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PubMed1992

Interpretation of epicardial mapping by means of computer simulations: applications to calcium, lidocaine and to BRL 34915.

The aim of this work was to compare experimental investigations on effects of lidocaine, calcium and, BRL 34915 on reentries to simulated data obtained by use of a model of propagation based on the Huygens' construction method already described in previous works. Calcium and lidocaine effects are investigated on anisotropic conduction conditions. In both cases, reduction in conduction velocities are observed. In lidocaine case, a refractory area is located along the longitudinal axis. In agreement with experimental electrical mapping, the simulations show that the stabilization of reentrant excitation is mainly due to the existence of this refractory area around which the reentrant circuit can develop. The experimental study shows that BRL 34915 has both arrhythmogenic and antiarrhythmic effects. A detailed electrophysiological analysis has shown that drug infusion act on normal cardiac cells by decreasing the relative and absolute refractory period. BRL 34915 action is simulated by a decrease in the refractory period showing that the time frequency of the reentrant activity is increased and that the spatial size where the reentry is developing is becoming smaller. These two effects are arrhythmogenic, the simulated data being so in good agreement with the experimental ones.

Animals↗
PubMed1987

Computer simulation of cardiac arrhythmias.

A mathematical model of the cardiac conduction system has been developed. The mechanisms of cardiac arrhythmias are described mathematically, and the heart is modeled as a network, where each element is defined by a unique set of time parameters from the action potential. The mathematical description is separated from the network structure, thus making it possible to run the model with different network sizes. Simulated ECG curves are produced in each case. This model is especially suited for rhythm studies, and a variety of different cardiac arrhythmia mechanisms has been simulated such as reentry, reflection, modulated parasystole, and different kinds of block.

Action Potentials↗
PubMed2006

Physiologic mechanisms can predict hematologic responses to iron supplements in growing children: a computer simulation model.

BACKGROUND: Iron deficiency is the most common preventable nutrition problem in developing countries. Several randomized clinical trials (RCTs) have been conducted to determine the effectiveness of various iron dosing schemes in multiple settings. OBJECTIVE: The objective was to determine whether enough is known about iron metabolism to predict hemoglobin and serum ferritin (SF) concentrations with a computer model and whether the model could be used as a substitute for new RCTs. DESIGN: Guided by the physiology of iron absorption and regulation, we used data from RCTs that tested iron Sprinkles to develop a computer model. Of 2 RCTs in Ghana, we used 1 to compute the amount of iron absorbed from a given dose in anemic and nonanemic children and the other to compute the resulting change in hemoglobin concentrations. We used this model to predict hemoglobin and SF concentrations in a new RCT in China and compared model-predicted values with actual values by using summary statistics (means and medians) and quantile-quantile plots. RESULTS: The model-predicted hemoglobin means were within +/-2 g/L, and SF medians were within +/-3 microg/L of the corresponding means and medians of the actual values. On quantile-quantile plots, the predicted hemoglobin quantiles were within +/-5 g/L, and SF quantiles were within +/-10 microg/L of the corresponding quantiles of the actual values. CONCLUSION: Our model of iron metabolism can accurately predict hemoglobin and SF concentrations after iron supplementation with Sprinkles in children; the model can thus obviate the need for repeating RCTs in multiple settings.

Anemia, Iron-Deficiency↗
PubMed1998

The effects of computer simulated facial plastic surgery on social perception by others.

Previous studies have demonstrated the remarkable impact of facial plastic surgery on the perception of facial features. However, pre- and postoperative differences other than the surgically changed features such as facial expression, hairstyle, make-up etc., have influenced the results of previous studies. To exclude these visual cues a computer composite photograph of the changed feature mounted upon the preoperative photograph, instead of the standard postoperative photograph, was presented to observers in this study. Computer graphic technology was used to superimpose the postoperative, surgically changed facial features such as the nose, ear and chin of 16 patients on standardized preoperative photographs. The randomized preoperative photographs and the 'postoperative' composed images were presented to 67 subjects, using a person-perception questionnaire. Multivariate analysis demonstrated a more favourable postoperative judgement in only two patients (12.5%). The exclusive effect of facial plastic surgery on the social perception of patients by others when excluding visual cues, such as facial expression, hairstyle, make-up etc, is limited. It is tentatively assumed that the role played by facial plastic surgery is one of initiating a positive cycle by changing the patient's self-perception rather than one of direct social impact from the changed features.

