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PubMed1991

Optimal control for the active above-knee prosthesis.

Control of an active above-knee prosthesis has been simulated for a selected gait activity using a hierarchical closed-loop method. An extension of finite-state control, referred to as artificial reflex control, was adopted at the strategic level of control. At the actuator level of control an optimal tracking method, based on dynamic programming, is applied. This deals mainly with the actuator level of control, but considers the interaction of the leg dynamics and the switching effects of artificial reflex control. Optimal tracking at the actuator level of the above-knee prosthesis reduces the on-off effects of finite-state methods, such as artificial reflex control. The proposed method can also be used for the design of prosthetic elements. Specific attention is paid to the limited torque and power in the prosthetic joint actuator, which are imposed by the principle of self-containment in the artificial leg. The hierarchical structure, integrating artificial reflex control and optimal tracking, can be used in real time, as estimated from the number of computer operations required for the suggested method.

Artificial Limbs↗
PubMed1990

A precise analytical method for calculating the electrostatic energy of macromolecules in aqueous solution.

A new method for calculating the total electrostatic free energy of a macromolecule in solution is presented. It is applicable to molecules of arbitrary shape and size, including membranes or macromolecular assemblies with substrate molecules and ions. The method is derived from integrating the energy density of the electrostatic field and is termed the field energy method. It is based on the dielectric model, in which the solute and the surrounding water are regarded as different continuous dielectrics. The field energy method yields both the interaction energy between all charge pairs and the self energy of single charges, effectively accounting for the interaction with water. First, the dielectric boundary and mirror charges are determined for all charges of the solute. The energy is then given as a simple function of the interatomic distances, and the standard atomic partial charges and volumes. The interaction and self energy are shown to result from three-body and pairwise interactions. Both energy terms explicitly involve apolar atoms, revealing that apolar groups are also subject to electrostatic forces. We applied the field energy method to a spherical model protein. Comparison with the Kirkwood solution shows that errors are within a small percentage. As a further test, the field energy method was used to calculate the electrostatic potential of the protein superoxide dismutase. We obtained good agreement with the result from a program that implements the numerical finite difference algorithm. The field energy method provides a basis for energy minimization and dynamics programs that account for the solvent and screening effect of water at little computational expense.

Electricity↗
PubMed1988

A flexible multiple sequence alignment program.

The 'regions' method for multisequence alignment used in the previously reported program MALIGN has been generalized to include recursive refinement so that unaligned portions between two regions at the current level of resolution can be handled with increased resolution. Additionally, there is incorporated a limiting of the number of regions to be used at any level of resolution from which to abstract an alignment. This provides a significant increase in speed over the unlimited version. The program GENALIGN uses this improved regions method to execute fast pairwise alignments in the framework of Taylor's multisequence alignment procedure using clustered pairwise alignments. Pairwise alignments by dynamic programming are also provided in the program.

Algorithms↗
PubMed1985

Left ventricular border recognition using a dynamic search algorithm.

Initial results obtained with a simple, fully automated algorithm for detection of left ventricular boundaries are presented. The strength of this approach is the use of dynamic programming search techniques, which allow determination of local border points to be influenced by the entire global border location. The relative contributions of mask mode subtraction and the dynamic search technique are evaluated with respect to accurate border definition. These computer-determined ventricular borders are compared with hand-traced borders on subtracted and unsubtracted images. The modular dynamic search algorithm is shown to perform better than previously described algorithms, which generally require operator interaction. It is also shown that for both manual and automated techniques, ventricular borders derived from subtracted images may be significantly different from borders derived from nonsubtracted images.

Angiocardiography↗
PubMed1989

A study of Supplemental Security Income awardees.

Since its enactment in 1974, the Supplemental Security Income (SSI) program has had a stable caseload of about 4 million recipients. Hidden by this unchanging total is the fact that nearly 9 million persons were served by the program from 1974 to 1986. This study explores some SSI program dynamics by following a group of SSI awardees for a period of 4 years from the initial receipt of award in 1981. Many of these awardees had previous contact with the program either through a previous award or a denial. About 60 percent of the awardees were eligible at the end of the 4-year period. Most persons who became ineligible did so within the first 6 months after the award.

Adolescent↗
PubMed1990

Restoring unassisted natural gait to paraplegics via functional neuromuscular stimulation: a computer simulation study.

