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PubMed2006

Computer simulation of native epidermal enzyme structures in the presence and absence of hydrogen peroxide (H2O2): potential and pitfalls.

The human epidermis is especially vulnerable to oxidative stress, which in turn leads to oxidation of important antioxidant enzymes, other proteins, and peptides. Molecular dynamic computer modelling is a new powerful tool to predict or confirm oxidative stress-mediated structural changes consequently altering the function of enzymes/proteins/peptides. Here we used examples of important epidermal antioxidant enzymes before and after hydrogen peroxide (H(2)O(2))-mediated oxidation of susceptible amino-acid residues (i.e. tryptophan, methionine, cysteine, and selenocysteine), which can affect enzyme active sites, cofactor binding, or dimerization/tetramerization domains. Computer modelling predicts that enzyme active sites are altered by H(2)O(2)-mediated oxidation in thioredoxin reductase (TR) and acetylcholinesterase (AchE), whereas cofactor nicotinamide adenine dinucleotide phosphate (reduced form) binding is affected in both catalase and TR but not in glutathione peroxidase. Dimerization is prevented in catalase. These structural changes lead to impaired functionality. Fourier transform-Raman- and Fluorescence spectroscopy together with enzyme kinetics support the results. There are limitations of modelling as demonstrated on the AchE substrate-binding domain, where the computer predicted deactivation, which could not be confirmed by enzyme kinetics. Computer modelling coupled with classical biochemical techniques offers a new powerful tool in cutaneous biology to explore oxidative stress-mediated metabolic changes in the skin.

Computer Simulation↗
PubMed2003

Computer simulation of prostate cryoablation--fast and accurate approximation of the exact solution.

OBJECTIVE: Cryosurgery is a minimally invasive cancer treatment that uses liquid nitrogen or supercooled argon to freeze and destroy tumors. To achieve complete ablation of the prostate, we have developed a computer program that can determine treatment effects by calculating iceball formation. This is based on a three-dimensional (3D) model of the patient's prostate constructed from ultrasound images. The program predicts the best set of cryoablation parameters and cryoprobe spatial positions, then displays these parameters in graphical or numerical form. The objective of this work was to improve our prostate cryoablation modeling software by making its partial differential equation (PDE) solver more accurate and faster. MATERIALS AND METHODS: CryoSim, our software package, accepts a set of acquired and processed 3D ultrasound images of the prostate, then models heat diffusion using numerical approximations of the heat equation. RESULTS: We describe the latest version of the CryoSim software, which models cryoablation therapy. Solving the problems of low spatial resolution (now down to a fraction of a millimeter, as compared to 5 mm in the old version) and modeling cryosurgery in a short time (down to few minutes versus hours) provides a platform for proper planning of cryosurgery and a tool for the training of surgeons. CONCLUSION: Changes in the PDE solver algorithm produce more accurate results, leading to an improved visualization of the iceball, with a precision of a few mm and a significant decrease in computation time.

Algorithms↗
PubMed2000

MR phase imaging to quantify bone volume fraction: computer simulations and in vivo measurements.

Magnetic resonance phase images can be used to assess trabecular bone by measuring the standard deviation of the phases in a region of interest. The standard deviation of regional phase measurements reflects the degree of magnetic field inhomogeneity caused by susceptibility differences between bone and marrow. A 3D computer model of trabecular bone was developed and then used to explore the influence of bone volume fraction and imaging parameters such as pixel size and slice width on the standard deviation of regional phase measurements. The results from these tests show that with appropriate selection of these parameters, phase spread strongly reflects variations in trabecular bone density (a correlation of R(2) = 0.98 with bone volume fraction between 0 and 10%). The technique was then applied in vivo on the radius of 25 patients who already had a bone density scan with peripheral quantitative tomography and a correlation between phase standard deviation and trabecular bone density was found (R(2) = 0.46).

Bone Density↗
PubMed2004

The addition of computer simulated noise to investigate radiation dose and image quality in images with spatial correlation of statistical noise: an example application to X-ray CT of the brain.

This study validates a method to add spatially correlated statistical noise to an image, applied to transaxial X-ray CT images of the head to simulate exposure reduction by up to 50%. 23 patients undergoing routine head CT had three additional slices acquired for validation purposes, two at the same clinical 420 mAs exposure and one at 300 mAs. Images at the level of the cerebrospinal fluid filled ventricles gave readings of noise from a single image, with subtraction of image pairs to obtain noise readings from non-uniform tissue regions. The spatial correlation of the noise was determined and added to the acquired 420 mAs image to simulate images at 340 mAs, 300 mAs, 260 mAs and 210 mAs. Two radiologists assessed the images, finding little difference between the 300 mAs simulated and acquired images. The presence of periventricular low density lesions (PVLD) was used as an example of the effect of simulated dose reduction on diagnostic accuracy, and visualization of the internal capsule was used as a measure of image quality. Diagnostic accuracy for the diagnosis of PVLD did not fall significantly even down to 210 mAs, though visualization of the internal capsule was poorer at lower exposure. Further work is needed to investigate means of measuring statistical noise without the need for uniform tissue areas, or image pairs. This technique has been shown to allow sufficiently accurate simulation of dose reduction and image quality degradation, even when the statistical noise is spatially correlated.

