Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Computer Simulation”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 289 records · Page 16Linked to original sources
PubMed1988

Algorithms for determining the fate of sites and domain boundaries in computer simulations of recombinant DNA procedures.

Structural and functional features within genomic sequences are best described by their position within the genomic structure. Cleavage sites can be conveniently described by single positions but genomic domains require the position of their two boundaries. The handling of these positions simultaneously to sequence manipulations in computer simulations of recombinant DNA procedures greatly improves the understanding of the resulting recombinant constructs. In addition, the algorithms describing the fate of domain boundaries can be used for the handling of nucleotide sequences in dynamic database environments handled by languages like Prolog which are particularly suitable for artificial intelligence implementations. This communication describes a set of algorithms for the automatic updating of single sites and double domain boundaries in linear and circular models for computer simulation of recombinant DNA procedures.

Algorithms↗
PubMedDate not supplied

[Monitoring high dose methotrexate therapy (HD MTX) in children with osteosarcoma and computer simulation using a pharmacokinetic model].

The pharmacokinetics of methotrexate (MTX) was studied in 15 children with osteosarcoma, treated (54 courses) with high-dose methotrexate (8, 10 i 12 g/m2; 4 h i.v. infusion). Pharmacokinetic analysis was performed by standard non-compartmental methods and using two-compartment nonlinear model with coexistence of additional, parallel linear route of elimination from central compartment. The model was used for computer simulation and prognosis of the serum-level curve course depending on the simulated dosage, enhanced diuresis and simulated kidney or liver insufficiency during the dose individualization. The usage of the pharmacokinetic model for computer simulations may improve understanding of the MTX kinetics and can optimise dosage regimens for the next cycles of chemotherapy.

Adolescent↗
PubMed1988

An analysis of the hyper-sharp phenomenon of myosin diffusion in an F-actin/ATP solution by computer simulation.

The diffusion of myosin molecules was demonstrated using schlieren optics and Rayleigh fringe optics. A hyper-sharp schlieren pattern appeared near the boundary between the upper and lower parts of the diffusion cell at a time when ATP in the lower part had almost been consumed. The mechanism underlying the appearance of the hyper-sharp peak was investigated by means of computer simulations based on random-walk theory. The schlieren pattern with the hyper-sharp peak could be reproduced on the computer with the assumptions that a myosin molecule can be detached from an actin filament only on binding of ATP and that it can then move along actin filaments or diffuse in the aqueous solution. The results of the computer simulations are in good agreement with the experimental data.

Actins↗
PubMed2006

Theoretical aspects and computer simulations of flexible charged oligomers in salt-free solutions.

The structural and thermodynamic properties of a model solution containing flexible charged oligomers and an equivalent number of counterions were studied by means of the canonical Monte Carlo simulation and integral equation theory. The oligomers were represented as freely jointed chains of charged hard spheres. In accordance with the primitive model of electrolyte solutions, the counterions were modeled as charged hard spheres and the solvent as a dielectric continuum. Simulations were performed for a set of model parameters, independently varying the chain length and concentration of the oligomers. Structural properties in the form of pair distribution functions were calculated as functions of model parameters. In addition, thermodynamic properties such as the excess energy of solution and the excess chemical potential of counterions were obtained. These properties were correlated with the conformational averages of oligomers as reflected in the end-to-end distances and radii of gyration obtained from the simulations. The relation with the experimental data for heats of dilution and for the activity coefficient is discussed. Finally, theories based on Wertheim's integral equation approach (product reactant Ornstein-Zernike approach) [J. Stat. Phys. 42, 477 (1986)] in the so-called polymer mean spherical and polymer hypernetted chain approximations were tested against the new and existing computer simulations. For the values of parameters examined in this study, the integral equation theory yields semiquantitative agreement with computer simulations.

Biopolymers↗
PubMedDate not supplied

Computer simulation analysis of blood donor queueing problems.

A computer simulation model was used to study work flow and queueing problems in blood collection. Donor scheduling strategies, such as stream and block arrivals, were compared with random arrival at a constant hourly rate. Controlling donor queueing required keeping donor arrivals from exceeding the system capacity, rather than using any one type of scheduling strategy. However, widely uneven arrivals compared to even arrivals at the same input level caused protracted queueing. Because men have a shorter average phlebotomy processing time, time can be saved in some situations by scheduling mostly men at the beginning of a drive. Nursing utilization appears optimal at donor arrival rates at or near system capacity. Techniques may be available to modify the collection system to ameliorate or prevent queueing when donor arrivals appear to be excessive.

