SEARCH · PubMed Health

Results for “energy optimization”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 757 records · Page 42Linked to original sources

PubMedDate not supplied

Theoretical studies on the conformation of saccharides. XIV. Structure and conformational properties of the glycosylamines.

The 2-methylaminotetrahydropyran was used as a model to study conformational properties of the N-glycosidic linkage in glycosylamines. Relaxed two-dimensional conformational (phi, psi) maps in 20 solvents were calculated by a method in which the total energy is divided into the energy of the isolated molecule and the solvation energy. Molecular geometry optimization has been carried out for each conformer using the quantum chemical method PCILO. The calculated variations of the geometry are consistent with the results obtained by the statistical analysis of available experimental data retrieved from the Cambridge Structural Database. The calculated abundances of conformers show that the polarity of the solvent has little effect on the anomeric ratio, and the form having the methylamino group equatorial is favored in all considered solvents.

Carbohydrate Conformation↗

PubMed2004

Synthesis and conformational analysis of novel N(OCH3)-linked disaccharide analogues.

N(OMe)-linked disaccharide analogues, isosteric to the corresponding natural disaccharides, have been synthesized by chemoselective assembly of unprotected natural monosaccharides with methyl 6-deoxy-6-methoxyamino-alpha-D-glucopyranoside in an aqueous environment. The coupling reactions were found to be chemo- and stereoselective affording beta-(1-->6) disaccharide mimics when using Glc and GlcNAc; in the case of Gal, the beta-anomer was prevalent (beta:alpha=7:1). An iterative method for the synthesis of linear N(OMe) oligosaccharide analogues was demonstrated, based on the use of an unprotected monosaccharide building block in which an oxime functionality at C-6 is converted during the synthesis into the corresponding methoxyamino group. The conformational analysis of these compounds was carried out by using NMR spectroscopy, ab initio, molecular mechanics, and molecular dynamics methods. Optimized geometries and energies of fourteen conformers for each compound have been calculated at the B3LYP/6-31G* level. Predicted conformational equilibria were compared with the results based on NMR experiments and good agreement was found. It appears that N(OMe)-linked disaccharide analogues exhibit a slightly different conformational behavior to their parent natural disaccharides.

Carbohydrate Conformation↗

PubMed2002

Chemical shift driven geometry optimization.

A new method for refinement of 3D molecular structures by geometry optimization is presented. Prerequisites are a force field and a very fast procedure for the calculation of chemical shifts in every step of optimization. To the energy, provided by the force field (COSMOS force field), a pseudoenergy, depending on the difference between experimental and calculated chemical shifts, is added. In addition to the energy gradients, pseudoforces are computed. This requires the derivatives of the chemical shifts with respect to the coordinates. The pseudoforces are analytically derived from the integral expressions of the bond polarization theory. Single chemical shift values attributed to corresponding atoms are considered for structural correction. As a first example, this method is applied for proton position refinement of the D-mannitol X-ray structure. A crystal structure refinement with 13C chemical shift pseudoforces is carried out.

Carbohydrate Conformation↗

PubMed2003

A computational study of conformational interconversions in 1,4-dithiacyclohexane (1,4-dithiane).

Ab initio molecular orbital theory with the 6-31G(d), 6-31G(d,p), 6-31+G(d), 6-31+G(d,p), 6-31+G(2d,p), 6-311G(d), 6-311G(d,p), and 6-311+G(2d,p) basis sets and density functional theory (BLYP, B3LYP, B3P86, B3PW91) have been used to locate transition states involved in the conformational interconversions of 1,4-dithiacyclohexane (1,4-dithiane) and to calculate the geometry optimized structures, relative energies, enthalpies, entropies, and free energies of the chair and twist conformers. In the chair and 1,4-twist conformers the C-Hax and C-Heq bond lengths are equal at each carbon, which suggest an absence of stereoelectronic hyperconjugative interactions involving carbon-hydrogen bonds. The 1,4-boat transition state structure was 9.53 to 10.5 kcal/mol higher in energy than the chair conformer and 4.75 to 5.82 kcal/mol higher in energy than the 1,4-twist conformer. Intrinsic reaction coordinate (IRC) calculations showed that the 1,4-boat transition state structure was the energy maximum in the interconversion of the enantiomers of the 1,4-twist conformer. The energy difference between the chair conformer and the 1,4-twist conformer was 4.85 kcal/mol and the chair-1,4-twist free energy difference (deltaG degrees (c-t)) was 4.93 kcal/mol at 298.15 K. Intrinsic reaction coordinate (IRC) calculations connected the transition state between the chair conformer and the 1,4-twist conformer. This transition state is 11.7 kcal/mol higher in energy than the chair conformer. The effects of basis sets on the 1,4-dithiane calculations and the relative energies of saturated and unsaturated six-membered dithianes and dioxanes are also discussed.

