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Results for “energy optimization”

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At least 19 recordsLinked to original sources

PubMed1998

Self-consistently optimized energy functions for protein structure prediction by molecular dynamics.

The protein energy landscape theory is used to obtain optimal energy functions for protein structure prediction via simulated annealing. The analysis here takes advantage of a more complete statistical characterization of the protein energy landscape and thereby improves on previous approximations. This schema partially takes into account correlations in the energy landscape. It also incorporates the relationships between folding dynamics and characteristic energy scales that control the collapse of the proteins and modulate rigidity of short-range interactions. Simulated annealing for the optimal energy functions, which are associative memory hamiltonians using a database of folding patterns, generally leads to quantitatively correct structures. In some cases the algorithm achieves "creativity," i.e., structures result that are better than any homolog in the database.

Artificial Intelligence↗

PubMed1997

Simultaneous and coupled energy optimization of homologous proteins: a new tool for structure prediction.

BACKGROUND: Homology-based modeling and global optimization of energy are two complementary approaches to prediction of protein structures. A combination of the two approaches is proposed in which a novel component is added to the energy and forces similarity between homologous proteins. RESULTS: The combination was tested for two families: pancreatic hormones and homeodomains. The simulated lowest-energy structure of the pancreatic hormones is a reasonable approximation to the native fold. The lowest-energy structure of the homeodomains has 80% of the native contacts, but the helices are not packed correctly. The fourth lowest energy structure of the homeodomains has the correct helix packing (RMS 5.4 A and 82% of the correct contacts). Optimizations of a single protein of the family yield considerably worse structures. CONCLUSIONS: Use of coupled homologous proteins in the search for the native fold is more successful than the folding of a single protein in the family.

Amino Acid Sequence↗

PubMed2005

Energy-optimal electrical excitation of nerve fibers.

We derive, based on an analytical nerve membrane model and optimal control theory of dynamical systems, an energy-optimal stimulation current waveform for electrical excitation of nerve fibers. Optimal stimulation waveforms for nonleaky and leaky membranes are calculated. The case with a leaky membrane is a realistic case. Finally, we compare the waveforms and energies necessary for excitation of a leaky membrane in the case where the stimulation waveform is a square-wave current pulse, and in the case of energy-optimal stimulation. The optimal stimulation waveform is an exponentially rising waveform and necessitates considerably less energy to excite the nerve than a square-wave pulse (especially true for larger pulse durations). The described theoretical results can lead to drastically increased battery lifetime and/or decreased energy transmission requirements for implanted biomedical systems.

Action Potentials↗

PubMed2000

Fluctuations and the energy-optimal control of chaos

The energy-optimal entraining of the dynamics of a periodically driven oscillator, moving it from a chaotic attractor to a coexisting stable limit cycle, is investigated via analysis of fluctuational transitions between the two states. The deterministic optimal control function is identified with the corresponding optimal fluctuational force, which is found by numerical and analog simulations.

Journal Article↗

PubMed1995

Energy optimization and bifurcation angles in the microcirculation.

Our purpose was to examine the relationship between bifurcation angle and energy optimization in the arteriolar microcirculation. We measured bifurcation angles and diameters for sequential branches along a third-order feed arteriole (25 microns) in the superfused cremaster muscle of anesthetized (pentobarbital, 70 mg/kg) Golden hamsters (N = 51). Predicted bifurcation angles were calculated using the diameter data in a model designed to minimize total energy or using four different models each designed to minimize a specific energy cost (vessel wall surface area, vascular volume, wall shear stress, power losses), these models each assuming constant viscosity and that branching occurs with perfect space filling (i.e. junction exponent, x, = 3). The range of the predicted bifurcation angles for any model was small (+/- 10 degrees), and they were not different for the sequential junctions along the feed arteriole, where the observed angles significantly decreased in angle along the feed (first junction, 115 +/- 4.4 degrees; second, 88 +/- 5.2 degrees; third, 76 +/- 4.8 degrees; and last, 57 +/- 3.4 degrees). We next corrected for a nonconstant viscosity by using our in vivo tube hematocrit data and a published relationship among diameter, tube hematocrit, and apparent viscosity. Again assuming that x = 3, the total energy minimization model now predicted that the bifurcation angle was always obtuse and not different for the sequential branches along the feed arteriole (first, 125 +/- 3.3 degrees; second, 124 +/- 3.4 degrees; third, 120 +/- 6.6 degrees; and last, 132 +/- 2.7 degrees); the predicted angles were not correlated with the observed angles (r = 0.25). Using the geometric resistance (diameters) and the angles measured in vivo, and assuming constant viscosity, we next calculated the value of chi for each of the bifurcation junctions for each of the four models described above. The average value of x was not equal to 3 for any of the four models. The value of x decreased along the feed arteriole (first to last branch) from 2.7 +/- 0.26 to 1.6 +/- 0.22 (surface) and from 4.2 +/- 0.36 to 2.9 +/- 0.23 (volume), and x increased along the feed from 3.0 +/- 0.35 to 15.5 +/- 2.6 (shear stress) and from 40 +/- 31 to 82 +/- 49 (power loss). These calculations suggest that both changing viscosity and a changing value for the junction exponent are likely important when examining the energy optimization within the arteriolar microcirculation.

