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PubMed1995

Computer simulations of morphologically reconstructed CA3 hippocampal neurons.

1. We tested several hypotheses with respect to the mechanisms and processes that control the firing characteristics and determine the spatial and temporal dynamics of intracellular Ca2+ in CA3 hippocampal neurons. In particular, we were interested to know 1) whether bursting and nonbursting behavior of CA3 neurons could be accounted for in a morphologically realistic model using a number of the known ionic conductances; 2) whether such a model is robust across different cell morphologies; 3) whether some particular nonuniform distribution of Ca2+ channels is required for bursting; and 4) whether such a model can reproduce the magnitude and spatial distribution of intracellular Ca2+ transients determined from fluorescence imaging studies and can predict reasonable intracellular Ca2+ concentration ([Ca2+]i) distribution for CA3 neurons. 2. For this purpose we have developed a highly detailed model of the distribution and densities of membrane ion channels in hippocampal CA3 bursting and nonbursting pyramidal neurons. This model reproduces both the experimentally observed firing modes and the dynamics of intracellular Ca2+. 3. The kinetics of the membrane ionic conductances are based on available experimental data. This model incorporates a single Na+ channel, three Ca2+ channels (CaN, CaL, and CaT), three Ca(2+)-independent K+ channels (KDR, KA, and KM), two Ca(2+)-dependent K+ channels (KC and KAHP), and intracellular Ca(2+)-related processes such as buffering, pumping, and radial diffusion. 4. To test the robustness of the model, we applied it to six different morphologically accurate reconstructions of CA3 hippocampal pyramidal neurons. In every neuron, Ca2+ channels, Ca(2+)-related processes, and Ca(2+)-dependent K+ channels were uniformly distributed over the entire cell. Ca(2+)-independent K+ channels were placed on the soma and the proximal apical dendrites. For each reconstructed cell we were able to reproduce bursting and nonbursting firing characteristics as well as Ca2+ transients and distributions for both somatic and synaptic stimulations. 5. Our simulation results suggest that CA3 pyramidal cell bursting behavior does not require any special distribution of Ca(2+)-dependent channels and mechanisms. Furthermore, a simple increase in the Ca(2+)-independent K+ conductances is sufficient to change the firing mode of our CA3 neurons from bursting to nonbursting. 6. The model also displays [Ca2+]i transients and distributions that are consistent with fluorescent imaging data. Peak [Ca2+]i distribution for synaptic stimulation of the nonbursting model is broader when compared with somatic stimulation. Somatic stimulation of the bursting model shows a broader distribution in [Ca2+]i when compared with the nonbursting model.(ABSTRACT TRUNCATED AT 400 WORDS)

Calcium↗
PubMed1993

Computer simulation of antibody binding specificity.

A Monte Carlo algorithm that searches for the optimal docking configuration of hen egg white lysozyme to an antibody is developed. Both the lysozyme and the antibody are kept rigid. Unlike the work of other authors, our algorithm does not attempt to explicitly maximize surface contact, but minimizes the energy computed using coarse-grained pair potentials. The final refinement of our best solutions using all-atom OPLS potentials (Jorgensen and Tirado-Rives8) consistently yields the native conformation as the preferred solution for three different antibodies. We find that the use of an exponential distance-dependent dielectric function is an improvement over the more commonly used linear form.

Algorithms↗
PubMedDate not supplied

Role of a striatal slowly inactivating potassium current in short-term facilitation of corticostriatal inputs: a computer simulation study.

Striatal output neurons (SONs) integrate glutamatergic synaptic inputs originating from the cerebral cortex. In vivo electrophysiological data have shown that a prior depolarization of SONs induced a short-term (</=1 sec) increase in their membrane excitability, which facilitated the ability of corticostriatal synaptic potentials to induce firing. Here we propose, using a computational model of SONs, that the use-dependent, short-term increase in the responsiveness of SONs mainly results from the slow kinetics of a voltage-dependent, slowly inactivating potassium A-current. This mechanism confers on SONs a form of intrinsic short-term memory that optimizes the synaptic input-output relationship as a function of their past activation.

Animals↗
PubMed1993

A burn patient resuscitation therapy designed by computer simulation (BET). Part 1: Simulation studies.

This study presents an analysis of the fluid, electrolyte and colloid needs of burn patients during the shock phase. A digital simulation technique was used which had previously been validated and published in burned patients (Roa et al., 1988). After analysing the repercussions of both burns and various resuscitation procedures, a fluid therapy method (BET) has been designed using a burn patient simulator, which has been characterized by its effectiveness and minimal side-effects. The characteristics of the BET method are a low volume of infusion resuscitation solution (220 ml/h/m2 burned body surface area (BBSA)) and a rapid and large volume of colloidal substances (with colloid concentrations of 10, 7.5 and 5 g/100 ml during the first three 8 h periods of the first postburn day and 2.5 g/100 ml until the 40th h postburn).

