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PubMed2003

Reducing uncertainties in volumetric image based deformable organ registration.

Applying volumetric image feedback in radiotherapy requires image based deformable organ registration. The foundation of this registration is the ability of tracking subvolume displacement in organs of interest. Subvolume displacement can be calculated by applying biomechanics model and the finite element method to human organs manifested on the multiple volumetric images. The calculation accuracy, however, is highly dependent on the determination of the corresponding organ boundary points. Lacking sufficient information for such determination, uncertainties are inevitable-thus diminishing the registration accuracy. In this paper, a method of consuming energy minimization was developed to reduce these uncertainties. Starting from an initial selection of organ boundary point correspondence on volumetric image sets, the subvolume displacement and stress distribution of the whole organ are calculated and the consumed energy due to the subvolume displacements is computed accordingly. The corresponding positions of the initially selected boundary points are then iteratively optimized to minimize the consuming energy under geometry and stress constraints. In this study, a rectal wall delineated from patient CT image was artificially deformed using a computer simulation and utilized to test the optimization. Subvolume displacements calculated based on the optimized boundary point correspondence were compared to the true displacements, and the calculation accuracy was thereby evaluated. Results demonstrate that a significant improvement on the accuracy of the deformable organ registration can be achieved by applying the consuming energy minimization in the organ deformation calculation.

Algorithms↗

PubMed1999

Toward designing the optimal total cavopulmonary connection: an in vitro study.

BACKGROUND: Understanding the total cavopulmonary connection (TCPC) hemodynamics may lead to improved surgical procedures which result in a more efficient modified circulation. Reduced energy loss will translate to less work for the single ventricle and although univentricular physiology is complex, this improvement could contribute to improved postoperative outcomes. Therefore to conserve energy, one surgical goal is optimization of the TCPC geometry. In line with this goal, this study investigated whether addition of caval curvature or flaring at the connection conserves energy. METHODS: TCPC models were made varying the curvature of the caval inlet or by flaring the anastomosis. Steady flow pressure measurements were made to calculate the power loss attributed to each connection design over a range of pulmonary flow splits (70:30 to 30:70). Particle flow visualization was performed for each design and was qualitatively compared to the power losses. RESULTS: Results indicate that curving the cavae toward one pulmonary artery is advantageous only when the flow rate from that cavae matches the flow to the pulmonary artery. Under other pulmonary flow split conditions, the losses in the curved models are significant. In contrast, fully flaring the anastomosis reduced losses over the range of pulmonary flow splits. Power losses were 56% greater for the curving as compared to flaring. Fully flaring without caval offset reduced losses 45% when compared to previous models without flaring. If flaring on all sides was implemented with caval offset, power losses reduced 68% compared to the same nonflared model. CONCLUSIONS: The results indicate that preferentially curving the cavae is only optimal under specific pulmonary flow conditions and may not be efficient in all clinical cases. Flaring of the anastomosis has great potential to conserve energy and should be considered in future TCPC procedures.

Anastomosis, Surgical↗

PubMed2003

Performance of hybrid methods for large-scale unconstrained optimization as applied to models of proteins.

Energy minimization plays an important role in structure determination and analysis of proteins, peptides, and other organic molecules; therefore, development of efficient minimization algorithms is important. Recently, Morales and Nocedal developed hybrid methods for large-scale unconstrained optimization that interlace iterations of the limited-memory BFGS method (L-BFGS) and the Hessian-free Newton method (Computat Opt Appl 2002, 21, 143-154). We test the performance of this approach as compared to those of the L-BFGS algorithm of Liu and Nocedal and the truncated Newton (TN) with automatic preconditioner of Nash, as applied to the protein bovine pancreatic trypsin inhibitor (BPTI) and a loop of the protein ribonuclease A. These systems are described by the all-atom AMBER force field with a dielectric constant epsilon = 1 and a distance-dependent dielectric function epsilon = 2r, where r is the distance between two atoms. It is shown that for the optimal parameters the hybrid approach is typically two times more efficient in terms of CPU time and function/gradient calculations than the two other methods. The advantage of the hybrid approach increases as the electrostatic interactions become stronger, that is, in going from epsilon = 2r to epsilon = 1, which leads to a more rugged and probably more nonlinear potential energy surface. However, no general rule that defines the optimal parameters has been found and their determination requires a relatively large number of trial-and-error calculations for each problem.

