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PubMed1992

Refined solution structure and ligand-binding properties of PDC-109 domain b. A collagen-binding type II domain.

We have determined, via 1H-n.m.r., the solution conformation of the collagen-binding b-domain of the bovine seminal fluid protein PDC-109 (PDC-109/b). The structure determination is based on 341 interproton distance estimates and 42 dihedral angle estimates: a set of 24 initial structures were computed; 12 using the variable target function program DIANA, and 12 using the metric matrix program DISGEO. These structures were optimized by restrained energy minimization and dynamic simulated annealing using the CHARMM and X-PLOR programs. The average pairwise root-mean-square difference (r.m.s.d) between the optimized DIANA (DISGEO) structures is 0.71 A (0.82 A) for the backbone atoms, and 1.73 A (2.03 A) for all atoms. Both sets of structures exhibit the same global fold, secondary structure and placement of most non-polar side-chains. Two central antiparallel beta-sheets, which lie roughly perpendicular to each other, and two irregular loops support a large, partially exposed, hydrophobic surface that defines a putative binding site. A test of a hybrid relaxation matrix-based distance refinement protocol (MIDGE program) was performed using a normalized 250 millisecond NOESY spectrum. The resulting distances were input to the molecular mechanics/dynamics procedures mentioned above in order to optimize the DIANA structures. Our results indicate that relaxation matrix refinement of distances is most useful when used conservatively for identifying underestimated distance constraints. 1H-n.m.r. monitored ligand titration experiments revealed definite, albeit weak, binding interactions for phenethylamine and leucine analogs (Ka less than or equal to 25 M-1). Residues perturbed by ligand binding include Tyr7, Trp26, Tyr33, Asp34 and Trp39. These results suggest that PDC-109/b may recognize specific leucine and/or isoleucine-containing sequences within collagen.

Amino Acid Sequence↗

PubMed2004

["Persistent" angina: rationale for a metabolic approach].

Despite increasing pharmacological and mechanical treatment options, ischemic heart disease continues to be associated with considerable patient mortality and morbidity. The estimates of the direct and indirect costs associated with chronic stable angina amount to billions of dollars. Given the epidemiological and economic magnitude of the problem, the need for more effective therapies is self-evident. Based on current guidelines, the management of ischemic heart disease has progressively broadened to include risk factor modification, patient education, and pharmacological therapy. The latter includes i) classic antianginal agents such as beta-blockers, calcium antagonists, and nitrates, and ii) drugs for secondary prevention, such as aspirin, clopidogrel, statins, and angiotensin-converting enzyme inhibitors. Tailoring therapy to individual needs has become even more challenging because of the marked changes in the clinical profile of patients with chronic ischemic heart disease. Compared with the past, today's patients tend to be older, to have undergone revascularization procedures, and to frequently have associated illnesses, including heart failure and diabetes. Significant progress has been made in recent years in understanding the role of cardiac energy metabolism in the pathogenesis of myocardial ischemia. A better understanding of metabolic derangements associated with ischemia and reperfusion is translating into innovative therapeutic approaches. Optimization of cardiac energy metabolism is based on promoting cardiac glucose oxidation. This has been proved to enhance cardiac function and protect myocardial tissue against ischemia-reperfusion injury. A new class of metabolic agents, known as the 3-ketoacyl coenzyme A thiolase inhibitors (trimetazidine), is able to elicit an increase in glucose and lactate combustion secondary to partial inhibition of fatty acid oxidation, producing clinical benefits in patients with ischemic heart disease.

Angina Pectoris↗

PubMed1991

Aging as a multi-step process characterized by a lowering of entropy production leading the cell to a sequence of defined stages.

