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PubMed2005

[Mathematical model of cardiac action potential and its computer simulations].

Malignant arrhythmias and ventricular fibrillation are generally accepted as one of the major causes of death in cardiovascular diseases. Based on the H-H equations, the mathematical model of the cardiac cell action potential consists of the ion channels, pumps, exchangers and transporters that are closely connected with intra- and extra-cellular ion concentrations, the channel's conditions, nerve transductors and drugs. It can build the link between cell electrophysiology and clinical pathophysiology. By altering the cellular environments the computer simulating study on this kind of model can help us look into the electrophysiological changes of the cardiac tissue and even the whole heart and investigate the mechanisms of the cardiac arrhythmias as well. The components of the model and its computer simulating study are introduced in the paper.

Action Potentials↗
PubMed1984

Monte Carlo computer simulation of the aqueous hydration of the glycine zwitterion at 25 degree C.

Monte Carlo computer simulation on a dilute aqueous solution of the glycine zwitterion are reported. The results are presented in terms of the Quasi-Component Distribution Functions (QCDF) of Ben Naim and partitioned into atomic and functional group contributions using the Proximity Criterion. The Proximity Criterion analysis has been extended to orientational properties and a new normalization procedure has been introduced for the radial distribution functions obtained by the Proximity Criterion. The solvation environment of the glycine zwitterion is found to contain, on the average, 14.4 water molecules out of which 3.2 belong to the ammonium group, 6.1 to the methylene group and 5.1 to the carboxyl group. The importance of the many-body statistical mechanical approach to hydration is emphasized by our finding that the configuration corresponding to the absolute minimum of the glycine zwitterion-water potential surface was found to have negligible statistical weight in the aqueous simulation.

Computer Simulation↗
PubMed2006

Framework for optimal design of porous scaffold microstructure by computational simulation of bone regeneration.

In bone tissue engineering using a biodegradable scaffold, geometry of the porous scaffold microstructure is a key factor for controlling mechanical function of the bone-scaffold system in the regeneration process as well as after the regeneration. In this study, we propose a framework for the optimal design of the porous scaffold microstructure by three-dimensional computational simulation of bone tissue regeneration that consists of scaffold degradation and new bone formation. The rate of scaffold degradation due to hydrolysis, that leads to decrease in mechanical properties, was simply assumed to relate to the water content diffused from the surface to the bulk material. For the new bone formation on both bone and scaffold surfaces, the rate equation of trabecular surface remodeling driven by mechanical stimulation was applied. Solving these two phenomena in the same time frame, the bone regeneration process in the bone-scaffold system was predicted by computational simulation using a voxel finite element method. The change in the mechanical function of the bone-scaffold system during the regeneration process was quantitatively evaluated by measuring the change in total strain energy, and this was used for the evaluation function to optimize the scaffold microstructure that provides the desired mechanical function during and after the bone regeneration process. A case study conducted for the scaffold with a simple microstructure demonstrated that the proposed simulation method could be applied to the design of a porous scaffold microstructure. In addition, the regeneration process was found to be very complex even though the simple rate equations for scaffold regeneration and new bone formation were used because of the coupling effects of these phenomena.

Animals↗
PubMed2005

Does three-dimensional computer simulation improve results of scaphoid nonunion surgery?

The purpose of this study was to clarify the effectiveness of the three-dimensional computer simulations in scaphoid nonunion surgery. Seven consecutive clinical patients with scaphoid nonunion at the middle third comprised the study group. Surface models of the scaphoid were constructed on the computer using computed tomography data of the bilateral wrists in neutral position. The distal and proximal fragments of the nonunion model were matched to the mirror image of the contralateral scaphoid model. The rotation of the distal fragment relative to the proximal fragment was calculated, and reduction of the displaced fragment of the scaphoid nonunion was simulated. Similarly, the estimated bone defect and the appropriate site and direction of the screw insertion were simulated. Full-sized hard models of the bone, including a model with simulated reduction and screw insertion, then were made using stereolithography based on the computer data. In the actual surgery, reduction, bone grafting, and screw insertion were achieved using the hard models as guides. All the patients obtained solid bone fusion and substantial clinical improvement with normalized scapholunate and radiolunate angles after surgery. Three-dimensional computer simulations were found as useful for accurate correction of scaphoid nonunions and proper screw placement, which consequently leads to good clinical results.

Adolescent↗
PubMed1990

The development of computer simulations of the geometries and thermodynamics of biological molecules.