Algorithms↗

PubMed1994

Red blood cell function in hypoxia at altitude and exercise.

Oxygen transport by red blood cells is regulated by erythropoiesis and Hb-O2-affinity. The O2 carrying capacity is characterized by changes in hematocrit, red blood count or the mass of circulating red blood cells. Erythropoiesis is controlled by the hormone erythropoietin, which induces slow changes of the O2-transport capacity. The Hb-O2-affinity is modified mainly by pH and 2,3-DPG. Despite their apparently diverse effects e.g. in hypoxia at high altitude, a compromise seems to be adopted optimizing both arterial O2-loading and peripheral O2-unloading. In contrast to erythropoiesis, adjustments of the Hb-O2-affinity occur fast and allow rapid adjustments of O2-binding and release. In the intact organism the significance of changes in Hb-O2-affinity for tissue oxygen supply relative to adjustments of cardiac output, microcirculation and O2-transport capacity is not completely understood yet, but beneficial effects were demonstrated in isolated organs. It is, however, the least energy-demanding way of optimizing tissue O2-supply, which might be of significance in extreme situations. In severe hypoxia adjustments of both, hematocrit and Hb-O2-affinity, are insufficient to maintain tissue O2-supply. Alterations of Hb-O2-affinity are also insufficient to compensate for severe anemia.

Altitude↗

PubMed2004

Optimized Jastrow-Slater wave functions for ground and excited states: application to the lowest states of ethene.

A quantum Monte Carlo method is presented for determining multideterminantal Jastrow-Slater wave functions for which the energy is stationary with respect to the simultaneous optimization of orbitals and configuration interaction coefficients. The approach is within the framework of the so-called energy fluctuation potential method which minimizes the energy in an iterative fashion based on Monte Carlo sampling and a fitting of the local energy fluctuations. The optimization of the orbitals is combined with the optimization of the configuration interaction coefficients through the use of additional single excitations to a set of external orbitals. A new set of orbitals is then obtained from the natural orbitals of this enlarged configuration interaction expansion. For excited states, the approach is extended to treat the average of several states within the same irreducible representation of the pointgroup of the molecule. The relationship of our optimization method with the stochastic reconfiguration technique by Sorella et al. is examined. Finally, the performance of our approach is illustrated with the lowest states of ethene, in particular with the difficult case of the 1(1)B(1u) state.

Journal Article↗

PubMed2006

Novel approach for alpha-helical topology prediction in globular proteins: generation of interhelical restraints.

The protein folding problem represents one of the most challenging problems in computational biology. Distance constraints and topology predictions can be highly useful for the folding problem in reducing the conformational space that must be searched by deterministic algorithms to find a protein structure of minimum conformational energy. We present a novel optimization framework for predicting topological contacts and generating interhelical distance restraints between hydrophobic residues in alpha-helical globular proteins. It should be emphasized that since the model does not make assumptions about the form of the helices, it is applicable to all alpha-helical proteins, including helices with kinks and irregular helices. This model aims at enhancing the ASTRO-FOLD protein folding approach of Klepeis and Floudas (Journal of Computational Chemistry 2003;24:191-208), which finds the structure of global minimum conformational energy via a constrained nonlinear optimization problem. The proposed topology prediction model was evaluated on 26 alpha-helical proteins ranging from 2 to 8 helices and 35 to 159 residues, and the best identified average interhelical distances corresponding to the predicted contacts fell below 11 A in all 26 of these systems. Given the positive results of applying the model to several protein systems, the importance of interhelical hydrophobic-to-hydrophobic contacts in determining the folding of alpha-helical globular proteins is highlighted.

Animals↗

PubMed2004

Screening and identification of glycosides in biological samples using energy-gradient neutral loss scan and liquid chromatography tandem mass spectrometry.