The principles of the thermodynamics of irreversible processes which occur in biological cells considered as open systems, have been reviewed and applied in order to describe a possible evolution of cells during aging. The main feature of such an approach is that cells operating in a steady state, optimize their free energy production by lowering their entropy production which is kept to a minimum. Instabilities can however occur which can lead the cell from one steady state to another characterized by a lower production of entropy. Concomitantly, the level of errors or entropy of the system will increase. The process will continue and the cell will go from one state to another until a critical level is attained where the cell can not cope any more with keeping its organization and will die. The effect of stresses and mitosis have been also considered in this model. Such an approach stresses that cells can only subsist as a whole in certain states which are the result of the genetic constitution but also of the optimalization of cellular functions given their requirement in energy and the fluctuations from the environmental changes. In this respect, it reconciles both programmed and stochastic theories of aging.

Aging↗

PubMed1983

Optimal control of antagonistic muscles.

Recently, a model for a pair of antagonistic muscles has been studied (Oğuztöreli and Stein, 1982). In the present paper we formulate and investigate the minimization of the costs associated with the time to complete the movement, the oscillation about the endpoint, the energy costs to the muscles to complete the movement, the cost to the nervous system to supply the inputs, and the cost of reliability in the face of perturbing forces. To solve these optimization problems the maximum principle of Pontryagin is employed. In all of these optimization problems, except the energy optimal problem, the optimal controls (active states or nervous inputs) are of the bang-bang type.

Animals↗

PubMed1990

Energy utilization in pregnant and lactating sows: modeling of energy requirements.

Data on energy metabolism and body composition changes of the pregnant and lactating sow have been considered in order to propose methods for determination of energy requirements according to a factorial approach. Daily requirements for maintenance at thermoneutrality amounts to about 105 and 110 kcal ME/kg BW.75 in pregnant and lactating sows, respectively. During pregnancy, maintenance represents 75 to 85% of the total requirements and is affected greatly by environmental temperature and activity of the animals. Requirements for total uterine gain are low, but they increase with advancement of pregnancy. In addition, the daily ME requirements during pregnancy depend on the amount and composition of maternal weight gain and on the previous lactation body weight loss. The factorial approach indicates clearly that daily ME recommendation in pregnant sows varies from 6 to more than 10 Mcal and must be adapted to each sow within a herd. A method for prediction of ME requirements in lactating sows that considers a relatively precise estimate of energy output in milk is proposed. Results indicate that daily ME requirements are particularly high (15 to more than 20 Mcal) and generally are not met by voluntary feed intake. Emphasis also has been given to prediction of body composition changes that occur over the reproductive life of the sow. Data from the factorial approach allow for optimization of sow energy nutrition to ensure a normal evolution of body weight changes and to avoid major changes in body weight and composition. However, no available data demonstrate whether such a strategy is concomitant with optimal lifetime reproductive performance.

Animals↗

PubMed2005

Quantum-chemical study of CHCl3-SO2 association.

CHCl(3)-SO(2) association is studied by high-level quantum-chemical calculations of stationary points of the dimer electronic potential-energy hypersurface, including correlated second-order Moller-Plesset and CCSD(T) calculations with basis sets up to 6-311++G(d,p). During geometry optimization, frequency, and energy calculations, a self-written computer code embedding the GAMESS ab initio program suite applies counterpoise correction of the basis set superposition error. A CH...O hydrogen-bonded complex (DeltaE(0)=-8.73 kJmol) with a 2.4 A intermolecular H...O distance and two very weak van der Waals complexes (DeltaE(0)=-3.78 and -2.94 kJmol) are located on the counterpoise-corrected potential-energy surface. The intermolecular interactions are characterized by Kitaura-Morokuma interaction energy decompositions and Mulliken electron population analyses. The unusual hydrogen bond is distinguished by a CH-bond contraction, a pronounced enhancement of the IR intensity and a shift to higher frequency ("blueshift") of the CH-stretching vibration compared to the CHCl(3) monomer. Spectroscopy and association in liquid solution is also discussed; our results provide an alternative explanation for features in the CH-stretching vibration spectrum of chloroform dissolved in liquid sulfur dioxide which have been attributed previously to an intermolecular Fermi resonance.

Algorithms↗

PubMed2006

Dual-stage soliton compression of a self-started additive pulse mode-locked erbium-doped fiber laser for 48 fs pulse generation.

