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Results for “energy optimization”

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At least 271 records · Page 15Linked to original sources

PubMed1987

Computer modeling of the neurotoxin binding site of acetylcholine receptor spanning residues 185 through 196.

A model of the complex between the acetylcholine receptor and the snake neurotoxin, cobratoxin, was built by molecular model building and energy optimization techniques. The experimentally identified functionally important residues of cobratoxin and the dodecapeptide corresponding to the residues 185-196 of acetylcholine receptor alpha subunit were used to build the model. Both cis and trans conformers of cyclic L-cystine portion of the dodecapeptide were examined. Binding residues independently identified on cobratoxin are shown to interact with the dodecapeptide AChR model.

Amino Acid Sequence↗

PubMed1977

Nutrient intake and stimulant drugs in hyperactive children.

Recent studies have demonstrated suppressed growth of height and weight in children receiving stimulant drugs for hyperactivity. For approximately twelve months, growth data and food records were collected on two subjects receiving different types and dosages of stimulant drugs. The two cases demonstrated that dextroamphetamine levels of 10 mg. or more and methylphenidate levels of 30 mg. or more decreased caloric intake significantly. This decrease may be limiting for long-term growth. Both subjects had a variety of feeding problems due to poor appetite. Careful nutritional evaluation and planning are important to insure optimal energy and nutrient intake in these children receiving stimulant drugs.

Ascorbic Acid↗

PubMedDate not supplied

[Structure of poly(dA).poly(dT) from data of x-ray diffraction, energy calculations and nuclear magnetic resonance].

The results of X-ray diffraction studies of poly(dA).poly(dT) have been compared with the results of energy optimization and with the NMR data in solution. Slight refinement of the X-ray and energetically optimal models leads to a very good quantitative agreement with the NMR data, that suggests similarity of the poly(dA).poly(dT) structure in a condensed state and in solution. One of the features distinguishing these models from the classic B form is a narrowed minor groove of the double helix. The anomalous properties of DNA with this sequence can be related specific organization of the water molecules near the polynucleotide.

Magnetic Resonance Spectroscopy↗

PubMedDate not supplied

[Various characteristics of the control of cyclic movements].

It was shown by studying control forces and phasic trajectories during oscillation of human forearm, locomotion and rocking of the body on the support that there was an image of accomplished movement in the central nervous system. This image seems to be realized by linear connected displacements of the muscle tension level and threshold of tonic stretch reflex. During the control process, velocity of the threshold and tension level is similarly transformed to that of the body part. The piece constant similarity coefficient is regulated centrally. The main result of such control is moving of the body along energy optimal trajectories.

Ankle Joint↗

PubMed1978

[Surgical refertilization by means of laser technic. Animal experimental study].

Animal experiments on rabbits with a CO2 laser concerning end-to-end-anastomosis of cornua uteri are reported. The rate of success of this laser technique by a before investigated optimal energy density of 64 Watt sec/cm2 (8 Watt,0,2 sec) was about 70% deliveries without any complication. This method could be an alternative to the presently used microsurgical methods of refertilisation in human tubar sterility.

Animals↗

PubMedDate not supplied

[Characteristics of glucose metabolism in rats with different preferences for alcohol].

Rats preferring ethanol were distinct from water-consuming animals in a decreased level of immunoreactive insulin im blood serum as well as in glucokinase activity of liver tissue. Per oral loading with glucose, 4 g/kg of body mass, enabled to detect a difference in the sugar phosphorylation via hexokinase and glucokinase reactions as well as the dissimilar sensitivity of the insulin system to glucose in the ethanol-, water-consuming and intermediate animals. Ethanol-consuming rats were more resistant to the effect of starvation during 48 hrs. The data obtained suggest that the characteristic properties of glucose metabolism in ethanol-consuming rats appear to be responsible for increased consumption of ethanol, which is used as optimal energy source, metabolized via pathways which did not involve the glycolytic pathway.

Alcohol Drinking↗

PubMedDate not supplied

[Simulation of DNA conformation possibilities by means of nonbonded interaction energy calculations of complementary dinucleoside phosphate complexes].

Nonbonded interaction energy calculations were performed for complementary deoxydinucleoside phosphate complexes dApdA with dUpdU and dUpdA with dUpdA. All dihedral and bond angles but nitrogen base angles were the variables in minimization of energy. Complex conformations resembling A- and B-family double-helical conformations were recieved as a result of calculations when intramolecular interaction energy approach minima. Dihedral angles of one molecule of the complex may differ from corresponding angles of another by several degrees. Energy optimal complex conformations in other space regions of conformation parameters were found. Biological consequences of possible dihedral and bond angle changes of double stranded nucleic acids at interactions with other molecules are discussed.