The historical development of computer simulations of molecular geometry and thermodynamics (molecular mechanics, force field method) is outlined. The advantages and disadvantages of techniques such as energy minimization, molecular dynamics and free energy perturbation are discussed. An example is included that shows how energy minimization studies of dopamine D-2 antagonists have been used to develop an understanding of the three-dimensional pharmacophore necessary for this pharmacological activity.

Computer Simulation↗
PubMed1995

A computer simulation program for MR imaging: application to RF and static magnetic field imperfections.

A computer simulation program capable of demonstrating various artifacts, such as image distortion caused by metallic implants in MR imaging, is presented. The structure of the program allows for the implementation of various imaging situations as long as spins only experience weak interaction, i.e., the Bloch equations are obeyed. The raw data are obtained by repeatedly applying the Bloch equations to the magnetization vector of each point of the simulated object, throughout the pulse sequence. With only a limited number of spins in each voxel, the effects of intravoxel dephasing and rephasing require special attention, and algorithms for this have been implemented.

Algorithms↗
PubMed1994

Computer simulation analysis of fracture dislocation of the proximal interphalangeal joint using the finite element method.

Stress is a proximal interphalangeal (PIP) joint model was analyzed by the two-dimensional and three-dimensional finite element methods (FEM) to study the onset mechanisms of the middle phalangeal base fracture. The structural shapes were obtained from sagittally sectioned specimens of the PIP joint for making FEM models. In those models, four different material properties were given corresponding to cortical bone, subchondral bone, cancellous bone and cartilage. Loading conditions were determined by estimating the amount and position of axial pressure added to the middle phalanx. A general finite element program (MARC) was used for computer simulation analysis. The results of the fracture experiments compared with the clinical manifestation of the fractures justify the applicability of the computer simulation models using FEM analysis. The stress distribution changed as the angle of the PIP joint changed. Concentrated stress was found on the volar side of the middle phalangeal base in the hyperextension position, and was found on the dorsal side in the flexion position. In the neutral position, the stress was found on both sides. Axial stress on the middle phalanx causes three different types of fractures (volar, dorsal and both) depending upon the angle of the PIP joint. These results demonstrate that the type of PIP joint fracture dislocation depends on the angle of the joint at the time of injury. The finite element method is one of the most useful methods for analyzing the onset mechanism of fractures.

Aged↗
PubMed2002

Experiences with computer simulation at two large wastewater treatment plants in northern Poland.

Mathematical modelling and computer simulation have became a useful tool in evaluating the operation of wastewater treatment plants (WWTPs) in terms of nutrient removal capability. In this study, steady-state simulation results for two large biological nutrient removal WWTPs are presented. The plants are located in two neighbouring cities Gdansk and Gdynia in northern Poland. Simulations were performed using a pre-compiled model and layouts (MUCT and Johannesburg processes) implemented in the GPS-X simulation package. The monthly average values of conventional parameters, such as COD, Total Suspended Solids, total N, N-NH4+, P-PO4- were used as input data. The measured effluent concentrations of COD, N-NH4+, N-NO3- and P-PO4- as well as reactor MLSS were compared with model predictions. During calibration, performed from the process engineering perspective, default values of only five model parameters were changed. The opportunities for further applications of such models in municipal WWTPs are discussed.

Biodegradation, Environmental↗
PubMed1993

Development of a software package for computer simulations: the use of a sorted event list for reduction of calculation times.

A new program for continuous simulation is described. The program is block oriented, simulating the function of an analogue computer. C structures containing pointers to the calculation of their input functions were used for the individual blocks. The actual calculation order was determined from a sorted event list. After calculation events were inserted at the appropriate place in this list again. This procedure allowed for a variable and independent stepsize for the main blocks and for the introduction of discrete events. With typical applications a speed increase of about 500% was attained.

Algorithms↗
PubMed1994

A computer simulation study of the relation between lipid and probe behaviour in bilayer systems.

