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Results for “Computer Simulation”

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PubMedDate not supplied

The initiator titration model: computer simulation of chromosome and minichromosome control.

The initiator titration model was formulated to explain the initiation control of the bacterial chromosome. In particular, features concerning the replication behaviour of minichromosomes, such as their high copy number and Escherichia coli's ability to coinitiate chromosome and many minichromosome origins, were considered during the formulation of the model. The model is based on the initiator protein DnaA and its binding sites, DnaA boxes, in oriC, in the dnaA promoter and at other positions on the chromosome. Another important factor in the model is the eclipse period created by the hemimethylation of a new oriC which makes it refractory to initiation. The model was analysed by computer simulations using a stochastic approach varying the different input parameters, and the resulting computer cells were compared with data on living E. coli cells. Here we present the outcome of a few of these simulations concerning the eclipse period, in silico-shift experiments blocking initiation or elongation of replication, and introduction of minichromosomes into the computer cells. We also discuss the synthesis of DnaA protein in the computer cells. From our simulations, we conclude that, whether true or not, the model can mimic the in vivo initiation control of E. coli.

Bacterial Proteins↗

PubMed1991

Protein-protein interaction: an analysis by computer simulation.

A survey of protein-protein interactions in structures derived by X-ray crystallography of protease-inhibitor and antigen-antibody complexes shows that they form close-packed interfaces from which water is excluded. The interfaces are of almost constant size, and they contain about ten hydrogen bonds. These features account for the stability of the complexes. To test whether they also account for specificity, we designed a computer simulation that searches for complementary surfaces on two protein molecules. In all cases tested, the simulation finds a number of complexes having interfaces and hydrogen bonds equivalent to those of the native complexes. These artificial complexes might represent secondary specificities, which can be detected when normal association is prevented by mutation or other means.

Computer Simulation↗

PubMed1990

[The computer simulation of orthodontic tooth movements].

A personal computer programme is presented which allows the prediction of orthodontic tooth movement under the influence of any given force and moment. The changes in position of the front teeth caused by the chosen forces appear on the monitor as a three-dimensional diagram and as a movie-like picture sequence.

Computer Simulation↗

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↗

PubMed1990

A computer simulation of conduction block: effects produced by actual block versus interphase cancellation.

A reduction in compound muscle action potential (CMAP) amplitude and area following proximal versus distal stimulation is the accepted clinical hallmark of conduction block; however, quantitative criteria for determining conduction block remain ambiguous. In this study, digitized records of individual motor unit action potentials (MUAPs) elicited by incremental stimulation in vivo were arithmetically combined in a computer simulation of CMAP generation. Through simulation of possible phase interaction patterns of individual MUAPs, we have shown that abnormal temporal dispersion alone can produce reductions in CMAP area of up to 50%, values that are commonly thought to represent conduction block. Furthermore, by simulating conduction block without excessive temporal dispersion in defined subpopulations of axons, we have demonstrated the importance of the fastest conducting (largest MUAP) axons in determining CMAP amplitude and area. In conclusion, measurements of CMAP amplitude and area in determining conduction block may be misleading if there is significant abnormal temporal dispersion, and quantitation of the degree of conduction block is difficult without knowledge of which subpopulations of axons are affected.

Action Potentials↗

PubMed1986

Computer simulations of nuclear reactions by protons with incident energies of 250, 300 and 500 MeV in a human body.

Computer simulations of nuclear reactions by protons in a human body were carried out at the incident energies of 250, 300 and 500 MeV. About 20% of the incident protons are absorbed by the body with nuclear interactions and the rest of the protons pass through the body at these energies. Radiation of gamma rays from the body and radioactivity of the body were estimated as a function of the time after irradiation with the proton beam.

Body Composition↗

PubMed1991

Model and computer simulations of the motion of DNA molecules during pulse field gel electrophoresis.