A rapid, selective, and reliable strategy has been developed for the screening and identification of glycosides in biological samples: a crude extract was directly infused to a triple-quadrupole MS/MS, and major glycosides were screened out with high confidence by an energy-gradient neutral loss scan (EGNLS) for the loss of sugar(s); then these glycosides were further identified with LC/MS/MS. The proposed EGNLS method was established and optimized with 16 representative glycosides (including ginsenosides and the glycosides of flavones, anthraquinones, and terpenoids). The EGNLS method has two major advantages over the conventional fixed-energy neutral loss scan: (1) The latter is liable to '"omit" some target compounds due to the usual mismatch between the preset collision energy and interested compounds' optimal collision energy (OCE), while EGNLS solves this problem by scanning over an energy range. (2) The EGNLS simultaneously measures the screened compounds' OCE, which not only are essential parameters for further LC/MS/MS analysis but also carry some structural information, as proved by this study. This strategy has been successfully demonstrated with the analysis of glycosides in Scutellaria viscidula Bge and transformed Panaxhairy roots (the glycoside constitutions of both had not been studied before): without laborious separation processes; comprehensive glycoside information on those two plants was obtained by a rapid and simple procedure. This strategy is valuable for the study of glycosides in complex samples.

Chromatography, High Pressure Liquid↗

PubMed1995

Implantable atrial defibrillators.

Due to the limited efficacy of antiarrhythmic drugs for atrial fibrillation, several nonpharmacologic therapeutic options have evolved. One of these is an implantable atrial defibrillator. Recent studies have shown that internal atrial defibrillation is feasible with relatively low energies. To date, the optimal electrode configuration involves large surface area catheters in the right atrium and coronary sinus. In humans, atrial defibrillation can generally be achieved with < 2 J using this electrode configuration and a biphasic shock waveform. For shocks < 5 J, there is no significant pathological damage to the atria or coronary sinus. Further investigation is needed to guarantee that atrial defibrillation shocks do not provoke ventricular arrhythmias. Preliminary data suggest that atrial defibrillation shocks synchronized to R waves that are not closely coupled are safe. In addition, the shocks are well tolerated if the shock energy is < 1.5 J. With additional studies to confirm the safety of implantable atrial defibrillators, further reduce shock energy, and improve patient tolerance, an implantable atrial defibrillator can become an acceptable therapy for patients with symptomatic, paroxysmal atrial fibrillation.

Animals↗

PubMed1997

A model of scorpion toxin binding to voltage-gated K+ channels.

Mutational studies have identified part of the S5-S6 loop of voltage-dependent K+ channels (P region) responsible for tetraethylammonium (TEA) block and permeation properties. Several scorpion peptide toxins-charybdotoxin (ChTX), kaliotoxin (KITX), and agitoxin (AgTX)-also block the channel with high affinity and specificity. Here, we examine the interaction predicted when the toxins are docked onto the molecular model of the K+ channel pore that we recently proposed. Docking with the model of the Kv1.3 channel started by location of Lys-27 side chain into the central axis of the pore, followed by energy minimization. In the optimal arrangement, Arg-24 of KITX or AgTX forms a hydrogen bond with the Asp-386 carboxyl of one subunit, and Asn-30 is in immediate contact with Asp-386 of the opposing subunit in the tetramer. Toxin residues in proximity to the side chain of Lys-27 (Phe-25, Thr-36, Met-29, and Ser-11 in KITX) interact with the four C-end His-404s. For ChTX the interaction with Asp-386 is reduced, but this is compensated by additional nonbonded interactions formed by Tyr-36 and Arg-34. Comparison of calculated energy of interaction of these specific toxin-channel residues with experimental studies reveals good agreement. The similar total calculated energy of interaction is consistent with the similar IC50 for Kv1.3 block by KITX and AgTX. Steric contacts of residues in position 380 of the S5-P linker with residues on the upper part of toxins permit reconstruction of the K+ channel outer vestibule walls, which are about 30 A apart and about 9 A high. Molecular modeling shows complementarity of the pore model to toxin spacial structures, and supports the proposal that the N-terminal borders of the P regions surround residues of their C-terminal halves.

Amino Acid Sequence↗

PubMed2006

Dietary intervention and oxidative phosphorylation capacity.

