PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “Dynamic Programming”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 631 records · Page 35Linked to original sources
PubMed1991

Molecular dynamics simulation on a network of workstations using a machine-independent parallel programming language.

Molecular dynamics simulations investigate local and global motion in molecules. Several parallel computing approaches have been taken to attack the most computationally expensive phase of molecular simulations, the evaluation of long range interactions. This paper develops a straightforward but effective algorithm for molecular dynamics simulations using the machine-independent parallel programming language, Linda. The algorithm was run both on a shared memory parallel computer and on a network of high performance Unix workstations. Performance benchmarks were performed on both systems using two proteins. This algorithm offers a portable cost-effective alternative for molecular dynamics simulations. In view of the increasing numbers of networked workstations, this approach could help make molecular dynamics simulations more easily accessible to the research community.

Algorithms↗
PubMed1999

Early protected motion after extensor tendon repair.

Thirty hands with 50 extensor tendon lacerations, excluding mallet finger injuries, were examined. They were treated with surgical repair followed by immediate motion which included a dynamic splinting and tendon mobilization program. The average follow-up period was 7 months (range, 8 weeks to 2 years). Forty-five of the 50 tendons regained full range of motion (average total active motion, 262 degrees) within an average time of 9 weeks; the remaining 5 tendons had extension lags of < or = 10 degrees. All patients regained at least 93% of their predicted normal strength within 9 to 12 weeks and returned to their previous level of activity in an average of 10 weeks. These results, which include complex lacerations, are an improvement from previously published data. This is probably due to the addition of a tendon mobilization program to dynamic splinting following extensor tendon repair.

Adolescent↗
PubMed1994

Evolution of a computer program for classifying protein segments as transmembrane domains using genetic programming.

The recently-developed genetic programming paradigm is used to evolve a computer program to classify a given protein segment as being a transmembrane domain or non-transmembrane area of the protein. Genetic programming starts with a primordial ooze of randomly generated computer programs composed of available programmatic ingredients and then genetically breeds the population of programs using the Darwinian principle of survival of the fittest and an analog of the naturally occurring genetic operation of crossover (sexual recombination). Automatic function definition enables genetic programming to dynamically create subroutines dynamically during the run. Genetic programming is given a training set of differently-sized protein segments and their correct classification (but no biochemical knowledge, such as hydrophobicity values). Correlation is used as the fitness measure to drive the evolutionary process. The best genetically-evolved program achieves an out-of-sample correlation of 0.968 and an out-of-sample error rate of 1.6%. This error rate is better than that reported for four other algorithms reported at the First International Conference on Intelligent Systems for Molecular Biology. Our genetically evolved program is an instance of an algorithm discovered by an automated learning paradigm that is superior to that written by human investigators.

Amino Acid Sequence↗
PubMedDate not supplied

Declarative simulation of dynamicals systems: the 812 programming language and its application to the simulation of genetic networks.

A major part of biological processes can be modeled as dynamical systems (DS), that is, as a time-varying state. In this article, we advocate a declarative approach for prototyping the simulation of DS. We introduce the concepts of collection, stream and fabric. A fabric is a multi-dimensional object that represents the successive values of a structured set of variables. A declarative programming language, called 8 1/2 has been developed to support the concept of fabrics. Several examples of working 8 1/2 programs are given to illustrate the relevance of the fabric data structure for simulation applications and to show how recursive fabric definitions can be easily used to model various biological phenomena in a natural way (a resolution of PDE, a simulation in artificial life, the Turing diffusion-reaction process and various examples of genetic networks). In the conclusion, we recapitulate several lessons we have learned from the 8 1/2 project.

Programming Languages↗
PubMed1992

Molecular dynamics simulation on a network of workstations using a machine-independent parallel programming language.

Molecular dynamics simulations investigate local and global motion in molecules. Several parallel computing approaches have been taken to attack the most computationally expensive phase of molecular simulations, the evaluation of long range interactions. This paper reviews these approaches and develops a straightforward but effective algorithm using the machine-independent parallel programming language, Linda. The algorithm was run both on a shared memory parallel computer and on a network of high performance Unix workstations. Performance benchmarks were performed on both systems using two proteins. This algorithm offers a portable cost-effective alternative for molecular dynamics simulations. In view of the increasing numbers of networked workstations, this approach could help make molecular dynamics simulations more easily accessible to the research community.