Aged↗
PubMed2002

Computer simulation of the inverse problem of electrocardiography: use of properties of harmonic functions.

The problem of reconstructing the pattern of heart excitation from body surface potentials is simulated. The problem is well known as the inverse problem of electrocardiography and in a general case this problem has a non-unique solution. The relationship of the problem with the inverse problem of potential theory is shown. From this relationship a new excitation propagation model for the heart ventricles is developed. The model is based on a classical multidipole cardiogenerator, but is stable, flexible, and provides a unique solution for the inverse problem of electrocardiography.

Body Surface Potential Mapping↗
PubMed1996

Computer simulation of human blood flow and vascular resistance.

Organ blood flows and associated vascular resistances have been investigated through the use of a Microsoft Windows-compatible computer program which employs Monte Carlo simulations based on the system's principal components. This approach replicates the system's behavior by maintaining proper correlations between all variables in the system as well as allowing for modulation of the system by its inherent uncertainties. By applying various external constraints, such as a specific age, weight, height and/or blood pressure, the simulations allow for insights to be obtained about the behavior of individual patients. In particular, patient specific organ blood flows and associated vascular resistances can be determined as a function of a patient's age, weight, height and blood pressure.

Adult↗
PubMed1993

Computer simulation of neutrophil transit through the pulmonary capillary bed.

One-half of the neutrophils that enter the pulmonary circulation become temporarily trapped in capillaries. The neutrophils that are impeded make complete stops between free-flowing movements. These observations, based on in vivo microscopy, suggest that pulmonary margination is caused by neutrophils being impeded at focal sites in the capillary bed. To investigate the frequency with which impeding sites had to occur in the pulmonary capillaries to trap one-half of the circulating neutrophils, we developed a computer model to simulate neutrophils encountering discrete obstructions in a capillary-like network. Surprisingly, if only 1% of the capillaries in the network acted as traps, one-half of the neutrophils stopped at least once. The trapping ability of a given percentage of obstructions was independent both of the geometry of the network was whether the obstructions occurred in the segments or junctions. To simulate neutrophil transit more realistically, both neutrophil and capillary diameters were randomly selected from published diameter distributions. Every neutrophil was trapped multiple times by this model, suggesting that cell deformation contributes importantly to neutrophil passage through the pulmonary capillary bed.

Animals↗
PubMed2004

Clinical evaluation of a computer simulated prediction model of contrast enhancement of the liver in spiral CT.

OBJECTIVE: A software program was developed simulating a compartmental model of blood circulation based on differential equations. The aim of this study was to compare software-simulated levels of hepatic enhancement with the true values in patients and to test how many patients reach the simulated hepatic enhancement level. METHODS: As software program the CT application software carebolus 2 (Siemens, Forchheim, Germany) was used. Hepatic contrast-enhancement curves were simulated prior to CT examinations to evaluate a patient specific time delay after contrast application. At the time delay, when the simulation curve showed an enhancement threshold of 40 Hounsfield Units (HU), the CT spiral scan was started applying 120 ml contrast media with 2 ml/s. The simulated curves were compared with the empiric curves of each patient. RESULTS: 25 of 28 patients (89%) achieved 40 HU. The mean enhancement of empiric patients curves was 46.32 +/- 11.9 HU, the mean simulated enhancement was 46.62 +/- 4.3 HU S.D. (P= 0.48). 4.4 values per patient liver could be compared with the simulation curve (122 points for 28 patients): 50% of the patient curves were within a range of 5 HU compared with the simulation curve. CONCLUSION: Software simulation of contrast enhancement curves of the liver is a feasible and valuable method to predict individual liver enhancement curves. Improvements concerning the integration of cardiovascular parameters and preexisting liver parenchymal diseases into the simulation software have to be arranged.

Adult↗
PubMed1980

Computer-simulated laboratory experiments in food science. I. The model.

A computer model and instructional material provide the student with the opportunity to learn basic information and gain expertise in solving problems which occur in foods. The model covers twenty-five simulations over a range of food types, permitting a variety of experiments of differing complexity. The student is assigned a problem or activity which may be partially or completely answered by using one of the simulations. The simulations give answers to a series of treatments and tests, properties, recipes, characteristics, and/or sensory parameters being investigated.

Computer-Assisted Instruction↗
PubMed1991

The computer simulation of RNA folding involving pseudoknot formation.

