair presents an interaction energy similar to that found on fully geometry-optimized structure, the water-mediated CU closing base pair energy interaction reaches less than half the optimal value.

Aptamers, Nucleotide↗

PubMed1998

Kinetic and thermodynamic principles determining the structural design of ATP-producing systems.

It is theoretically analysed whether the structural design of ATP-producing pathways, in particular the design of glycolysis, may be explained by optimization principles. On the basis of kinetic and thermodynamic principles conclusions are derived concerning the stoichiometry of these pathways in states of high ATP production rates. One of the extensions to previous investigations is that the concentrations of the adenine nucleotides are taken into account as variable quantities. This necessitates the consideration of an interaction of the ATP-producing system I with an external ATP-consuming system II. A great variety of pathways is studied which differ in the number and location of ATP-consuming reactions, ATP-producing reactions and reactions involving inorganic phosphate. The corresponding number of possible pathways may be calculated in an explicit manner as a function of the number of those reactions which do not couple to ATP or inorganic phosphate. The kinetics of the individual reactions are described by linear or bilinear functions of reactant concentrations and all rate equations are expressed in terms of equilibrium constants and characteristic times. A thermo-dynamical analysis of the two coupled systems yields upper and lower limits for the concentration of ATP and an explicit expression for the maximal difference between the number of ATP-producing and ATP-consuming reactions of system I. The following results of the optimization are obtained. (i) The ATP production rate always increases if the ATP-producing reactions as well as those reactions characterized by an uptake of inorganic phosphate are shifted as far as possible towards the end of system I. (ii) Explicit conditions for the optimal location of the ATP-consuming reactions are presented. The results are discussed in the context of characteristic times as well as in terms of enzyme kinetic parameters. (iii) For two sets of characteristic times the resulting stoichiometries and their corresponding steady-state fluxes are investigated in detail. One of these stoichiometries shows a close correspondence to contemporary standard glycolysis. (iv) It is shown that most possible pathways result in a very low steady-state flux, that is, the optimal stoichiometry is characterized by a significant selective advantage. (v) The standard free energy profile of a pathway with an optimal stoichiometry is discussed. It differs significantly from the free energy profiles of nonoptimized pathways.

Adenosine Triphosphate↗

PubMed2002

Influence of pedalling rate on the energy cost of cycling in humans.

To determine the optimal pedalling rate that minimises both the oxygen consumption (fV(O2,min)) and the energy cost of cycling (f(Cr,min)), 22 male subjects were asked to cycle on an ergometer on five occasions of 4 min each at a constant power output of 150 W and at pedalling rates of 40, 60, 80, 100 and 120 rpm. The oxygen consumption (V(O2) in millilitres per minute per kilogram) and the energy cost (Cr in joules per kilogram per metre) were determined during each period. The individual V(O2)-pedalling rate and Cr-pedalling rate relationships were fitted by parabolic regressions which allowed the determination for each individual of fV(O2,min) [mean (SD) 57.0 (4.9) rpm] and f(Cr,min) [101.1 (3.2) rpm], respectively. Contrary to the values obtained for fV(O2,min), those for f(Cr,min) were in agreement with the pedalling rates (90-110 rpm) usually selected in road cycling. It is therefore suggested that the minimisation of Cr is the main factor that determines the pedalling rate in field conditions. The lack of a significant correlation between fV(O2,min) and f(Cr,min) further indicated that, although fV(O2,min) is often used for determining the metabolic capacities of subjects, f(Cr,min) is a better index of optimal mechanical parameters of cycling in field conditions.

Adult↗

PubMed1978

The energy cost of overweight in the United States.

We have calculated the total fossil energy equivalent of the food calories saved by reducing the present degree of overweight (2.3 billion pounds for the adult United States population) to optimum body weight and the annual fossil energy reduction once all Americans reached their optimum weight. The energy saved by dieting to reach optimal weight is equivalent to 1.3 billion gallons of gasoline and the annual energy savings would more than supply the annual residential electrical demands of Boston, Chicago, San Francisco, and Washington, DC.

Adolescent↗

PubMed2006

Density functional theory investigation of product distribution following reaction of acrylonitrile on diamond (001)-2 x 1 surface.

The reaction of acrylonitrile with the C(001)-2 x 1 surface has been investigated by employing density functional cluster model calculations. The calculations revealed eight possible reaction pathways for acrylonitrile with the surface dimer. Full geometry optimized structures were obtained for all adducts, including intra- and interdimer reaction products. These results were analyzed in terms of both the total energy values and the detailed optimized geometries. We find that the reaction of acrylonitrile with the diamond (001) surface occurs primarily through its nonpolar C=C group and the intradimer [2+2](cc) product is the dominant product. All these results are in good agreement with the experimental work by Schwartz. It is noteworthy that the isomerization process plays an important role in the chemisorption process. Both intradimer [4+2] product and interdimer [2+2](cc) product can isomerize to the intradimer [2+2](cc) product. The present study shows that the isomerization between intradimer [4+2] product and intradimer [2+2](cc) product is slightly favorable over the direct path to formation of the intradimer [2+2](cc) product.

Journal Article↗

PubMed2004

Application of evolutionary algorithm methods to polypeptide folding: comparison with experimental results for unsolvated Ac-(Ala-Gly-Gly)5-LysH+.