Algorithms↗
PubMed1994

Dynamic simulation of molecular and ionic materials.

Two new programs perform molecular dynamics simulations on molecular and ionic materials, respectively. The first simulates systems of small molecules, treated dynamically as rigid bodies, with interactions of the site-site Lennard-Jones form, plus point charges. The second simulates systems of point ions, which may be made polarizable by means of the shell model, treated by the method of adiabatic dynamics. Both programs handle Coulombic interactions in periodic boundaries by means of the Ewald sum. Force evaluations make use of efficient neighbor-search algorithms. The programs incorporate extensive analysis options in terms of structural and dynamic correlation functions. The programs are controlled by a command language, Dynamo, which provides a good environment for further development, as well as ease of use and flexibility in the choice of simulation protocol.

Algorithms↗
PubMed2005

Correspondence between spin-dynamic phases and pulse program phases of NMR spectrometers.

Spin state selective experiments have become very useful tools in solution NMR spectroscopy, particularly in the context of TROSY line narrowing. However, the practical implementation of such pulse sequences is frequently complicated by unexpected instrument behavior. Furthermore, a literal theoretical analysis of sequences published with specific phase settings can fail to rationalize such experiments and can seemingly contradict experimental findings. In this communication, we develop a practical approach to this ostensible paradox. Spin-dynamic design, rationalization, and simulation of NMR pulse sequences, as well as their confident and reliable implementation across current spectrometer hardware platforms, require precise understanding of the underlying nutation axis conventions. While currently often approached empirically, we demonstrate with a simple but general pulse program how to uncover these correspondences a priori in the general case. From this, we deduce a correspondence table between the spin-dynamic phases used in NMR theory and simulation on the one hand and pulse program phases of current commercial spectrometers on the other. As a practical application of these results, we analyze implementations of the original (1)H-(15)N TROSY experiment and illustrate how steady-state magnetization can be predictably, rather than empirically, added to a desired component. We show why and under which circumstances a literal adoption of phases from published sequences can lead to incorrect results. We suggest that pulse sequences should be consistently given with spin-dynamically correct (physical) phases, rather than in spectrometer-specific (software) syntax.

Carbon Isotopes↗
PubMed2005

Brownian dynamics simulations of the self- and collective rotational diffusion coefficients of rigid long thin rods.

Recently a microscopic theory for the dynamics of suspensions of long thin rigid rods was presented, confirming and expanding the well-known theory by Doi and Edwards [The Theory of Polymer Dynamics (Clarendon, Oxford, 1986)] and Kuzuu [J. Phys. Soc. Jpn. 52, 3486 (1983)]. Here this theory is put to the test by comparing it against computer simulations. A Brownian dynamics simulation program was developed to follow the dynamics of the rods, with a length over a diameter ratio of 60, on the Smoluchowski time scale. The model accounts for excluded volume interactions between rods, but neglects hydrodynamic interactions. The self-rotational diffusion coefficients D(r)(phi) of the rods were calculated by standard methods and by a new, more efficient method based on calculating average restoring torques. Collective decay of orientational order was calculated by means of equilibrium and nonequilibrium simulations. Our results show that, for the currently accessible volume fractions, the decay times in both cases are virtually identical. Moreover, the observed decay of diffusion coefficients with volume fraction is much quicker than predicted by the theory, which is attributed to an oversimplification of dynamic correlations in the theory.

Journal Article↗
PubMed1990

Dynamic training and circulating levels of corticotropin-releasing factor, beta-lipotropin and beta-endorphin in rheumatoid arthritis.

