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At least 595 records · Page 33Linked to original sources
PubMed1984

On computer simulation methods used to study models of two-component lipid bilayers.

We show that the use of a computer simulation method introduced to calculate the equilibrium thermodynamic properties of a model of a two-component lipid bilayer membrane [Freire, E., & Snyder, B. (1980) Biochemistry 19, 88-94] is incorrect. This is done by comparing the method to that of Metropolis, which has been proven to generate equilibrium distribution of that model, and by showing that back-processes have been omitted in the implicit master equation of Freire and Snyder. We have illustrated this explicitly by first generating distributions according to the method of Freire and Snyder and then allowing the system to relax via the Kawasaki method, which uses the technique of Metropolis. We show that relaxation to a different distribution occurs. We also remark that the cluster distributions generated by the Freire-Snyder method are substantially different from those occurring in equilibrium distributions. Thus, conclusions about equilibrium thermodynamic properties such as specific heats and transition enthalpies or about transport properties or cluster properties at equilibrium cannot be drawn from the results obtained by using this method. Finally, we point out that the method of Freire and Snyder is appropriate to so-called aggregation models, which have been used to study irreversible growth; and we suggest biological systems that might be simulated by their method.

Computers↗
PubMed1994

On the mechanisms of growth cone locomotion: modeling and computer simulation.

In this paper we put forward a model for growth-cone locomotion in which the actin cytoskeleton is represented by a two-dimensional contractile network and the growth-cone membrane is represented by contractile segments coupled with the actin network. Our computer simulation suggests that many mechanisms, such as the actin polymerization and depolymerization, the attachment of actin filaments to the substratum, the transformation of the growth-cone neck into the axon, and the axonal transport, co-operate to generate growth-cone movement.

Actins↗
PubMed1993

Computer simulation of tumour cell invasion by a stochastic growth model.

The structure and function of biological systems are considered to be closely related. The present study addresses the question of how histological patterns of tumours are related to specific functional properties of the tumour cells. A mathematical model was developed, which facilitates the simulation of tumour growth and invasion by computer. The degree of cell division, migration and death can be interactively set and the simulation results can be observed on the screen. Additionally, these basic functional properties of a particular cell can be influenced by autocrine and paracrine factors. The study shows that the resulting morphological patterns closely depend on the preset functional properties of the tumour cells. Furthermore, each autocrine or paracrine factor, or combinations of these factors, induce peculiar modifications of the tumour pattern. These results provide evidence that histological tumour patterns reflect functional properties of the tumour cells and their interaction with the micro-environment. Qualitative and quantitative comparison of real tumour specimens with patterns simulated by computer may thus provide a logical base for a functional interpretation of static histological images.

Cell Death↗
PubMed1997

The EWMA control chart: properties and comparison with other quality-control procedures by computer simulation.

A quality-control chart based on exponentially weighted moving averages (EWMA) has, in the past few years, become a popular tool for controlling inaccuracy in industrial quality control. In this paper, I explain the principles of this technique, present some numerical examples, and by computer simulation compare EWMA with other control charts currently used in clinical chemistry. The EWMA chart offers a flexible instrument for visualizing imprecision and inaccuracy and is a good alternative to other charts for detecting inaccuracy, especially where small shifts are of interest. Detection of imprecision with EWMA charts, however, requires special modification.

Algorithms↗
PubMed1991

How many probes are needed for HLA-DPB1 typing with sequence-specific oligonucleotide probes? A theoretical approach using computer simulation.

HLA-DP genotyping with sequence-specific oligonucleotides is used to detect known sequence variations in the polymorphic segments of the DPB1 second exon. This approach is a valuable method replacing the tedious cellular definition of DP polymorphism. We have addressed, by computer simulation, the question: what is the minimum number of probes needed to provide an unambiguous assignment of HLA-DP alleles by genotyping of heterozygous individuals? We were able to reduce the number of probes in a set defining the presently known 22 different alleles and most of the heterozygous combinations to 18 probes. Only two pairs of allelic combinations cannot be distinguished by this method, neither with our optimized set of probes nor with any larger set comprising probes of reasonable length. This is because two pairs of alleles may be the result of a reciprocal genetic exchange. These two pairs, however, could be distinguished by family analysis, direct sequencing, or DNA amplification using specific primers chosen from the polymorphic ends of the DPB1 second exon.

Alleles↗
PubMedDate not supplied

Computational simulations of mitral regurgitation quantification using the flow convergence method: comparison of hemispheric and hemielliptic formulae.

