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PubMed1984

Computer simulation modeling of abnormal behavior: a program approach.

A need for modeling abnormal behavior on a comprehensive, systematic basis exists. Computer modeling and simulation tools offer especially good opportunities to establish such a program of studies. Issues concern deciding which modeling tools to use, how to relate models to behavioral data, what level of modeling to employ, and how to articulate theory to facilitate such modeling. Four levels or types of modeling, two qualitative and two quantitative, are identified. Their properties are examined and interrelated to include illustrative applications to the study of abnormal behavior, with an emphasis on schizophrenia.

Association Learning↗
PubMed2004

Phasic coordination between locomotor and respiratory rhythms in Lymnaea. Real behavior and computer simulation.

In the pond snail Lymnaea stagnalis, a firm phase-locked coupling of pneumostome movements to the locomotor cycle was observed during terrestrial locomotion, thus demonstrating that the coordination between locomotor and respiratory rhythms is a natural behavioral event in this animal. The results of computational modelling suggest a possible scheme of coordination between these motor rhythms which is based on inhibitory projection from the central pattern generator for locomotion to that for respiration. These findings allow the neuronal mechanisms underlying coordination of two rhythmic behaviors to be investigated.

Animals↗
PubMed2003

Computer simulation of inhibition-dependent binding in a neural network.

Reverberating dynamics of neural network is modeled on PC in order to illustrate possible role of inhibition as binding controller in the network. The network is composed of binding neurons. In the binding neuron model [BioSystems 48 (1998) 263], the degree of temporal coherence between synaptic inputs is decisive for triggering, and slow inhibition is expressed in terms of the degree, which is necessary for triggering. Two learning mechanisms are implemented in the network, namely, adjusting synaptic strength and/or propagation delays. By means of forced playing of external pattern, the network is taught to support dynamics with disconnected and bound patterns of activity. By choosing either high, or low inhibition, one can switch between the disconnected and bound patterns, respectively. This is interpreted as inhibition-controlled binding in the network.

Computer Simulation↗
PubMed2006

Computer simulations reveal properties of the cell-cell signaling network at the shoot apex in Arabidopsis.

The active transport of the plant hormone auxin plays a major role in the initiation of organs at the shoot apex. Polar localized membrane proteins of the PIN1 family facilitate this transport, and recent observations suggest that auxin maxima created by these proteins are at the basis of organ initiation. This hypothesis is based on the visual, qualitative characterization of the complex distribution patterns of the PIN1 protein in Arabidopsis. To take these analyses further, we investigated the properties of the patterns using computational modeling. The simulations reveal previously undescribed properties of PIN1 distribution. In particular, they suggest an important role for the meristem summit in the distribution of auxin. We confirm these predictions by further experimentation and propose a detailed model for the dynamics of auxin fluxes at the shoot apex.

Arabidopsis↗
PubMed2003

Statistical thermodynamics of internal rotation in a hindering potential of mean force obtained from computer simulations.

A method of statistical estimation is applied to the problem of one-dimensional internal rotation in a hindering potential of mean force. The hindering potential, which may have a completely general shape, is expanded in a Fourier series, the coefficients of which are estimated by fitting an appropriate statistical-mechanical distribution to the random variable of internal rotation angle. The function of reduced moment of inertia of an internal rotation is averaged over the thermodynamic ensemble of atomic configurations of the molecule obtained in stochastic simulations. When quantum effects are not important, an accurate estimate of the absolute internal rotation entropy of a molecule with a single rotatable bond is obtained. When there is more than one rotatable bond, the "marginal" statistical-mechanical properties corresponding to a given internal rotational degree of freedom are reduced. The method is illustrated using Monte Carlo simulations of two public health relevant halocarbon molecules, each having a single internal-rotation degree of freedom, and a molecular dynamics simulation of an immunologically relevant polypeptide, in which several dihedral angles are analyzed.

Algorithms↗
PubMed2005

Flocculation in brewing yeasts: a computer simulation study.

A new simulator, INDISIM-FLOC, based on the individual-based simulator INDISIM, is used to examine the predictions of two different models of yeast flocculation. The first, proposed by Calleja is known as the "addition" model. The second, proposed by Stratford is known as the "cascade" model. The simulations show that the latter exhibits a better qualitative agreement with available experimental data.

Computer Simulation↗
PubMed1999

Comparison of prostate biopsy schemes by computer simulation.