The study aimed at evaluating the effects of a dynamic training program on circulating levels of corticotropin-releasing factor (CRF), beta-lipotropin (beta-LPH), and beta-endorphin (beta-EP) in 8 patients (5 females and 3 males, aged 39-65 years) with classical/definite rheumatoid arthritis (RA). Blood samples were collected immediately before, in the middle of, and after a 6-week high-intensity training period as well as after a subsequent 1-year period of low-intensity training. In addition, baseline data were obtained 3 weeks before the start of the training program. Use of multivariate analyses of variance, and of analyses of variance of contrast variables, indicated a short-term effect of the high-intensity training program for beta-EP with increased levels (P less than 0.05) between the 3rd and the 6th weeks, no significant differences being obtained for CRF or beta-LPH here. Corresponding analyses with regard to the combined high and low-intensity training program revealed CRF (P less than 0.01), and beta-LPH (P less than 0.01) levels to increase over time, no long-term effect being found for beta-EP. Despite the intensity of the dynamic training program, no change was found in pain experience as measured on a visual analogue scale.

Adult↗
PubMed2003

Disentangling the dynamic core: a research program for a neurodynamics at the large-scale.

My purpose in this paper is to sketch a research direction based on Francisco Varela's pioneering work in neurodynamics (see also Rudrauf et al. 2003, in this issue). Very early on he argued that the internal coherence of every mental-cognitive state lies in the global self-organization of the brain activities at the large-scale, constituting a fundamental pole of integration called here a "dynamic core". Recent neuroimaging evidence appears to broadly support this hypothesis and suggests that a global brain dynamics emerges at the large scale level from the cooperative interactions among widely distributed neuronal populations. Despite a growing body of evidence supporting this view, our understanding of these large-scale brain processes remains hampered by the lack of a theoretical language for expressing these complex behaviors in dynamical terms. In this paper, I propose a rough cartography of a comprehensive approach that offers a conceptual and mathematical framework to analyze spatio-temporal large-scale brain phenomena. I emphasize how these nonlinear methods can be applied, what property might be inferred from neuronal signals, and where one might productively proceed for the future. This paper is dedicated, with respect and affection, to the memory of Francisco Varela.

Brain↗
PubMed1999

Dynamic treatment of displaced proximal phalangeal fractures.

We report a splint system for a protected mobilization program (termed dynamic treatment) of proximal phalangeal fractures. This program can be used for nonoperative treatment or after operative treatment. Intra-articular fractures of the proximal phalanx at the metacarpophalangeal joint were included. The custom-molded 2-component thermoplastic splint allows motion of the proximal and distal interphalangeal joints. It was developed to allow bone healing and recovery of motion at the same time. We evaluated the clinical and radiologic results of a consecutive series of 48 displaced proximal phalangeal fractures in 45 patients who received dynamic treatment. Fracture consolidation was achieved in all patients and bone healing and recovery of full active motion was achieved simultaneously in all but 4 patients by 6 weeks. The advantage of this splint system is the variability of its application. The splint can be used both for nonsurgical and surgical management. It can be removed to change dressings and for radiologic evaluations. The period of dynamic treatment can be determined individually in each case.

Adult↗
PubMedDate not supplied

Co-production dynamics and time dollar programs in community-based child welfare initiatives for hard-to-serve youth and families.

Hard-to-serve youth and families residing in high-poverty communities often have multiple, interlocking needs. These needs necessitate complex service models. The complex model described in this article combines a unique approach to wraparound services with a coproduction framework and related theories. The model aims to improve outcomes for vulnerable youth and their families, simultaneously strengthening communities by employing residents and engaging participants in community service. Examples derived from current pilot projects illustrate co-production's importance for other child welfare initiatives.

Child↗
PubMed1996

MDMovie: a molecular dynamics viewing tool.

The graphics program MDMovie (Molecular Dynamics Movie), written in C using IRIS GL graphics library calls, is designed to facilitate the visualization and interpretation of empirical force field data. MDMovie was created and initially adapted in accord with the needs of physical chemists and thereafter became an expandable analysis tool. Capabilities include the display of chemical structure, animation of molecular dynamics and Monte Carlo trajectories, and the visual representation of various vector and scalar dynamical properties. In addition to being a research tool, MDMovie has features for creating presentation videos and hardcopy output. A library is also available for linking to Fortran simulation codes running on a remote machine and connecting to MDMovie via a socket connection. MDMovie continues to be an ongoing research project and new features are actively being added in collaboration with various research groups. Future plans include porting to OpenGL and the design of an XII-based user interface.

Computer Graphics↗