A dual-stage single-mode fiber (SMF) and large-effective-area fiber (LEAF) link for generating 48 fs pedestal-free pulses from a 40 MHz self-started additive pulse mode-locked erbium-doped fiber laser (APM-EDFL) with output peak power and pulse energy of 16 kW and 500 pJ, respectively, is demonstrated. With the SMF+LEAF link, a maximum pulse-width compression ratio of 7 and an optimized pulse-energy confining ratio of up to 85% can be achieved, and the soliton self-frequency shift effect of the APM-EDFL pulse can be greatly suppressed.

Journal Article↗

PubMed1990

Bond-optimized ring closure for proline: comparison of conformations and semiempirical energies with small molecule X-ray structures.

A method is described for generating proline ring structures by successive addition of atoms, wherein ring closure is achieved by optimizing the fit to known ring bond-angles and one closing bond-length ("bond-optimized ring closure"). Two ring torsion angles are fixed independently within broad, allowed ranges, and the remaining torsion angles are determined uniquely in most cases. The independent torsion angles are chosen as phi and chi 2, and ring closure is achieved without prohibitive strain through most of the ranges -130 degrees less than phi less than -20 degrees and -60 degrees less than chi 2 less than 60 degrees. Comparisons of predicted ring structures to 191 X-ray diffraction structures from the literature, starting with the known values of phi and chi 2, yielded root-mean-square deviations of 4.8 degrees in chi 1, 4.7 degrees in chi 3, 8.3 degrees in chi 4, and 0.3-2% in the ring bond angles and the N-C delta distance. Semiempirical energies were calculated for the optimized structures using three sets of energy parameters from the literature. The energy surfaces show broad minima coinciding with the torsion angle regions in which the highest concentrations of observed structures are found. Two of the sets of energy parameters produce double minima corresponding to the "up" and "down" puckered conformations.

Molecular Conformation↗

PubMed1986

HeNe laser irradiation delivered transcutaneously: its effect on the sciatic nerve of rats.

For our study of the effect of low energy laser irradiation (LELI) on living tissue we used HeNe laser on rats. The exponential absorption was reaffirmed in the living tissues overlying the sciatic nerve. An optimal range of energy between 3.5 and 7 J--associated with energy concentration of 4-10 J/cm2 delivered transcutaneously--was found to cause a significant increase in action potential in the sciatic nerve. The effect lasted for more than 8 months after the irradiation session.

Action Potentials↗

PubMed1989

Errors in estimating energy expenditure in critically ill surgical patients.

Thirty-one critically ill surgical patients were receiving central parenteral nutrition. All were intubated, and 29 were receiving mechanical ventilatory support. Nutritional and metabolic data were recorded at the time of indirect calorimetry. Measured energy expenditure (MEE) was compared with predictions of basal energy expenditure (BEE) and calculated energy expenditure, defined as the product of BEE and a stress factor estimated by the nutrition support service to account for severity of illness and activity. The MEE was significantly greater than the BEE and significantly less than the calculated energy expenditure. The estimated stress factor was significantly greater than the actual MEE/BEE ratio, and the correlation between these values was poor. Clinical assessment may overestimate energy expenditure in critically ill patients because of the apparent degree of illness used to determine the stress factor. Bedside indirect calorimetry may be useful to assess more accurately energy expenditure and optimize nutritional support.

Adolescent↗

PubMed1990

Codon usage pattern in alpha 2(I) chain domain of chicken type I collagen and its implications for the secondary structure of the mRNA and the synthesis pauses of the collagen.

A stability map of local secondary structure of the mRNA of the triple-helical alpha 2(I) chain domain of chicken type I collagen was obtained by plotting the free energy of the optimal secondary structure of a local segment in mRNA against the segment position along a base sequence of the mRNA. It was found that the positions of the minima of free energy in the plot coincide with the positions where synthesis pauses of the alpha-chain polypeptides of the corresponding sizes translated from the mRNA have been reported to occur (1). The codon usage pattern of each of the three major amino acids of the alpha-chain domain of the collagen, Gly, Pro and Ala, fluctuates considerably along the base sequence segments of the mRNA and a deviation of the pattern from that of the average of the whole alpha 2(I) chain domain mRNA, particularly for Gly codons, leads to a loss of the stability of the local secondary structure of the mRNA. The results suggest that selection has operated on the codon usage to optimize the secondary structure characteristic of the mRNA of the chicken collagen alpha 2(I) chain domain which leads to a nonuniform polypeptide elongation pattern.

