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PubMedDate not supplied

Computational simulation of platelet deposition and activation: II. Results for Poiseuille flow over collagen.

We have previously described the development of a two-dimensional computational model of platelet deposition onto biomaterials from flowing blood (Sorensen et al., Ann. Biomed. Eng. 27:436-448, 1999). The model requires estimation of four parameters to fit it to experimental data: shear-dependent platelet diffusivity and three platelet-deposition-related reaction rate constants. These parameters are estimated for platelet deposition onto a collagen substrate for simple parallel-plate flow of whole blood in both the presence and absence of thrombin. One set of experimental results is used as a benchmark for model-fitting purposes. The "trained" model is then validated by applying it to additional test cases from the literature for parallel-plate Poiseuille flow over collagen at both higher and lower wall shear rates, and in the presence of various anticoagulants. The predicted values agree very well with the experimental results for the training cases, and good reproduction of deposition trends and magnitudes is obtained for the heparin, but not the citrate, validation cases. The model is formulated to be easily extended to synthetic biomaterials, as well as to more complex flows.

Adenosine Diphosphate↗
PubMed1989

Computer simulation of arcuate and radial incisions involving the corneoscleral limbus.

We have created a computer model of the eye that improves upon previous models with two assumptions: (1) the cornea is considered anisotropic, and (2) the strain tensor is non-linear for large displacements. Values used include those for Young's modulus, Poisson's ratio, and three coefficients of anisotropia. A finite element computer program was used to stimulate the behaviour of the eye. Four simulations were done: (1) a full thickness arcuate limbal cataract incision, (2) a partial thickness arcuate corneal relaxing incision, (3) a partial thickness radial incision extending across the limbus, (4) a partial thickness radial incision confined to the cornea. A full thickness corneal arcuate incision for cataract induced more change in corneal shape than a limbal incision. However, the gaping is more important in the limbal incision. Partial thickness arcuate corneal relaxing incisions were found to be more effective with a clear zone 3-5 mm in diameter. Radial incision simulation demonstrated little enhancement of the effect of the incisions when across the limbus.

Astigmatism↗
PubMed2006

[Computer simulation by passenger wound analysis of vehicle collision].

OBJECTIVE: To reconstruct the course of vehicle collision, so that to provide the reference for forensic identification and disposal of traffic accidents. METHODS: Through analyzing evidences left both on passengers and vehicles, technique of momentum impulse combined with multi-dynamics was applied to simulate the motion and injury of passengers as well as the track of vehicles. RESULTS: Model of computer stimulation perfectly reconstructed phases of the traffic collision, which coincide with details found by forensic investigation. CONCLUSION: Computer stimulation is helpful and feasible for forensic identification in traffic accidents.

Accidents, Traffic↗
PubMed1975

Analysis of motor conduction velocity in the human median nerve by computer simulation of compound muscle action potentials.

A digital computer was used to reconstruct compound muscle action potentials recorded from the human thenar eminence after stimulation of the median nerve. The programme allowed the following parameters to be varied: (1) the dimensions of a representative single motor unit potential; (2) the number of motor units in the muscle and the range and distribution of conduction velocities in their nerve fibres; and (3) the distance along the nerve from the point of stimulation to the muscle. The reconstructed compound muscle action potentials were similar to real compound potentials recorded from normal subjects. The number of single motor units and the range of conduction velocities required for the reconstruction correlated with quantitative histologic studies of the recurrent branch of the median nerve to the thenar muscles. By altering the distribution of conduction velocities it was possible to study the effect of abnormal patterns of nerve conduction on the configuration of the simulated compound muscle action potentials. It was found that abnormally slow conduction caused an increased discrepancy between the main parameters of compound potentials corresponding to stimulation of the nerve at proximal and distal sites. These observations suggest that a careful analysis of the differences between pairs of compound muscle action potentials may provide a method for more detailed assessment of conduction velocity in clinical studies of peripheral nerve disorders.

Action Potentials↗
PubMed1995

Computational simulation of blood flow in human systemic circulation incorporating an external force field.

A quasi-one-dimensional non-linear mathematical model for the computation of the blood flow in the human systemic circulation is constructed. The morphology and physical modelling of the whole system (arteries, capillaries and veins) are completed by different methods for the different vessel generations. A hybrid method is used to solve the problem numerically, based on the governing equation (continuity, momentum and state equations), the input boundary conditions and the predetermined initial conditions. The two-step Lax-Wendroff finite-difference method is used to compute variables for each individual vessel, and the characteristic method is employed for the computation of internal boundary conditions of the vessel connection and the input and output system boundary conditions. Using this approach, blood flow, transmural pressure and blood velocity are computed at all vessel sites and for each time step. The pressure and flow waveforms obtained show reasonable agreement with clinical data and results reported in the literature. When an external conservative force field is applied to the system, the results computed from the model are intuitively correct. The term representing the external pressure added to the system by the muscle, which represents active control on the cardiovascular system, is also embodied in this model.

