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At least 883 records · Page 49Linked to original sources
PubMed1984

A computer simulation of geometrical configurations during cell division.

A process of cell division in the blastular wall of the starfish, Asterina pectinifera, was observed, and an attempt was made to model with a computer simulation the way in which cell number increases in such a tissue. Dividing cells at stages between the 2(11)-cell and the beginning of rotation were observed to shift these positions to the outer surface of the cell sheet by rounding up, after which they divide and slip back into the sheet as two columnar daughter cells. The change of a polygonal pattern of the blastular wall by cell division was simulated by making use of geometrical models of polygonal cells and the rule of the direction of cell division which was confirmed by observation. The simulation proves valid for describing changes of polygonal patterns of cell sheets including dividing cells.

Animals↗
PubMed1989

Reversed-phase chromatographic method development for peptide separations using the computer simulation program ProDigest-LC.

A computer program, ProDigest-LC, has been developed that assists scientists in devising methods of size-exclusion, cation-exchange and reversed-phase high-performance liquid chromatography for the analytical separation and purification of biologically active peptides and peptide fragments from enzymatic and chemical digests of proteins. ProDigest-LC accurately predicts the retention behaviour of peptides of known composition, containing 2-50 amino acid residues, and simulates the elution profiles in all three modes of chromatography. In addition, ProDigest-LC is a user-friendly program, designed as a teaching aid for both students and researchers in selecting the correct conditions for chromatography, that is, the mode of chromatography, column selection and mobile-phase selection, and has the ability to examine the effects of gradient-rate, flow-rate and sample size on the separation. The simulation capabilities of ProDigest-LC as they apply to the reversed-phase chromatography of peptides were examined. The development of the reversed-phase simulation features of the program is described, stressing the importance of peptide standards in the development, testing and practical use of ProDigest-LC. The ease of use of the program is clearly demonstrated by presenting a step-by-step procedure to produce several of the simulations illustrated in the paper. The predictive accuracy of the program was rigorously tested by its application to retention time prediction, at different gradient-rates and flow-rates, for a sample mixture containing peptides exhibiting a wide range of size (11-50 residues), charge (+1 to +8 net charge), hydrophobicity and conformation (random coil to considerable alpha-helical structure). The excellent accuracy of these peptide retention time predictions complemented the successful simulation (in terms of peptide retention times, peptide resolution, peak heights and peak widths) of the effects of gradient-rate and flow-rate on the elution profile of a mixture of closely related peptide analogues.

Chromatography, High Pressure Liquid↗
PubMed1984

Quality control of manual visual field examination by computer simulation.

Quality control of manual visual field examination is impaired because the process is difficult to monitor, and because examiners have minimal formal training and supervision, and are subject to rapid turnover. Computer simulation can be used both to teach perimetry and to provide a reference standard against which performance may be measured.

Community Health Services↗
PubMed1984

Estimation of the rising phase of EPSP analyzed by computer simulation of the coding process.

Based on data obtained from intracellular recordings of cat alpha-motoneurons in the stretch reflex, the firing process of these motoneurons was computer-simulated. The impulse response EPSP (IR-EPSP) was simulated to correspond to a monosynaptic mass EPSP elicited by a spindle afferent volley, while the returning potential was simulated to correspond to a potential gradient rising toward an augmenting depolarization of the membrane (augmentative EPSP) after motoneuronal spike generation. The IR-EPSPs were generated by input at random intervals and added to each other, linearly, on the returning potential. As soon as the resultant potential attained the critical threshold level, Vth, motoneuron firing occurred. Then IR-EPSPs were again added to the returning potential until another motoneuron firing occurred. This process was repeated continuously, and the time relation between input and output, lag-time distribution (PT(T], was determined Distribution of the bias potential, PV(V), from which the motoneuron spike triggering EPSP started to rise, was also calculated. The relations between PT(T), PV(V) and a waveform of the IR-EPSP were obtained analytically. The relation indicated that the shape of PT(T) corresponds to a time derivative of the rising phase of the IR-EPSP if the PV(V) distribution is uniform. In this study, we investigated the possibility of making the PV(V) distribution uniform.

Animals↗
PubMed2006

Microscopic description of the low-temperature anomalies in silica and lithium silicate via computer simulations.

Information about the nature of the low-temperature anomalies and in particular the properties of the tunneling systems in silica and lithium silica glasses are revealed via computer simulations. The potential energy landscape of these systems is systematically explored for adjacent pairs of local minima which may act as double-well potentials (DWPs) at low temperatures. Three different types of DWPs are distinguished, related to perfectly coordinated silica, intrinsic silica defects, and extrinsic defects. Their properties such as the spatial extension and the dipole moment are characterized in detail. Furthermore, the absolute number of tunneling systems, that is, symmetric DWPs, is estimated. The results are compared with dielectric echo, specific heat, and acoustic experiments on Suprasil I and Suprasil W. A semiquantitative agreement for all relevant features is obtained.

Journal Article↗
PubMed2006

Self-organization and pattern formation of janus particles in two dimensions by computer simulations.