Mitral regurgitation results from the incomplete closure of the mitral valve, and the noninvasive diagnosis of this disease remains an important clinical goal. In this study, steady flow computer simulations were used to evaluate flow convergence method for flow rate estimation. The hemispheric and hemielliptic formulae were compared for accuracy in the presence of complicating factors such as ventricular confinement, orifice shape, and aortic outflow. Results showed that in the absence of aortic outflow and ventricular confinement, there was a plateau zone where the hemispheric formula approximated the true flow rate, independent of orifice shape. However, in the presence of complicating factors such as aortic outflow and ventricular confinement, there was no clear zone where the hemispheric formula could be applied. The hemielliptic formula, however, worked in all cases, regardless of chamber size or magnitude of aortic outflow. Therefore, application of the hemielliptic formula should be considered in future clinical studies.

Aorta, Thoracic↗
PubMed1994

Estimation of growth hormone secretory patterns in children with use of a numerical deconvolution technique: experimental design with use of computer simulation.

Growth hormone (GH) secretion rates were estimated from 24-hour plasma GH concentration profiles using a model-based numerical deconvolution method. The basic kinetic parameters describing GH distribution and elimination were obtained from studies using single intravenous injections in GH-deficient children. Computer simulation techniques were used to produce 24-hour GH secretion profiles, which could serve as reference curves for analysis of the impact of certain practical aspects of the estimation of GH secretion, such as the method of blood sampling (discrete or integrated), sampling frequency and analytical errors. The results show that sampling intervals of 20 min are acceptable even in the presence of analytical errors, and that with this sampling interval, discrete blood sampling does not seem to be preferable to continuous withdrawal of blood.

Blood Specimen Collection↗
PubMedDate not supplied

Auditory brainstem response threshold estimation: subjective threshold estimation by experienced clinicians in a computer simulation of the clinical test.

Little research has been undertaken into the extent to which auditory brainstem response (ABR) threshold estimation varies between experienced professionals. In this paper, results are presented for 16 professionals who estimated ABR threshold for 12 sets of data in a computer simulation of the clinical test. The design differs from previous research in this area in that subjects had control over the creation of the set of traces from which they would estimate threshold, much as they would in the clinical situation. No agreement for threshold was found for any of the 12 sets of test data across the 16 subjects, and for nine of the sets, the difference between highest and lowest estimated threshold was 40 dB or greater. The maximum difference between highest and lowest estimated threshold was 60 dB. It is argued that the variability is not accounted for by experimental design. The implications for clinical practice are discussed.

Adult↗
PubMed1992

Computer simulations of EPSP-spike (E-S) potentiation in hippocampal CA1 pyramidal cells.

Long-term potentiation of hippocampal excitatory synapses is often accompanied by an increase in the probability of spiking to an EPSP of fixed strength (E-S potentiation). We used computer simulations of a CA1 pyramidal neuron to test the plausibility of the hypothesis that E-S potentiation is caused by changes in dendritic excitability. These changes were simulated by adding "hot spots" of noninactivating voltage-sensitive Ca2+ conductance to various dendritic compartments. This typically caused spiking in response to previously subthreshold synaptic inputs. The magnitude of the simulated E-S potentiation depended on the passive electrical properties of the cell, the excitability of the soma, and the relative locations on the dendrites of the synaptic inputs and hot spots. The specificity of the simulated E-S potentiation was quantified by colocalizing the hot spots with a subset (40 of 80) of the synaptic contacts, denoted "tetanized," and then comparing the effects of the hot spots on these and the remaining (untetanized) synaptic contacts. The simulated E-S potentiation tended to be specific to the tetanized input if the untetanized contacts were, on average, electrically closer to the soma than the tetanized contacts. Specificity was also high if the tetanized and untetanized contacts were segregated to different primary dendrites. The results also predict, however, that E-S potentiation by this mechanism will appear to be nonspecific (heterosynaptic) if the synapses of the untetanized input are sufficiently far from the soma relative to the tetanized synapses. Experimental confirmation of this prediction would support the hypothesis that changes in postsynaptic excitability can contribute to hippocampal E-S potentiation.

Animals↗
PubMed1995

Biological significance of tumor thickness. Theoretical considerations based on computer simulation.

Maximum vertical tumor thickness is a highly significant prognostic criterion in cutaneous melanoma. To date, little is known about the problem, why thick lesions are more capable of metastatic spread than thin ones. To evaluate theoretical possibilities of the biological impact of thick lesions, computer simulation of tumor growth was performed. In a set of 35,000 simulated tumors, the thickness of the resulting tumor was measured and the functional simulation settings contributing to tumor thickness were identified by statistical methods. It turned out that in this theoretical model of tumor growth, besides time, which is the most important factor, other factors contribute to tumor thickness. These are tumor cell motility, particularly when stimulated by stromal elements, a decreased rate of tumor cell loss, and pronounced proliferation associated with high numbers of cell cycle generations in the tumor cells. These findings are in agreement with experimental data indicating that metastatic capacity may depend on increased motility, stroma-induced motility stimulation, evasion from the host immune system, and genetic instability manifesting during cell cycling. Thus the observations may help to clarify the relationship of vertical tumor thickness and poor clinical outcome in cutaneous melanomas.

