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PubMed2006

A computer simulation of in vivo tumour growth and response to radiotherapy: new algorithms and parametric results.

The aim of this paper is to present the newest algorithms and simulation results of a computer model of in vivo tumour growth and response to radiotherapy. The new algorithms are analytically presented. A set of parametric simulations has been performed with special emphasis on the influence of the genetic profile of a tumour on its radiosensitivity. The results of the simulation procedure are three-dimensionally visualized and critically surveyed. The long-term goal of this work is twofold: the development of a computational tool for getting insight into cancer biology and the development of a patient-specific decision support system.

Algorithms↗
PubMed1991

A stochastic model for predator-prey systems: basic properties, stability and computer simulation.

A simple stochastic description of a model of a predator-prey system is given. The evolution of the system is described by means of Itô's stochastic differential equations (SDEs), which are the natural stochastic generalization of the Lotka-Volterra deterministic differential equations. Since these SDEs do not satisfy the usual conditions for the existence and uniqueness of the solution, we state a theorem of existence; moreover we study the stability of the equilibrium point and perform a computer simulation to study the behaviour of the trajectories of solutions with given initial data and to estimate first and second moments.

Animals↗
PubMedDate not supplied

A computer simulation model of the natural history and economic impact of chronic obstructive pulmonary disease.

OBJECTIVE: Chronic obstructive pulmonary disease (COPD) is a major health problem with high societal costs. The Global Initiative for Chronic Lung Disease (GOLD) has identified a need for health economics data for COPD. For chronic diseases, such as COPD, where the natural history of disease is lifetime, a modeling approach for economic evaluation may be more realistic than prospective, piggy-backed clinical trials or specific COPD cohort studies. Simulation models can be used to extrapolate clinical data beyond the limited time frame of clinical trials, to analyze subgroups of patients or to explore uncertainty regarding the results by using sensitivity analysis techniques. Our purpose has been to develop a flexible computer simulation model for COPD that will represent disease progression and GOLD recommendations, useful for economic evaluations of new medicines to meet the needs of various payer requirements for reimbursement and resource allocation. METHODS: This article describes a two-dimensional Markov model, which uses data from multiple sources about disease progression, exacerbation frequency and duration, mortality, costs, burden of illness, and the relationships between those variables. The model is evaluated using stochastic uncertainty analysis, it allows comparison of treatments affecting different disease mechanisms, and it uses primary data validated against published sources. RESULTS: We have evaluated two hypothetical interventions treating different features of the disease (lung function decline and acute exacerbations). These analyses show that reducing lung function decline must be a long-term strategy compared to reducing the number of exacerbations. It was necessary to have a long term like 30 years, with 10,000 patients and 20% increase in price, or 20 years with equal prices to show cost-effectiveness with statistical significance for a treatment that reduces lung function decline. CONCLUSIONS: Our study shows the value of modeling as a tool for evaluating different scenarios and for combining several sources of data, to provide estimates that would otherwise be unavailable. Clinical trials of this size and duration would be unrealistic.

Computer Simulation↗
PubMed2002

Computational simulation of the docking of Prochlorothrix hollandica plastocyanin to potosystem I: modeling the electron transfer complex.

We have used several docking algorithms (GRAMM, FTDOCK, DOT, AUTODOCK) to examine protein-protein interactions between plastocyanin (Pc)/photosystem I (PSI) in the electron transfer reaction. Because of the large size and complexity of this system, it is faster and easier to use computer simulations than conduct x-ray crystallography or nuclear magnetic resonance experiments. The main criterion for complex selection was the distance between the copper ion of Pc and the P700 chlorophyll special pair. Additionally, the unique tyrosine residue (Tyr(12)) of the hydrophobic docking surface of Prochlorothrix hollandica Pc yields a specific interaction with the lumenal surface of PSI, thus providing the second constraint for the complex. The structure that corresponded best to our criteria was obtained by the GRAMM algorithm. In this structure, the solvent-exposed histidine that coordinates copper in Pc is at the van der Waals distance from the pair of stacked tryptophans that separate the chlorophylls from the solvent, yielding the shortest possible metal-to-metal distance. The unique tyrosine on the surface of the Prochlorothrix Pc hydrophobic patch also participates in a hydrogen bond with the conserved Asn(633) of the PSI PsaB polypeptide (numbering from the Synechococcus elongatus crystal structure). Free energy calculations for complex formation with wild-type Pc, as well as the hydrophobic patch Tyr(12)Gly and Pro(14)Leu Pc mutants, were carried out using a molecular mechanics Poisson-Boltzman, surface area approach (MM/PBSA). The results are in reasonable agreement with our experimental studies, suggesting that the obtained structure can serve as an adequate model for P. hollandica Pc-PSI complex that can be extended for the study of other cyanobacterial Pc/PSI reaction pairs.

Algorithms↗
PubMed1993

VNTR allele frequency distributions under the stepwise mutation model: a computer simulation approach.