Burns↗
PubMed1997

Chiral interactions in capillary zone electrophoresis: computer simulation and comparison with experiment.

Chiral interaction in capillary electrophoresis can be modeled using pK values, mobilities of analytes, and their formation constants with the chiral selector. An existing steady-state simulation program for CE (HPCESIM) was recently extended with a chiral submenu involving the chiral parameters listed above. These were experimentally determined in both our laboratories for mandelic acid and terbutaline using hydroxypropylated beta-cyclodextrin as chiral selector. A comparison was made between both sets of parameters and between experimental electropherograms and those obtained from simulation. Error analysis of the results indicate the sensitivity of the obtained results.

Computer Simulation↗
PubMed2000

Pulling chromatin fibers: computer simulations of direct physical micromanipulations.

A low-resolution molecular model, which combines the known mechanical properties of protein-free DNA with the accumulating picture of chromatosome structure, has been developed to account for the stretching of single chromatin fibers by an imposed external force. Force-extension characteristics of sets of chains accumulated by Monte Carlo sampling are consistent with recently observed findings in the non-destructive regime (<20 pN imposed force), where the structure of the chromatosome remains intact. The correspondence between simulation and the relaxation phase of the experiment limits the equilibrium entry-exit angle of linker DNA on the chromatosome to W=50(+/-10) degrees and the effective DNA linker length to L(eff)=40(+/-5) bp. The computed force-extension characteristics are relatively insensitive to other parameters of the model, precluding their accurate estimation. The introduction of an attractive potential between closely spaced nucleosomes reproduces the added initial resistance of single fibers to extension at high salt conditions. The consideration of elastic linkers also improves the fitting of assorted classical measurements of unstressed chromatin structure in solution. The overall picture of chromatin that emerges is an irregular, fluctuating, three-dimensional, zig-zag structure with intact, mechanically stable chromatosome units and deformable linkers. The modeled fiber undergoes large-scale configurational rearrangements without significant perturbation of the constituent chromatosome beads, collapsing into a highly condensed form in response to small (<2kT) inter-nucleosomal attractions.

Calibration↗
PubMed2004

AIPAR: ab initio parametrization of intermolecular potentials for computer simulations.

An unambiguous, fully ab initio and automated technique denoted AIPAR ("ab initio parametrization") implemented in the SJBR program has been proposed to yield intermolecular interaction potentials between polar molecules and water. The AIPAR procedure has been applied to several organic molecules covering a wide range of structure and functional groups, namely methanol, acetone (propanone), methanethiol (methyl mercaptan), imidazole (1,3-diazole), oxazole and furan. The AIPAR-derived sets of parameters compare well with the empirical OPLS ones, mainly when the all-atoms model is employed in the OPLS procedure. Monte Carlo simulations were performed for an aqueous solution of methanol and for an equimolar binary mixture methanol-water using the AIPAR and OPLS parameters. The thermodynamic and geometric results obtained with the parameters obtained with the AIPAR procedure compare favorably with the OPLS simulations, even for the binary mixture, demonstrating the precision, robustness and transferability of the parameters obtained with the AIPAR procedure.

Computer Simulation↗
PubMed1997

Extraction of cilium beat parameters by the combined application of photoelectric measurements and computer simulation.

Photoelectric signals were created and used to investigate the features of the signals as a function of the ciliary beat parameters. Moreover, correlation between the simulated and the measured signals permitted measurement of the cilium beat parameters. The simulations of the signals were based on generation of a series of time-frozen top-view frames of an active ciliary area and determination of the amount of light passing through an observation area in each of these frames. All the factors that might contribute to the shape of the signals, namely, partial ciliary transmittance of light, three-dimensional ciliary beat (composed of recovery, effective, and pause parts), phase distribution on the ciliary surface, and the large number of cilia that contribute to the photoelectric signal, were taken into account in generation of the signals. Changes in the ciliary parameters influenced the shape of the photoelectric signals, and the different phases of the beat could not be directly and unequivocally identified in the signals. The degree of temporal asymmetry of the beat and the portion of the cycle occupied by the pause significantly influenced the shapes of both the lower and the upper parts of the signal and the slopes of the signal. Increases in the angle of the arc swept by the cilium during the effective stroke smoothed the signals and increased the duration of the upper part of the signal. The angle of the arc projected by the cilium onto the cell surface during the recovery stroke had minor effects on the signal's shape. Characteristics of the metachronal wave also influenced the signal's shape markedly. Decreases in ciliary spacing smoothed the signals, whereas ciliary length had a minor influence on the simulated photoelectric signals. Comparison of the simulated and the measured signals showed that the beat parameters of the best-fitting simulated signals converged to values that agree well with the accepted range of beat parameters in mucociliary systems.