Cell Cycle↗
PubMed2000

Computer simulation of haemodynamic parameters changes with left ventricle assist device and mechanical ventilation.

Left Ventricular Assist Device is used for recovery in patients with heart failure and is supposed to increase total cardiac output, systemic arterial pressure and to decrease left atrial pressure. Aim of our computer simulation was to assess the influence of Left Ventricular Assist Device (LVAD) on chosen haemodynamic parameters in the presence of ventilatory support. The software package used for this simulation reproduces, in stationary conditions, the heart and the circulatory system in terms of pressure and volume relationships. Different circulatory sections (left and right heart, systemic and pulmonary arterial circulation, systemic and pulmonary venous circulation) are described by lumped parameter models. Mechanical properties of each section are modelled by RLC elements. The model chosen for the representation of the Starling's law of the heart for each ventricle is based on the variable elastance model. The LVAD model is inserted between the left atrium and the aorta. The contractility of the heart and systemic arterial resistance were adjusted to model pathological states. Our simulation showed that positive thoracic pressure generated by mechanical ventilation of the lungs dramatically changes left atrial and pulmonary arterial pressures and should be considered when assessing LVAD effectiveness. Pathological changes of systemic arterial resistance may have a considerable effect on these parameters, especially when LVAD is applied simultaneously with mechanical ventilation. Cardiac output, systemic arterial and right atrial pressures are less affected by changes of thoracic pressure in cases of heart pathology.

Animals↗
PubMed1993

Computer simulations of the differentiated pay structure model.

The differentiated pay structure (DPS) model determines a nurse's base pay on the basis of education, position, and expertise level, adjusting that base for part-time employment, differentials for nonbusiness hours, and single payment bonuses to reward longevity. Using computer simulations, the model was tested with data from two urban hospitals. The findings show that the model can be applied in a manner that is acceptable in terms of budget. By using the DPS model, administration can compensate for those objective employee behaviors that employers value the most.

Computer Simulation↗
PubMed2005

[The application of a systematic-dynamic model to study the computer simulation of severe acute respiratory syndrome transmission and the impact of control measures].

OBJECTIVE: (1) Building a macroscopical systematic-dynamic model of severe acute respiratory syndrome (SARS) transmission and disease control process. (2) To determine key variables on the control of SARS epidemic through computer simulation methodology, especially to analyze the effect of "screening for fever" practice during the epidemics. (3) To provide evidence for related decision-making. METHODS: Parameters in the model were collected from local hospitals and municapal CDC through interview, questionnaire survey, literature review and case analysis. A systematic-dynamic model was built under similar studies. 'What-if' analysis was used during the simulation process. RESULTS: (1) The mean duration between disease onset and hospital admission, rate of contacts of each infectious individual as well as the rate of contacts in hospital of each infectious individual appeared to be the key variables in the process of SARS transmission. (2) Physician's alertness/sense and practice of self-protection on SARS, measures on quarantine and isolation to the patients, ventilation and disinfection process in the wards appeared to be the key variables for the control of epidemics. (3) "Screening for fever" practice on each patient at the entrance of the hospital did not seem to act as an important factor to the control of the epidemics. CONCLUSION: The health system in Beijing can control SARS epidemic rapidly based on current applied disease control measures and plan.

China↗
PubMed1996

Production of proteinase A by Saccharomyces cerevisiae in a cell-recycling fermentation system: experiments and computer simulations.

Overproduction of proteinase A by recombinant Saccharomyces cerevisiae was investigated by cultivations in a cell-recycling bioreactor. Membrane filtration was used to separate cells from the broth. Recycling ratios and dilution rates were varied and the effect on enzyme production was studied both experimentally and by computer simulations. Experiments and simulations showed that cell mass and product concentration were enhanced by high ratios of recycling. Additional simulations showed that the proteinase A concentration decreased drastically at high dilution rates and the optimal volumetric productivities were at high dilution rates just below washout and at high ratios of recycling. Cell-recycling fermentation gave much higher volumetric productivities and stable product concentrations in contrast to simple continuous fermentation.

Aspartic Acid Endopeptidases↗
PubMed1990

A model for computer simulation of P-glycoprotein and transmembrane delta pH-mediated anthracycline transport in multidrug-resistant tumor cells.