The algorithm and the program for the prediction of RNA secondary structure with pseudoknot formation have been proposed. The algorithm simulates stepwise folding by generating random structures using Monte Carlo method, followed by the selection of helices to final structure on the basis of both their probabilities of occurrence in a random structure and free energy parameters. The program versions have been tested on ribosomal RNA structures and on RNAs with pseudoknots evidenced by experimental data. It is shown that the simulation of folding during RNA synthesis improves the results. The introduction of pseudoknot formation permits to predict the pseudoknotted structures and to improve the prediction of long-range interactions. The computer program is rather fast and allows to predict the structures for long RNAs without using large memory volumes in usual personal computer.

Algorithms↗
PubMed1991

A didactic computer simulation of the environmental impact of a pollution discharge.

Algorithms for simulating the response of a benthic animal community and several abiotic environmental variables to organic pollution are described. An IBM PC compatible computer program incorporating these methods has been written. The program simulates the abundance response of 23 species, the redox potential depth profile and several other sediment variables at any distance from a point source of pollution. The program has been designed as a teaching tool and examples of its use to study pollution biology and biometrics are given.

Algorithms↗
PubMed2001

Visualization of computer simulated heart temperature during topical cooling.

A local hypothermia is often used during cardiac operations to slow down the tissue metabolism. The heart is cooled down with cold cardioplegic solution. Sometimes even the topical cooling with or without ice slush is used. Different heart models have been used earlier to simulate heart temperature distribution, but the resolution of the model has always been limited by the speed of the computer. We used the computer heart model derived from Visible Human Dataset with the spatial resolution of 1 mm. In this article, the step-by-step generation of 3D computer heart model is described. The heat transfer was modeled by a diffusion equation that was discretised in space and time and solved by a parallel algorithm. Finally, the cooling of heart during an operation, with and without topical ice slush, was simulated on a cluster of 9 PC-based computers, which assured sufficient computing power. The simulated results are presented as images of cross sections in different planes with temperatures shown by different colors.

Body Temperature↗
PubMed1988

Computer simulations in zeolite chemistry.

Recent developments in molecular modelling techniques have provided us with a new and powerful tool for the simulation and better understanding of the complex chemistry of zeolites. The range of applications include cation distributions, acid strengths of catalytic sites, intergrowth phenomena, derivation of new structures, molecular adsorption and selective diffusion of organic molecules through zeolite frameworks. A perspective summary of a number of simulation methods and their specific areas of applicability is given in this article.

Aluminum Silicates↗
PubMed1992

Transcription regulation by steroid hormones: a computer simulation study.

Three-dimensional structures of complexes of 66 amino acid-DNA binding domains of human progesterone (hPR), estrogen (hER) and glucocorticoid (hGR) receptors (proteins), with ten base pair DNA duplexes: d(AGGTCATGCT).d(AGCATGACCT) and d(AGAACATGCT).d(AGCATGTTCT) were obtained using computer modeling and molecular mechanics techniques. Cartesian coordinates for the proteins were obtained from: 1) structural data of hER and hGR by NMR spectroscopy; 2) steric constraints imposed by tetrahedral coordination of the zinc ion to Cys residues, and 3) energy minimization in torsional and cartesian space. The proteins were made to interact with DNA (in B-form) in major groove through alpha-helical linker between the two zinc fingers. The geometry of the complexes was obtained by allowing them to slide, glide, penetrate in to and out of the groove, and to rotate about the helical axis. The complexes were energy minimized. Also maximized was the number of H-bonds between proteins and DNA. The complex structures were refined by molecular mechanics using AMBER 3.0. Structural parameters of DNA were analyzed in each complex and compared with those of native DNA optimized separately. The stereochemical differences of the complexes are discussed.

Amino Acid Sequence↗
PubMed1991

Computer simulation model of swine production systems: I. Modeling the growth of young pigs.

Theoretical concepts and relationships were used to develop a deterministic pig growth model. The model predicts, in a continuous form, growth and body composition of boars, barrows, and gilts according to genotype, diet, and management conditions. The model is aggregated at the whole-animal level with three main elements of body composition; total body DNA, total body protein mass (PT), and total body mass of lipids, with PT determining the secondary elements of ash and moisture. The primary factors regulating growth were associated with cellular hyperplasia and hypertrophy in agreement with the basic concepts described by Baldwin and Black (1979). Differential equations representing DNA accretion and protein synthesis and degradation were adapted from Oltjen et al. (1985). Normal pig protein growth was characterized from published data. Body PT was used to reflect several metabolic activities related to animal size and age, as in some prior models. Dietary energy and protein were used in sequence until requirements are satisfied, first for maintenance, then for protein growth, and finally for fat deposition. A comparison between experimental and simulated results illustrates that the model may simulate growth and body composition of young pigs adequately.

Animals↗