We present an evolutionary method for finding the low-energy conformations of polypeptides. The application, called FOLDAWAY,is based on a generic framework and uses several evolutionary operators as well as local optimization to navigate the complex energy landscape of polypeptides. It maintains two complementary representations of the structures and uses the CHARMM force field for evaluating the energies. The method is applied to unsolvated Met-enkephalin and Ac-(Ala-Gly-Gly)(5)-Lys(+)H(+). Unsolvated Ac-(Ala-Gly-Gly)(5)-Lys(+)H(+) has been the object of recent experimental studies using ion mobility measurements. It has a flat energy landscape where helical and globular conformations have similar energies. FOLDAWAY locates several large groups of structures not found in previous molecular dynamics simulations for this peptide, including compact globular conformations, which are probably present in the experiments. However, the relative energies of the different conformations found by FOLDAWAY do not accurately match the relative energies expected from the experimental observations.

Algorithms↗

PubMed2004

Experimental design for the formulation and optimization of novel cross-linked oilispheres developed for in vitro site-specific release of Mentha piperita oil.

A Plackett-Burman design was employed to develop and optimize a novel crosslinked calcium-aluminum-alginate-pectinate oilisphere complex as a potential system for the in vitro site-specific release of Mentha piperita, an essential oil used for the treatment of irritable bowel syndrome. The physicochemical and textural properties (dependent variables) of this complex were found to be highly sensitive to changes in the concentration of the polymers (0%-1.5% wt/vol), crosslinkers (0%-4% wt/vol), and crosslinking reaction times (0.5-6 hours) (independent variables). Particle size analysis indicated both unimodal and bimodal populations with the highest frequency of 2 mm oilispheres. Oil encapsulation ranged from 6 to 35 mg/100 mg oilispheres. Gravimetric changes of the crosslinked matrix indicated significant ion sequestration and loss in an exponential manner, while matrix erosion followed Higuchi's cube root law. Among the various measured responses, the total fracture energy was the most suitable optimization objective (R2 = 0.88, Durbin-Watson Index = 1.21%, Coefficient of Variation (CV) = 33.21%). The Lagrangian technique produced no significant differences (P > .05) between the experimental and predicted total fracture energy values (0.0150 vs 0.0107 J). Artificial Neural Networks, as an alternative predictive tool of the total fracture energy, was highly accurate (final mean square error of optimal network epoch approximately 0.02). Fused-coated optimized oilispheres produced a 4-hour lag phase followed by zero-order kinetics (n > 0.99), whereby analysis of release data indicated that diffusion (Fickian constant k1 = 0.74 vs relaxation constant k2 = 0.02) was the predominant release mechanism.

Chemistry, Pharmaceutical↗

PubMed2006

Protein-ligand binding affinity predictions by implicit solvent simulations: a tool for lead optimization?

Continuum electrostatics is combined with rigorous free-energy calculations in an effort to deliver a reliable and efficient method for in silico lead optimization. The methodology is tested by calculation of the relative binding free energies of a set of inhibitors of neuraminidase, cyclooxygenase2, and cyclin-dependent kinase 2. The calculated free energies are compared to the results obtained with explicit solvent simulations and empirical scoring functions. For cyclooxygenase2, deficiencies in the continuum electrostatics theory are identified and corrected with a modified simulation protocol. For neuraminidase, it is shown that a continuum representation of the solvent leads to markedly different protein-ligand interactions compared to the explicit solvent simulations, and a reconciliation of the two protocols is problematic. Cyclin-dependent kinase 2 proves more challenging, and none of the methods employed in this study yield high quality predictions. Despite the differences observed, for these systems, the use of an implicit solvent framework to predict the ranking of congeneric inhibitors to a protein is shown to be faster, as accurate or more accurate than the explicit solvent protocol, and superior to empirical scoring schemes.

Cyclin-Dependent Kinase 2↗

PubMed2002

Solvation of copper ions by acetone. structures and sequential binding energies of Cu+(acetone)x, x = 1-4 from collision-induced dissociation and theoretical studies.

Collision-induced dissociation of Cu+(acetone)(x), x = 1-4, with Xe is studied as a function of kinetic energy using guided ion beam mass spectrometry. In all cases, the primary and lowest energy dissociation channel observed is endothermic loss of one acetone molecule. The primary cross section thresholds are interpreted to yield 0 and 298 K bond energies after accounting for the effects of multiple ion-neutral collisions, internal energy of the complexes, and dissociation lifetimes. Density functional calculations at the B3LYP/6-31G* level of theory are used to determine the structures of these complexes and provide molecular constants necessary for the thermodynamic analysis of the experimental data. Theoretical bond dissociation energies are determined from single point calculations at the B3LYP/6-311+G(2d,2p) and MP2(full)/6-311+G(2d,2p) levels, using the B3LYP/6-31G* optimized geometries. The experimental bond energies determined here are in good agreement with previous experimental measurements made in a high-pressure mass spectrometer for the sum of the first and second bond energy (i.e., Cu+(acetone)2 --> Cu+ + 2 acetone) when these results are properly anchored. The agreement between theory and experiment is reasonable in all cases, but varies both with the size of the cluster and the level of theory employed. B3LYP does an excellent job for the x = 1 and 3 clusters, but is systematically low for the x = 2 and 4 clusters such that the overall trends in sequential binding energies are not parallel. In contrast, all MP2 values are somewhat low, but the overall trends parallel the measured values for all clusters. The trends in the measured Cu+(acetone), binding energies are explained in terms of 4s-3d sigma hybridization effects and ligand-ligand repulsion in the clusters.

Journal Article↗