Journal Article↗

PubMed2004

Solvation model induced structural changes in peptides. A quantum chemical study on Ramachandran surfaces and conformers of alanine diamide using the polarizable continuum model.

Potential energy surfaces of the model peptide HCO-L-Ala-NH2 were calculated using polarizable continuum model (PCM) for the description of aqueous solution at RHF/3-21G, RHF/6-31+G(d), and B3LYP/6-31+G(d) levels of theory. Energy minima were optimized at all three levels as well as at B3LYP/PCM/6-311++G(d,p) level of theory. Results were correlated to experimental data of protein structures retrieved from PDB SELECT. It is concluded that alanine residues of proteins are modeled better by PCM results than by gas-phase calculations on the alanine diamide model (frequently called alanine dipeptide model). The currently available version of the PCM model implemented in Gaussian 03 provides a reasonable alternative to anticipate solvation effects without the computational costs of introducing explicit solvent molecules into the model system. Frequencies calculated at RHF/PCM/6-31+G(d) and B3LYP/PCM/6-31+G(d) levels of theory show high correlation; thus, RHF results have their own merit.

Alanine↗

PubMed2006

Doping effects on proton incorporation and conduction in SrZrO3.

The doping effects on the proton incorporation and protonic conductivity of perovskite-type SrZrO3 were investigated using the density functional theory (DFT) with the generalized gradient approximation (GGA). The optimized geometries, formation energies of hydrogen defect and activation energies for hydrogen diffusion in SrZrO3 doped with Al, Sc, Ga, Y, Rh, In, and Yb were calculated. It was shown that the doping leads to large local distortions around hydrogen and dopant ion, affecting the protonic conduction in these oxides. The alignment of hydrogen levels varies with the dopant introduced into the SrZrO3. In In-, Y-, Sc-, Ga-, and Al-doped SrZrO3, the H+ is the lowest energy state in all the bandgap. But for Yb- and Rh-doped SrZrO3, the H+ is the lowest energy state only when the Fermi energy below 2.37 and 2.66 eV, respectively. The estimates of the activation energy show good agreement between the measured and calculated activation energies. Also, the hydrogen diffusion seems to become more difficult as the distance between hydrogen and dopant ion decreases.

Journal Article↗

PubMed2006

Microwave- and ultrasound-assisted extraction of vanillin and its quantification by high-performance liquid chromatography in Vanilla planifolia.

Microwave-assisted extraction (MAE), ultrasound-assisted extraction (UAE) and conventional extraction of vanillin and its quantification by HPLC in pods of Vanilla planifolia is described. A range of nonpolar to polar solvents were used for the extraction of vanillin employing MAE, UAE and conventional methods. Various extraction parameters such as nature of the solvent, solvent volume, time of irradiation, microwave and ultrasound energy inputs were optimized. HPLC was performed on RP ODS column (4.6 mm ID x 250 mm, 5 microm, Waters), a photodiode array detector (Waters 2996) using gradient solvent system of ACN and ortho-phosphoric acid in water (0.001:99.999 v/v) at 25 degrees C. Regression equation revealed a linear relationship (r2 > 0.9998) between the mass of vanillin injected and the peak areas. The detection limit (S/N = 3) and limit of quantification (S/N = 10) were 0.65 and 1.2 microg/g, respectively. Recovery was achieved in the range 98.5-99.6% for vanillin. Maximum yield of vanilla extract (29.81, 29.068 and 14.31% by conventional extraction, MAE and UAE, respectively) was found in a mixture of ethanol/water (40:60 v/v). Dehydrated ethanolic extract showed the highest amount of vanillin (1.8, 1.25 and 0.99% by MAE, conventional extraction and UAE, respectively).

Antimutagenic Agents↗

PubMed2006

Ab initio prediction of peptide-MHC binding geometry for diverse class I MHC allotypes.