Chemical Phenomena↗

PubMed1993

Effect of KTP laser ablation of endochondral bone on bone healing.

The advantages of using a laser to cut a hole in the ossicular chain include increased precision, decreased likelihood of disarticulation, and elimination of noise-induced threshold shift associated with conventional drills. This study was designed to determine optimal energy settings and cooling technique to minimize tissue injury. Laser ablated holes were cut in rabbit femurs with different endostat fibers at power settings of 1.6 to 5.0 watts. Comparable burr holes were cut by a high-speed drill and the animals were sacrificed at different time intervals. Specimens were evaluated microscopically for tissue injury by the amount of cell necrosis of the surrounding osteocytes, bone marrow changes, and denaturation of bone matrix. Changes in healing were assessed by the production and ossification of the granulation tissue. Laser ablated holes created with 1.6 to 2.0 watts at 2 to 7 days demonstrated thermal damage comparable to conventionally drilled holes. At 14 to 28 days these holes demonstrated advanced healing and integrated lamellar bone. In contrast, higher power (> 3.5 watts) at 2 to 7 days demonstrated Significantly more osteocyte loss, marked bone marrow fibrosis, and bone matrix denaturation. At 14 to 28 days these holes showed evidence of delayed healing and osseous plugs not integrated with the surrounding bone.

Animals↗

PubMed1997

Modeling of erbium: YAG laser-mediated explosive photovaporization: implications for vitreoretinal surgery.

BACKGROUND AND OBJECTIVE: Motivated by the potential for highly precise tissue removal, investigators are exploring fiberoptic microsurgical maneuvers with the erbium:YAG (Er:YAG) laser. Tissue is disrupted and removed by direct ablation and the acousto-mechanical sequelae of explosive vaporization of the tissue water. The authors investigated the scaling laws for photoablative and photodisruptive interactions and interpreted these results to optimize energy delivery for vitreoretinal surgical maneuvers. MATERIALS AND METHODS: A model for laser-generated-bubble expansion is presented based on energy principles and adiabatic gas expansion. Comparisons are made with the authors' previous studies of ablation rate and thermometry. RESULTS: The authors' modeling studies generated predictions similar to experimental data. The maximum bubble diameter increases as the cube root of the pulse energy. At constant radiant exposure, the maximum bubble diameter increases as the probe tip diameter raised to the two-thirds power. The authors demonstrated that tissue ablation depends on radiant exposure (J/cm2), whereas temperature increases, bubble size, and peak pressure depend on total pulse energy. CONCLUSIONS: Mechanical injury should be minimized and efficient ablation preserved by delivering low-pulse energy through small-diameter probe tips at high repetition rates.

Laser Therapy↗

PubMed1998

The carboxyl-terminal region of protein C is essential for its secretion.

We have previously reported a mutated protein C, designated protein C Nagoya (PCN), characterized by the deletion of a single guanine residue (8857G). This frameshift mutation results in the replacement of the carboxyl-terminal 39 amino acids of wild-type protein C (G381-P419) by 81 abnormal amino acids. This elongated mutant was not effectively secreted, and was retained in the endoplasmic reticulum. To determine why PCN is not secreted, we constructed a series of mutants from which some or all of the 81 amino acids were deleted. None of these shortened proteins were secreted from producing cells, indicating that the carboxyl-terminal extension is not mainly responsible for the intracellular retention of PCN, and that the 39 carboxyl-terminal amino acids of wild-type protein C are required for secretion. To determine which residues are essential for the secretion of protein C, deletion mutants of the carboxyl-terminal region (D401-P419) were prepared. Metabolic labeling showed that mutants of protein C truncated before W417, Q414, E411, or K410 were efficiently secreted. On the other hand, the mutants truncated before D409 were retained and degraded intracellularly. Immunofluorescence and immunoelectron microscopy showed that truncation before D409 blocks the movement from rough endoplasmic reticulum to the Golgi apparatus. To understand the conformational change in the carboxyl-terminal region, two models of truncated activated protein C were constructed using energy optimization and molecular dynamics with water molecules.

Amino Acid Sequence↗

PubMed2006

Multiple neutral loss monitoring (MNM): a multiplexed method for post-translational modification screening.