Blood Donors↗
PubMed1999

Computer simulations of actin polymerization can explain the barbed-pointed end asymmetry.

Computer simulations of actin polymerization were performed to investigate the role of electrostatic interactions in determining polymerization rates. Atomically detailed models of actin monomers and filaments were used in conjunction with a Brownian dynamics method. The simulations were able to reproduce the measured barbed end association rates over a range of ionic strengths and predicted a slower growing pointed end, in agreement with experiment. Similar simulations neglecting electrostatic interactions indicate that configurational and entropic factors may actually favor polymerization at the pointed end, but electrostatic interactions remove this trend. This result would indicate that polymerization at the pointed end is not only limited by diffusion, but faces electrostatic forces that oppose binding. The binding of the actin depolymerizing factor (ADF) and G-actin complex to the end of a filament was also simulated. In this case, electrostatic steering effects lead to an increase in the simulated association rate. Together, the results indicate that simulations provide a realistic description of both polymerization and the binding of more complex structures to actin filaments.

Actin Cytoskeleton↗
PubMed2003

Determining the number of beds in the postanesthesia care unit: a computer simulation flow approach.

UNLABELLED: Designing a new operating room (OR) suite is a difficult process owing to the number of caregivers involved and because decision-making managers try to minimize the direct and indirect costs of operating the OR suite. In this study, we devised a computer simulation flow model to calculate, first, the minimum number of beds required in the postanesthesia care unit (PACU). In a second step, we evaluated the relationship between the global performance of the OR suite in terms of OR scheduling and number of staffed PACU beds and porters. We designed a mathematical model of OR scheduling. We then developed a computer simulation flow model of the OR suite. Both models were connected; the first one performed the input flows, and the second simulated the OR suite running. The simulations performed examined the number of beds in the PACU in an ideal situation or in the case of reduction in the number of porters. We then analyzed the variation of number of beds occupied per hour in the PACU when the time spent by patients in the PACU or the number of porters varied. The results highlighted the strong impact of the number of porters on the OR suite performance and particularly on PACU performances. IMPLICATIONS: Designing new operating room (OR) facilities implies many decisions on the number of ORs, postanesthesia care unit (PACU) beds, and on the staff of nurses and porters. To make these decisions, managers can use rules of thumb or recommendations. Our study highlights the interest of using flow simulation to validate these choices. In this case study we determine the number of PACU beds and porter staff and assess the impact of decreasing the number of porters on PACU bed requirements.

Algorithms↗
PubMed1984

A computer simulation of cell stacking for even thickness in mammalian epidermis.

The method of even stacking of epidermal cells in mammalian skin was studied by computer simulation. The epidermis consists of neat vertical columns of stacked, flattened, tetrakaidecahedral cells. Cells which have been proliferated in a basal layer migrate upwards, occupy the bottom regions of vertical columns, and become members constituting columns. Computer simulations demonstrated that the column height becomes considerably varied if the cells are randomly supplied from the basal layer. In contrast, if the cells are assumed to have an ability to find the uppermost region among the column's bases consisting of one base where the cell has reached and its neighbouring bases, the cells stack into columns whose heights are remarkably uniform even if the cells are randomly supplied. The results indicated that an epidermal structure consisting of the flattened polyhedral cells could itself function as a control mechanism of the epidermal thickness.

Animals↗
PubMed1993

Computer simulations in comparison with in vivo measurements of nifedipine-induced changes in renal allograft hemodynamics.

Analysis of Doppler spectrum waveforms is increasingly used in the differential diagnosis of human renal allograft dysfunction. The physiologic interpretation of changes in Doppler spectra obtained from renal allografts, however, remains a major problem. Computer simulation models of the renal circulation may provide insight into the physiologic mechanisms responsible for changes in Doppler spectrum characteristics. The results of measurements of renal allograft hemodynamics with both determinations of PAH clearance and Doppler spectrum analysis in 11 kidney allograft recipients were explained physiologically using a computer simulation model of kidney allograft hemodynamics. Using PAH clearance and blood pressure measurements a significant decrease in RVR was found (from 0.32 +/- 0.17 to 0.20 +/- 0.07 mm Hg x min/ml, P < 0.05) after administration of the vasodilatory drug nifedipine. The Doppler spectrum waveform obtained from interlobar renal arteries showed a decrease in the RI (from 0.60 +/- 0.04 to 0.56 +/- 0.06; P < 0.05) and Tmax (from 133 +/- 32 to 98 +/- 32 ms; P < 0.05). The user-designed simulation model of renal hemodynamics showed comparable changes of the waveform when, in the model, the analogs of blood pressure, impedance of the artery, and the impedance of the peripheral vascular bed were altered proportionally.