OBJECTIVES: To compare the ability of different biopsy schemes to detect cancer and predict tumor volume using our previously described prostate biopsy simulation system. In addition, we used the simulation system to evaluate the optimal location of transition zone biopsies. METHODS: Digital reconstructions of 180 radical prostatectomy specimens were used. Forty simulations were performed on each prostate for 10 biopsy schemes, including a previously reported five-region peripheral zone biopsy pattern and a new 11-core multisite-directed scheme consisting of sextant, two transition zone, one midline, and two anterior horn biopsies. For simulation of the transition zone biopsies, paired near-midline biopsies were simulated, with needle insertion points from the apex to the base of the prostate and with needle advances of 1 to 4 cm before firing. A total of 1,180,800 individual biopsy tracks were simulated. RESULTS: The 11-core multisite-directed biopsy scheme had the highest detection rate for cancers greater than 0.5 cc. This scheme reliably detected cancer in 94% (138 of 147) of the cases. These results were significantly better than those of the sextant biopsy scheme (P <0.001) and the five-region 18-core peripheral zone scheme (P = 0.03). Compared with other schemes, there were increases in small-volume (0.5 cc or less) cancer detection by both the 11-core multisite-directed and five-region schemes, but they were not statistically significant. The multisite and the sextant plus four transition zone biopsy schemes had the best correlation of mean total core cancer length with total cancer volume. In the simulation of the transition zone biopsies, the highest detection rate was observed when the biopsies were initiated at the most apical section and inserted for a depth of 3 cm before firing. CONCLUSIONS: Our simulation results suggest that the detection rate of prostate biopsies is not related solely to the number of cores taken. Core placement (the regions of the prostate from which samples are taken) is also important. The 11-core multisite-directed biopsy scheme performed the best, with improved cancer detection rates and tumor volume correlation over other schemes. On the basis of our simulations, this scheme has been chosen for clinical evaluation.

Biopsy↗
PubMed2003

[Computer simulation of DOI-PET detector (1) -analysis of DOI discrimination accuracy in a detector block-].

A detector proposed by Murayama et al. for detection of depth-of-interaction (DOI) in PET consists of three-dimensionally arranged crystal elements with proper optical reflectors and is coupled to an array of photomultiplier tubes. This detector has a great advantage in easiness and cost in fabrication. We implemented a simulator of this detector that allows us to find appropriate values of parameters such as optical properties of crystal or detector unit geometry before making detectors. The simulator is based on the Monte Carlo method that traces the migration of optical photons generated by interaction of a gamma ray with crystal. First, the simulator performance was validated by comparing with the experimental data obtained with some prototype detectors. Then, on some parameters including refractive index of inter-crystal material, reflectance of optical reflector and detector geometry, appropriate values were investigated for accurate discrimination of crystal element of interaction.

Computer Simulation↗
PubMedDate not supplied

Computer simulation as a method for evaluating the copper sulfate test for hemoglobin in diverse populations.

The copper sulfate hemoglobin screening method was separately evaluated for three local population groups which do not conform to accepted normal standards of hemoglobin and/or plasma specific gravity (SG). This was carried out by a computer which simulated the distribution of plasma specific gravity and hemoglobin levels in random samples of blood donors. Simulations of 1,000 were carried out for males and for females in each of the three main population groups in Natal (Caucasians, Negroes and Asians). These were compared with a simulation of hypothetical normal subjects whose hemoglobin and plasma SG conformed to accepted standards. Variations in accuracy, relating to differences in plasma specific gravity and in hemoglobin, were demonstrated. Acceptances of donors who should be rejected (Type II errors) were most common in Negroes, but did not occur in the normal group. Type II errors did not occur in males with hemoglobin levels below 12.5 gm/dl or in females under 11.5 gm/dl. Erroneous rejections of prospective donors who, in fact, satisfied the criterion of acceptance (Type I errors) occurred in all groups, but were fewest in the normal group.

Computers↗
PubMed2001

Importance of accurate geometry in the study of the total cavopulmonary connection: computational simulations and in vitro experiments.

Previous in vitro studies have shown that total cavopulmonary connection (TCPC) models incorporating offset between the vena cavae are energetically more efficient than those without offsets. In this study, the impact of reducing simplifying assumptions, thereby producing more physiologic models, was investigated by computational fluid dynamics (CFD) and particle flow visualization experiments. Two models were constructed based on angiography measurements. The first model retained planar arrangement of all vessels involved in the TCPC but incorporated physiologic vessel diameters. The second model consisted of constant-diameter vessels with non-planar vascular features. CFD and in vitro experiments were used to study flow patterns and energy losses within each model. Energy losses were determined using three methods: theoretical control volume, simplified control volume, and velocity gradient based dissipation. Results were compared to a simplified model control. Energy loss in the model with physiologically more accurate vessel diameters was 150% greater than the simplified model. The model with nonplanar features produced an asymmetric flow field with energy losses approximately 10% higher than simplified model losses. With the velocity gradient based dissipation technique, the map of energy dissipation was plotted revealing that most of the energy was dissipated near the pulmonary artery walls.