A model is presented for the motion of individual molecules of DNA undergoing pulse field gel electrophoresis (PFGE). The molecule is represented by a chain of charged beads connected by entropic springs, and the gel is represented by a segmented tube surrounding the beads. This model differs from earlier reptation/tube models in that the tube is allowed to leak in certain places and the chain can double over and flow out of the side of the tube in kinks. It is found that these kinks often lead to the formation of U shapes, which are a major source of retardation in PFGE. The results of computer simulations using this model are compared with real DNA experimental results for the following cases: steady field motion as seen in fluorescence microscopy, mobility in steady fields, mobility in transverse field alternation gel electrophoresis (TFAGE), mobility in field inversion gel electrophoresis (FIGE), and linear dichroism (LD) of DNA in agarose gels during PFGE. Good agreement between the simulations and the experimental results is obtained.

Chemical Phenomena↗

PubMed1982

A theory for the origin of a self-replicating chemical system. II. Computer simulation of the autogen.

In order to better understand the feasibility and limitations of the autogen (White 1980), a computer simulation based on the fluctuating clay environment was used to test whether autocatalytic growth would occur under various conditions. The results suggest that overall accuracies of replication and translation in the range of 90% and 10%, and protoenzyme turnover numbers of 10--120 monomers/protoenzyme/day are adequate for exponential growth. Nucleation of the components of the autogen from random background oligomers would be extremely rapid if oligomers lengths 2--6 were adequately functional, whereas oligomer lengths much greater than 10 are prohibited. The autogen would most likely nucleate and grow to dominance either rapidly (10--100 cycles of roughly 1 day each) or not at all.

Computers↗

PubMed1987

Effectiveness of a salt transport cascade in the renal medulla: computer simulations.

Based on morphological observations, it has been concluded that the upper parts of the long descending limbs of Henle's loops should be able to secrete salts into the tubular fluid (Kriz, W. Federation Proc. 42:2379-2385, 1983). In the same article, a hypothesis is given depicting how this active transport in concert with certain characteristics of the medullary architecture might produce a transport cascade toward the papillary tip, thus supporting the accumulation of salts in this region. The effectiveness of the proposed mechanism can be judged by a mathematical model only. The computer simulations of the present study demonstrate that this mechanism indeed leads to an increase of the concentrating capability of the renal countercurrent system.

Biological Transport, Active↗

PubMed1988

A computer simulation of hearing aid response and the effects of ear canal size.

The response of a hearing aid is affected by many factors which include the head and outer ear, the microphone, amplifier, and receiver used in the hearing aid, the properties of the ear canal and the eardrum, and acoustic feedback through the vent. This article presents a computer simulation of an in-the-ear (ITE) hearing aid that includes all of the above factors. The simulation predicts the pressure at the eardrum for a frontal free-field sound source. The computer model was then used to determine the effects on the hearing aid response due to variations in the size of the ear canal. The simulation indicates that, for an unvented hearing aid, changes in the size of the ear canal shift the overall sound-pressure level at the eardrum but have only small effects on the shape of the frequency response. The situation is more complicated when a vent is present, however, since changes in the size of the ear canal that cause apparently small perturbations in the acoustic feedback signal may, nonetheless, have large effects on the overall system response.

Computer Simulation↗

PubMed1979

A theoretical approach to precipitin reactions: insight from computer simulation.

The theoretical consequences of different hypotheses of the mechanism of precipitin reactions have been evaluated by means of computer simulation. It has been found that the formation of compositionally different complexes in different antigen/antibody mixtures provides a valid explanation of the zoning phenomenon, but this concept fails to explain the absence of free antigen and of antigen in soluble complexes at the point of maximum percipitation. It is found that the following hypothesis provides an improved qualitative and quantitative explanation of percipitin reactions. In the first stage of the total reaction a series of compositionally different complexes is formed. As the second stage of the total reaction two kinds of processes are proposed. Inherently insoluble complexes precipitate causing the remaining soluble complexes to participate in mutual rearrangements to re-establish a new state of equilibrium in the supernatant. The inherently insoluble complexes, moreover, create a hydrophobic phase, distinct from the supernatant and cause the remaining otherwise soluble complexes to distribute themselves between the two phases according to a partition coefficient. A mathematical apparatus to study the consequences of this hypothesis is presented, and it is demonstrated that the features of precipitin curves can be explained nearly completely this way.