Animals↗

PubMed2000

Optimal method to achieve consistently low defibrillation energy requirements.

Reduction of the defibrillation energy requirement offers the opportunity to decrease implantable cardioverter defibrillator (ICD) size and to increase device longevity. Therefore, the purpose of this prospective study was to obtain confirmed defibrillation thresholds (DFTs) of < or = 15 J in each patient with an endocardial dual-coil lead system incorporating an active pectoral pulse generator (TRIAD lead system: RV- --> SVC+ + CAN+). According to our previous clinical and experimental studies, we tried to lower DFTs that were > 15 J by repositioning the distal coil of the endocardial lead system in the right ventricle. A total of 190 consecutive patients requiring ICDs for ventricular fibrillation and/or recurrent ventricular tachycardia were investigated at the time of ICD implantation (42 women, 148 men; mean age 61.9 +/- 12.0 years; mean left ventricular ejection fraction 42.7 +/- 16.6%). Coronary artery disease was present in 139 patients; nonischemic dilated cardiomyopathy in 34 patients; and other etiologies in 17 patients; 47 patients had undergone previous cardiac surgery. Regardless of optimal pacing and sensing parameters, for patients having DFTs > 15, we repositioned the distal coil of the endocardial lead system toward the intraventricular septum to include this part of both ventricles within the electrical defibrillating field. In 177 of 190 patients, induced ventricular fibrillation was successfully terminated with < or = 15 J (group I) using the initial lead position. Repositioning of the endocardial lead was necessary in 13 patients whose DFT(plus) (DFT(plus) = second additional success at lowest energy level) were > 15 J (group II). In all patients, repositioning was successful within a 15 J energy level (100% success). The mean DFT(plus) was 7.3 +/- 3.5 J (group I) and 11.0 +/- 4.5 J (group II; p<0.005). The mean DFT(plus) of all patients enrolled in the study was 7.6 +/- 3.7 J (range: 2 to 15 J). In 87% of all patients, DFT(plus) of < or = 10 J was achieved. Repositioning of the endocardial lead in the right ventricle is a simple and effective method to reduce intraoperative high DFTs. As a result of this procedure, ICDs with a 20 J output should be sufficient for the vast majority (87%) of our patients. Furthermore, we were able to avoid additional subcutaneous or epicardial electrodes in all patients.

Aged↗

PubMed2004

A hierarchical approach to all-atom protein loop prediction.

The application of all-atom force fields (and explicit or implicit solvent models) to protein homology-modeling tasks such as side-chain and loop prediction remains challenging both because of the expense of the individual energy calculations and because of the difficulty of sampling the rugged all-atom energy surface. Here we address this challenge for the problem of loop prediction through the development of numerous new algorithms, with an emphasis on multiscale and hierarchical techniques. As a first step in evaluating the performance of our loop prediction algorithm, we have applied it to the problem of reconstructing loops in native structures; we also explicitly include crystal packing to provide a fair comparison with crystal structures. In brief, large numbers of loops are generated by using a dihedral angle-based buildup procedure followed by iterative cycles of clustering, side-chain optimization, and complete energy minimization of selected loop structures. We evaluate this method by using the largest test set yet used for validation of a loop prediction method, with a total of 833 loops ranging from 4 to 12 residues in length. Average/median backbone root-mean-square deviations (RMSDs) to the native structures (superimposing the body of the protein, not the loop itself) are 0.42/0.24 A for 5 residue loops, 1.00/0.44 A for 8 residue loops, and 2.47/1.83 A for 11 residue loops. Median RMSDs are substantially lower than the averages because of a small number of outliers; the causes of these failures are examined in some detail, and many can be attributed to errors in assignment of protonation states of titratable residues, omission of ligands from the simulation, and, in a few cases, probable errors in the experimentally determined structures. When these obvious problems in the data sets are filtered out, average RMSDs to the native structures improve to 0.43 A for 5 residue loops, 0.84 A for 8 residue loops, and 1.63 A for 11 residue loops. In the vast majority of cases, the method locates energy minima that are lower than or equal to that of the minimized native loop, thus indicating that sampling rarely limits prediction accuracy. The overall results are, to our knowledge, the best reported to date, and we attribute this success to the combination of an accurate all-atom energy function, efficient methods for loop buildup and side-chain optimization, and, especially for the longer loops, the hierarchical refinement protocol.