Functional neuromuscular stimulation (FNS) of paralyzed muscles has enabled spinal-cord-injured patients to regain a semblance of lower-extremity control, for example to ambulate while relying heavily on the use of walkers. Given the limitations of FNS, specifically low muscle strengths, high rates of fatigue, and a limited ability to modulate muscle excitations, it remains unclear, however, whether FNS can be developed as a practical means to control the lower extremity musculature to restore aesthetic, unsupported gait to paraplegics. A computer simulation of FNS-assisted bipedal gait shows that it is difficult, but possible to attain undisturbed, level gait at normal speeds provided the electrically-stimulated ankle plantarflexors exhibit either near-normal strengths or are augmented by an orthosis, and at least seven muscle-groups in each leg are stimulated. A combination of dynamic programming and an open-loop, trial-and-error adjustment process was used to find a suboptimal set of discretely-varying muscle stimulation patterns needed for a 3-D, 8 degree-of-freedom dynamic model to sustain a step. An ankle-foot orthosis was found to be especially useful, as it helped to stabilize the stance leg and simplified the task of controlling the foot during swing. It is believed that the process of simulating natural gait with this model will serve to highlight difficulties to be expected during laboratory and clinical trials.

Computer Simulation↗
PubMed1992

Distal pocket residues affect picosecond ligand recombination in myoglobin. An experimental and molecular dynamics study of position 29 mutants.

Time courses for intramolecular NO and O2 recombination to native and three position 29 mutants of sperm whale myoglobins were measured after laser photolysis on picosecond and nanosecond time scales. The rates for the first phase of NO recombination were 1.8, 2.5, 29, and > or = 100 ns-1 for Ala29, Val29, Leu29 (native), and Phe29 myoglobin, respectively, at room temperature. This order is not correlated with the overall association rate constants for NO binding which were all in the range 20-50 x 10(6) M-1 s-1 and is the opposite of that observed for the rate constants for the overall thermal dissociation of NO which were 5.0, 2.8, 0.98, and 0.21 x 10(-4) s-1 for Ala29, Val29, Leu29 (native), and Phe29 myoglobin, respectively, at 20 degrees C. This inverse correlation suggests that photo- and thermally dissociated ligand molecules experience similar kinetic and equilibrium barriers to rebinding. The larger side chains of Leu29 and Phe29 inhibit rapid movement of the ligand away from the iron atom facilitating geminate recombination. The smaller side chains of Val29 and Ala29 increase the space available to the ligand, decreasing the rate of geminate recombination and enhancing complete dissociation. Diffusion of NO in the distal pocket of myoglobin was simulated using a variant of the molecular dynamics program CHARMM that includes the locally enhanced sampling protocol (Elber, R., and Karplus, M. (1991) J. Am. Chem. Soc. 112, 9161-9175; Roitberg, A., and Elber, R. (1991) J. Chem. Phys. 95, 9277-9287) and the x-ray structures of Carver et al. (Carver, T. E., Brantley, R. E., Jr., Singleton, E. W., Arduini, R. M., Quillin, M. L., Phillips, G. N., Jr., and Olson, J. S. (1992) J. Biol. Chem. 267, 14443-14450). Both accelerated (5,000 K) and room temperature ligands were used, and comparisons were made between simulations with a complete hydration shell surrounding the protein and those with only eight water molecules near the distal histidine. Photodissociated ligands initially move away from the heme plane, past Leu29, and toward Leu32, Phe33, Ile107, and Ile111. These theoretical results confirm that a complete description of picosecond ligand recombination must include the dynamics of ligand movement in the distal portion of the heme pocket.

Animals↗
PubMed2025

Pioneer in Molecular Biology: Conformational Ensembles in Molecular Recognition, Allostery, and Cell Function.