Since determining the crystallographic structure of all peptide-MHC complexes is infeasible, an accurate prediction of the conformation is a critical computational problem. These models can be useful for determining binding energetics, predicting the structures of specific ternary complexes with T-cell receptors, and designing new molecules interacting with these complexes. The main difficulties are (1) adequate sampling of the large number of conformational degrees of freedom for the flexible peptide, (2) predicting subtle changes in the MHC interface geometry upon binding, and (3) building models for numerous MHC allotypes without known structures. Whereas previous studies have approached the sampling problem by dividing the conformational variables into different sets and predicting them separately, we have refined the Biased-Probability Monte Carlo docking protocol in internal coordinates to optimize a physical energy function for all peptide variables simultaneously. We also imitated the induced fit by docking into a more permissive smooth grid representation of the MHC followed by refinement and reranking using an all-atom MHC model. Our method was tested by a comparison of the results of cross-docking 14 peptides into HLA-A*0201 and 9 peptides into H-2K(b) as well as docking peptides into homology models for five different HLA allotypes with a comprehensive set of experimental structures. The surprisingly accurate prediction (0.75 A backbone RMSD) for cross-docking of a highly flexible decapeptide, dissimilar to the original bound peptide, as well as docking predictions using homology models for two allotypes with low average backbone RMSDs of less than 1.0 A illustrate the method's effectiveness. Finally, energy terms calculated using the predicted structures were combined with supervised learning on a large data set to classify peptides as either HLA-A*0201 binders or nonbinders. In contrast with sequence-based prediction methods, this model was also able to predict the binding affinity for peptides to a different MHC allotype (H-2K(b)), not used for training, with comparable prediction accuracy.

Binding Sites↗

PubMed2006

ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility.

Protein-small molecule docking algorithms provide a means to model the structure of protein-small molecule complexes in structural detail and play an important role in drug development. In recent years the necessity of simulating protein side-chain flexibility for an accurate prediction of the protein-small molecule interfaces has become apparent, and an increasing number of docking algorithms probe different approaches to include protein flexibility. Here we describe a new method for docking small molecules into protein binding sites employing a Monte Carlo minimization procedure in which the rigid body position and orientation of the small molecule and the protein side-chain conformations are optimized simultaneously. The energy function comprises van der Waals (VDW) interactions, an implicit solvation model, an explicit orientation hydrogen bonding potential, and an electrostatics model. In an evaluation of the scoring function the computed energy correlated with experimental small molecule binding energy with a correlation coefficient of 0.63 across a diverse set of 229 protein- small molecule complexes. The docking method produced lowest energy models with a root mean square deviation (RMSD) smaller than 2 A in 71 out of 100 protein-small molecule crystal structure complexes (self-docking). In cross-docking calculations in which both protein side-chain and small molecule internal degrees of freedom were varied the lowest energy predictions had RMSDs less than 2 A in 14 of 20 test cases.

Algorithms↗

PubMed1990

Bundles of amphipathic transmembrane alpha-helices as a structural motif for ion-conducting channel proteins: studies on sodium channels and acetylcholine receptors.

Channel proteins are transmembrane symmetric (or pseudosymmetric) oligomers organized around a central ionic pore. We present here a molecular model of the pore forming structures of two channel proteins with different primary structures and oligomeric size: the voltage-sensitive sodium channel and the nicotinic cholinergic receptor. We report low-energy arrangements of alpha-helical bundles calculated by semiempiricial potential energy functions and optimization routines and further refined using molecular dynamics. The ion-conducting pore is considered to be a symmetric or pseudosymmetric homooligomer of 3-5 amphipathic alpha-helices arranged such that the polar residues line a central hydrophilic pathway and the apolar residues face the hydrophobic bilayer interior. The channel lining exposes either charged (Asp, Glu, Arg, Lys) or polar-neutral (Ser, Thr) residues. A bundle of four parallel helices constrained to C4 symmetry, the helix axis aligned with the symmetry axis, and the helices constrained to idealized dihedral angles, produces a structure with a pore of the size inferred for the sodium channel protein (area approximately 16 A2). Similarly, a pentameric array optimized with constraints to maintain C5 symmetry and backbone torsions characteristic of alpha-helices adopts a structure that appears well suited to form the lining of the nicotinic cholinergic receptor (pore area approximately 46 A2). Thus, bundles of amphipathic alpha-helices satisfy the structural, energetic, and dynamic requirements to be the molecular structural motif underlying the function of ionic channels.

Amino Acid Sequence↗

PubMed1981

Cell death: questions for histochemists concerning the causes of the various cytological changes.