Algorithms↗
PubMed2001

Assembly of a tetrameric alpha-helical bundle: computer simulations on an intermediate-resolution protein model.

Discontinuous molecular dynamics (DMD) simulation on an intermediate-resolution protein model is used to study the folding of an isolated, small model peptide to an amphipathic alpha-helix and the assembly of four of these model peptides into a four-helix bundle. A total of 129 simulations were performed on the isolated peptide, and 50 simulations were performed on the four-peptide system. Simulations efficiently sample conformational space allowing complete folding trajectories from random initial configurations to be observed within 15 min for the one-peptide system and within 15 h for the four-peptide system on a 500-MHz workstation. The native structures of both the alpha-helix and the four-helix bundle are consistent with experimental characterization studies and with results from previous simulations on these model peptides. In both the one- and four-peptide systems, the native state is achieved during simulations within an optimal temperature range, a phenomenon also observed experimentally. The ease with which our simulations yield reasonable estimates of folded structures demonstrates the power of the intermediate-resolution model developed for this work and the DMD algorithm and suggests that simulations of very long times and of multiprotein systems may be possible with this model.

Amino Acids↗
PubMed1990

Computer simulation of supraventricular tachycardia with the Wolff-Parkinson-White syndrome using three-dimensional heart models.

Supraventricular tachycardias with the Wolff-Parkinson-White (WPW) syndrome have been successfully simulated using a newly developed simulation system. The heart model, including atria and ventricles, was constructed of about 50,000 discrete elements (model cells) in three dimensions with 1.5-mm spatial resolution. The model cells covered all of the types of cells in the actual heart, including the normal myocardium, special conduction system and abnormal cells, such as the bundle of Kent (accessory pathway) and ectopic pacemaker (premature beat). Different model cells were specified by their electrophysiologic parameters, such as action potential, refractory period, and conduction velocity. The WPW syndrome was simulated by setting an accessory pathway between the right atrium and ventricle. Based on this model a premature atrial beat was introduced, which initialized the tachycardia. By adjusting the parameters, three types of reciprocal supraventricular tachycardia were simulated with the reentry circuits (1) formed anterogradely by the A-V node and retrogradely by the accessory pathway, (2) formed anterogradely by the accessory pathway and retrogradely by the A-V node, and (3) confined within the A-V node. Time relations for initializing and maintaining the tachycardias were evaluated. The simulated ECGs were in good agreement with the clinical findings.

Computer Simulation↗
PubMed2001

[A biomechanical model of left ventricle regional ischemia: a computer simulation].

Objective. To analyze the biomechanical mechanism of left ventricular regional ischemia and to investigate the changes of myocardial contractilities in different ventricular regions during regional ischemia. Method. A time-dependent mathematical model for simulating left ventricle regional ischemia has been developed basing on geometry of left ventricle, spatial angle distribution, propagation of electrical activation signals and biomechanical properties of cardiac muscle fibers. Then the model was incorporated into a multi-element circulatory model established by us previously. By using this model, some simulation experiments relating myocardium contractility to regional ischemia in inner or outer layers of ventricular wall were performed. Result. Myocardial contractility of the ischemic layers decreased whereas that of normal layers increased significantly. Compared with ischemia in outer layers of ventricular wall, ischemia in inner layers of ventricular wall had more effects upon cardiac function. Conclusion. The myocardium of normal region had the ability to increase its contractility in order to maintain a normal cardiac function. A method to simulate the relationship between cardiovascular function and left ventricular regional ischemia was developed.

Biomechanical Phenomena↗
PubMed1990

The use of computer simulation in the design and analysis of cell proliferation experiments.

The simulation language CELLSIM is used to model a population of cells undergoing proliferation, death and migration. It is shown that standard analytical methods can successfully describe the system in its unperturbed state, but may be considerably in error if the system has recently been subjected to cytotoxic insult. It is suggested that laboratory experiments should be performed on perturbed systems only if simulations have shown that the methods of data analysis will be satisfactorily powerful and accurate.

Animals↗