In 1978, for my PhD, I developed the efficient O(n3) dynamic programming algorithm for the-then open problem of RNA secondary structure prediction. This algorithm, now dubbed the "Nussinov algorithm", "Nussinov plots", and "Nussinov diagrams", is still taught across Europe and the U.S. As sequences started coming out in the 1980s, I started seeking genome-encoded functional signals, later becoming a bioinformatics trend. In the early 1990s I transited to proteins, co-developing a powerful computer vision-based docking algorithm. In the late 1990s, I proposed the foundational role of conformational ensembles in molecular recognition and allostery. At the time, conformational ensembles and free energy landscapes were viewed as physical properties of proteins but were not associated with function. The classical view of molecular recognition and binding was based on only two conformations captured by crystallography: open and closed. I proposed that all conformational states preexist. Proteins always have not one folded form-nor two-but many folded forms. Thus, rather than inducing fit, binding can work by shifting the ensembles between states, and this shifting, or redistributing the ensembles to maintain equilibrium, is the origin of the allosteric effect and protein, thus cell, function. This transformative paradigm impacted community views in allosteric drug design, catalysis, and regulation. Dynamic conformational ensemble shifts are now acknowledged as the origin of recognition, allostery, and signaling, underscoring that conformational ensembles-not proteins-are the workhorses of the cell, pioneering the fundamental idea that dynamic ensembles are the driving force behind cellular processes. Nussinov was recognized as pioneer in molecular biology by JMB.

Molecular Biology↗
PubMed1992

Optimizing model: insemination, replacement, seasonal production, and cash flow.

Dynamic programming to solve the Markov decision process problem of optimal insemination and replacement decisions was adapted to address large dairy herd management decision problems in the US. Expected net present values of cow states (151,200) were used to determine the optimal policy. States were specified by class of parity (n = 12), production level (n = 15), month of calving (n = 12), month of lactation (n = 16), and days open (n = 7). Methodology optimized decisions based on net present value of an individual cow and all replacements over a 20-yr decision horizon. Length of decision horizon was chosen to ensure that optimal policies were determined for an infinite planning horizon. Optimization took 286 s of central processing unit time. The final probability transition matrix was determined, in part, by the optimal policy. It was estimated iteratively to determine post-optimization steady state herd structure, milk production, replacement, feed inputs and costs, and resulting cash flow on a calendar month and annual basis if optimal policies were implemented. Implementation of the model included seasonal effects on lactation curve shapes, estrus detection rates, pregnancy rates, milk prices, replacement costs, cull prices, and genetic progress. Other inputs included calf values, values of dietary TDN and CP per kilogram, and discount rate. Stochastic elements included conception (and, thus, subsequent freshening), cow milk production level within herd, and survival. Validation of optimized solutions was by separate simulation model, which implemented policies on a simulated herd and also described herd dynamics during transition to optimized structure.

Animals↗
PubMed1986

Optimal harvesting of a logistic population in an environment with stochastic jumps.

Dynamic programming is employed to examine the effects of large, sudden changes in population size on the optimal harvest strategy of an exploited resource population. These changes are either adverse or favorable and are assumed to occur at times of events of a Poisson process. The amplitude of these jumps is assumed to be density independent. In between the jumps the population is assumed to grow logistically. The Bellman equation for the optimal discounted present value is solved numerically and the optimal feedback control computed for the random jump model. The results are compared to the corresponding results for the quasi-deterministic approximation. In addition, the sensitivity of the results to the discount rate, the total jump rate and the quadratic cost factor is investigated. The optimal results are most strongly sensitive to the rate of stochastic jumps and to the quadratic cost factor to a lesser extent when the deterministic bioeconomic parameters are taken from aggregate antarctic pelagic whaling data.

Animals↗
PubMedDate not supplied

The equilibrium partition function and base pair binding probabilities for RNA secondary structure.

A novel application of dynamic programming to the folding problem for RNA enables one to calculate the full equilibrium partition function for secondary structure and the probabilities of various substructures. In particular, both the partition function and the probabilities of all base pairs are computed by a recursive scheme of polynomial order N3 in the sequence length N. The temperature dependence of the partition function gives information about melting behavior for the secondary structure. The pair binding probabilities, the computation of which depends on the partition function, are visually summarized in a "box matrix" display and this provides a useful tool for examining the full ensemble of probable alternative equilibrium structures. The calculation of this ensemble representation allows a proper application and assessment of the predictive power of the secondary structure method, and yields important information on alternatives and intermediates in addition to local information about base pair opening and slippage. The results are illustrated for representative tRNA, 5S RNA, and self-replicating and self-splicing RNA molecules, and allow a direct comparison with enzymatic structure probes. The effect of changes in the thermodynamic parameters on the equilibrium ensemble provides a further sensitivity check to the predictions.