Algorithms↗

PubMed2006

Modeling product formation in anaerobic mixed culture fermentations.

The anaerobic conversion of organic matter to fermentation products is an important biotechnological process. The prediction of the fermentation products is until now a complicated issue for mixed cultures. A modeling approach is presented here as an effort to develop a methodology for modeling fermentative mixed culture systems. To illustrate this methodology, a steady-state metabolic model was developed for prediction of product formation in mixed culture fermentations as a function of the environmental conditions. The model predicts product formation from glucose as a function of the hydrogen partial pressure (P(H2)), reactor pH, and substrate concentration. The model treats the mixed culture as a single virtual microorganism catalyzing the most common fermentative pathways, producing ethanol, acetate, propionate, butyrate, lactate, hydrogen, carbon dioxide, and biomass. The product spectrum is obtained by maximizing the biomass growth yield which is limited by catabolic energy production. The optimization is constrained by mass balances and thermodynamics of the bioreactions involved. Energetic implications of concentration gradients across the cytoplasmic membrane are considered and transport processes are associated with metabolic energy exchange to model the pH effect. Preliminary results confirmed qualitatively the anticipated behavior of the system at variable pH and P(H2) values. A shift from acetate to butyrate as main product when either P(H2) increases and/or pH decreases is predicted as well as ethanol formation at lower pH values. Future work aims at extension of the model and structural validation with experimental data.

Adenosine Triphosphate↗

PubMed2001

Optimal posture control of a musculo-skeletal arm model.

In this paper maximal performance posture control of the human arm is investigated by means of model simulations. Recent experiments (F.C.T. van der Helm, submitted, 2000) have shown that the reflexive feedback during postural control varies with the bandwidth of the applied force disturbances. This paper focusses on the influence of the frequency content of force disturbances on the reflexive feedback gains by means of optimization. The arm is modelled by a nonlinear musculo-skeletal model with two degrees of freedom and six muscles. To facilitate the optimization of the model parameters, the arm model is linearized. A performance criterion is minimized for stochastic force disturbances in a two-step procedure: (1) optimization of static muscle activations using an additional energy criterion to obtain a unique and energy-efficient solution; antid (2) optimization of reflex gains using an additional control effort criterion to obtain a unique solution. The optimization reveals that for the given task and posture, the shoulder muscles have the largest contribution, whereas the bi-articular muscles have a relatively small contribution to the behaviour. The dynamics at the endpoint level are estimated so that a comparison can be made with the experiments. Compared to the experiments, the intrinsic damping of the model is relatively large (about 150%), whereas the intrinsic stiffness is relatively small (about 60%). These differences can be attributed to unmodelled mechanical effects of crossbridges in Hill-type muscle models. The optimized reflex gains show remarkable similarities with the values found in the experiments, implying that humans can adjust their reflexive feedback gains in an optimal way, weighting the performance and energy. The approach in this paper could be useful in the study of various posture tasks, for example in the prediction of the relation between the control parameters of various musculo-skeletal models and different experimental variables.

Arm↗

PubMed2006

Optimization of a flat-panel based real time dual-energy system for cardiac imaging.