Post-translational modifications of proteins are involved in determining the activity of proteins and are essential for proper protein function. Current mass spectrometric strategies require one to specify a particular type of modification, in some cases also a particular charge state of a protein or peptide that is to be studied before the actual analysis. Due to these requirements, most of the modifications on proteins are not considered in such an experiment and, thus, a series of similar analyses need to be performed to ensure a more extensive characterization. A novel scan strategy has been developed, multiple neutral loss monitoring (MNM), allowing for the comprehensive screening of post-translational modifications (PTM) on proteins that fragment as neutral losses in a mass spectrometer. MNM method parameters were determined by performing product ion scans on a number of modified peptides over a range of collision energies, providing neutral loss energy profiles and optimal collision energies (OCE) for each modification, supplying valuable information pertaining to the fragmentation of these modifications and the necessary parameters that would be required to obtain the best analysis. As the optimal collision energy was highly dependent on the type of modification and the charge state of the peptide, the MNM scan was operated with a collision energy gradient. Autocorrelation analyses identified the type of modification, and convolution mapping analyses identified the associated peptide. The MNM scan with the new collision energy parameters was successfully applied to a mixture of four modified peptides in a BSA digest. The implementation of this technique will allow for comprehensive screening of all modifications that fragment as neutral losses.

Algorithms↗

PubMed2004

A parameter study to determine the optimal source neutron energy in boron neutron capture therapy of brain tumours.

The values of the parameters used in boron neutron capture therapy (BNCT) to calculate a given dose to human tissue vary with patients due to different physical, biological and/or medical circumstances. Parameters include the tissue dimensions, the 10B concentration and the relative biological effectiveness (RBE) factors for the different dose components associated with BNCT. Because there is still no worldwide agreement on RBE values, more often than not, average values for these parameters are used. It turns out that the RBE-problem can be circumvented by taking into account all imaginable parameter values. Approaching this quest from another angle: the outcome will also provide the parameters (and values) which influence the optimal source neutron energy. For brain tumours it turns out that the 10B concentration, the RBE factors for 10B as well as fast neutrons, together with the dose limit set for healthy tissue, affect the optimal BNCT source neutron energy. By using source neutrons of a few keV together with neutrons of a few eV, it ensures that, under all imaginable circumstances, a maximum of alpha (and lithium) particles can be delivered in the tumour.

Algorithms↗

PubMed2006

Modeling the influence of a laser pulse on the potential energy surface in optimal molecular control theory.

Understanding and modeling the interaction between light and matter is essential to the theory of optical molecular control. While the effect of the electric field on a molecule's electronic structure is often not included in control theory, it can be modeled in an optimal control algorithm by a set or toolkit of potential energy surfaces indexed by discrete values of the electric field strength where the surfaces are generated by Born-Oppenheimer electronic structure calculations that directly include the electric field. Using a new optimal control algorithm with a trigonometric mapping to limit the maximum field strength explicitly, we apply the surface-toolkit method to control the hydrogen fluoride molecule. Potential energy surfaces in the presence and absence of the electric field are created with two-electron reduced-density-matrix techniques. The population dynamics show that adjusting for changes in the electronic structure of the molecule beyond the static dipole approximation can be significant for designing a field that drives a realistic quantum system to its target observable.

Journal Article↗

PubMed2005

Structured dietary advice incorporating walnuts achieves optimal fat and energy balance in patients with type 2 diabetes mellitus.

OBJECTIVE: A cardioprotective dietary fat profile is recommended for the treatment of type 2 diabetes. The clinical feasibility of advice strategies targeting specific fatty acid intakes and the extent to which they can be achieved by free-living populations needs to be tested. Walnuts, with high n-3 polyunsaturated fatty acid (PUFA) content, may help optimize fatty acid intakes, but regular consumption might increase total fat and energy intakes. This study examined whether advice that refers to a total dietary pattern inclusive of walnuts would result in low-fat energy-controlled diets with optimal dietary fat proportions for patients with type 2 diabetes mellitus. RESEARCH DESIGN AND METHODS: A parallel-design, controlled trial was completed by 55 free-living men and women with established type 2 diabetes mellitus. Participants were randomly assigned to one of three groups: low-fat (general advice), modified low-fat (total diet advice using exchange lists to differentiate PUFA-rich foods), walnut-specific (modified low fat including 30 g walnuts/day). Dietary intakes and clinical outcomes were measured at baseline, and at 3 and 6 months. Dietary goals were: less than 10% of energy from saturated fat, 7% to 10% of energy from PUFA, adequate n-3 PUFA (>or=2.22 g alpha-linolenic acid, >or=0.65 g eicosapentaenoic acid [EPA]+docosahexaenoic acid [DHA]) and n-6 to n-3 ratio less than 10. The proportion of subjects achieving dietary goals and major food sources of fat were determined. RESULTS: At baseline, dietary intakes were not significantly different between groups. No group and few individuals (10%) were consuming adequate PUFA, with meat the main source of dietary fat (22% total dietary fat). At 3 and 6 months, energy and macronutrient intakes were similar among groups. The walnut group, however, was the only group to achieve all fatty acid intake targets (P <.01), and had the greatest proportion of subjects achieving targets ( P <.05). Walnuts were the main source of dietary fat (31%) and n-3 PUFA (50%), while 350 g oily fish/day provided a further 17% n-3 PUFA consumed by this group. CONCLUSIONS: Specific advice for the regular inclusion of walnuts in the context of the total diet helps achieve optimal fat intake proportions without adverse effects on total fat or energy intakes in patients with type 2 diabetes mellitus.