The question of cell death is accessible to study by histochemists and many questions remain to be resolved. From a physiological point of view, the most important are the causal relationships. (1) At what phase in cell death is the synthesis of RNA disrupted and at what phase is the rate of degradation of RNA increased? (2) Does the disruption of synthesis result from a direct genetic command, or does it result indirectly from gradual deterioration of energy resources or optimal ionic conditions? (3) What properties, presumably of the substrate organelles, marks them for specific absorption into autophagic vacuoles? (4) What proteases and other hydrolases operate currently undetected in the cytoplasm? How are they controlled and regulated? (5) Why does the physiologically dying cell shrink and appear more dense? To what extent is a cell in this state able to regulate any metabolic parameter? The advent of newer, more sensitive and quantitative techniques, and greater attention to the controls and causes as opposed to the phenomena, should help to resolve these questions.

Animals↗

PubMed1976

Biophysical questions in ecology and environmental research. Part 2: The extremes of an ecosystem (author's transl).

Some basic differences and developmental aspects of ecosystems are demonstrated. Maximum "energy conductivity" and the pathways of energy flow through ecosystems are discussed as the force, potential, or principle to drive the evolution of the system. A working hypothesis is offered: Ecosystems maximize the total energy flow to optimize temperature stability. The paper stresses in general the need and search for new approaches to analyze the evolution of ecosystems. The hypothesis presented in this paper should be regarded as stimulation for further research.

Ecology↗

PubMed2005

Human disease-associated mitochondrial mutations fixed in nonhuman primates.

A number of human disease-associated sequences have been reported in other species, such as rodents, but compensatory changes appear to prevent these deleterious mutations from being expressed. The aim of this work was to compare the mitochondrial DNA of multiple primates to ascertain whether mitochondrial disease-causing sequences in humans are fixed in nonhuman primates. Indeed, 46 sequences related to human pathology were identified in 1 or more of the 12 studied nonhuman primates, the majority of which were associated with late-onset diseases. Most of these sequences can be explained by the presence of secondary compensatory changes that render these mutations phenotypically inert. Nonetheless, and since humans not only are the longest-lived primate but feature the largest brain, one hypothesis is that a gradual optimization of the human mitochondrion occurred in the hominid lineage driven by the need to optimize the aerobic energy metabolism to delay neurodegeneration. Therefore, it is also proposed that some of these disease-associated sequences in nonhuman primates may be linked to the evolution of human longevity and intelligence, indicating a general pattern of selection on longevity in the course of evolution of the human mitochondrion.

Animals↗

PubMed2006

Simultaneous control of apparent extract and volatile compounds concentrations in low-malt beer fermentation.

Volatile compounds cause undesirable flavor when their concentrations exceed threshold values in beer fermentation. The objective of this study is to develop a system for controlling apparent extract concentration, which indicates the fermentation degree and which should be decreased below a targeted value at a fixed time under a constraint of tolerable amounts of volatile compounds. In beer fermentation, even though the production of volatile compounds is suppressed by maintaining a low fermentation temperature, a low temperature causes a delay in the control of apparent extract concentration. Volatile compound concentration was estimated on-line, and the simulation of apparent extract consumption and volatile compound production was performed. To formulate various beer tastes and conserve energy for attemperation, optimal temperature profiles were determined using a genetic algorithm (GA). The developed feedback control of the brewing temperature profile was successfully applied, and apparent extract and volatile compound concentrations at a fixed time reached their target concentrations. Additionally, the control technique developed in this study enables us to brew a wide variety of beers with different tastes.

Acids↗

PubMed2000

A novel "cooled-wet" electrode for radiofrequency ablation.

In the light of growing demands for improved applicability of radiofrequency ablation (RFA), recently we have developed a novel "cooled-wet" electrode by taking the advantages of both internally cooled and saline-enhanced electrodes. The efficacy of the electrode was evaluated in both ex vivo and in vivo liver RFA under both low and high power output levels. The ablation volume created with the "cooled-wet" electrode appeared to be much larger than that reported up to now with the use of other monopolar electrodes. The mechanisms on how this device optimizes the RF energy delivery are also discussed.

Animals↗

PubMed2004

Age-related changes in glucose utilization and fatty acid oxidation in a muscle-specific manner during rabbit growth.

