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PubMed1975

Computer simulation of flagellar movement. III. Models incorporating cross-bridge kinetics.

A computer simulation procedure is used to analyze the generation of propagated bending waves by flagellar models in which active sliding is generated by a cycle of cross-bridge activity. Two types of cross-bridge cycle have been examined in detail. In both cycles, cross-bridge attachment is followed immediately by a configurational change in the cross-bridge, which transfers energy to a stretched elastic element and generates a shearing force between the filaments. In the first model, which has cross-bridge behavior close to current ideas about cross-bridge behavior in muscle, cross-bridge attachment is proportional to curvature of the flagellum and detachment is an exponential decay process. The configurational change is equivalent to an angular deviation of pi/5 radians. In the second type of cross-bridge cycle, cross-bridge attachment occurs rapidly when a critical curvature is reached, and detachment occurs when a critical curvature in the opposite direction is reached. With this cycle, an unrealistically large angular deviation of the cross-bridges, equivalent to 3.0 radians, is required to obtain bending waves of normal amplitude. Both models generate bending wave patterns similar to those obtained in earlier work. However, the behavior of the second type of cross-bridge model more closely matches the actual behavior of flagella under experimental conditions: the chemical turnover rate per beat cycle remains constant as the viscosity is increased, and reduction in the number of active cross-bridges can cause a reduction in beat frequency, with little change in amplitude or wavelength.

Binding Sites↗
PubMed1975

Urea handling by the renal countercurrent system: insights from computer simulation.

The renal handling of urea has been investigated with the aid of a computer model of the countercurrent system in which active electrolyte reabsorption occurs along the entire ascending limb of Henle's loop. In this model, summarized in Fig.9, the buildup of a corticopapillary gradient for urea is optimized if there is net addition of urea to loops of Henle only in the outer medulla. This added urea remains within the tubular system until it is reabsorbed from collecting ducts in the inner medulla. Thus, a net transfer of urea from outer to inner medulla is accomplished (via distal tubule and cortical collecting duct). There is no net addition of urea to loops of Henle within the inner medulla; in this region, the loops act simply as countercurrent exchangers for urea. Computer simulation of systematic variation in the urea permeabilities of each nephron segment shows that interference with any element of the above schema results in impairment of the medullary accumulation of urea relative to plasma. Simulation of varying rates of urinary urea excretion demonstrates that this model can account for the ability of the kidney to excrete substantial amounts of urea without an accompanying osmotic loss of water. The major insight gained from this study is that net addition of urea to loops of Henle in the outer medulla greatly enhances the medullary accumulation of urea, whereas, net addition of urea to loops within the inner medulla tends to defeat such accumulation and hence the urinary concentrating process. This general principle applies also to an alternate model of the countercurrent system, in which electrolyte reabsorption from thin ascending limbs of Henle is passive.

Computers↗
PubMed1976

Computer simulation of the precordial QRS complex: effects of simulated changes in ventricular wall thickness and volume.

The cardiac electric field generated by depolarization of the human ventricle is simulated with a computer model which utilizes 1,500 dipoles. The configuration of the ventricles utilized in the model assumed that the cross-sectional shape of the left ventricle was circular and the right ventricular free wall was a portion of an ellipse. The torso was assumed to be homogeneous and infinite. The activation sequence was based on the measurements of Durrer. The depolarizational wave was simulated by dipole layers. The output of the model is presented as a standard multilead precordial ECG. The ECG complexes generated by the model closely resemble the precordial QRS complexes of normal man. Simulated increases in wall thickness (1 to 2.2 X control) were associated with changes in the calculated precordial QRS complexes which were characteristic of left ventricular hypertrophy. Voltage (R in V5 or V6 and S in V1) and QRS duration increased linearly as a function of calculated left ventricular mass. Increases in ventricular activation time were related nonlinearly to changes in left ventricular mass and did not occur in the absence of a simulated increase in wall thickness. The effects of simulated changes in left ventricular volume (0.6 to 3.0 X control) on the QRS complex were mainly dependent on the resultant increase in left ventricular mass. This model may be useful in simulating the precordial QRS complexes that result from isolated or combined changes in ventricular volume or wall thickness or other disorders of the heart. Furthermore, it may be useful whenever a simulation of a QRS generator is needed.

Cardiac Volume↗
PubMed1979

Computer simulation of flow-dependent absorption in microperfused short Henle's loop of rats.