Variable numbers of tandem repeats (VNTRs) are a class of highly informative and widely dispersed genetic markers. Despite their wide application in biological science, little is known about their mutational mechanisms or population dynamics. The objective of this work was to investigate four summary measures of VNTR allele frequency distributions: number of alleles, number of modes, range in allele size and heterozygosity, using computer simulations of the one-step stepwise mutation model (SMM). We estimated these measures and their probability distributions for a wide range of mutation rates and compared the simulation results with predictions from analytical formulations of the one-step SMM. The average heterozygosity from the simulations agreed with the analytical expectation under the SMM. The average number of alleles, however, was larger in the simulations than the analytical expectation of the SMM. We then compared our simulation expectations with actual data reported in the literature. We used the sample size and observed heterozygosity to determine the expected value, 5th and 95th percentiles for the other three summary measures, allelic size range, number of modes and number of alleles. The loci analyzed were classified into three groups based on the size of the repeat unit: microsatellites (1-2 base pair (bp) repeat unit), short tandem repeats [(STR) 3-5 bp repeat unit], and minisatellites (15-70 bp repeat unit). In general, STR loci were most similar to the simulation results under the SMM for the three summary measures (number of alleles, number of modes and range in allele size), followed by the microsatellite loci and then by the minisatellite loci, which showed deviations in the direction of the infinite allele model (IAM). Based on these differences, we hypothesize that these three classes of loci are subject to different mutational forces.

Alleles↗
PubMed2001

Effect of blood flow, tumour and cold stress in a female breast: a novel time-accurate computer simulation.

Breast cancer is a dreadful disease among women and early detection helps in achieving a cure. The mammogram is presently the standard tool for detecting breast abnormality, but its sensitivity is lower for women with dense breasts. It has been found that women with an abnormal thermogram are at a higher risk and have a poorer prognosis. However, performing and interpreting thermograms requires meticulous training. Computer simulations can be an additional tool to help the clinician in the interpretation. In this paper, a novel and flexible finite element model of a female breast is developed. Both steady state and time-dependent solutions are obtained. Steady state solutions globally match experimental thermographic results with the proper choice of blood perfusion source terms, tissue thickness and geometric scaling factor. Although the simulations may not be useful in providing a unique solution (i.e. exact size and location of the tumour owing to the complex physiological relationship between the tumour and the breast surface temperature), it would nevertheless help in the 'analysis by elimination'. An example of this type of analysis is also presented.

Body Temperature↗
PubMed1986

Cross-correlation analysis of intracellularly recorded synaptic activities: an evaluation of the method through computer simulation.

Cross-correlation of 'spontaneous' synaptic activities intracellularly recorded from pairs of neurons may be used to detect shared synaptic input, which could remain hidden in the raw data by the non-synchronized postsynaptic potentials (PSPs); besides, if a normalized cross-correlation function is adopted, the fraction of synchronized activity may be quantitatively estimated. To evaluate power and limits of this method, computer-simulated synaptic activities of pairs of neurons, in which a given percentage of PSPs were simultaneous, were subjected to this type of analysis. It was shown that percentages of shared activities as low as 4% and in some cases 2% could be revealed, with a conspicuity which was influenced by the types of associated PSPs.

Action Potentials↗
PubMed2004

Structure and diffusion in amorphous aluminum silicate: a molecular dynamics computer simulation.

The amorphous aluminum silicate (Al2O3)2(SiO2) [AS2] is investigated by means of large scale molecular dynamics computer simulations. We consider fully equilibrated melts in the temperature range 6100 K> or =T> or =2300 K as well as glass configurations that were obtained from cooling runs from T=2300 to 300 K with a cooling rate of about 10(12) K/s. Already at temperatures as high as 4000 K, most of the Al and Si atoms are fourfold coordinated by oxygen atoms. Thus, the structure of AS2 is that of a disordered tetrahedral network. The packing of AlO4 tetrahedra is very different from that of SiO4 tetrahedra in that Al is involved with a relatively high probability in small-membered rings and in triclusters in which an O atom is surrounded by four cations. We find as typical configurations two-membered rings with two Al atoms in which the shared O atoms form a tricluster. On larger length scales, the system shows a microphase separation in which the Al-rich network structure percolates through the SiO2 network. The latter structure gives rise to a prepeak in the static structure factor at a wave number q=0.5 A(-1). A comparison of experimental x-ray data with the results from the simulation shows good agreement for the structure function. The diffusion dynamics in AS2 is found to be much faster than in SiO2. We show that the self-diffusion constants for O and Al are very similar and that they are by a factor of 2-3 larger than the one for Si.

Journal Article↗
PubMed2004

Raman spectra of ionic liquids: interpretation via computer simulation.

Theoretical Raman spectra of the complex-forming ionic liquids LaCl3 and ScCl3, derived from molecular dynamics computer simulations, are presented. These simulations, which use polarizable ion interaction models, have previously been shown to predict structural properties in excellent agreement with diffraction experiments. The dependence of the polarizability of the melt on the ionic positions, which determines the Raman spectrum through the time dependence of the polarizability correlation function, is modeled on the basis of ab initio electronic structure calculations carried out on alkali chlorides. New simulation techniques are introduced in order to allow the spectrum to be calculated with acceptable statistics. The calculated spectra are in semiquantitative agreement with experimental data. The distinctive bands which appear in the spectra of such complex melts are linked to the vibrations of the transient coordination complexes which form in these melts and new interpretations for the origin of several well-known features are proposed. The simulations thus enable a link between the structure of a melt as perceived through Raman spectroscopy and through diffraction experiments to be made.