The optimal utilization of energy substrates in muscle fibers is of primary importance for muscle contraction and whole body physiology. This study aimed to investigate the age-related changes in some indicators of glucose catabolism and fatty acid oxidation in muscles of growing rabbits. Longissimus lumborum (fast-twitch, LL) and semimembranosus proprius (slow-twitch, SMP) muscles were collected at 10 or 20 weeks of age ( n=6 per age). Glucose transporter GLUT4 content was investigated by immunoblot assay. Activity levels of five enzymes were measured: lactate dehydrogenase (LDH) and phosphofructokinase (PFK) for glycolysis; citrate synthase (CS), isocitrate dehydrogenase (ICDH) and -3-hydroxyacyl-coenzyme A dehydrogenase (HAD) for oxidation. Mitochondrial and peroxisomal oxidation rates were assessed on fresh homogenates using [1-14C]-oleate as substrate. At both ages, mitochondrial and peroxisomal oxidations rates, as well as activities of oxidative enzymes were higher in SMP than in LL. In both muscles, the apparent rate of fatty acid oxidation by the mitochondria did not differ between the two ages. However, a decrease in the activities of the three oxidative enzymes was observed in LL, whereas activities of CS and HAD and peroxisomal oxidation rate of oleate increased between the two ages in SMP muscle. In both muscles, LDH activity increased between 10 and 20 weeks, without variations in glucose uptake (GLUT4 transporter content) and in the first step of glucose utilization (PFK activity). In conclusion, mitochondrial oxidation rate of fatty acids and activities of selected mitochondrial enzymes were largely unrelated. Moreover, regulation of energy metabolism with advancing age differed between muscle types.

Aging↗

PubMed1993

Measurement of strain and analysis of stress in resting rat left ventricular myocardium.

A technique has been developed for measuring two-dimensional strains in the left ventricle of the isolated arrested rat heart subjected to passive ventricular loading. The pressure-volume relationship was found in eight hearts during inflation of a left ventricular balloon. With the zero-pressure state as reference, in-plane strain components were determined using a triangle of ultrasonic dimension transducers (0.6-0.8 mm diameter) placed 3-6 mm apart in the midwall of the left ventricle. Mean circumferential (fiber) strain was larger than longitudinal (cross-fiber) strain (0.108 +/- 0.045, 0.055 +/- 0.045, respectively, at 11 mmHg), and shear strain (-0.048 +/- 0.029) was negative, consistent with left-handed torsion. The in-plane angle of greatest stretch was uniform with inflation (range = -26.5 degrees to -34.5 degrees). The equatorial region of the left ventricle was modeled with finite element analysis of a transversely isotropic thick-walled cylindrical shell subjected to internal loading and axial forces. The material parameters of an exponential strain energy function were optimized so that the least-squares difference between the predicted and the measured midwall strains was minimized. Material properties, stress and strain in the rat heart were compared to values predicted for the dog. In both species the tissue was stiffer in the fiber direction than in the cross-fiber direction. The ratio of fiber to cross-fiber stiffness was lower in the rat (2.50) than in the dog (5.24) at low loads and approximately equal at higher loads (1.63 and 1.39, respectively). The computational and experimental analyses showed that the larger shear strain and more nonuniform in-plane extension in the rat may be an indication of significantly different anisotropic material properties in these two species, and implies differences in the collagen ultrastructure.

Animals↗

PubMed1992

Comparison of gas chromatographic-mass spectrometric methods for screening of chlorotriazine pesticides in soil.

The performance of a coupled technique resulting from the combination of gas chromatography with a selective mass spectrometric technique (tandem mass spectrometry) (GC-MS-MS) with collisionally activated dissociation (CAD) and multi-reaction monitoring (MRM) was compared with that of GC-low resolution MS (GC-LRMS) at a resolving power of 1000 and GC-high-resolution MS (GC-HRMS) at resolving powers of 5000 and 10,000 for the determination of atrazine, simazine, cyanazine, deethylatrazine and deisopropylatrazine in polluted soil samples. GC-MS-MS daughter ion spectra for the parent ions [M]+. and [M - CH3]+ were generated using collisionally activated dissociation and studied. Also, by optimizing the collision energy for maximum sensitivity a method for screening chlorotriazines by MRM was developed. Analyses of soil sample extracts showed that GC-MS-MS overcomes interferences from other chlorotriazines and interfering compounds that could not be removed by GC-HRMS or GC-LRMS at resolving powers of 10,000 and 1000, respectively. The limits of detection for GC-MS-MS and GC-HRMS at a signal-to-noise ratio of 10 ranged between 1 and 24 pg, with a mean relative standard deviation of 25-30%. Soil samples known to contain chlorotriazines and their degradation products were analysed by GC-MS-MS and the results obtained were compared with those given by GC-HRMS at resolving powers of 5000 and 10,000, with quantification differences of 25-30%.

Gas Chromatography-Mass Spectrometry↗