Animals↗
PubMed1999

Computer simulation of field distribution and excitation of denervated muscle fibers caused by surface electrodes.

In the course of this study, 2 submodels have been developed and combined, the 2-D finite element modeling of the electrical potential distribution in the human thigh and a Hodgkin and Huxley (HH) type model to calculate fiber excitation and action potential propagation. To determine the excitation of the target muscle fiber with the help of the activating function, the fiber's orientation within the muscle has to be known. The electric field along the fiber has to be calculated as a function of the applied electric current and the potential at the electrodes, respectively. The excitement of the muscle fibers varies across a wide range depending on the active and passive membrane parameters and the intracellular and extracellular mediums. Persisting denervation leads to a decay of muscle cells, and a partial substitution by fibroblasts occurs. The electrical activation of these tissues is more difficult, and biphasic stimulation pulses up to 200 ms in duration and 60-100 V in amplitude are needed to cause a contraction of the denervated muscle. An example shows the field distribution and the simulated activity in one representative muscle fiber of a well trained m. rectus femoris.

Action Potentials↗
PubMed2003

Computer simulation of Clostridium botulinum strain 56A behavior at low spore concentrations.

It is generally assumed that spore behavior is independent of spore concentration, but recently published mathematical models indicate that this is not the case. A Monte Carlo simulation was employed in this study to further examine the independence assumption by evaluating the inherent variance in spore germination data. All simulations were carried out with @Risk software. A total of 500 to 4,000 iterations were needed for each simulation to reach convergence. Lag time and doubling time from a higher inoculum concentration were used to simulate the time to detection (TTD) at a lower inoculum concentration under otherwise identical environmental conditions. The point summaries of the simulated and observed TTDs were recorded for the 26 simulations, with kinetic data at the target inoculum concentration. The ratios of the median (R(m) = median(obs)/median(sim)) and 90% range (R(r) = 90% range(obs)/90% range(sim)) were calculated. Most R(m) and R(r) values were greater than one, indicating that the simulated TTDs were smaller and more homogeneous than the observed ones. R(r) values departed farther from one than R(m) values. Ratios obtained when simulating 1 spore with 10,000 spores deviated the farthest from one. Neither ratio was significantly different from the other when simulating 1 spore with 100 spores or simulating 100 spores with 10,000 spores. When kinetic data were not available, the percent positive observed at the 95th percentile of the simulated TTDs was obtained. These simulation results confirmed that the assumption of independence between spores is not valid.

Clostridium botulinum↗
PubMed1991

Computer simulation model of swine production systems: III. A dynamic herd simulation model including reproduction.

A dynamic herd simulation model for a swine production unit has been developed. The model is discrete and stochastic and the appropriate random distributions have been defined from the literature or empirically estimated. Theoretical concepts and relationships presented previously are used to simulate growth and the overall life cycle of individual animals. Simulated animals are young pigs (from birth to slaughter age), gilts, and sows. Animal events are farrowing, weaning, mating, end-nursery (transfer from nursery to the growing-finishing facility), and slaughter and are processed individually using a next-event scheduling orientation package. Animals within the herd are culled for different health and reproductive reasons. Genetic parameters, diet composition, and herd management are input variables chosen by the user. The effects of nutrition, genetics, season, and other factors on several reproductive parameters are considered. Model evaluation is performed by studying the output of the model under specified herd situations. The herd model adequately simulates animal flow and dynamics of the herd.

Animal Nutritional Physiological Phenomena↗
PubMed1990

Computer simulation of the kinetics of the sodium pump.

A simple kinetic model for the membrane-bound enzyme, 'Na+, K(+)-ATPase', is presented. An equation for the efflux of Na+ and influx of K+ is derived. This also explains multiple ligand binding of homospecies of these cations and competition between heterospecies of these cations. The equation is computed by a small BASIC program and its validity is sought by comparing the results with a few experimental data.

Computer Simulation↗
PubMed1999

Computer simulation of intracranial pressure changes during induction of anesthesia: comparison of thiopental, propofol, and etomidate.