Secondary deterioration of mitochondrial function has been reported in patients with anorexia and cancer-related malnutrition. Inadequate nutrition, failure to thrive and feeding problems are also common symptoms in children with primary oxidative phosphorylation defects. As a standard intervention protocol we advise an age-appropriate diet and energy intake in our patients diagnosed with a mitochondrial dysfunction. By comparing the results of the first and the second samples from a group of children who underwent repeated muscle biopsies, we observed biochemical improvement in the mitochondrial function in 7 out of 10 patients following dietary advice and intervention. We suggest evaluating the nutritional state by interpretation of the skeletal muscle biochemistry in patients with a suspected oxidative phosphorylation defect. Since an insufficient dietary intake could play a role in secondary mitochondrial dysfunction, nutritional intervention should be performed prior to the biopsy. On the other hand, our data suggest that optimizing the nutritional and energy intake might also improve the utilization of the residual mitochondrial energy-generating capacity in patients with primary oxidative phosphorylation defects.

Adenosine Triphosphate↗

PubMed2006

Computational models with thermodynamic and composition features improve siRNA design.

BACKGROUND: Small interfering RNAs (siRNAs) have become an important tool in cell and molecular biology. Reliable design of siRNA molecules is essential for the needs of large functional genomics projects. RESULTS: To improve the design of efficient siRNA molecules, we performed a comparative, thermodynamic and correlation analysis on a heterogeneous set of 653 siRNAs collected from the literature. We used this training set to select siRNA features and optimize computational models. We identified 18 parameters that correlate significantly with silencing efficiency. Some of these parameters characterize only the siRNA sequence, while others involve the whole mRNA. Most importantly, we derived an siRNA position-dependent consensus, and optimized the free-energy difference of the 5' and 3' terminal dinucleotides of the siRNA antisense strand. The position-dependent consensus is based on correlation and t-test analyses of the training set, and accounts for both significantly preferred and avoided nucleotides in all sequence positions. On the training set, the two parameters' correlation with silencing efficiency was 0.5 and 0.36, respectively. Among other features, a dinucleotide content index and the frequency of potential targets for siRNA in the mRNA added predictive power to our model (R = 0.55). We showed that our model is effective for predicting the efficiency of siRNAs at different concentrations. We optimized a neural network model on our training set using three parameters characterizing the siRNA sequence, and predicted efficiencies for the test siRNA dataset recently published by Novartis. On this validation set, the correlation coefficient between predicted and observed efficiency was 0.75. Using the same model, we performed a transcriptome-wide analysis of optimal siRNA targets for 22,600 human mRNAs. CONCLUSION: We demonstrated that the properties of the siRNAs themselves are essential for efficient RNA interference. The 5' ends of antisense strands of efficient siRNAs are U-rich and possess a content similarity to the pyrimidine-rich oligonucleotides interacting with the polypurine RNA tracks that are recognized by RNase H. The advantage of our method over similar methods is the small number of parameters. As a result, our method requires a much smaller training set to produce consistent results. Other mRNA features, though expensive to compute, can slightly improve our model.

Artificial Intelligence↗

PubMed2006

Theoretical search for the growth-temperature relationship in plants.

In this article we deal with the definition of a new phenomenological model with physical bases for the response of short-term cell expansion growth to temperature. Although the interest on both the biomechanical bases of elongation growth and on temperature responses has a long lasting development in plant biology and biophysics, yet the question of the mode of actions of temperature is a very relevant and still open one. The purpose of our paper was not to deal with all the complexity of the possible effects of temperature on a growing cell but to concentrate on two more focused questions: i) whether it is possible to specify an optimal temperature for growth responses all along development by defining some phenomenological equations for temperature response, ii) can we learn something from that on the temperature dependence of the cell wall expansion process using a minimal analytical modelling? To answer both questions we introduce (by extending Lockhart approach) the notion of temperature by simple thermodynamical reasoning. Assuming incompressibility of water (by the constant molar density n/V ) we also accounted for the role of osmosis and consequently - the role of water uptake in growing cell. This approach allowed us (by comparing theoretical solutions and experimental results) not only to determine the specific (resonance) temperature (or corresponding absorption energy kBT*) of the optimal growth but also draw conclusions about the cell wall extensibility dependence on temperature and its evolution in time. A straightforward application of our method to determine optimum growth temperature for different plant species in a greenhouse practice (as its simple implication) can also be recommended.