Adolescent↗
PubMed2005

Computer simulation of flagellar movement IX. Oscillation and symmetry breaking in a model for short flagella and nodal cilia.

A computer model of flagella in which oscillation results from regulation of active sliding force by sliding velocity can simulate the movements of very short flagella and cilia. Of particular interest are the movements of the short (2-3 microm) nodal cilia of the mammalian embryo, which determine the development of the asymmetry of the internal organs. These cilia must generate a counterclockwise (viewed from base to tip) circling motion. A three-dimensional computer model, with active force generated by a simple mathematical formulation and regulated by sliding velocity, can generate this circling motion if a time delay process is included in the control specification. Without the introduction of a symmetry-breaking mechanism, the computer models start randomly in either direction, and maintain either clockwise or counterclockwise circling. Symmetry can be broken by at least two mechanisms: (1) control of dynein activity on one outer doublet by sliding velocity can be influenced by the sliding velocity experienced on an adjacent outer doublet, or (2) a constant twist of the axoneme caused by an off-axis component of dynein force. This second mechanism appears more reasonable, but its effectiveness is highly dependent upon specifications for the elastic resistances of the model. These symmetry-breaking mechanisms need to be present only at the beginning of circling. With these models, once a circling direction is established, it remains stable even if the symmetry-breaking mechanism is removed.

Animals↗
PubMed1986

Isotachophoretic determination of mobility and pKa by means of computer simulation. IV. Evaluation of m0 and pKa of twenty-six amino acids and assessment of the separability.

Isotachophoretic qualitative indices, RE, of twenty-six amino acids were measured at several pHL values in the range of 8.6-9.6. The absolute mobility, m0, and pKa values were evaluated by the use of a least-squares method utilizing a simulation of the isotachophoretic steady state. The pKa values were in good agreement with values cited in the literature. The RE values simulated using the evaluated constants were in good agreement with RE values converted from step heights observed previously. By comparing the previously observed separation behaviour of amino acids with their simulated effective mobilities, it is concluded that when the effective mobility of samples differs by ca. 1 X 10(-5) cm2 V-1 s-1 at the steady state, ca. 10-nmol samples can be separated by the use of a 80 cm X 0.5 mm I.D. tube. The simulated effective mobilities of twenty-two amino acids were tabulated to assess the separability under some typical electrolyte conditions.

Amino Acids↗
PubMed2004

Image reconstruction of anisotropic conductivity tensor distribution in MREIT: computer simulation study.

We describe a novel method of reconstructing images of an anisotropic conductivity tensor distribution inside an electrically conducting subject in magnetic resonance electrical impedance tomography (MREIT). MREIT is a recent medical imaging technique combining electrical impedance tomography (EIT) and magnetic resonance imaging (MRI) to produce conductivity images with improved spatial resolution and accuracy. In MREIT, we inject electrical current into the subject through surface electrodes and measure the z-component Bz of the induced magnetic flux density using an MRI scanner. Here, we assume that z is the direction of the main magnetic field of the MRI scanner. Considering the fact that most biological tissues are known to have anisotropic conductivity values, the primary goal of MREIT should be the imaging of an anisotropic conductivity tensor distribution. However, up to now, all MREIT techniques have assumed an isotropic conductivity distribution in the image reconstruction problem to simplify the underlying mathematical theory. In this paper, we firstly formulate a new image reconstruction method of an anisotropic conductivity tensor distribution. We use the relationship between multiple injection currents and the corresponding induced Bz data. Simulation results show that the algorithm can successfully reconstruct images of anisotropic conductivity tensor distributions. While the results show the feasibility of the method, they also suggest a more careful design of data collection methods and data processing techniques compared with isotropic conductivity imaging.

Algorithms↗
PubMed2000

[Computer simulation programs as an alternative for classical nerve, muscle and heart experiments using frog tissues].