With computer simulation we examined the extent to which current theories and experimental data explain function of single microperfused superficial Henle's loops in rats. In the model standard phenomenological equations describe transport; two sets of transport parameters labeled rat and rabbit were taken from published experiments; Michaelis-Menten kinetics in the ascending thick limb were adjusted arbitrarily; tubular radius is either constant or depends on luminal pressure with compliance based on experimental observations; the interstitium is an infinite sink with salt and urea concentrations constant in the cortex and exponentially increasing in the outer medulla; concentrations resemble those found in hydropenic or saline diuretic rats. The following predictions were obtained. The model with rabbit parameters does not recirculate urea and will not operate with high medullary urea concentrations; with rat parameters too much urea recirculates an the results of perfusion with equilibrium solution are not reproduced. Using a compromise between rat and rabbit parameters, the model reproduces water absorption, salt reabsorption, and urea recirculation as observed in vivo in rat loops perfused at 5-40 nl/min. It also simulates perfusion with saline, equilibrium solution, saline plus furosemide, and 300 mM mannitol. When the model includes a short early distal segment, effluent salt concentration reaches a minimum at a 15 nl/min perfusion rate as observed in vivo; however, concentration at the macula densa is a monotonically increasing function of flow. When permeation rate is a function of wall surface area and thickness a better fit to experimental results is produced. However, the effect is small: water absorption alters by 4% or less and effluent salt concentration is reduced by up to 10% at low perfusion rates. Comparison of rigid and compliant loops shows no relationship between transit time per se and reabsorption.

Animals↗
PubMed1976

Implications of fertility patterns in the Republic of Korea: a study by computer simulation.

Implications of various fertility patterns in the Republic of Korea (ROK) are studied by computer simulation. These patterns include the factors: age of marriage, sex preference, abortion (induced), contraception and sterilisation. As a result of studying a large number of combinations of these factors, the following tentative conclusions, among others, are reached. If future cohorts of women in the ROK become limiters after two live births and marry according to an observed high level marriage distribution, at least two of the methods of birth control--abortion, contraception, and sterilisation--will have to be used extensively to yield a mean number of live births (MNLB) in these cohorts of the order 2-2. However, if these women marry later than the observed high level marriage distribution and, in addition, accept effective methods of contraception more widely and use them more effectively, then the MNLB experienced by these cohorts could move below 2-5 wihtout the extensive utilisation of abortion and sterilisation.

Abortion, Induced↗
PubMed1977

Computer simulation of rat heart metabolism after adding glucose to the perfusate.

An experiment where perfused rat hearts receiving no substrate are suddenly given glucose with insulin in the perfusate is simulated with a computer model of cardiac energy metabolism. Mitochondrial metabolism is quantitatively reorganized under cytoplasmic control, with fatty acid oxidation undergoing a two-step decrease. There is an unspanning of the Krebs cycle (different reactions going at different rates) due primarily to slowing of alpha-ketoglutarate dehydrogenase; this ends when cytoplasmic glucose reaches a new steady state. Mitochondria in vitro are known to have higher pH than their surroundings; it is found here that this also holds in situ. Under these conditions, glycolysis is coherently substrate controlled, as is phosphofructokinase, usually considered the typical example of an allosteric enzyme. Limitations on simple methods of analyzing metabolic data of this type, e.g., use of lactate/pyruvate ratios to calculate NADH/NAD ratios, are discussed. Here a large volume of enzyme and other biochemical information has been integrated into a physiologically meaningful system.

Amino Acids↗
PubMed1976

Active enzyme gel chromatography: II. Computer simulations.

The behavior of an enzyme undergoing reaction while on a gel chromatography column has been studied by computer simulation using the steady state assumtion for a system with a single enzyme-substrate complex. The profiles of the enzyme-substrate complex, product, and substrate were examined varying the parameters of kcat, flow rate, partition coefficient dispersion, and time. These investigations confirm that much information about both the active enzyme and the product may be obtained by examining the product profile alone, varying the power of applying scanning gel chromatography to active enzyme systems.

Binding Sites↗
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↗
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↗
PubMed1976

Computer simulation of brainstem respiratory activity.

A mathematical model of the medullary respiratory oscillator, composed of two mutually inhibiting populations (inspiratory and expiratory) of computer-simulated neurons, is presented. Each population consists of randomly interconnected subpopulations of excitatory and inhibitory neurons, is presented. Each population consists of randomly interconnected subpopulations of excitatory and inhibitory neurons. Neuronal coupling is such that either the inspiratory or expiratory population alone is capable of cyclic activity. Weak inhibitory connections between inspiratory and expiratory populations provide satisfactory reciprocating activity independent of the natural frequency of either population alone. Initiation and persistence of rhythmic activity is dependent on a diffused noncyclic excitatory input. Vagal discharge, simulated by phasic inhibition of inspiratory neurons, results in increased respiratory frequency with decreased inspiratory activity. In the absence of simulated vagal discharge, uniform facilitation of synaptic connections increases averaged activities of inspiratory and expiratory populations, with minor effect on frequency. In the presence of simulated vagal discharge, facilitation of synaptic connections increases both frequency and amplitude. The simulated effects of synaptic facilitation, with and without vagal discharge, mimic the physiological response to CO2 in the intact and vagotimized animal.

Computers↗
PubMed1975

Computer simulation study of hexokinase II from Ehrlich ascites cells.

A study of the mechanism of hexokinase II from ascites cells the effects of its binding to mitochondrial membranes has been carried out by computer simulation. This is based on experimental data of Kosow and Rose and of Gumaa and McLean, and the theoretical methods of cleveland. For the soluble enzyme the mechanism is random with ternary produce-inhibition complexes; when bound to mitochondria, the mechanism becomes ordered-on, random-off, as the binding of ATP to the free enzymes becomes negligibly slow. The requirements of experimental data for mechanistic studies are discussed.