Biomechanical Phenomena↗

PubMed1982

Enzymatic activity of Trp 62-modified lysozyme.

The time-courses of action of Trp 62-modified lysozymes on the initial substrate chitopentaose were measured by means of high-performance gel-filtration. The activities of the modified lysozymes, represented by the rate of disappearance of the initial substrate (overall rate) were lowered to various extents depending on the method of the modification. On the other hand, the time-courses were calculated by changing the values of rate constants, using the binding free energy of each subsite estimated by the optimization technique (Kuhara et al. (1982) J. Biochem.). For NBS- and NPS-lysozymes, the calculated time-courses were not in good agreement with the experimental ones, when the binding free energies estimated by the optimization technique were used for the calculation. Therefore, the binding free energies of the subsites were estimated from the experimental time-courses with the assumption that the values of the rate constants do not change upon modification of Trp 62 in subsite C. As a result, it was found that, though the modification was at subsite C, the binding free energy of subsite A was profoundly lowered, while that of subsite B remained almost unchanged.

Energy Metabolism↗

PubMed2005

Theoretical determination of standard oxidation and reduction potentials of chlorophyll-a in acetonitrile.

QM/MM calculations were performed on ethyl chlorophyllide-a and its radical cation and anion, by using the density functional (DF) B3LYP method to determine the molecular characteristics, and a molecular mechanics (MM) method to simulate the solvating medium. The presence of the solvent was accounted for during the optimization of the geometry of the 85-atom chlorophyll-a system by using an ONIOM methodology. A total of 24 solvent molecules were explicitly considered during the optimization process, and these were treated by the universal force field (UFF) method. Initially, the split-valence 3-21G basis set was used for optimizing the geometry of the 85-atom species, neutral, cation and anion. Electronic energies were then determined for the optimized species by making use of the polarized 6-31G(d) basis set. The ionization energy calculated (6.0 eV) is in very good agreement with the observed one (6.1 eV). The MM+ force field was used to investigate the dynamics of the acetonitrile molecules around the neutral species as well as the radical ions of chlorophyll. The required atomic charges on all the atoms were obtained from calculations on all involved molecules at the DFT/6-31G(d) level. Randomly sampled configurations were used to determine the first solvation layer contribution to the free energy of solvation of various species. A truncated 46-atom model of ethyl chlorophyllide-a was used to evaluate the thermal energies of neutral chlorophyll molecule relative to its two radical ions in the gas phase. Born energy, Onsager energy, and the Debye-Huckel energy of the chlorophyll-solvent aggregate were added as perturbative corrections to the free energy of solvation that was initially obtained through molecular dynamics method for the same complex. These calculations yield the oxidation potential as 0.75 +/- 0.32 V and the reduction potential -1.18 +/- 0.31 V at 298.15 K. The calculated values are in good agreement with the experimental midpoint potentials of +0.76 and -1.04 V, respectively.

Journal Article↗

PubMed2006

Density-functional geometry optimization of the 150,000-atom photosystem-I trimer.

We present a linear-scaling method based on the use of density-functional theory (DFT) for the system-wide optimization of x-ray structural coordinates and apply it to optimize the 150,000 atoms of the photosystem-I (PS-I) trimer. The method is based on repetitive applications of a multilevel ONIOM procedure using the PW916-31G(d) DFT calculations for the high level and PM3 for the lower level; this method treats all atoms in the structure equivalently, a structure in which the majority of the atoms can be considered as part of some internal "active site." To obtain a realistic single structure, some changes to the original protein model were necessary but these are kept to a minimum in order that the optimized structure most closely resembles the original x-ray one. Optimization has profound effects on the perceived electronic properties of the cofactors, with, e.g., optimization lowering the internal energy of the chlorophylls by on average 53 kcal mol(-1) and eliminates the enormous 115 kcal mol(-1) energy spread depicted by the original x-ray heavy-atom coordinates. A highly precise structure for PS-I results that is suitable for analysis of device function. Significant qualitative features of the structure are also improved such as correction of an error in the stereochemistry of one of the chlorophylls in the "special pair" of the reaction center, as well as the replacement of a water molecule with a metal cation in a critical region on the C3 axis. The method also reveals other unusual features of the structure, leading both to suggestions concerning device functionality and possible mutations between gene sequencing and x-ray structure determination. The optimization scheme is thus shown to augment the molecular modeling schemes that are currently used to add medium-resolution structural information to the raw scattering data in order to obtain atomically resolved structures. System-wide optimization is now a feasible process and its use within protein x-ray data refinement should be considered.

