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The first order probability distribution for the distance between adjacent zeros of a Gaussian process has been estimated using computer simulations of the process. The results are compared to theoretical approximate results found in the literature.
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.
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.
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.
We have developed a computer model of chest-mounted counterlungs, which accounts for counterlung shape, effective volume, and pressure centroid. The model has been validated and the principles are applicable to other counterlung systems. The highly non-linear and discontinuous behavior of a counterlung is predicted by use of a sophisticated numerical integration method that computes variables such as pressure and volume in the time domain. Three separate stiffness (reciprocal of compliance) terms have been used which contribute to the diver's work of breathing: material elastic stiffness, "gas" stiffness, and "hydrostatic" stiffness. The model provides a significant advance in the understanding of counterlung behavior, allowing the performance of practical equipment to be predicted.
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.
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.
1. As a human subject slowly increases the amount of force exerted by a muscle, the discharge rates of low-threshold motor units saturate at a rather low level, whereas higher-threshold units continue to be recruited and undergo increases in their discharge rates. The presently known intrinsic properties of motor units do not produce this "rate limiting." 2. Using computer simulations of a model motoneuron pool, we tested the hypothesis that rate limiting can be accounted for on the basis of the known distributions of synaptic input from different sources. The properties of the simulated motor units and their synaptic inputs were based as closely as possible on the available experimental data. A variety of simulated synaptic input organizations were applied to the pool, and the resulting outputs were compared with the data on rate limiting in human subjects. 3. We found that the data on rate limiting in human subjects greatly constrained the possible organizations of characterized synaptic input systems. Only when the synaptic organization included a gradual "crossover" between two specific types of input systems could the human data be accurately reproduced. Low input/output levels relied on a system organized like the monosynaptic Ia input, which produces greater effective synaptic currents in low- than in high-threshold motor units. Above a sharply defined crossover level, all further increases in output were produced by a system organized like the oligosynaptic rubrospinal input, which generates the opposite pattern.
We describe a method to study the monomer-dimer equilibrium of human growth hormone (hGH) making use of a very short size exclusion high-performance liquid chromatographic column and rapid flow rates. By adjusting the flow rate and thus the retention time on the column, the dissociation of the hGH dimer can be observed. Using computer simulation, both the equilibrium constant for dissociation and the dissociation rate constant can be determined directly, followed by the indirect determination of the association rate constant. This method is potentially useful for determining the thermodynamic the kinetic parameters of aggregation of many protein-protein (homodimers and heterodimers) and protein-ligand systems whose rates of interaction are too rapid to be studied by conventional techniques.
Estimation of acceptably safe levels of biological contaminants in drinking water requires fitting a mathematical model to infection rates observed in small samples of human subjects. Because of obvious constraints on exposing human subjects to infective conditions, it is not feasible to compare the utilities of alternative sampling strategies and research designs using data from real experiments. Computer simulation methods were used to generate sample data having known probabilities of infection determined by an exponential or log-linear infectivity model. Experimental conditions that were examined included variations in the total available sample size, strategies for allocating subjects among different test concentrations, and methods for fitting a prediction model to the observed data. Results confirmed that data obtained by exposing most subjects to a concentration that produces an infection rate approximating 50% and calculating the sample regression coefficient for the log-linear model as the average infectivity-to-concentration ratio provided the best estimates of safe concentration. Exposing a single subject to each successively higher test level until an initial infection is observed, and exposing all remaining subjects at that level, or an adjacent log-concentration level is a tactic supported by the empirical results.
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.
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.
Local vascular drug delivery systems provide elevated concentrations in target arterial tissues while minimizing systemic side effects; however, definition of their precise pharmacokinetics remains elusive. The standard labeled tracer assays used in experimental vascular pharmacokinetic studies of these systems are limited because they quantify the arterial average drug concentration as opposed to transmural concentration profiles, require many animal experiments to elucidate the time-varying deposition, and track label rather than intact biologically active drug. In this study, computational simulations of drug deposition and distribution in vascular tissues after release from these systems have provided two important insights. First, simulations of arteries that were uniformly loaded with heparin predicted that most of the drug is cleared in < 1 h, illustrating the need for sustained modes of delivery. Second, some of the limitations of labeled tracers can be over come by combining experimental data with simulations that provided high spatial resolution. This enabled us to describe the kinetics of the deposited drug and distinguish soluble from reversibly bound and internalized drug within cells. The latter can help differentiate biologically viable drug from its committed inactive form or metabolites. These points have been illustrated through simulations of a novel endovascular hydrogel heparin-delivery system that has been applied to the porcine coronary artery. The basic models used in these simulations are generalized, and with the appropriate boundary conditions, binding and distribution constants can be used to study the physical interactions between any compound and tissue.
Oral anticoagulant therapy (OAT) has a well-established efficacy in prophylaxis and treatment of thromboembolic disorders. Because complications are related to intensity of OAT, optimal control of treatment is mandatory. In studies of OAT, as many as 30% of International Normalized Ratio (INR) measurements for prothrombin times fall outside the therapeutic interval. Preanalytical, analytical, and biological variation all contribute to this. Computer simulations of serial INR measurements were performed for various assumed in-treatment setpoints within the therapeutic interval INR 2.0-3.0 and for an "in-treatment within-subject variation" (CV) of 10.1%. Results are presented in difference plots with therapeutic intervals and critical differences. If the in-treatment setpoint is mid-interval (INR = 2.5), only 5% of simulated INR values fall outside the therapeutic interval. Setpoints deviating from the mid-interval and increases in the in-treatment within-subject variation considerably increase the number of observations outside the therapeutic interval and the critical differences. In conclusion, random variation, biological or analytical, and setpoints (targets) deviating from mid-interval explain a substantial number of the INR values outside therapeutic intervals observed in clinical studies. Analytical imprecision should be kept < 5% and analytical bias < +/- 0.2 INR.
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.
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.
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.
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.