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PubMed2005

Computer simulation of polypeptide translocation through a nanopore.

A simplified model of polypeptide chains was designed and studied by means of computer simulations. Chains were represented by a sequence of united atoms located at the positions of the alpha-carbons. A further assumption was the lattice approximation for the chains. We used a (310) lattice, which was found useful for studying properties of proteins. The force field used consisted of a long-range contact potential between amino-acid residues and a local preference for forming alpha-helical states. The chain consisted of two kinds of residues: hydrophilic (P) and hydrophobic (H) ones forming model helical septets--HHPPHPP--in a sequence. The chains were placed near an impenetrable surface with a square hole in it. The size of the hole was comparable or smaller than the size of a chain. The properties of these model chains were determined using the Monte-Carlo simulation method. During the simulations, translocation of the chain through the hole in the wall was observed. The influence of the chain length, the temperature differences on both sides of the wall and the force field on the chain properties were investigated. It was shown that the translocation time scales as N(2.2) and it was found that the presence of the local helical potential significantly slows down the process of translocation. [Figure: see text]. The snapshots of typical chain's conformation obtained during the simulation for chain consisted of N = 60. The values of the local potential epsilon(loc) = -8.

Computer Simulation↗
PubMedDate not supplied

A computer simulation for the entry-level RN: enhancing clinical decision making.

Staff development educators struggle to prepare today's entry-level RN for effective decision making in a new healthcare climate that demands both skill and expertise with patients with high acuity levels. The clinical decision making simulator is an innovative approach to teaching and learning decision-making skills. The authors discuss the development and use of a computer simulation that provides repeated opportunities for clinical decision making for the newly licensed nurse without jeopardizing patient safety.

Clinical Competence↗
PubMed1984

Formation of specific amino acid sequences during carbodiimide-mediated condensation of amino acids in aqueous solution, and computer-simulated sequence generation.

Carbodiimide-mediated peptide synthesis in aqueous solution has been studied with respect to self-ordering of amino acids. The copolymerisation of amino acids in the presence of glutamic acid or pyroglutamic acid leads to short pyroglutamyl peptides. Without pyroglutamic acid the formation of higher polymers is favoured. The interactions of the amino acids and the peptides, however, are very complex. Therefore, the experimental results are rather difficult to explain. Some of the experimental results, however, can be explained with the aid of computer simulation programs. Regarding only the tripeptide fraction the copolymerisation of pyroGlu, Ala and Leu, as well as the simulated copolymerisation lead to pyroGlu-Ala-Leu as the main reaction product. The amino acid composition of the insoluble peptides formed during the copolymerisation of Ser, Gly, Ala, Val, Phe, Leu and Ile corresponds in part to the computer-simulated copolymerisation data.

Amino Acid Sequence↗
PubMed1991

Clinical decision making of critical care nurses managing computer-simulated tachydysrhythmias.

The purposes of this study were to describe the clinical decision making of critical care nurses managing computer-simulated tachydysrhythmias and to assess the major sources of error related to the management of two tachydysrhythmias: atrial flutter and ventricular tachycardia. In this descriptive study, 142 critical care nurses each completed four computerized clinical simulations (two atrial flutter and two ventricular tachycardia). Simulation performance was measured by proficiency score (comparison with expert performance), patient outcome (cure or die), and amount of data collected before the first intervention. Mean proficiency scores were 51% for atrial flutter and 35% for ventricular tachycardia. Thirteen percent of the atrial flutter and 35% of the ventricular tachycardia simulations ended in patient death. Failure to recognize ventricular tachycardia and unfamiliarity with second- and third-line treatments were major sources of error. Medication errors were the cause of death in 87% of the simulations ending in patient death. These results document the need for emphasis on dysrhythmia management in the critical care curriculum.

Arrhythmias, Cardiac↗
PubMed1996

Influence of boundary effects on minimum spanning tree features. A computer simulation.