Animals↗
PubMed1992

Solution structures of cyclic and dicyclic analogues of growth hormone releasing factor as determined by two-dimensional NMR and CD spectroscopies and constrained molecular dynamics.

Solution structures were determined for a linear analogue of growth hormone releasing factor (GRF), and cyclic and dicyclic analogues in which the side chains of aspartyl and lysyl residues spaced at positions i-(i + 4) were joined to form a lactam. The four analogues were [Ala15]-GRF-(1-29)-NH2 and its cyclo8-12, cyclo21-25, and dicyclo8-12;21-25 derivatives. The peptides were studied in two solvent systems: 75% methanol/25% water at pH 6.0; and 100% water at pH 3.0. CD spectroscopy was used to assess the overall alpha-helical content. Nuclear magnetic resonance spectroscopy was used to determine the structures in more detail. Nearly complete proton resonance assignments were made for each of the peptides, in both solvents. Nuclear Overhauser effects were converted into distance constraints and applied in the molecular dynamics program CHARMM to evaluate the range of low-energy structures that satisfied the nmr data. In 75% methanol, all of the peptides are comprised of a single alpha-helical segment with fraying of one to three residues at each end. The linear analogue has a tendency to kink. In water, the analogues have two helical segments with flexible regions between them and at the termini of the peptides. The linear analogue is helical at residues 7-14 and 21-28. In the cyclo8-12 analogue, the N-terminal helical region extends to include residues 7-19, while the other helical region is slightly shortened. In the cyclo21-25 analogue, the C-terminal helical region is extended to include residues 19-28, while the N-terminal helical region is destabilized. The dicyclic analogue has the largest N-terminal helix, spanning residues 7-20, but its helical segment at residues 21-28 is not well ordered. All of the analogues exhibit substantial biological activity. The cyclic and dicyclic analogues show dramatically increased resistance to degradation during incubation with human plasma. The i-(i + 4) lactam, therefore, appears to be a synthetic means of stabilizing a local alpha-helical conformation, which may be of general use in the design of active, stable peptides.

Amino Acid Sequence↗
PubMed1990

Automatically inferred Markov network models for classification of chromosomal band pattern structures.

A structural pattern recognition approach to the analysis and classification of metaphase chromosome band patterns is presented. An operational method of representing band pattern profiles as sharp edged idealized profiles is outlined. These profiles are nonlinearly scaled to a few, but fixed number of "density" levels. Previous experience has shown that profiles of six levels are appropriate and that the differences between successive bands in these profiles are suitable for classification. String representations, which focuses on the sequences of transitions between local band pattern levels, are derived from such "difference profiles." A method of syntactic analysis of the band transition sequences by dynamic programming for optimal (maximal probability) string-to-network alignments is described. It develops automatic data-driven inference of band pattern models (Markov networks) per class, and uses these models for classification. The method does not use centromere information, but assumes the p-q-orientation of the band pattern profiles to be known a priori. It is experimentally established that the method can build Markov network models, which, when used for classification, show a recognition rate of about 92% on test data. The experiments used 200 samples (chromosome profiles) for each of the 22 autosome chromosome types and are designed to also investigate various classifier design problems. It is found that the use of a priori knowledge of Denver Group assignment only improved classification by 1 or 2%. A scheme for typewise normalization of the class relationship measures prove useful, partly through improvements on average results and partly through a more evenly distributed error pattern. The choice of reference of the p-q-orientation of the band patterns is found to be unimportant, and results of timing of the execution time of the analysis show that recent and efficient implementations can process one cell in less than 1 min on current standard hardware. A measure of divergence between data sets and Markov network models is shown to provide usable estimates of experimental classification performance.

Chromosome Banding↗
PubMed1992

Fast structure alignment for protein databank searching.