Binding Sites↗

PubMed2003

Boltzmann-type distribution of side-chain conformation in proteins.

We analyze packing imperfections in globular proteins as reflected in deviations of torsion angles from the equilibrium values for the isolated side chains. The distribution of conformations of methionine and lysine residues in a database of high-resolution structures is compared with energies of model compounds calculated with high-level quantum-mechanics. The distribution of the C-C and C-S torsion angles (chi(3)) correlates well with the Boltzmann factor of the torsion energy, exp(-betaE) of the model compounds C(2)H(5)-C(2)H(5) and C(2)H(5)-S-CH(3). An exponential relation was again found between the relative occurrence of g+, g- and t conformations for C(alpha)-C(beta) bonds in long side chains and the energy differences of rotamers of alpha-amino n-butyric acid, when dependence on backbone conformation was taken into account. The distribution of all 27 rotamers of methionine was correlated with the energy differences between the model's rotamers, corrected for clashes with nearby residues, the correlation being good for a set with backbone in the beta-conformation, but less clear for backbone alpha-conformation. In all correlations, the value of the coefficient beta corresponds to a temperature of circa 300 K. These results can be interpreted with a model that considers the structure of a folded protein as resulting from packing imperfectly complementary parts, with a requirement of an overall low energy. Compromises are required to optimize the fit of nonbonded contacts with surrounding groups, and side chains assume conformations away from the energy minimum. An exponential distribution is a most probable distribution, and this can be established easily under conditions other than thermal equilibrium.

Butanes↗

PubMed2006

Optimal HP configurations of proteins by combining local search with elastic net algorithm.

The prediction of protein conformation from its amino-acid sequence is one of the most prominent problems in computational biology. But it is NP-hard. Here, we focus on an abstraction widely studied of this problem, the two-dimensional hydrophobic-polar protein folding problem (2D HP PFP). Mathematical optimal model of free energy of protein is established. Native conformations are often sought using stochastic sampling methods, but which are slow. The elastic net (EN) algorithm is one of fast deterministic methods as travelling salesman problem (TSP) strategies. However, it cannot be applied directly to protein folding problem, because of fundamental differences in the two types of problems. In this paper, how the 2D HP protein folding problem can be framed in terms of TSP is shown. Combination of the modified elastic net algorithm and novel local search method is adopted to solve this problem. To our knowledge, this is the first application of EN algorithm to 2D HP model. The results indicate that our approach can find more optimal conformations and is simple to implement, computationally efficient and fast.

Algorithms↗

PubMed2000

Optimization of the extraction of polycyclic aromatic hydrocarbons from wood samples by the use of microwave energy.

A simple and rapid microwave-assisted extraction (MAE) procedure was developed and optimized for benzo[a]anthracene, benzo[e]pyrene, benzo[b]fluoranthene, benzo[k]fluoranthene and benzo[a]pyrene in wood samples. The spiked wood used was prepared 3 months before analysis to simulate weathering processes and to allow the formation of analyte-matrix interaction. The samples, immersed in acetonitrile were irradiated with microwaves in a closed-vessel system. Optimization of the method was achieved by using a factorial design approach on parameters such as extraction time, temperature and sample amount. The analysis of extracts has been carried out by reversed-phase high-performance liquid chromatography with fluorescence detection for quantification and UV-diode-array detection for confirmation. The MAE procedure yielded extracts that could be analyzed directly without any preliminary clean-up or solvent exchange steps.

Chromatography, High Pressure Liquid↗