Journal Article↗
PubMed2000

Computer simulations of liquid silica: equation of state and liquid-liquid phase transition.

We conduct extensive molecular dynamics computer simulations of two models for liquid silica [the model of Woodcock, Angell and Cheeseman, J. Phys. Chem. 65, 1565 (1976); and that of van Beest, Kramer, and van Santen, Phys. Rev. Lett. 64, 1955 (1990)] to determine their thermodynamic properties at low temperature T across a wide density range. We find for both models a wide range of states in which isochores of the potential energy U are a linear function of T(3/5), as recently proposed for simple liquids [Rosenfeld and P. Tarazona, Mol. Phys. 95, 141 (1998)]. We exploit this behavior to fit an accurate equation of state to our thermodynamic data. Extrapolation of this equation of state to low T predicts the occurrence of a liquid-liquid phase transition for both models. We conduct simulations in the region of the predicted phase transition, and confirm its existence by direct observation of phase separating droplets of atoms with distinct local density and coordination environments.

Journal Article↗
PubMed1999

Middle cerebral artery anatomy and characteristics of embolic signals: a dual gate computer simulation study.

In terms of microembolic signal (MES) detection, the anatomy of the middle cerebral artery (MCA) mainstem has only scarcely been considered. The vessel itself, however, could be at least partly responsible for the enormous variation when calculating the essential time difference (deltat) values of MES using the dual-gate technique. Therefore, we studied the time characteristics of MES in a computer simulation applying an anatomically realistic vessel and a dual-gate TCD approach. Three different MCA anatomies and two MES to blood intensities were simulated as well as two different sample volume settings. The MES length (proximal sample volume t1; distal sample volume t2) and deltat were calculated for different angles of insonation and sample volume depths. The calculations of the time characteristics of MES showed extreme variation, with only modest changes of the insonation angle (t1 4-34 ms; deltat 9-27 ms) or the sample volume depth (t1 7-27 ms; deltat 6-32 ms). The variation could be considerably reduced with modified TCD settings i.e., a shorter gate separation combined with a shorter receiver gate time in the distal sample volume (deltat with changing insonation angles 6-19 ms; deltat with changing insonation depths 13-17 ms). These results not only urge us to a cautious interpretation of the properties of single MES, but also contribute to an understanding of the marked deltat variation using the dual-gate technique.

Cerebral Arteries↗
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↗
PubMed2005

Computer simulation studies of the effects of dynamic shimming on susceptibility artifacts in EPI at high field.

Dynamic shimming in multi-slice imaging aims to achieve optimal magnetic field homogeneity by updating the shim coil currents for each slice in real time. Dynamic shimming may reduce the signal loss and geometric distortion caused by magnetic susceptibility variations between tissues and is likely to be valuable for fast T2*-sensitive imaging techniques like EPI. A computer simulation of dynamic shimming using real image data has been developed to demonstrate the effectiveness of higher order dynamic shimming for echo planar imaging at high magnetic field, and to investigate the potential benefits of different orders of shim coil. Geometric distortions and signal intensities for different degrees of dynamic shimming were simulated and the results are compared with the images obtained with a conventional shimming technique. These results demonstrate the effectiveness, necessity and difficulty of high order dynamic shimming.

Artifacts↗
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↗
PubMed2005

Computer simulation of the last support phase of the long jump.

PURPOSE: The purpose was to examine the interacting roles played by the approach velocity, the explosive strength (represented by vertical ground reaction force [VGRF]), and the change in angular momentum about a transverse axis through the jumper's center of mass (deltaHzz) during the last support phase of the long jump, using a computer simulation technique. METHODS: A two-dimensional inverted-pendulum-plus-foot segment model was developed to simulate the last support phase. Using a reference jump derived from a jump performance reported in the literature, the effects of varying individual parameters were studied using sensitivity analyses. In each sensitivity analysis, the kinematic characteristics of the longest jumps with the deltaHzz considered and not considered when the parameter of interest was altered were noted. A sensitivity analysis examining the influence of altering both approach velocity and VGRF at the same time was also conducted. RESULTS AND CONCLUSION: The major findings were that 1) the jump distance was more sensitive to changes in approach velocity (e.g., a 10% increase yielded a 10.0% increase in jump distance) than to changes in the VGRF (e.g., a 10% increase yielded a 7.2% increase in jump distance); 2) the relatively large change in jump distance when both the approach velocity and VGRF were altered (e.g., a 10% increase in both parameters yielded a 20.4% increase in jump distance), suggesting that these two parameters are not independent factors in determining the jump distance; and 3) the jump distance was overestimated if the deltaHzz was not considered in the analysis.

Algorithms↗
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↗
PubMed1993

Computer simulation of counterlungs.

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.

Computer Simulation↗