A fast method is described for searching and analyzing the protein structure databank. It uses secondary structure followed by residue matching to compare protein structures and is developed from a previous structural alignment method based on dynamic programming. Linear representations of secondary structures are derived and their features compared to identify equivalent elements in two proteins. The secondary structure alignment then constrains the residue alignment, which compares only residues within aligned secondary structures and with similar buried areas and torsional angles. The initial secondary structure alignment improves accuracy and provides a means of filtering out unrelated proteins before the slower residue alignment stage. It is possible to search or sort the protein structure databank very quickly using just secondary structure comparisons. A search through 720 structures with a probe protein of 10 secondary structures required 1.7 CPU hours on a Sun 4/280. Alternatively, combined secondary structure and residue alignments, with a cutoff on the secondary structure score to remove pairs of unrelated proteins from further analysis, took 10.1 CPU hours. The method was applied in searches on different classes of proteins and to cluster a subset of the databank into structurally related groups. Relationships were consistent with known families of protein structure.

Amino Acid Sequence↗
PubMed1992

Optimal checking procedures for monitoring laboratory analyses.

Many clinical, environmental, and epidemiologic studies rely heavily upon biochemical data, and the quality of these data is of paramount importance to the validity of study conclusions. Traditionally, far more attention has been given to the analysis of study data than has been given to monitoring the quality of the data. In this paper we draw an analogy between monitoring a laboratory system and an industrial production process and discuss the limitations of industrial quality control plans when applied in a laboratory setting. We derive methods for computing optimal checking schedules for laboratory analyses. These schedules formalize traditional laboratory practices of periodic checking and provide guidelines for the frequency and placement of checks within a finite batch of analyses. When laboratory system failure can be reasonably approximated by an exponential or geometric distribution, optimal checking schedules are relatively easy to compute. For more complex failure distributions, we present a dynamic programming approach. We describe an application to the measurement of selenium status in plasma samples using an electrothermal atomic absorption spectrophotometry procedure.

Algorithms↗
PubMed1976

Frequency of insertion-deletion, transversion, and transition in the evolution of 5S ribosomal RNA.

The problem of choosing an alignment of two or more nucleotide sequences is particularly difficult for nucleic acids, such as 5S ribosomal RNA, which do not code for protein and for which secondary structure is unknown. Given a set of 'costs' for the various types of replacement mutations and for base insertion or deletion, we present a dynamic programming algorithm which finds the optimal (least costly) alignment for a set of N sequences simultaneously, where each sequence is associated with one of the N tips of a given evolutionary tree. Concurrently, protosequences are constructed corresponding to the ancestral nodes of the tree. A version of this algorithm, modified to be computationally feasible, is implemented to align the sequences of 5S RNA from nine organisms. Complete sets of alignments and protosequence reconstructions are done for a large number of different configurations of mutation costs. Examination of the family of curbes of total replacements inferred versus the ratio of transitions/transversions inferred, each curve corresponding to a given number of insertions-deletions inferred, provides a method for estimating relative costs and relative frequencies for these different types of mutations.

Base Sequence↗
PubMed1991

A fast unbiased comparison of protein structures by means of the Needleman-Wunsch algorithm.

A fast dynamic programming algorithm for the spatial superposition of protein structure without prior knowledge of an initial alignment has been developed. The program was applied to serine proteases, hemoglobins, cytochromes C, small copper-binding proteins, and lysozymes. In most cases the existing structural homology could be detected in a completely unbiased way. The results of the method presented are in general agreement with other studies. Applying our method, the different alignment results obtained by other authors for serine proteases and cytochromes C can be classified in terms of different alignment parameters such as gap penalties or cut-off length. Limitations of the method are discussed.

Algorithms↗
PubMed1991

Knowledge-based system for the three-dimensional reconstruction of blood vessels from two angiographic projections.

A knowledge-based system for the three-dimensional reconstruction of blood vessels from wide-angle coronary and stereoscopic cerebral angiographic projections is developed. For the reconstruction of the coronary vessels, the left coronary artery (LCA) is automatically labelled on standard RAO and LAO projections, using anatomical models of the LCA. The labelling system succeeds in giving the most important coronary arteries a correct anatomical label. These labelling results enable us to find corresponding segments in both images. In the case of the reconstruction of the cerebral vessels however, such an anatomical model is clearly unavailable. To find corresponding segments, small-angle projections must be relied on, resulting in very similar images. Owing to the small angular separation between both projections, the three-dimensional reconstruction will be less accurate. Once the corresponding segments in both projections are obtained, the three-dimensional artery trajectory is reconstructed with dynamic programming techniques. The three-dimensional reconstructed coronary vessels are also used for an automatic quantification of stenotic lesions.

Blood Vessels↗