Algorithms↗
PubMed2003

Computer simulation system for orthognathic surgery.

OBJECTIVE: The system aimed to make a simulation model of an orthognathic patient without using his/her computed tomography data. DESIGN: The morphological data of the teeth and face were obtained by laser scanner. All the data were integrated in the reference coordinate system of frontal and lateral cephalograms using projection matching technique. SETTING: A case of mandibular prognathism was analyzed and presented. EXPERIMENTAL VARIABLE: About 7 mm (left side) to 6 mm (right side) of mandibular setback with a small rotation was performed on this case. RESULTS: Simulated osteotomies and bone movements help us to analyze the movement of bone and soft tissue. Collisions and gaps generated between bone segments and facial changes are shown. CONCLUSION: This simulation system will be particularly useful for the selection of an optimal operative method in cases in which the change in facial soft tissue shape should be carefully deliberated.

Cephalometry↗
PubMed1995

Computer simulation of antisense DNA containing enantio-deoxynucleotides in the double helix.

Computer modeling of DNA double helices containing L-oligodeoxynucleotides and their complementary D-beta-strands in different orientations and conformations was performed using empirical force-field and semiempirical methods. In particular, the parallel and antiparallel orientations of L-alpha and L-beta-configured strands have been extensively simulated. The parallel oriented double helix with L-alpha-2'-deoxynucleotides has been found to be the enantio-deoxynucleotides. The energy difference between this enantio-DNA and native DNA is approximately 6kcal/mol per base pair, favoring the latter. The theoretical results compared well with preliminary experimental data on the hybridization of recently synthesized 11-mer L-oligodeoxynucleotides, L-d-5' (TpCpGpCpTpGpCpTpTpCpT)3' and L-d-5' (TpCpTpTpCpGpTpCpGpCpT)3' containing the complementary D-beta-oligodeoxynucleotides. As predicted by the calculations, experimental results can be interpreted by assuming that hybridization occurs only in the parallel L-alpha-2'-oligodeoxynucleotides.

Base Sequence↗
PubMed2001

Dynamics of internal water in fatty acid binding protein: computer simulations and comparison with experiments.

Multiple molecular dynamics (MD) simulations of fully solvated rat intestinal fatty acid binding protein (I-FABP) were conducted to investigate the dynamics of internal water molecules. Although the long time average of the number of internal water molecules in I-FABP is 22 as shown by the X-ray crystal structure, MD simulations predict large variations in the instantaneous number of internal water molecules on the nanosecond time scale. The computational model employed predicts that w135 (internal) and w217 (located on the protein surface) may be the water molecules with long residence times observed in previously reported magnetic relaxation dispersion studies. The average residence time of approximately 20 internal water molecules occupying the fatty acid binding cavity is estimated to be between 0.6 and 2.0 nanoseconds. Exchange of internal water in I-FABP appears to occur almost exclusively through the interface of beta-strands EF with the rest of the protein, which has significant implications for the pathways of the fatty acid entry and exit from the binding cavity. Proteins 2001;43:65-72.

Animals↗
PubMed1993

An approximate but efficient method to calculate free energy trends by computer simulation: application to dihydrofolate reductase-inhibitor complexes.

Derivatives of free energy differences have been calculated by molecular dynamics techniques. The systems under study were ternary complexes of Trimethoprim (TMP) with dihydrofolate reductases of E. coli and chicken liver, containing the cofactor NADPH. Derivatives are taken with respect to modification of TMP, with emphasis on altering the 3-, 4- and 5-substituents of the phenyl ring. A linear approximation allows the encompassing of a whole set of modifications in a single simulation, as opposed to a full perturbation calculation, which requires a separate simulation for each modification. In the case considered here, the proposed technique requires a factor of 1000 less computing effort than a full free energy perturbation calculation. For the linear approximation to yield a significant result, one has to find ways of choosing the perturbation evolution, such that the initial trend mirrors the full calculation. The generation of new atoms requires a careful treatment of the singular terms in the non-bonded interaction. The result can be represented by maps of the changed molecule, which indicate whether complex formation is favoured under movement of partial charges and change in atom polarizabilities. Comparison with experimental measurements of inhibition constants reveals fair agreement in the range of values covered. However, detailed comparison fails to show a significant correlation. Possible reasons for the most pronounced deviations are given.

Animals↗