Computer simulations are presented of the behaviour of elongated probe molecules anchored to the interface of lipid bilayers above the phase transition of the hydrocarbon chains. The simulations thus mimic the behaviour of the fluorescent probe 1-(4-(trimethylammonio)phenyl)-6-phenyl-1,3,5-hexatriene (TMA-DPH) and Cholestane spin label in lipid systems. In contrast to any experimental technique the simulations follow the behaviour of both the lipid molecules and the probe within the bilayer structure. Thus, the relation between the behaviour of the probe molecules and the order and dynamics of the lipid chains can be studied in detail. We find that the presence of probe molecules, at the low concentrations used experimentally, causes only a marginal perturbation in the intrinsic properties of the lipid chains. The simulations presented support the conventional prescription for describing the orientational behaviour of probe molecules in lipid bilayers in terms of a local effective orienting potential. They indicate, however, that the potential arises from the confinement of the probe molecules between long segments of lipid chains in elongated free-volume cavities within the bilayer structure. In this sense the orienting potential concept needs to be refined in order to take into account the combined effect of the restricted free rattling motions of the probes within the free-volume cavities and the orientations of the cavities themselves relative to the normal to the bilayer plane. The time scale of the motions of the cavities within the bilayer is determined by the rotational motions of long segments of the lipid chains. These observations justify the use of rigid probe molecules such as TMA-DPH and Cholestane spin labels for monitoring the orientational order and dynamics in lipid bilayer systems.

1,2-Dipalmitoylphosphatidylcholine↗
PubMed1992

Synthesis and conformational properties of the lanthionine-bridged opioid peptide [D-AlaL2,AlaL5]enkephalin as determined by NMR and computer simulations.

We report the synthesis and conformational analysis by means of NMR and computer simulations of a novel opioid peptide with the sequence [formula: see text], which we write as [formula: see text], abbreviated [D-AlaL2,L-AlaL5]EA, where AlaL denotes each of the lanthionine amino acid ends linked by a monosulfide bridge and EA indicates enkephalinamide. Data from 2D NMR (HOHAHA and ROESY) provide short-range NOEs that are used as constraints in molecular modeling; measurement of coupling constants shows that chi 1 (D-AlaL2) is predominantly in either the t or g- conformation, and temperature coefficient data suggest the participation of the AlaL5 amide proton in an intramolecular hydrogen bond. The use of NOE and hydrogen-bond constraints in a distance-geometry program yields a large number of initial conformations compatible with the data. Energy minimization of these structures using CHARMM results in three families of backbone ring conformations, labled A1, A2, and B. The torsion chi 1 in D-AlaL2 remains close to trans for all three conformations. Molecular dynamics in vacuo at 300 K show that these three families of conformers interconvert, with concerted shifts in two of the three torsions psi(Phe), phi(AlaL5), and chi(AlaL5). The [D-AlaL2,L-AlaL5]EA is superactive in the guinea pig ileum (GPI) and mouse vas deferens (MVD) in vitro tests and also in the rat hot plate test in vivo. At the same time, this analog with a constrained 13-membered ring shows virtually no selectivity with a ratio IC50 (MVD)/IC50 (GPI) of 0.882.

Amino Acid Sequence↗
PubMed1998

Computer simulation to estimate the effectiveness of carotid endarterectomy.

OBJECTIVES: To investigate the benefit of carotid endarterectomy relative to medical treatment, by comparing the outcome for different groups of patients following transient ischaemic attacks. METHODS: A Markov model was used to describe the survival and quality of life of patients treated for a transient ischaemic attack. The benefit is measured in terms of quality adjusted life months (QALMs). The outcome was estimated using a computer simulation with parameters based on published studies on the probability of events following treatment. The benefit of carotid endarterectomy was explored using a baseline set of parameters and a sensitivity analysis. RESULTS: The baseline scenario of a 65-year-old male patient with the model factors set at an intermediate level showed a benefit for surgery of 3 QALMs compared with medical treatment alone. The sensitivity analysis showed that the most favourable combination of factors had a benefit of 13.4 QALMs and the least favourable a loss of 2 QALMs. Of all 128 factor combinations, 79.9% showed a benefit for surgery, 5.5% showed equal benefit, and 15.6% showed a benefit for medical treatment. CONCLUSIONS: Computer simulations have the potential for deriving estimates of benefit for different patient groups from the results of clinical trials. Combined with reliable information on costs, the technique could also demonstrate variations in cost-effectiveness for these groups. For patients following a transient ischaemic attack, the results from this simulation and limited cost information suggest that carotid endarterectomy is unlikely to be a cost-effective intervention in the UK for many patient groups despite a reduction in the risk of stroke.

Aged↗
PubMed2006

Estimating resting motor thresholds in transcranial magnetic stimulation research and practice: a computer simulation evaluation of best methods.