OBJECTIVE: To assess the influence of boundary effects on quantitative data derived from the minimum spanning tree (MST). STUDY DESIGN: In a computer simulation, 10 patterns of points (resembling populations of nuclei in tumor tissue) were generated, ranging from completely regular to very irregular. This allowed for assessing the influence of boundary effects in populations with different degrees of disorder. A stepwise reduction of the size of the sampling window enabled the analysis of the influence of boundary effects at different sample sizes (from 1,024 down to 9 points). RESULTS: Both the mean and coefficient of variation of all features remained rather constant with decreasing sample size down to a sample size of 64 points per MST. CONCLUSION: Based on this model, it is concluded that boundary effects have only a minor influence on the outcome of MST features when the sample size is larger than 64 points.

Computer Simulation↗
PubMed2006

Self-assembly of peptide scaffolds in biosilica formation: computer simulations of a coarse-grained model.

The self-assembly of model peptides is studied using Brownian dynamics computer simulations. A coarse-grained, bead-spring model is designed to mimic silaffins, small peptides implicated in the biomineralization of certain silica diatom skeletons and observed to promote the formation of amorphous silica nanospheres in vitro. The primary characteristics of the silaffin are a 15 amino acid hydrophilic backbone and two modified lysine residues near the ends of the backbone carrying long polyamine chains. In the simulations, the model peptides self-assemble to form spherical clusters, networks of strands, or bicontinuous structures, depending on the peptide concentration and effective temperature. The results indicate that over a broad range of volume fractions (0.05-25%) the characteristic structural lengthscales fall in the range 12-45 nm. On this basis, we suggest that self-assembled structures act as either nucleation points or scaffolds for the deposition of 10-100 nm silica-peptide building blocks from which diatom skeletons and synthetic nanospheres are constructed.

Computer Simulation↗
PubMed1995

Investigation of protein unfolding and stability by computer simulation.

Structural, dynamic and energetic properties of proteins in solution can be studied in atomic detail by molecular dynamics computer simulation. Protein unfolding can be caused by a variety of driving forces induced in different ways: increased temperature or pressure, change of solvent composition, or protein amino acid mutation. The stability and unfolding of four different proteins (bovine pancreatic trypsin inhibitor, hen egg white lysozyme, the surfactant protein C and the DNA-binding domain of the 434 repressor) have been studied by applying the afore-mentioned driving forces and also to some artificial forces. The results give a picture of protein (in)stability and possible unfolding pathways, and are compared to experimental data where possible.

Amino Acid Sequence↗
PubMed2006

Dioxygen affinity in heme proteins investigated by computer simulation.

We present an investigation of the molecular basis of the modulation of oxygen affinity in heme proteins using computer simulation. QM-MM calculations are applied to explore distal and proximal effects on O(2) binding to the heme, while classical molecular dynamics simulations are employed to investigate ligand migration across the polypeptide to the active site. Trends in binding energies and in the kinetic constants are illustrated through a number of selected examples highlighting the virtues and the limitations of the applied methodologies. These examples cover a wide range of O(2)-affinities, and include: the truncated-N and truncated-O hemoglobins from Mycobacterium tuberculosis, the mammalian muscular O(2) storage protein: myoglobin, the hemoglobin from the parasitic nematode Ascaris lumbricoides, the oxygen transporter in the root of leguminous plants: leghemoglobin, the Cerebratulus lacteus nerve tissue hemoglobin, and the Alcaligenes xyloxidans cytochrome c'.

Animals↗
PubMed1997

[First comparisons with laser vibrometry measurements and computer simulation of ear ossicle movements].

The dynamic behavior of the ossicular chain is very complex and is frequency-dependent. To date, this has still not been fully investigated or understood. There remains a lack of measurement procedures to pick up the motion of the ossicles and ear drum simultaneously with sufficient resolution. The presented paper reports simultaneous measurements with laser-Doppler vibrometry at two points of the ossicular chain of cadaver specimens. Motions not observed were derived using mechanical simulation models on a computer and then evaluating appropriate mathematical equations. Using a sound stimulus, the displacement velocities of the umbo and stapes footplate were measured, and the corresponding transfer functions were derived by Fourier transform. Results were used for verification of the computer models. In the current investigations these models were refined and allow for the detailed investigation of the dynamic behavior of the ossicular chain, facilitating the optimal design of passive and active middle-ear implants.

Computer Simulation↗
PubMed1995

Impact of electroosmosis on isotachophoresis in open-tubular fused-silica capillaries: analysis of the evolution of a stationary steady-state zone structure by computer simulation and experimental validation.