The phase behavior and associated pattern formation of two-dimensional systems of hard disks decorated with amphiphilic coronae (Janus disks) are studied by means of Monte Carlo computer simulations. A primitive interaction potential that captures the essential interparticle interactions is introduced. Despite its simplicity, the system exhibits a very rich phase polymorphism. Apart from the isotropic phase and depending upon the coronal thickness, the simulated systems self-organize in a number of two-dimensional mesophases of various symmetries exhibiting a variety of novel patterns. The results of these simulations suggest that 2D Janus particles are promising candidates for bottom-up design of precise two-dimensional templates.

Journal Article↗
PubMed1972

Computer simulation of radial immunodiffusion. I. Selection of an algorithm for the diffusion process.

Theories of diffusion with chemical reaction are reviewed as to their contributions toward developing an algorithm needed for computer simulation of immunodiffusion. The Spiers-Augustin moving sink and the Engelberg stationary sink theories show how the antibody-antigen reaction can be incorporated into boundary conditions of the free diffusion differential equations. For this, a stoichiometric precipitate was assumed and the location of precipitin lines could be predicted. The Hill simultaneous linear adsorption theory provides a mathematical device for including another special type of antibody-antigen reaction in antigen excess regions of the gel. It permits an explanation for the lowered antigen diffusion coefficient, observed in the Oudin arrangement of single linear diffusion, but does not enable prediction of the location of precipitin lines. The most promising mathematical approach for a general solution is implied in the Augustin alternating cycle theory. This assumes the immunodiffusion process can be evaluated by alternating computation cycles: free diffusion without chemical reaction and chemical reaction without diffusion. The algorithm for the free diffusion update cycle, extended to both linear and radial geometries, is given in detail since it was based on gross flow rather than more conventional expressions in terms of net flow. Limitations on the numerical integration process using this algorithm are illustrated for free diffusion from a cylindrical well.

Antigen-Antibody Reactions↗
PubMed1971

Population control potential of heterozygous translocations as determined by computer simulations.

A possible method for genetic control of insect vector species involves the use of translocation heterozygotes. The potential of single and double heterozygotes already available in Aedes aegypti has been investigated with computer simulations of release strategies. Such simulations indicate a possible role for translocation heterozygotes of these types in an insect population characterized by a 5-fold population growth per generation, or less.

Aedes↗
PubMed2005

Transient electric birefringence of wormlike macromolecules in electric fields of arbitrary strength: a computer simulation study.

We have studied the birefringence decay of linear models of macromolecules for two different types of flexibility, the broken-rod chain and the wormlike chain, using a computer simulation of a transient electric birefringence experiment. We have paid particular attention to the influence of the intensity of the orienting field, including two orienting mechanisms, the induced dipole, and the permanent dipole. We have compared wormlike and broken-rod models of the same radius of gyration, finding that they present a different decay curve under the influence of the same intensity of the field. We have seen that these differences are due to the faster relaxation times (smaller in the wormlike chain model) and amplitudes, because, regardless of the type of flexibility, the overall size of a molecule (measured by the radius of gyration) essentially determines the longest relaxation time. We have also analyzed how the relaxation process is affected by the degree of flexibility, the orientation mechanisms, and the intensity of the field. Studying a different aspect, we have paid attention to the deformation of a molecule in a transient electric birefringence experiment as a source of information. In this work we have developed equations to characterize this deformation in terms of one of the components of the gyration tensor, if a dynamic light scattering experiment under the influence of an electric field could be performed. To develop this work we have simulated the Brownian dynamics of the different models, relaxing after the removal of an orienting external electric field of arbitrary strength. A comparison with other methods such a the rigid body treatment or the correlation analysis of Brownian trajectories has also been included. We have seen that differences between the two Brownian dynamics methods are small and that the rigid-body treatment is only an acceptable approximation to obtain the longest relaxation time.

Journal Article↗
PubMed1984

Analytical isotachophoresis utilizing computer simulation. II. Assessment of optimum separation conditions for urinary trifluoroacetic acid metabolized from anaesthetic halothane.

Experimentally determined optimum separation conditions for a metabolite of anaesthetic halothane in urine, trifluoroacetic acid, were assessed by means of computer simulation of the isotachophoretic steady-state. The simulation confirmed that urinary acids and trifluoroacetic acid can be separated in the limited pH range of 3.5-3.7 buffered by beta-alanine, as far as the pH dependence of effective mobility is utilized. The separated fraction of the trifluoroacetic acid zone was identified by mass spectrometry. The simulated coefficient of the calibration curve agreed well with the observed value.

Computers↗
PubMed1992

Computer simulation and modelling of tumor spheroid growth and their relevance for optimization of fractionated radiotherapy.