Courses in Physiology include different methodical approaches such as exercises with living animals, experiments using organs or tissues from killed or slaughtered animals, application of diagnostic techniques in humans and theoretical seminars. In addition to these classical approaches computer programs for multimedia simulation of nerve, muscle and heart physiology are now a regular component of courses in Physiology at the School of Veterinary Medicine in Hannover. It is the aim of the present paper to give the first experiences about these new components.

Animal Testing Alternatives↗
PubMed1999

Application and validation of three-dimensional data sets from a phase contrast MR angiography for preoperative computer simulation of brain tumors.

We applied a three-dimensional (3D) phase contrast magnetic resonance angiography as the source for generating integrated 3D images for surgical planning of brain tumors. In the 3D model, we defined the Cingulomarginal sulcus and subsequently the central sulcus in the interhemispheric plane. This method solved the misregistration problem caused by the combination of multi-sequence data sets and can be feasible for surgical planning.

Adenocarcinoma↗
PubMed1995

Computer simulations to predict the availability of peptides with known HLA class I motifs possibly generated by proteolysis of HIV-1 proteins in infected cells.

Cytotoxic T cells that recognize HIV-1 peptides generated from all viral proteins were reported. To predict the cleavage pattern of HIV-1 proteins by cytoplasmic proteasomes into peptides with motifs fitting known HLA class I molecules, the computer program Findpatterns was used. In this paper the combined amino acids patterns for proteolytic cleavages and the HLA class I haplotype-restricted peptides motifs are studied. It was noted that peptides with motifs of HLA class I A2 and A68 were abundant compared with HLA class 5B2, B8, B53, and B35.

Amino Acid Sequence↗
PubMed1990

A generalized approach to random noise synthesis: theory and computer simulation.

A generalized approach to the synthesis of Gaussian and non-Gaussian random noises as well as purely impulsive waveforms having a preselected amplitude spectrum has been developed. The basic idea behind the synthesis is to construct the amplitude-time waveform from the frequency domain, i.e., from the amplitude and phase spectra. By maintaining a predetermined (reference) amplitude spectrum and performing certain specific manipulations of the phase spectrum within any selected band of frequencies and then applying the inverse discrete Fourier transform (IDFT), peaks in the non-Gaussian random waveform can be constructed from the selected band of frequencies that have been phase manipulated. Entire families of signals can thus be produced having the same energy spectrum, but statistical characteristics that vary along the continuum from Gaussian (skewness = 0 and kurtosis = 3) through non-Gaussian (variable skewness, kurtosis, and crest factor) to purely impulsive (shock/transient) signals. The theoretical background and the results of a series of numerical simulations will be presented which demonstrate the functional relation between various phase spectrum manipulations and the descriptors of the synthesized random noise. The results show that the approach is viable and that the synthesized random waveforms can be easily tailored to simulate a variety of real-world acoustic/vibration signals, e.g., high kurtosis (impulsive) industrial noises, helicopter noises, missile vibrational signals, etc.

Acoustic Stimulation↗
PubMed2004

Computer simulation of small molecule permeation across a lipid bilayer: dependence on bilayer properties and solute volume, size, and cross-sectional area.

Cell membrane permeation is required for most drugs to reach their biological target, and understanding this process is therefore crucial for rational drug design. Recent molecular dynamics simulations have studied the permeation of eight small molecules through a phospholipid bilayer. Unlike experiments, atomistic simulations allow the direct calculation of diffusion and partition coefficients of solutes at different depths inside a lipid membrane. Further analyses of the simulations suggest that solute diffusion is less size-dependent and solute partitioning more size-dependent than was commonly thought.

Algorithms↗
PubMedDate not supplied

Computer simulation study of the shape of motor unit action potential.

Motor unit action potentials (MUAPs) of brachial biceps were simulated. A simulated MUAP was obtained as a sum of single fibre action potentials (SFAPs) from all the muscle fibres of a motor unit (MU). The influence of the following factors on MUAP shape for different kinds of recording electrode was studied: fibre density, neuromuscular jitter, temporal dispersion and electrode displacements. The simulation confirms that typical MUAPs recorded with needle electrodes from muscles of low fibre density such as brachial biceps are usually triphasic. Increased fibre density produces MUAPs of more complex shape and higher amplitude. Normal neuromuscular jitter is responsible for the variability of shape of subsequent potentials from the same MU as well as for electromyographic shimmer. Pathologic (increased) jitter makes the shapes of subsequent potentials unrecognizable. The influence of temporal dispersion is interconnected with other factors but rather of minor importance. The simulation shows how big changes in MUAP shape can be expected due to electrode displacements during single experiment or during estimation of MU territory.