Adult↗

PubMed2006

Dynamic analysis of optimality in myocardial energy metabolism under normal and ischemic conditions.

To better understand the dynamic regulation of optimality in metabolic networks under perturbed conditions, we reconstruct the energetic-metabolic network in mammalian myocardia using dynamic flux balance analysis (DFBA). Additionally, we modified the optimal objective from the maximization of ATP production to the minimal fluctuation of the profile of metabolite concentration under ischemic conditions, extending the hypothesis of original minimization of metabolic adjustment to create a composite modeling approach called M-DFBA. The simulation results are more consistent with experimental data than are those of the DFBA model, particularly the retentive predominant contribution of fatty acid to oxidative ATP synthesis, the exact mechanism of which has not been elucidated and seems to be unpredictable by the DFBA model. These results suggest that the systemic states of metabolic networks do not always remain optimal, but may become suboptimal when a transient perturbation occurs. This finding supports the relevance of our hypothesis and could contribute to the further exploration of the underlying mechanism of dynamic regulation in metabolic networks.

Computer Simulation↗

PubMed2005

Analytic energy gradients of the optimized effective potential method.

The analytic energy gradients of the optimized effective potential (OEP) method in density-functional theory are developed. Their implementation in the direct optimization approach of Yang and Wu [Phys. Rev. Lett. 89, 143002 (2002)] and Wu and Yang [J. Theor. Comput. Chem. 2, 627 (2003)] are carried out and the validity is confirmed by comparison with corresponding gradients calculated via numerical finite difference. These gradients are then used to perform geometry optimizations on a test set of molecules. It is found that exchange-only OEP (EXX) molecular geometries are very close to the Hartree-Fock results and that the difference between the B3LYP and OEP-B3LYP results is negligible. When the energy is expressed in terms of a functional of Kohn-Sham orbitals, or in terms of a Kohn-Sham potential, the OEP becomes the only way to perform density-functional calculations and the present development in the OEP method should play an important role in the applications of orbital or potential functionals.

Journal Article↗

PubMed2004

An adaptive immune optimization algorithm for energy minimization problems.

Based on the immune theory of biology, a novel evolutionary algorithm, adaptive immune optimization algorithm (AIOA), is proposed. In AIOA, density regulation and immune selection is adopted to control the individual diversity and the convergence adaptively. By an application of the algorithm to the optimization of test functions, it is shown that the algorithm is a highly efficient optimization method compared with other stochastic optimization methods. The algorithm was also applied to the optimization of Lennard-Jones clusters, and the results show that the method can find the optimal structure of N</=80 with a very high efficiency. The proposed algorithm may be a good tool for fast global optimization in chemical or biological molecular simulations.

Journal Article↗

PubMed2006

Excited state geometry optimizations by analytical energy gradient of long-range corrected time-dependent density functional theory.

An analytical excitation energy gradient of long-range corrected time-dependent density functional theory (LC-TDDFT) is presented. This is based on a previous analytical TDDFT gradient formalism, which avoids solving the coupled-perturbed Kohn-Sham equation for each nuclear degree of freedom. In LC-TDDFT, exchange interactions are evaluated by combining the short-range part of a DFT exchange functional with the long-range part of the Hartree-Fock exchange integral. This LC-TDDFT gradient was first examined by calculating the excited state geometries and adiabatic excitation energies of small typical molecules and a small protonated Schiff base. As a result, we found that long-range interactions play a significant role even in valence excited states of small systems. This analytical LC-TDDFT gradient was also applied to the investigations of small twisted intramolecular charge transfer (TICT) systems. By comparing with calculated ab initio multireference perturbation theory and experimental results, we found that LC-TDDFT gave much more accurate absorption and fluorescence energies of these systems than those of conventional TDDFTs using pure and hybrid functionals. For optimized excited state geometries, LC-TDDFT provided fairly different twisting and wagging angles of these small TICT systems in comparison with conventional TDDFT results.

Journal Article↗