We have developed a computer model of cerebrovascular hemodynamics that interacts with a pharmacokinetic drug model. We used this model to examine the effects of various stimuli occurring during anesthesia on cerebral blood flow (CBF) and intracranial pressure (ICP). The model is a seven-compartment constant-volume system. A series of resistances and compliances relate blood and cerebrovascular fluid fluxes to pressure gradients between compartments. Variable arterial-arteriolar resistance (Ra-ar) and arteriolar-capillary resistance (Rar-c) simulate autoregulation and drug effects, respectively. Rar-c is also used to account for the effect of CO2 on the cerebral circulation. A three-compartment pharmacokinetic model predicts concentration-time profiles of intravenous induction agents. The effect-site compartment is included to account for disequilibrium between drug plasma and biophase concentrations. The simulation program is written in VisSim dynamic simulation language for an IBM-compatible personal computer. Using the model, we have predicted ICP responses during induction of anesthesia for a simulated patient with normal as well as elevated ICP. Simulation shows that the induction dose of intravenous anesthetic reduces ICP up to 30% (propofol > thiopental > etomidate). The duration of this effect is limited to less than 5 minutes by rapid drug redistribution and cerebral autoregulation. Subsequent laryngoscopy causes acute intracranial hypertension, exceeding the initial ICP. ICP elevation is more pronounced in a nonautoregulated cerebral circulation. Simulation results are in good agreement with the available experimental data. The presented model allows comparison of various drug administration schedules to control ICP.

Anesthetics, Intravenous↗
PubMed2005

Enhancing design of immobilized enzymatic microbioreactors using computational simulation.

In continuous-flow enzymatic microbioreactors, enzymes on the channel walls catalyze reaction(s) among feed chemicals, resulting in the production of some desirable material or the destruction of some undesirable material. Computational models of microbioreactors were developed using the CFD-ACE+ multiphysics simulation package. These models were validated via comparison with experimental data for the destruction of urea, catalyzed by urease. Similar models were then used to assess the impact of internal features on destruction efficiency. It was found that triangular features within the channels enhanced the destruction efficiency more than could be attributed to the increase in surface area alone.

Catalysis↗
PubMed2006

Four-bar linkage modelling in teleost pharyngeal jaws: computer simulations of bite kinetics.

The pharyngeal arches of the red drum (Sciaenops ocellatus) possess large toothplates and a complex musculoskeletal design for biting and crushing hard prey. The morphology of the pharyngeal apparatus is described from dissections of six specimens, with a focus on the geometric conformation of contractile and rotational elements. Four major muscles operate the rotational 4th epibranchial (EB4) and 3rd pharyngobranchial (PB3) elements to create pharyngeal bite force, including the levator posterior (LP), levator externus 3/4 (LE), obliquus posterior (OP) and 3rd obliquus dorsalis (OD). A biomechanical model of upper pharyngeal jaw biting is developed using lever mechanics and four-bar linkage theory from mechanical engineering. A pharyngeal four-bar linkage is proposed that involves the posterior skull as the fixed link, the LP muscle as input link, the epibranchial bone as coupler link and the toothed pharyngobranchial as output link. We used a computer model to simulate contraction of the four major muscles, with the LP as the dominant muscle, the length of which determined the position of the linkage. When modelling lever mechanics, we found that the effective mechanical advantages of the pharyngeal elements were low, resulting in little resultant bite force. By contrast, the force advantage of the four-bar linkage was relatively high, transmitting approximately 50% of the total muscle force to the bite between the toothplates. Pharyngeal linkage modelling enables quantitative functional morphometry of a key component of the fish feeding system, and the model is now available for ontogenetic and comparative analyses of fishes with pharyngeal linkage mechanisms.

Animals↗
PubMedDate not supplied

Computational simulation of chronic persistent virus infection: factors determining differences in clinical outcome of HHV-6, HIV-1 and HTLV-1 infections including aplastic, hyperplastic and neoplastic responses.

A computational model was recently designed to simulate cellular changes in the T cell immune system. The model was validated by simulating cell changes in viral infections which target the same CD4+ T cell, yet cause either hyperplastic, aplastic or neoplastic responses. Respective case material for comparison was available from human infections with human herpesvirus-6 (HHV-6), human immunodeficiency virus (HIV-1) or human T cell leukemia virus (HTLV-1). Starting with cell values for a healthy human individual, factorial changes that influence the individual course of the various infections were determined by an algorithm search procedure. Such factorial differences determining a clinical course with aplasia, hyperplasia or neoplasia are outlined and further discussed in this paper.

Algorithms↗