OBJECTIVES: Resting motor threshold is the basic unit of dosing in transcranial magnetic stimulation (TMS) research and practice. There is little consensus on how best to estimate resting motor threshold with TMS, and only a few tools and resources are readily available to TMS researchers. The current study investigates the accuracy and efficiency of 5 different approaches to motor threshold assessment for TMS research and practice applications. METHODS: Computer simulation models are used to test the efficiency and accuracy of 5 different adaptive parameter estimation by sequential testing (PEST) procedures. For each approach, data are presented with respect to the mean number of TMS trials necessary to reach the motor threshold estimate as well as the mean accuracy of the estimates. RESULTS: A simple nonparametric PEST procedure appears to provide the most accurate motor threshold estimates, but takes slightly longer (on average, 3.48 trials) to complete than a popular parametric alternative (maximum likelihood PEST). Recommendations are made for the best starting values for each of the approaches to maximize both efficiency and accuracy. CONCLUSIONS: In light of the computer simulation data provided in this article, the authors review and suggest which techniques might best fit different TMS research and clinical situations. Lastly, a free user-friendly software package is described and made available on the world wide web that allows users to run all of the motor threshold estimation procedures discussed in this article for clinical and research applications.

Computer Simulation↗
PubMed1989

Positron emission tomographic measurement of blood-to-brain and blood-to-tumour transport of 82Rb. I: Error analysis and computer simulations.

Unidirectional blood-to-brain and blood-to-tumour transport rate constants (K1) for 82Rb (half-life 76 s) and plasma water volume per unit mass of brain/tumour tissue (Vp) can be estimated in vivo using dynamic positron emission tomography (PET). The accuracy of these estimates depends upon the accuracy of PET measurements of regional brain/tumour radioactivity and scintillation well detector measurements of whole-blood radioactivity, which, in turn, depend upon the time course of arterial blood radioactivity. A two-compartmental model has been employed to derive estimates for K1, k2 (efflux rate constant) and Vp from 82Rb/PET data. Errors in these parameter estimates have been studied (1) qualitatively using sensitivity function analysis and (2) quantitatively using computer simulations. The effect of adding a third irreversible compartment and its unidirectional rate constant, k3, has also been investigated. The advantages and disadvantages of bolus injection vs continuous infusion protocols are discussed. Precision in estimated parameters from actual patient data is compared to that obtained from computer simulations in part II of this paper.

Blood↗
PubMed2002

Computational simulations of stress shielding and bone resorption around existing and computer-designed orthopaedic screws.

Failure of an orthopaedic fixation due to stress shielding and consequent screw loosening is a major concern among surgeons: the loosened screws could not only interfere with the healing process but also endanger adjacent anatomical structures. In this study, the effect of the screw's engineering design (dimensions, profile shape and material properties) on the load sharing with adjacent bone and consequent bone resorption was tested, using a set of two-dimensional computational (finite element) models. An algorithm simulating local bone adaptation to strain energy density (SED) mechanical stimuli was developed and used to evaluate the biomechanical performances of different commercial screws. Two new designs, a 'graded-stiffness' composite screw, with a reduced-stiffness titanium core and outer polymeric threads, and an active-compression hollow screw that generates compressive stresses on the surrounding bone, were also evaluated. A dimensionless set of stress transfer parameters (STPs) were utilised for ranking the performances of the different screws according to the expected screw-bone load sharing and its evolution with adaptation of the surrounding tissue. The results indicated that commercial wide (6 mm thread diameter) trapezoidal and rectangular screw profiles have superior biomechanical compatibility with bone (i.e. predicted to be stable after 2 years). The graded-stiffness and active-compression screws provided the best biomechanical performances: bone loading around them was predicted to decrease by no more than 15% after 3 years, compared with a decrease of 55-70% in bone loading around commercially available screws. Computer simulations of bone adaptation around orthopaedic screws are demonstrated to be effective means for objective and quantitative evaluation of the biomechanical aspects of implant-tissue compatibility.

Bone Resorption↗
PubMed1975

Analysis of expert diagnosis of a computer simulation of congenital heart disease.

Analysis of data from five expert cardiologists indicates substantial agreement on the first step to be taken in response to an emergency case of computer-simulated congenital heart disease. There was little or no agreement among these same subjects on the specific steps undertaken following their initial response. The problem was solved in 11, 10, 8, and 6 steps by four of the cardiologists. The problem-solving sequence employed by one expert resulted in the patient's death. It is concluded that while the behavior of experts in the hospital and clinic is the primary means of evaluating successful student performance, computer simulations of patient cases offer the opportunity to use expert data in the calibration of student error.

Computers↗