Administration, Oral↗
PubMedDate not supplied

Stopping enteral feeding for arbitrary gastric residual volume may not be physiologically sound: results of a computer simulation model.

BACKGROUND: During tube feeding, it is a common practice to check gastric residual volume frequently for indications of pathologic impairment of gastric emptying. The volume threshold standards for holding feedings are applied nonselectively, disregarding slowing of gastric emptying by nutrient-triggered intestinogastric inhibitory feedback. We developed a computer simulation model considering this feedback to test the hypothesis that gastric residual volume increases with slower gastric emptying and faster formula delivery but reaches a plateau volume (equilibrium between input and output) at volumes commonly seen in the postprandial stomach. METHODS: A computer simulation model using Microsoft Excel 4.0 calculated the cumulative gastric residual volume over time when the input volume into the stomach is 125 mL/h (endogenous secretions)+ 0 to 125 mL/h (formula delivery rate) and the output volume out of the stomach is equal to gastric emptying rates that varied between 0% and 50%/h. The model simulated nasogastric feeding with nine different rates of gastric emptying and six different rates of formula delivery. Measurements consisted of the cumulative gastric residual volume at the end of each hour for a minimum of 48 hours. RESULTS: (1) Gastric residual volumes 1.5 to 6 times the commonly applied "stop feeding" threshold volume of 150 mL are encountered at gastric emptying rates of 20% to 50%/h; (2) gastric residual volume stabilizes to a plateau of 225 to 900 mL between 3 and 13 hours after start of formula delivery at these rates; and (3) at 0% gastric emptying, gastric residual volume does not reach a plateau. CONCLUSIONS: At gastric emptying rates expected with nutrient-triggered inhibitory feedback and at formula delivery rates common in nutrition support, gastric residual volume reaches a plateau rapidly and at volumes commonly encountered in normal postprandial stomachs. On the basis of the results of this model, the current practice of stopping enteral feeding when gastric residual volume exceeds an arbitrarily selected volume threshold may not be physiologically sound. Clinical studies are needed to verify this model.

Computer Simulation↗
PubMed1998

Total knee arthroplasty kinematics. Computer simulation and intraoperative evaluation.

The goal of this work was to develop computer simulations for intraoperative testing of the passive kinematics of knee prostheses. These are based on an anatomic model of the reconstructed joint, represented in the sagittal plane. A femoral component and a tibial component are linked by 3 springs that model the relevant ligaments, with the posterior cruciate providing the primary constraint. The components' behavior at each flexion angle is obtained by minimizing the total strain energy stored in the ligaments. Simulations were performed in vivo on 10 Interax implants (Howmedica International, Stain, UK) and showed good agreement with intraoperative observations, allowing monitoring of new parameters such as contact point motion, ligament strains, and the energetic state of the knee. This work contributes to the comprehension of individual knee kinematics after total knee arthroplasty, to improve long-term results and standardize the evaluation of the results of joint restoration.

Arthroplasty, Replacement, Knee↗
PubMed1997

Improving outpatient clinic efficiency using computer simulation.

To assess and plan alterations in outpatient clinic structure, produces a computer simulation of an outpatient clinic based on detailed time and role measurements from the authors' clinic. The stimulation which used an object-oriented design method is able to indicate the impact of changes in clinic structure using patient and doctor waiting times in clinic as endpoint measures. The effects of changes in clinic size, consultation time, patient mix, appointment scheduling and non-attendance were examined. We found that patient waiting time could be shortened considerably by using an optimizing appointment scheduler to determine appointment intervals. Clinic mix influences patient waiting time, which was shorter with a 1 in 4 ratio of new to follow-up patients. In mixed clinics, new patients appointments are optimally spread throughout the clinic to reduce patient waiting time. In all new or all follow-up clinics, waiting time is improved if the appointment interval reflects the consultation time. Computer modelling can help in optimizing clinic management so improving the delivery of care in outpatient services.

Appointments and Schedules↗
PubMed1986

Computer simulations of the kinetics of irreversible enzyme inhibition by an unstable inhibitor.

Computer simulations of the irreversible inhibition of an enzyme by an unstable inhibitor are presented. Data obtained at the end point of reaction are shown to conform poorly in many situations with relationships derived from integrated rate equations by setting t = infinity, and the implications concerning the experimental use of this method to determine kinetic constants describing inactivation are considered. The alternative approach of conducting experiments under conditions of inhibitor excess over enzyme is further discussed, and a graphical procedure is suggested for the description of time courses of reaction of enzyme with unstable inhibitor when an enzyme-inhibitor adsorptive complex is involved.