Antigen-Antibody Complex↗

PubMed1995

Neural network control of functional neuromuscular stimulation systems: computer simulation studies.

A neural network control system has been designed for the control of cyclic movements in Functional Neuromuscular Stimulation (FNS) systems. The design directly addresses three major problems in FNS control systems: customization of control system parameters for a particular individual, adaptation during operation to account for changes in the musculoskeletal system, and attaining resistance to mechanical disturbances. The control system was implemented by a two-stage neural network that utilizes a combination of adaptive feedforward and feedback control techniques. A new learning algorithm was developed to provide rapid customization and adaptation. The control system was evaluated in a series of studies on a computer simulated musculoskeletal model. The model of electrically stimulated muscle used in the study included nonlinear recruitment, linear dynamics, and multiplicative nonlinear torque-angle and torque-velocity scaling factors. The skeletal model consisted of a one-segment planar system with passive constraints on joint movement. Results of the evaluation have demonstrated that the control system can provide automated customization of the feedforward controller parameters for a given musculoskeletal system. It can account for changes in the musculoskeletal system by adapting the feedforward controller parameters on-line and it can resist the effects of mechanical disturbances. These results suggest that this design may be suitable for the control of FNS systems and other dynamic systems.

Adaptation, Physiological↗

PubMed1991

The potential and limitations of opportunistic screening: data from a computer simulation of a general practice screening programme.

Given the continuing emphasis on preventive medicine in general practice, there is considerable interest in the relative effectiveness of different ways of inviting patients to attend for screening. Recently, opportunistic methods have been advocated as being particularly useful but these methods often fail to reach a high proportion of the target population. Many patients do not consult and when they do they are not always invited to attend for screening. In this study a computer simulation model has been used to examine the effects of these variables in more detail. The notes of a random sample of 190 patients (97 women, 93 men) aged 30-50 years, registered with one general practitioner, were used to provide data for the model. The simulation model showed that increasing the number of screening appointments available each week has only a small effect on screening rates and that a ceiling is reached when 25 appointments per 1000 patients are available. In contrast, increasing the proportion of eligible consulting patients who are invited has a substantial effect such that it could take nearly 12 years to screen 90% of a target population if only one out of every four patients were invited compared with under four years if three out of every four patients were invited. The results suggest therefore that opportunistic screening methods are unlikely to achieve desired screening rates within acceptable time limits. It is argued that to achieve target levels of screening, practices will need to combine opportunistic methods with more formal methods of invitation.

Computer Simulation↗

PubMedDate not supplied

Conversion from intravenous aminophylline to sustained-release theophylline: computer simulation versus in vivo results.

The accuracy of computer-predicted theophylline serum concentrations compared with actual serum concentrations in patients whose drug therapy was being converted from aminophylline infusions to an oral sustained-release theophylline product (Theo-Dur) was measured. The SIMKIN computer program was used to simulate theophylline serum-concentration curves in nine patients receiving an initial dose of sustained-release theophylline at the time their maintenance aminophylline infusions were discontinued. The sustained-release theophylline doses were calculated using individual patient theophylline clearance values to produce mean theophylline serum concentrations in the normal therapeutic range. Pharmacokinetic variables used in the SIMKIN program were derived from individual patients' serum concentrations and average literature values. Theophylline serum concentrations were measured before the initial dose of the sustained-release product and periodically for 12 hours. Mean SIMKIN-predicted serum theophylline concentrations were within 10% of actual measurements 39% of the time, but data from individual patients varied considerably. Two patients had prolonged absorption lag times that could not be explained. Computer-simulation programs using population-based pharmacokinetic variables to predict theophylline serum concentrations must be tested against in vivo measurements to verify their accuracy.

Adult↗

PubMed1985

Effect of resolution improvement on required count density in ECT imaging: a computer simulation.