As previous papers show, our group developed computer models simulating spatial (3D) tumor growth of an in vitro tumor spheroid. These models were extended by implementing irradiation models based on the linear-quadratic survival function in order to simulate and optimize radiation therapy schemes. The key idea in this study is to simulate different fractionation schemes (standard-, super-, hyperfractionation, irradiation with a weekly high dose) and to compare the model results with regard to their tumor effectiveness. After introducing simplified model assumptions the following treatment plans, as a result, represent an optimal scheduling: 1. the hyperfractionation (3 x 1...1.5 Gy per day) in the case of rapidly growing tumors; 2. the hyperfractionation (3 x 1...1.5 Gy per day) for moderately fast growing tumors; and 3. the treatment with a weekly high single dose (1 x 6 Gy per week) in the case of slowly growing tumors. The transfer of the results gained by simulating in vitro-experiments to clinical tumors are discussed. Single observations in clinical practice concerning the therapeutical benefit indicate a rather good agreement with the simulation results. Thereby, the possibility is given to comprehend in vitro tumor growth and clinical therapy schemes in a model and to successfully simulate optimal treatment schedules by computer experiments. This method enables a reduction of time-consuming studies prior to clinical therapy.

Brain Neoplasms↗
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↗
PubMed1999

Computer Simulations for the Growth Process of Peanut-Type Hematite Particles.

The growth process of a monodispersed peanut-type hematite particle consisting of much smaller elongated subcrystals has been reproduced by computer simulation. On the basis of the microscopic internal structure, the simulation was performed by replacing the sequential events of surface nucleation and the subsequent growth of each subcrystal in the actual process with an arranged deposition of rectangular segments of fixed dimensions under different conditions in their site-dependent deposition rate and in the flexibility of their tilt angles. The most successful simulation model was obtained on the assumptions of a relatively fast deposition of the segments on the outermost side-surface of the ellipsoidal particle and the flexible tilt angle of each segment depending on the position of a neighboring new segment placed afterward. The result of the simulation strongly supported the previous elucidation of the growth mechanism in terms of the outward bending of adjoining subcrystals by nucleation and growth of a new subcrystal in each space between them. Enhancement of the outward bending of subcrystals by a large amount of sulfate ions adsorbed to the growing subcrystals was also suggested. Copyright 1999 Academic Press.

Journal Article↗
PubMed1986

An evaluation of screening policies for cervical cancer in England and Wales using a computer simulation model.

Several screening policies have been recommended for implementation in England and Wales in the last 20 years, although no evidence as to their relative effectiveness or efficiency has been provided. Using a computer simulation model, the outcomes expected from those policies had they been implemented over a 30 year period (1961-90) have been examined. The original policies based on five-yearly testing of women aged over 35 appear to be the most cost-effective, and extension of screening to younger age groups leads to loss of efficiency. Attempts to use non-screening health care contacts in order to take cervical smears (eg, during pregnancy, family planning, at gynaecology clinics) produce few advantages and considerably complicate the establishment of regular testing for the individual. The achievement of higher attendance rates is as important to the outcome of screening as concentration on more intensive or complex policies.

Adult↗
PubMed1982

Oculomotor effects of intermittent conduction block in myasthenia gravis and Guillain-Barré syndrome. An oculographic study with computer simulations.

Five abnormal oculographic patterns were identified in eight patients with either myasthenia gravis or Guillain-Barré syndrome (GBS). These could be differentiated into three intrasaccadic and two postsaccadic abnormalities. From our studies of computer simulations, and considering the established pathophysiology of myasthenia gravis and GBS, we believe that our oculographic findings were a consequence of defects in peripheral neural and neuromuscular conduction, together with a simple adaptive increase in duration of the saccadic burst of central innervation. We conclude that the eye movement abnormalities we observed are explained by intermittent block of peripheral conduction, and suggest that any disease causing intermittent blockage of neural signals to extraocular muscles will produce similar abnormalities of eye movement.

Adolescent↗
PubMed1998

Computer simulation of damped oscillations during peroxidase-catalyzed oxidation of indole-3-acetic acid.

Oscillation patterns in horseradish peroxidase (HRP)-catalyzed oxidation of indole-3-acetic acid (IAA) at neutral pH were studied using computer simulation. Under certain conditions, such as the presence of a reaction promoter and continuous intake of oxygen from the gaseous phase, the simulated system exhibits damped oscillations of the concentrations of oxygen in the aqueous phase, [O(2)](aq), and of all the reaction intermediates. The critical concentration of oxygen in aqueous phase, [O(2)](cr)(aq), was used to describe the nature of the oscillations. The critical concentration is the concentration at which the system abruptly changes its properties. If [O(2)](aq) is higher than [O(2)](cr)(aq) then the reaction develops as an avalanche, otherwise, the reaction stops. The nature of oscillations is accounted for by the interaction of two processes: the consumption/accumulation of oxygen and the accumulation/consumption of reaction intermediates. Oscillations are always damped. Neither HRP or umbelliferone (Umb) deactivation nor IAA consumption can account for the damping. The nature of the damping is determined by the termination reactions of free radical intermediates and ROOH. The three major parameters of oscillations: period of oscillations, initial amplitude of oscillations and the rate of damping were studied as functions of: (i) oxygen concentration in the gaseous phase, (ii) initial oxygen concentration in aqueous phase, (iii) the concentration of IAA and (iv) the initial concentration of HRP.

Journal Article↗