Animals↗

PubMed2004

Reducing exposure from 57Co sources during breast lymphoscintigraphy by optimizing energy windows and other suggested enhancements of acquisition and the display of images.

UNLABELLED: We set out to measure the reduction in exposure attained by using a weak 57Co sheet source with optimal energy windows. METHODS: Two groups of 10 lymphoscintigraphy studies were analyzed. Group 1 consisted of 10 studies obtained with a stronger source of 57Co, 59 MBq (1.6 mCi) at the time of data acquisition, with transmission images acquired at 3 energy windows of 115-129, 130-134, and 135-150 keV. Group 2 consisted of 10 studies with a weaker sheet source of 57Co, 11 MBq (0.3 mCi). Transmission images were acquired at 3 energy windows of 112-132, 130-134, and 135-150 keV. Same-sized regions of interest (ROIs) were drawn on the patient's torso (PT) and on the nonattenuated image of the transmission source itself (TS), all 1-min images. The counts in each ROI obtained over 1 min and the ratios between the TS ROI and the PT ROI were calculated for all of the energies. Dosimetry calculations based on measured exposure rates and the activity of the sheet sources were used to calculate the patient equivalent dose at 30 cm. RESULTS: For the 57Co energy window, group 1 had an average ROI count of 1,955 in the TS region and 135 counts in the PT region. The average ratio of TS/PT was 15.4. Similarly, group 2 had an average ROI count of 646.4 in the TS region and 91.2 counts in the PT region. The average ratio of TS/PT was 8.6. The relative "outlining performance," when comparing the 57Co and 99mTc windows, showed an average improvement when using the 57Co window of 4.4 and 5.8 times for group 1 and group 2, respectively (TS/PT at 57Co window)/(TS/PT at 99mTc window). Estimates of the patient equivalent dose per study were 2.30 microSv for the stronger 57Co flood source and 0.46 microSv for the weaker 57Co flood source, a 5-fold reduction in equivalent dose. Technologists received less than half of the above doses. CONCLUSION: Use of expanded, separate energy windows optimized for the primary 122-keV photon of 57Co greatly improves transmission scan image quality compared with the standard 140-keV 99mTc windows used for the delineation of the sentinel node. This markedly reduces exposure for all, by allowing the use of a weaker source, and can save time.

Breast↗

PubMed1998

Optimizing energy potentials for success in protein tertiary structure prediction.

BACKGROUND: Success in solving the protein structure prediction problem relies on the choice of an accurate potential energy function. for a single protein sequence, it has been shown that the potential energy function can be optimized for predictive success by maximizing the energy gap between the correct structure and the ensemble of random structures relative to the distribution of the energies of these random structures (the Z-score). Different methods have been described for implementing this procedure for an ensemble of database proteins. Here, we demonstrate a new approach. RESULTS: For a single protein sequence, the probability of success (i.e the probability that the folded state is the lowest energy state) is derived. We then maximize the average probability of success for a set of proteins to obtain the optimal potential energy function. This results in maximum attention being focused on the proteins whose structures are difficult but not impossible to predict. CONCLUSIONS: Using a lattice model of proteins, we show that the optimal interaction potentials obtained by our method are both more accurate and more likely to produce successful predictions than those obtained by other averaging procedures.