Computer Simulation↗
PubMed1990

Computer simulation of the hemodynamic determinants of myocardial oxygen supply and demand.

A computer program was developed that uses a mathematical model of the cardiovascular system to predict myocardial oxygen supply and demand as well as cardiac hemodynamics. This model combines the time-varying elastance model of the left ventricle, the modified Windkessel model of the arterial system, and the left ventricular pressure-volume area prediction of myocardial oxygen demand. The computer simulation permits independent control of variables, thus providing the opportunity to design "experiments" and to observe the results. The model predicts that tachycardia leads to reduced myocardial oxygen supply and increased demand. Hypertension caused by increased systemic vascular resistance increases supply more than it increases demand. On the other hand, increased contractility or left ventricular end-diastolic pressure increases demand more than supply, and may cause ischemia in the presence of coronary artery stenosis. The model is an aid in understanding how hemodynamic variables affect the balance between myocardial oxygen supply and demand. It can be used for education and to analyze study protocols prior to animal experimentation.

Animals↗
PubMed1972

A computer simulation of conduction in demyelinated nerve fibres.

1. The theoretical effects of demyelination on conduction of a propagated impulse have been examined in a computer simulated myelinated nerve fibre. Demyelination was simulated by increasing the capacitance and conductance of the myelin sheath of individual internodes or parts of internodes.2. Internodal conduction time increased as myelin thickness was decreased. The increase in internodal conduction time became more precipitous as the myelin became thinner. Propagation continued past a single demyelinated internode until myelin thickness was uniformly reduced to less than 2.7% of normal myelin thickness.3. Paranodal demyelination was more effective in slowing impulse conduction than was uniform demyelination of an entire internode with an equivalent rise in overall internodal capacitance and conductance.4. The effects on conduction of demyelination of two adjacent internodes or of two internodes separated by a normal internode were more than the sum of the effects of demyelination of each internode individually.5. Propagation across a severely demyelinated internode was blocked with an increase in internal sodium concentration which had a trivial effect on conduction in a normal fibre.6. Propagation across a severely demyelinated internode was blocked with increased temperature at a temperature at which propagation proceeds normally across normal internodes.7. The similarity between the findings of the computer simulations and the experimental findings in demyelinated fibres is discussed.

Action Potentials↗
PubMed1982

Oligonucleotide mapping: evaluation of its sensitivity by computer-simulation.

A frequently used method of comparing large RNA molecules employs the two-dimensional display of oligonucleotides generated through the action of specific RNases (oligonucleotide mapping, fingerprinting). Using computer simulations and simple analytic expressions the number of large RNase T1-resistant oligonucleotides obtained from random RNA sequences can be estimated. The computer simulations also permit estimation of the number of large oligonucleotides which remain unchanged as random variations are introduced into a random RNA sequence. In addition, computer analysis also provides a means of estimating statistical confidence limits to be used in a quantitative comparison of fingerprints of different RNA molecules. The model shows that two RNA sequences which differ overall by 1%, 5% or 10% share, on average, only 85%, 50% or 25%, respectively, of their large oligonucleotides. Thus, the use of fingerprint analysis is recommended only when closely related RNAs or regions of RNAs are compared (sequence homology greater than 90%).

Base Sequence↗
PubMedDate not supplied

[Pharmacokinetics of methotrexate and therapeutic drug monitoring in children with osteosarcoma. Computer simulation using a pharmacokinetic model].

The pharmacokinetics of methotrexate (MTX) and the therapeutic drug monitoring (TDM) in children treated-with high-dose of MTX (HD MTX) have been discussed. The pharmacokinetics of MTX was studied in 15 children (54 courses) with osteosarcoma, treated with HD MTX (8, 10 and 12 g/m2; 4 h i.v. infusion). Pharmacokinetic analysis was performed by standard non-compartmental methods and using two-compartment nonlinear model with coexistence of additional, parallel linear route of elimination from the central compartment. This proposed model can be used for computer simulation and prognosis of the serum-level curve course depending on the simulated dosage, enhanced diuresis and simulated kidney or liver insufficiency during the dose individualisation. The usage of the pharmacokinetic model for computer simulations may improve the understanding of MTX kinetics and can optimalise dosage regimens for the next cycles of chemotherapy.

Adolescent↗