A dynamic computer model for simulation of open-tubular capillary electrophoresis that includes in situ calculation of electroosmosis along the fused-silica capillary column has been applied to the characterization of an anionic isotachophoretic system in presence of a cathodic electroosmotic flow. For each column segment, electroosmosis is calculated with the use of a wall mobility, the voltage gradient and the degree of dissociation of the silanol surface groups of the capillary wall. Then, the bulk capillary flow is taken to be the average of all of the segment flows and considered to represent a plug flow. This simple approach enables the combined simulation of the temporal behavior of an isotachophoretic zone structure in presence of electroosmosis. For a model anionic isotachophoretic configuration at pH 6, simulation data reveal the asymptotic formation of a stationary steady-state zone configuration in which electrophoretic and electroosmotic zone displacements are opposite and of equal magnitude. The position of the stationary boundaries are predicted to be dependent on the selected wall pK and mobility values. For two different instruments, qualitative agreement between experimental data and simulation results obtained with a wall pK between 5 and 6 is demonstrated. However, for the two experimental setups, significant differences in electroosmotic pumping (i.e. wall mobility values) are noted.

Anions↗
PubMed1980

Disordered inhibition in internuclear ophthalmoplegia: analysis of eye movement recordings with computer simulations.

High resolution infra-red oculographic recordings were obtained in 19 patients with clinically evident internuclear ophthalmoplegia. The major findings were attenuated phasic and tonic components of adducting saccades, fractionated phasic components of abducting saccades, equally long durations for phasic components of adducting and abducting saccades with refixation, and nasal drift of the abducting eye which initiated abducting nystagmus. Ipsilateral gaze paresis and abduction lag were occasionally associated with primarily unilateral cases of internuclear ophthalmoplegia. These findings were interpreted using available anatomical, electromyographic and oculographic data as well as computer simulations of internuclear ophthalmoplegia. We concluded that deficient excitation of the ipsilateral medial rectus was due to interruption of burst-tonic neurons within the medial longitudinal fasciculus which mediate horizontal eye movements. This resulted in a decreased pulse height and step of the agonist neural controller signal. We were also able to determine that variably slowed fractionated abducting saccades were caused by deficient intrasaccadic inhibition of the antagonist medial rectus. When medial rectus excitation was more deficient than medial rectus inhibition of the opposite eye, then a typical internuclear ophthalmoplegia resulted; when the amount of medial rectus excitation was equal to the amount of medial rectus inhibition of the opposite eye, then a gaze paresis occurred; and when medial rectus excitation was less deficiennt than medial rectus inhibition of the opposite eye, abduction lag resulted in the oculographic appearance of internuclear ophthalmoplegia of abduction. Abducting nystagmus appeared to be initiated by a tendency for the abducted eye to drift nasally from the increased level of tonic inhibition of the antagonist medial rectus. Some oculographic patterns were attributed to higher level adaptive changes in innervation. These changes were a consequence of disordered excitatory and inhibitory controller signals at the lower, internuclear level. Possible anatomical pathways which might carry these inhibitory controller signals were discussed. High resolution eye movement recordings of patients with internuclear ophthalmoplegia were interpreted directly and by computer simulations as being most consistent with disordered inhibitory and excitatory control of the medial rectus motor pool during rapid eye movements and eccentric gaze.

Adolescent↗
PubMed1994

Electrically controlled focusing of proteins and ampholytes between two modified electrolytes. Computer simulation.

Properties of the focusing in simple electrolyte systems using four-pole electrophoretic capillary column was evaluated by a computer simulation. Simulated concentration, pH and conductivity profiles confirm the previous experimentally observed features of the technique, i.e., high concentration capabilities, separation of the ampholytes and proteins into individual adjacent zones, sharp profile of zones and presence of only background electrolyte in the zone. Moreover, the influence of the magnitude of the solvolytic fluxes on the position of the zones in the column is demonstrated.

Buffers↗
PubMed1998

Learning with technology: use of case-based physical and computer simulations in professional education.