Computer Simulation↗

PubMed2003

ICM-DISCO docking by global energy optimization with fully flexible side-chains.

The ICM-DISCO (Docking and Interface Side-Chain Optimization) protein-protein-docking method is a direct stochastic global energy optimization from multiple starting positions of the ligand. The first step is performed by docking of a rigid all-atom ligand molecule to a set of soft receptor potentials precalculated on a 0.5 A grid from realistic solvent-corrected force-field energies. This step finds the correct solution as the lowest energy conformation in almost 100% of the cases in which interfaces do not change on binding. The second step is needed to deal with the induced changes and includes the global optimization of the interface side-chains of up to 400 best solutions. The CAPRI predictions were performed fully automatically with this method. Available experimental information was included as a filtering step to favor expected docking surfaces. In three of the seven proposed targets, the ICM-DISCO method found a good solution (>50% of correct contacts) within the five submitted models. The procedure is global and fully automated. We demonstrate that the algorithm handles the induced changes of surface side-chains but is less successful if the backbone undergoes large-scale rearrangements.

Algorithms↗

PubMed1992

Energy-optimized structure of antifreeze protein and its binding mechanism.

A combination of Monte Carlo simulated annealing and energy minimization was utilized to determine the conformation of the antifreeze protein from the fish winter flounder. It was found from the energy-optimized structure that the hydroxyl groups of its four threonine residues, i.e. Thr2, Thr13, Thr24, Thr35, are aligned on almost the same line parallel to the helix axis and separated successively by 16.1, 16.0 and 16.2 A, respectively, very close to the 16.6 A repeat spacing along [0112] in ice. Based on such a space match, a zipper-like model is proposed to elucidate the binding mechanism of the antifreeze protein to ice crystals. According to the current model, the antifreeze protein may bind to an ice nucleation structure in a zipper-like fashion through hydrogen bonding of the hydroxyl groups of these four Thr residues to the oxygen atoms along the [0112] direction in ice lattice, subsequently stopping or retarding the growth of ice pyramidal planes so as to depress the freeze point. The calculated results and the binding mechanism thus derived accord with recent experimental observations. The mechanistic implications derived from such a special antifreeze molecule might be generally applied to elucidate the structure-function relationship of other antifreeze proteins with the following two common features: (1) recurrence of a Thr residue (or any other polar amino acid residue whose side-chain can form a hydrogen bond with water) in an 11-amino-acid period along the sequence concerned; and (2) a high percentage of Ala residue component therein. Further experiments are suggested to test the ice binding model.

Amino Acid Sequence↗

PubMed2004

Fully quantum mechanical energy optimization for protein-ligand structure.

We present a quantum mechanical approach to study protein-ligand binding structure with application to a Adipocyte lipid-binding protein complexed with Propanoic Acid. The present approach employs a recently develop molecular fractionation with a conjugate caps (MFCC) method to compute protein-ligand interaction energy and performs energy optimization using the quasi-Newton method. The MFCC method enables us to compute fully quantum mechanical ab initio protein-ligand interaction energy and its gradients that are used in energy minimization. This quantum optimization approach is applied to study the Adipocyte lipid-binding protein complexed with Propanoic Acid system, a complex system consisting of a 2057-atom protein and a 10-atom ligand. The MFCC calculation is carried out at the Hartree-Fock level with a 3-21G basis set. The quantum optimized structure of this complex is in good agreement with the experimental crystal structure. The quantum energy calculation is implemented in a parallel program that dramatically speeds up the MFCC calculation for the protein-ligand system. Similarly good agreement between MFCC optimized structure and the experimental structure is also obtained for the streptavidin-biotin complex. Due to heavy computational cost, the quantum energy minimization is carried out in a six-dimensional space that corresponds to the rigid-body protein-ligand interaction.

Carrier Proteins↗

PubMed2000

On the optimal energy of epithermal neutron beams for BNCT.

The optimal neutron energy for the treatment of deep-seated tumours using boron neutron capture therapy is studied by analysing various figures of merit. In particular, analysis of the therapeutic gain as a function of the neutron energy indicates that, with the currently available 10B carriers, the most useful neutrons for the treatment of deep-seated tumours, in particular glioblastoma multiforme, are those with an energy of a few keV. Based on the results of the simulations, a method is presented which allows us to evaluate the quality of epithermal neutron beams of known energy spectrum, thus allowing us to compare different neutron-producing reactions and beam-shaping assembly configurations used for accelerator-based neutron sources.