A simulation study was conducted to evaluate the effects of high-energy beam filtration, dual-gain operation and noise reduction on dual-energy images using a digital flat-panel detector. High-energy beam filtration increases image contrast through greater beam separation and tends to reduce total radiation exposure and dose per image pair. It is also possible to reduce dual-energy image noise by acquiring low and high-energy images at two different detector gains. In addition, dual-energy noise reduction algorithms can further reduce image noise. The cumulative effect of these techniques applied in series was investigated in this study. The contrast from a small thickness of calcium was simulated over a step phantom of tissue equivalent material with a CsI phosphor as the image detector. The dual-energy contrast-to-noise ratio was calculated using values of energy absorption and energy variance. A figure-of-merit (FOM) was calculated from dual-energy contrast-to-noise ratio (CNR) and patient effective dose estimated from values of entrance exposure. Filter atomic numbers in the range of 1-100 were considered with thicknesses ranging from 0-2500 mg/cm2. The simulation examined combinations of the above techniques which maximized the FOM. The application of a filter increased image contrast by as much as 45%. Near maximal increases were seen for filter atomic numbers in the range of 40-60 and 85-100 with masses above 750 mg/cm2. Increasing filter thickness beyond 1000 mg/cm2 increased tube loading without further significant contrast enhancement. No additional FOM improvements were seen with dual gain before or after the application of any noise reduction algorithm. Narrow beam experiments were carried out to verify predictions. The measured FOM increased by more than a factor of 3.5 for a silver filter thickness of 800 microm, equal energy weighting and application of a noise clipping algorithm. The main limitation of dynamic high-energy filtration is increased tube loading. The results of this study can be used to help develop an optimal dual-energy imaging system.

Algorithms↗

PubMed2004

The trust-region self-consistent field method: towards a black-box optimization in Hartree-Fock and Kohn-Sham theories.

The trust-region self-consistent field (TRSCF) method is presented for optimizing the total energy E(SCF) of Hartree-Fock theory and Kohn-Sham density-functional theory. In the TRSCF method, both the Fock/Kohn-Sham matrix diagonalization step to obtain a new density matrix and the step to determine the optimal density matrix in the subspace of the density matrices of the preceding diagonalization steps have been improved. The improvements follow from the recognition that local models to E(SCF) may be introduced by carrying out a Taylor expansion of the energy about the current density matrix. At the point of expansion, the local models have the same gradient as E(SCF) but only an approximate Hessian. The local models are therefore valid only in a restricted region-the trust region-and steps can only be taken with confidence within this region. By restricting the steps of the TRSCF model to be inside the trust region, a monotonic and significant reduction of the total energy is ensured in each iteration of the TRSCF method. Examples are given where the TRSCF method converges monotonically and smoothly, but where the standard DIIS method diverges.

Journal Article↗

PubMedDate not supplied

Progress of an electrohydraulic total artificial heart system with a separate energy converter.

We have been developing an electrohydraulic total artificial heart (EHTAH) system. The system consists of diaphragm blood pumps, an abdominally placed energy converter, an internal controller, a transcutaneous energy transfer (TET) system, a transcutaneous optical information transfer system, and internal and external lithium-ion (Li-ion) batteries. The energy converter was optimized to obtain better oil transfer. Maximum cardiac output and efficiency of the EHTAH were increased from 8 L/min to 10 L/min and from 10% to 12%, respectively. The volume of the energy converter was reduced from 280 to 210 ml. The pumping unit was successfully implanted in 68-85 kg calves without anatomic problems, and the calves survived up to 10 days with good circulatory results. The maximum temperature rise of the implanted energy converter was only 1 degrees C. Stable performance of the TET system was confirmed in goats for more than 1 month. DC-DC energy transfer efficiency with 20 W of energy transmission remained within the range of 80% to 85%, and no significant temperature rise was observed in the implanted circuit. The internal Li-ion battery was also evaluated in a goat, and the maximum temperature rise during the charging period was 1.5 degrees C, while the charging and discharging times were 72 and 58 min, respectively. We conclude that our system has progressed in its development as a practical implantable system.

Animals↗