Anthracycline resistance in multidrug-resistant (MDR) tumor cells is due in part to a reduced cellular drug accumulation. Using a simple kinetic model and numerical computer simulations, we have analyzed mathematically the following possible mechanisms controlling fluxes of the membrane permeable anthracyclines in MDR cells: (1) active outward transport via a specific drug transporter (P-glycoprotein), (2) exocytotic drug export via the endosomal vesicle system, and (3) pH-gradients across the plasma membrane. Model calculations were based on morphometric and kinetic data previously presented in the literature for daunorubicin transport in wild-type Ehrlich ascites tumor cells (EHR2) and the corresponding daunorubicin (DNR)-resistant cell line EHR2/DNR+. The results confirm the possible importance of the cell-surface pH in controlling DNR accumulation in the cells. With P-glycoprotein as the main efflux pump, a catalytic constant of the protein greater than 40 mol DNR transported/mol protein per min is predicted by the model calculations. Changes in the drug binding affinity of P-glycoprotein (Km = 10(-9)-10(-6) M) is of little importance in influencing its effectiveness to reduce DNR accumulation, which could explain the broad substrate specificity of the MDR efflux pump system. The conditions to evaluate unidirectional fluxes of DNR across the plasma membrane in cells with active P-glycoprotein are defined. An efflux mechanism which relies solely on pH-dependent drug trapping in a pH 5 endosomal compartment by a simple diffusion process followed by exocytosis, appears inadequate to account for the high rate of DNR efflux in EHR2/DNR+ cells.

Animals↗
PubMed2006

Computer simulations of Alzheimer's amyloid beta-protein folding and assembly.

Pathological folding and aggregation of the amyloid beta-protein (Abeta) are widely perceived as central to understanding Alzheimer's disease (AD) at the molecular level. Experimental approaches to study Abeta self-assembly are limited, because most relevant aggregates are quasi-stable and inhomogeneous. In contrast, simulations can provide significant insights into the problem, including specific sites in the molecule that would be attractive for drug targeting and details of the assembly pathways leading to the production of toxic assemblies. Here we review computer simulation approaches to understanding the structural biology of Abeta. We discuss the ways in which these simulations help guide experimental work, and in turn, how experimental results guide the development of theoretical and simulation approaches that may be of general utility in understanding pathologic protein folding and assembly.

Alzheimer Disease↗
PubMed2003

Computer simulation of the human leg subjected to impact loading.

One of the most important tasks in clinical practice is to determine accurately the forces and displacements of the various anatomical structural components of the human leg, especially when subjected to impact loading. This paper therefore develops a computer simulation which describes the biodynamic response of the human lower extremity for realistic activities such as kicking by foot etc. Firstly, the paper derives the nonlinear equations of motion and nonlinear constraint equation governing the sagittal plane response of the human leg subjected to impact loading. The equations are then solved using numerical techniques and the results are presented. Special attention is given to the ligament, contact and muscle group forces, the location of contact points, anterior-posterior displacements and the motion trajectories of the femur and the tibia.

Computer Simulation↗
PubMed1998

Computer simulation of changes in nursing productivity from early tracheal extubation of coronary artery bypass graft patients.

STUDY OBJECTIVE: To determine whether the results from a clinical trial, which showed that early extubation of elective coronary artery bypass graft (CABG) patients can reduce hospital costs by more rapid discharge of patients from the intensive care unit (ICU), are likely to apply to other hospitals. DESIGN: Discrete-event computer simulation. MEASUREMENTS AND MAIN RESULTS: We (1) generated simulated CABG patients, (2) had them "flow" from one condition to the next according to specified rules, and (3) calculated the labor productivity of simulated nurses who would be caring for the patients. We defined nursing labor productivity as the number of patients undergoing elective CABG cared for each year per nursing full-time equivalent working 40 hours per week. Our simulations predict that the increase in nursing labor productivity achieved by early extubation of CABG patients is sensitive to the number of elective CABG cases performed each year at the hospital and the method of compensating nurses. Hospitals with an "hourly workforce" and many cases per year are predicted to achieve a greater increase in productivity from early extubation than are hospitals with a "salaried workforce" and less active volume. At hospitals with a salaried workforce, increasing the percentage of patients extubated early may have no effect on labor productivity. CONCLUSIONS: Although "fast-tracking" protocols may offer benefits other than increasing nursing labor productivity (i.e., saving money), the results of clinical trials that demonstrate cost savings from clinical pathways that include early tracheal extubation are likely to apply only to hospitals that have similar annual CABG volume and method of compensating nurses as those in the clinical trial. To estimate the likely economic impact from early extubation protocols, a hospital should complete a simulation study with parameter values appropriate to its institution.

Computer Simulation↗