The effects of changes in spatial resolution and total number of counts on image quality were investigated for positron and single photon emission computed tomography (ECT) systems. A variety of high contrast phantoms were generated in a computer simulation and count density and spatial resolution were varied independently over a wide range. As system spatial resolution is improved, significantly fewer counts are needed to give images of comparable visual quality. Using 100% object contrast, it was found that the number of counts could be reduced by a factor of four for a 2 mm improvement in spatial resolution over a wide range of parameters. This is due to the fact that image contrast increases rapidly with spatial resolution improvements in high contrast objects such as those used in this simulation and typically encountered in brain and cardiac ECT studies.

Computers↗

PubMed1989

Computer simulations of globular protein folding and tertiary structure.

In summary, although a large number of disparate techniques have been applied to predict the tertiary structure of globular proteins from their amino acid sequence, the solution is not yet at hand. Methodologies for predicting the conformation of constrained, small protein fragments appear to be successful. As the size of the system increases, the level of detail of the treatment decreases; approaches that employ very detailed potentials appear to be limited to about 30-40 residues. Although this is a major advance, methods that reduce the effective number of degrees of freedom are clearly required. Lattice representations coupled to highly efficient Monte Carlo procedures appear to be one such approach. Thus, although a number of theoretical advances in the computer simulation of globular protein structure have been made, much work remains to be done before the globular protein folding problem is solved.

Computer Simulation↗

PubMed1994

The 'shortmer' approach to nucleic acid sequence analysis. I: Computer simulation of sequencing projects to find economical primer sets.

In principle it is most economical to sequence large DNA fragments consecutively ('primer walking'), provided there is an immediate supply of sequencing primers. To solve the problem of primer supply we previously suggested generating a bank of short oligonucleotide primers ('shortmers'). In every sequencing reaction shortmers would have to be selected from this bank that are suitable to hybridize adjacently on the sequencing template. After their ligation the shortmers would form a long, and hence more specific, primer in the subsequent sequencing reaction. In the present study a computer simulation of large sequencing projects revealed a reduced set of approximately 12,000 selected octanucleotides (out of all 65,536) retaining maximum priming flexibility and minimum redundant information on the simulated sequence analyses. Establishing routine protocols for nucleic acid sequencing following the shortmer approach will abolish the tightest bottleneck of the consecutive sequencing route (primer supply) and hence may render this general scheme more attractive than the shotgun sequencing scheme. A twofold (or more) speed-up of genome sequencing projects by the shortmer approach may be assumed.

Algorithms↗

PubMed1978

Burst generation by electrically coupled network in the snail helisoma: analysis using computer simulation.

The effectiveness of electrical coupling between neurons as a mechanism for mediating single and repetitive bursts is investigated here using computer simulation. The cyberchron network in the snail Helisoma generates repetitive bursts controlling the animal's feeding behavior and served as the basic model for the simulation studies described in this paper. The action potential properties of individual neurons were modeled by the Rall equations describing generalized action potentials. Several properties of electrical coupling and its role in burst generation were demonstrated, including: (1) A neuron in an electrically coupled network can generate action potentials at a higher frequency than an isolated neuron with similar membrane properties due to the loading through the electrical junctions. However, the ability of electrically coupled neurons to generate high-frequency bursts of action potentials requires a concomitantly greater amount of driving current to overcome the junctional loading. (2) Temporal and spatial summation of synaptic input onto a neuron is maintained at its most effective level because the postsynaptic current is integrated across the long postsynaptic membrane time constant. (3) Initial simulations concentrated on a pair of electrically coupled neurons which were below threshold. Stimulation of one of the two neurons with a short pulse resulted in a reverberation or regenerative excitation between the two neurons. The reverberation terminated after a number of action potentials dependent on the specific model parameters. Similar results were obtained with a network containing a greater number (20) of model neurons if approximately one-half of the neurons were stimulated simultaneously. However, none of the cases studied produced more than a single discrete burst. (4) Simulations were also conducted on 20-neuron networks containing two subpopulations of model neurons differing in their values of coupling resistance and excitability. Some networks of this type required stimulation of only one cell to make the two subpopulations of model neurons reverberate with one another. Such simulations suggest the possibility that 'preferred' input pathways involving a small number of neurons would be capable of 'turning on' the activity of the entire network.

Animals↗