This presentation will clarify contemporary ideas on the role of technology in education and how it can be employed to improve student learning experiences and outcomes. The paper will emphasise RMIT's role in providing quality education that is relevant to today's world and professional practice. It will examine a specific collaborative (RMIT & ACU), interdisciplinary project 'Pregnancy Simulator: Developing and Enhancing Student Learning of Assessment Skills'. This project consist of a physical pregnancy model connected to a multi-media computer-assisted learning package for the purpose of enhancing student learning of abdominal assessment skills. Our paper outlines an innovative technology-based teaching project and includes current educational issues or problems encountered in professional education, steps already taken to address these difficulties and how this project intends to facilitate learning. It identifies expected learning outcomes for midwives, nurses and medical students, and examines pedagogical principles applied to technological applications designed to provide guided discovery for allowing students to build confidence and competence in professional education. The case-based physical and computer simulations contextualise learning to assist transfer of learning to real world situations. This paper will also discuss how technology-based projects can be evaluated and integrated into university curricula to enhance student learning.

Computer Simulation↗
PubMed1996

Determining the size of a total purchasing site to manage the financial risks of rare costly referrals: computer simulation model.

OBJECTIVE: To estimate the financial risks of 15 categories of rare costly referrals for total purchasing sites of different population sizes. DESIGN: Computer simulation of 100 fund years assuming Poisson distribution of referrals. SETTING: British general practices that have opted to become total purchasing sites. Referral rates and price estimates were supplied by South and West Devon Health Commission. MAIN OUTCOME MEASURES: Variation in referral costs to purchasers in relation to size of risk pool (person years at risk). RESULTS: Random variation in referral costs increased as the size of the risk pool decreased. Variation increased greatly below 30,000 person years. The mean simulated cost of the referral categories considered was 2.8% of total NHS hospital and community service costs, and the maximum simulated cost for 7000 person years was 6.8%. Simulated variation was robust to assumption about prices and referral rates for specific types of referral. CONCLUSION: Rare costly referrals seem unlikely to bankrupt total purchasing sites. The management of risk is not in itself justification for total purchasing to be based in several general practices in order to generate large populations. There are other ways of managing risk. Sites can easily explore options by simulations using local referral rates and prices.

Computer Simulation↗
PubMed1987

Computer simulation of the metabolic consequences of the combined deficiency of 6-phosphogluconolactonase and glucose-6-phosphate dehydrogenase in human erythrocytes.

Computer simulation of the human erythrocyte hexose monophosphate shunt was used to investigate whether the severity of hemolysis, caused by deficiency of glucose-6-phosphate dehydrogenase, could be influenced by an accompanying deficiency of 6-phosphogluconolactonase. The known kinetics of the enzymes involved in the oxidative part of the hexose monophosphate shunt suggest that partial deficiency of 6-phosphogluconolactonase would not restrict the rate of reduced nicotinamide-adenine dinucleotide phosphate production significantly. It is therefore concluded that the metabolic consequences of a combined deficiency of the two enzymes are unlikely to be responsible for the interpatient variability of the hematologic response to deficiency of glucose-6-phosphate dehydrogenase.

Carboxylic Ester Hydrolases↗
PubMed2003

Topical cardiac cooling--computer simulation of myocardial temperature changes.

Topical cardiac cooling (TC) is often used in cardiac surgery. We used a computer simulation to study temperature changes in the heart, especially in the right ventricular wall. A three-dimensional computer heart model, derived from Visible Human Data set, National Library of Medicine was used. The model is made from cubes, with spatial resolution of 1mm. Explicit Finite Different method and temperature diffusion equation were used to calculate new temperatures. Three different simulations were performed and simulated temperatures were drawn on a cross-section of heart model in different colors. The results show that areas not immersed into TC solution are less protected against ischemia. It is important not to rely solely on topical cooling but use appropriate method of myocardial protection technique.

Anatomy, Cross-Sectional↗
PubMedDate not supplied

Computer simulation study of Siemens star x-ray image artifacts.

In the Siemens star image, exact determination of the first disappearance frequency, which is used to measure the focal spot size, is difficult since the disappearance band has a finite width and the image also has other artifacts. The origin of these artifacts and their appearance was studied by Siemens star image simulation on a digital computer. The simulated images were manipulated by using many different modulation and phase transfer functions. It is shown that the bending of spokes is not related to zero contrast; exact triplet splitting can occur only at the disappearance frequency, and therefore splitting is a valuable indicator of that frequency.

Computers↗