Adenosine Triphosphate↗
PubMed1978

A computer simulation study of optimal thyroid radiation protection during investigations involving the administration of radioiodine-labelled pharmaceuticals.

The administration of iodide for thyroid blocking is now known to carry its own risks, at least in certain categories of patients. We have therefore made a theoretical study by computer simulation of the efficacy of various thyroid blocking regimes. In the case of injected 125I- or 131I-iodide, substantial thyroid protection may theoretically be achieved by a single oral dose of inorganic iodide, for example a 90% reduction in radiation dose is produced by only 20 mg iodide. Repeating the initial blocking dose is of little value. A single blocking dose, however, affords poor protection against radioiodine released from labelled plasma proteins. Both for short-lived proteins such as fibrinogen, and for the longer-lived proteins such as albumin, the optimum dosage schedule appears to be stable iodide given daily for two to three weeks. For instance, 10 mg daily for a fortnight will reduce thyroid irradiation by a factor of ten following injection of 125I-fibrinogen.

Albumins↗
PubMed1978

Aspects of temperature regulation in harp seal pups evaluated by in vivo experiments and computer simulations.

Temperature regulation in harp seal pups (Pagophilus groenlandicus) has been studied by in vivo measurements of oxygen consumption, body temperatures and in vitro determinations of the thermal values of a fur sample. The experimental animals were restrained and exposed to natural wheather conditions. Solar irradiance above 600 W/m (global radiation) caused hyperthermia. Computer simulations based on the thermal values of the fur indicated that heat dissipation from primarily the limbs is a prerequisite for avoiding hyperthermia under natural weather conditions. Further simulations showed that the lower critical temperature of a lean newborn harp seal pup with standard metabolism is only--1 degree C while it is depressed to--59 degree C as the pup grows, aquire a 10 cm thick layer of blubber and the metabolism increases to 1.5 times standard. High metabolism and tolerance to low deep body temperatures (35 degree C) seems a prerequisite for thermal balance in the harp seal pup under cold conditions.

Animals↗
PubMed1978

On investigating the statistical properties of the populous path algorithm by computer simulation. Counterconclusions to those of Tateno and Nei.

Goodman et al.'s (1974) populous path algorithm for estimating hidden mutational change in protein evolution is designed to be used as an adjunct to the maximum parsimony method. When the algorithm is so used, the augmented maximum parsimony distances, far from being overestimates, are underestimates of the actual number of nucleotide substitutions which occur in Tateno and Nei's (1978) computer simulation by the Poisson process model, even when the simulation is carried out at two and a half times the sequence density. Although underestimates, our evidence shows that they are nevertheless more accurate than estimates obtained by a Poisson correction. In the maximum parsimony reconstruction, there is a bias towards overrepresenting the number of shared nucleotide identities between adjacent ancestral and descendant nodal sequences with the bias being stronger in those portions of the evolutionary tree sparser in sequence data. Because of this particular property of maximum parsimony reconstructed sequences, the conclusions of Tateno and Nei concerning the statistical properties of the populous path algorithm are invalid. We conclude that estimates of protein evolutionary rates by the maximum parsimony--populous path approach will become more accurate rather than less as larger numbers of closely related species are included in the analysis.

Biological Evolution↗
PubMed1976

Changes in the shape of the developing vertebrate nervous system analyzed experimentally, mathematically and by computer simulation.

Two forces are necessary and sufficient to produce the transformation of the newt neural plate from a hemispheric sheet of cells one cell thick to a keyhole shape. These forces are: (1) a regionally programmed shrinkage of the surface of the neural plate (accomplished by contraction of the apical surfaces of the neural plate cells and elongation of these cells perpendicular to the plate); and (2) displacement of the whole sheet caused by elongation of either the notochord or the overlying neural plate cells in the antero-posterior direction. A computer simulation and mathematical analysis ("morphodynamics"), together with experiments and observations on embryos, were used to deduce the morphogenesis of the neural plate from these forces.

Animals↗
PubMed1978

Conduction through demyelinated plaques in multiple sclerosis: computer simulations of facilitation by short internodes.

Clinical and laboratory observations both suggest that it may be possible for action potentials to traverse, in a continuous manner and without interruption, demyelinated zones along some axons. This continuous mode of conduction requires the presence of sufficient numbers of sodium channels in the demyelinated region. One of the factors which will tend to prevent such conduction is the impedance mismatch at sites of focal demyelination, which may result in a reduction in current density sufficient to cause conduction failure. As part of an effort to examine the conditions which would promote conduction into, and beyond, the demyelinated region, we examined, using computer simulations, the effects of reduction in length of the proximal internodes closest to the demyelinated region. Our results indicate that reduction in length of the two internodes closest to the demyelinated region. to approximately one-third of normal length or less, will facilitate conduction beyond the plaque. The results suggest that reductions in internode length, which have been histologically observed along some demyelinated fibres, may have functional significance in terms of facilitating conduction past focally demyelinated zones.

Action Potentials↗