Boron↗

PubMed2000

Optimized energy calculation in lattice systems with long-range interactions

We discuss an efficient approach to the calculation of the internal energy in numerical simulations of spin systems with long-range interactions. Although, since the introduction of the Luijten-Blote algorithm, Monte Carlo simulations of these systems no longer pose a fundamental problem, the energy calculation is still an O(N2) problem for systems of size N. We show how this can be reduced to an O(N log N) problem, with a break-even point that is already reached for very small systems. This allows the study of a variety of, until now hardly accessible, physical aspects of these systems. In particular, we combine the optimized energy calculation with histogram interpolation methods to investigate the specific heat of the Ising model and the first-order regime of the three-state Potts model with long-range interactions.

Journal Article↗

PubMed1997

Flexible protein-ligand docking by global energy optimization in internal coordinates.

Eight protein-ligand complexes were simulated by using global optimization of a complex energy function, including solvation, surface tension, and side-chain entropy in the internal coordinate space of the flexible ligand and the receptor side chains [Abagyan, R.A., Totrov, M.M. J. Mol. Biol. 235: 983-1002, 1994]. The procedure uses two types of efficient random moves, a pseudobrownian positional move [Abagyan, R.A., Totrov, M.M., Kuznetsov, D.A. J. Comp. Chem. 15:488-506, 1994] and a Biased-Probability multitorsion move [Abagyan, R.A., Totrov, M.M. J. Mol. Biol. 235: 983-1002, 1994], each accompanied by full local energy minimization. The best docking solutions were further ranked according to the interaction energy, which included intramolecular deformation energies of both receptor and ligand, the interaction energy, surface tension, side-chain entropic contribution, and an electrostatic term evaluated as a boundary element solution of the Poisson equation with the molecular surface as a dielectric boundary. The geometrical accuracy of the docking solutions ranged from 30% to 70% according to the relative displacement error measure at a 1.5 A scale. Similar results were obtained when the explicit receptor atoms were replaced with a grid potential.

Computer Simulation↗

PubMed2004

Improvement of comparative model accuracy by free-energy optimization along principal components of natural structural variation.

Accurate high-resolution refinement of protein structure models is a formidable challenge because of the delicate balance of forces in the native state, the difficulty in sampling the very large number of alternative tightly packed conformations, and the inaccuracies in current force fields. Indeed, energy-based refinement of comparative models generally leads to degradation rather than improvement in model quality, and, hence, most current comparative modeling procedures omit physically based refinement. However, despite their inaccuracies, current force fields do contain information that is orthogonal to the evolutionary information on which comparative models are based, and, hence, refinement might be able to improve comparative models if the space that is sampled is restricted sufficiently so that false attractors are avoided. Here, we use the principal components of the variation of backbone structures within a homologous family to define a small number of evolutionarily favored sampling directions and show that model quality can be improved by energy-based optimization along these directions.

Models, Molecular↗

PubMed2006

QBES: predicting real values of solvent accessibility from sequences by efficient, constrained energy optimization.

Solvent accessibility, one of the key properties of amino acid residues in proteins, can be used to assist protein structure prediction. Various approaches such as neural network, support vector machines, probability profiles, information theory, Bayesian theory, logistic function, and multiple linear regression have been developed for solvent accessibility prediction. In this article, a much simpler quadratic programming method based on the buriability parameter set of amino acid residues is developed. The new method, called QBES (Quadratic programming and Buriability Energy function for Solvent accessibility prediction), is reasonably accurate for predicting the real value of solvent accessibility. By using a dataset of 30 proteins to optimize three parameters, the average correlation coefficients between the predicted and actual solvent accessibility are about 0.5 for all four independent test sets ranging from 126 to 513 proteins. The method is efficient. It takes only 20 min for a regular PC to obtain results of 30 proteins with an average length of 263 amino acids. Although the proposed method is less accurate than a few more sophisticated methods based on neural network or support vector machines, this is the first attempt to predict solvent accessibility by energy optimization with constraints. Possible improvements and other applications of the method are discussed.