Action Potentials↗
PubMed1996

Modeling DNA in aqueous solutions: theoretical and computer simulation studies on the ion atmosphere of DNA.

This article provides a review of current theoretical and computational studies of the ion atmosphere of DNA as related to issues of both structure and function. Manning's elementary yet elegant concept of "counterion condensation" is revisited and shown to be well supported by current state-of-the-art molecular simulations. Studies of the ion atmosphere problem based on continuum electrostatics, integral equation methods, Monte Carlo simulation, molecular dynamics, and Brownian dynamics are considered. Grand canonical Monte Carlo and non-linear Poisson Boltzmann studies have recently focussed on the determination and significance of the index of non-ideality in solution known as the "preferential interaction coefficient," for which the relevant current literature is cited. The review concludes with a survey of applications to ligand binding problems involving drug-DNA and protein-DNA interactions.

Computer Simulation↗
PubMed2006

Computer simulation of the role of SOCS family protein in helper T cell differentiation.

The Th1/Th2 balance determines the nature of an immune response, and particular cytokines, IL-4 and IL-12, determine the direction at the initial stage of activation through TCRs. To investigate how cytokine networks and related signaling pathways impact upon the Th1/Th2 balance, we have developed a computer model for the simulation of Th differentiation. The model includes the IL-4, IL-12 and IFN-gamma signal transduction pathways, a positive and negative feedback mechanism for cytokine signaling and cytokine-induced negative regulators such as suppressors of cytokine signaling (SOCS)1, SOCS3 and SOCS5. In the present study, we propose a 'Th0 model', in which naive T cells differentiate neither into Th1 nor into Th2 states in unskewed cytokine conditions. The model was found to be consistent with experimental results in BALB/c mice. The results of in silico analysis in the condition with SOCS- and signal transducer and activator of transcription (STAT) family-deficient and transgenic states were well fitted to ex vivo experimental results for Th1 and Th2 differentiation profiles in the deficient and transgenic mice. The Th0 model suggested the possibility that dominant Th1 differentiation in STAT4/STAT6 double-deficient mice may be due to a positive feedback effect of initial IFN-gamma production from T cells. The in silico assessment of beneficial effects of inhibitory drugs by simulation analysis with our Th0 model indicated that Janus kinase 3-specific inhibitors might be suitable candidates for the modification of Th2-dominant immune responses. Our results demonstrate that models for the simulation of signaling network, such as our Th0 model, are useful tools for the in silico evaluation of novel drug candidates.

Animals↗
PubMed1995

Computer simulations to predict the availability of peptides with known HLA class I motifs generated by proteolysis of dengue fever virus (DFV) type 1 structural and nonstructural proteins in infected cells.

Cytotoxic T cells that recognize dengue fever viral (DFV) peptides were reported. To predict the cleavage pattern of DFV proteins by cytoplasmic proteasomes into nonapeptides with motifs fitting known HLA class I molecules, the computer program "Findpatterns" was used. In this study the combined amino acid motifs for proteolytic cleavages and the HLA class I haplotype-restricted peptides were analyzed. It was noted that putative peptides with motifs of HLA A2 and A68 were abundant compared with nonapeptides with motifs HLA A24, B8, B35, and B53. The possible interpretation of the computer analysis in explaining the cellular immune response in endogenous populations of endemic DF is discussed.

Amino Acid Sequence↗
PubMed2001

Computer simulations for biological aging and sexual reproduction.

The sexual version of the Penna model of biological aging, simulated since 1996, is compared here with alternative forms of reproduction as well as with models not involving aging. In particular we want to check how sexual forms of life could have evolved and won over earlier asexual forms hundreds of million years ago. This computer model is based on the mutation-accumulation theory of aging, using bits-strings to represent the genome. Its population dynamics is studied by Monte Carlo methods.

Aging↗