Protein Conformation↗

PubMed2004

Synchrotron radiation-based experimental determination of the optimal energy for cell radiotoxicity enhancement following photoelectric effect on stable iodinated compounds.

This study was designed to experimentally evaluate the optimal X-ray energy for increasing the radiation energy absorbed in tumours loaded with iodinated compounds, using the photoelectric effect. SQ20B human cells were irradiated with synchrotron monochromatic beam tuned at 32.8, 33.5, 50 and 70 keV. Two cell treatments were compared to the control: cells suspended in 10 mg ml(-1) of iodine radiological contrast agent or cells pre-exposed with 10 microM of iodo-desoxyuridine (IUdR) for 48 h. Our radiobiological end point was clonogenic cell survival. Cells irradiated with both iodine compounds exhibited a radiation sensitisation enhancement. Moreover, it was energy dependent, with a maximum at 50 keV. At this energy, the sensitisation calculated at 10% survival was equal to 2.03 for cells suspended in iodinated contrast agent and 2.60 for IUdR. Cells pretreated with IUdR had higher sensitisation factors over the energy range than for those suspended in iodine contrast agent. Also, their survival curves presented no shoulder, suggesting complex lethal damages from Auger electrons. Our results confirm the existence of the 50 keV energy optimum for a binary therapeutic irradiation based on the presence of stable iodine in tumours and an external irradiation. Monochromatic synchrotron radiotherapy concept is hence proposed for increasing the differential effect between healthy and cancerous tissue irradiation.

Carcinoma, Squamous Cell↗

PubMed1993

Towards protein folding by global energy optimization.

Different components of the theoretical protein folding problem are evaluated critically. It is argued that: (i) as a rule, small- and medium-sized proteins are in the free energy minimum; (ii) long-living metastable states may either appear occasionally with growing protein size, or be selected by evolution for a specific function; (iii) functions discriminating against incorrect folds would fail if they were used directly in the global optimization, unless they approximate the true free energy accurately; (iv) surface and electrostatic free energies should be treated separately; (v) conformational entropy (of side chains in particular) should be taken into account; (vi) Monte Carlo procedures considering all free energy terms and combining global knowledge-based random moves with local optimization have the largest potential for success.

Electrochemistry↗

PubMed1986

Optimal energy management in grain drying.

Grain drying is very specific to the geographic location, kind of drying system, and the type of grain. Under a given set of conditions, the optimal system can be selected based on careful evaluation. However, a good choice of drying systems, procedures, and management practices can be made from the information already available. The review of several grain-drying procedures has provided some insight in making a quick evaluation of the process and arriving at the most suitable system for a particular application. Despite extensive research efforts, the present knowledge of grain drying is yet insufficient to optimally design each drying process with respect to capacity, quality, and energy requirement. There is a need for incorporating grain and air parameters more accurately. It is also important to develop comprehensive drying simulation models to encompass agronomic practices, such as planting and harvesting. Recent efforts indicate a strong influence of planting and harvesting strategies on optimal drying and storage system selection. Results of the varietal trials at Ohio State University indicate that it is now possible to select midseason varieties, which dry down rapidly, without sacrificing yield. Also, low moisture at harvest is important to the energy management process because it affects total drying time and energy required. It is also important from a quality standpoint because kernel damage increases rapidly at harvesting moisture levels above 25%. The trend in grain-dryer design has shifted from focusing on drying capacity and operation reliability to energy consumption. The development in design of energy efficient continuous-flow dryers has been significant. Multistage concurrentflow dryers are excellent examples. Various aspects of dryer staging for efficient operation and control are yet to be determined. Recirculation of the exhaust air is a proven method of improving energy efficiency. Likewise, in batch-in-bin systems, stirring and intermittent drying are worth considering. Further research is required to formulate the best procedures for exhaust air recirculation and intermittent drying. Low temperature drying has a great potential in the U.S. corn belt. The suitability of low temperature drying at other places and for grains other than corn has not yet been well established. Energy savings resulting from low temperature drying entail careful planning and management on the part of the operator. Poor design and operation can result in a serious deterioration in grain quality.(ABSTRACT TRUNCATED AT 400 WORDS)

Conservation of Energy Resources↗