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PubMed2002

Direct calculation and computer simulation of the enantiomerization barrier of oxazepam in dynamic HPLC experiments--a comparative study.

Dynamic chromatographic methods constitute a versatile approach to the rapid and precise determination of enantiomerization barriers of stereolabile drugs. In the present study enantioselective dynamic high-performance liquid chromatography (DHPLC) was employed to determine the enantiomerization barrier of oxazepam. Dynamic elution profiles, exhibiting plateau formation and/or peak broadening between 20 and 60 degrees C at pH 2.6 and pH 8 were obtained in the presence of the chiral stationary phase (CSP) Nucleodex-beta-PM (permethylated beta-cyclodextrin chemically bonded to silica) using a 6:4 mixture of phosphate buffer and methanol as mobile phase. Evaluation of the experimental chromatograms was performed by the novel approximation function (AF) (without computer simulation), and by the stochastic model implemented in the ChromWin simulation software (with computer simulation) furnishing the respective apparent forward rate constants, k(1)(app)(T). From the rate constants, k(1)(app)(T), measured at variable temperatures, the kinetic Eyring activation parameters, deltaG(T)(#), deltaH(#) and deltaS(#), of the enantiomerization of oxazepam were obtained. By variation of the flow rate of the mobile phase, the expected independence of the enantiomerization barrier from the chromatographic time scale was demonstrated for the first time.

Chromatography, High Pressure Liquid↗
PubMed2003

Dynamic computer simulation of Clostridium perfringens growth in cooked ground beef.

The objective of this study was to develop a computer simulation algorithm to dynamically estimate and predict the growth of Clostridium perfringens in cooked ground beef. The computational algorithm was based on the implicit form of the Gompertz model, the growth kinetics of C. perfringens in cooked ground beef, and the fourth-order Runge-Kutta numerical method. This algorithm was validated using a cocktail of three strains of C. perfringens spores grown under isothermal, square-waved, linear cooling, and exponential cooling temperature profiles. In general, the results of computer simulation matched closely with the experimental data with the absolute errors less than 0.5 log(10) CFU/g. This method may be a useful tool for the food industry, regulatory agencies, distributors, and retailers to predict the effect of temperature abuse on the microbial safety of C. perfringens and other foodborne pathogens in processed meat products.

Animals↗
PubMed2002

Computer simulations and neutron reflectivity of proteins at interfaces.

Computer simulations in conjunction with neutron reflectivity is an excellent combination for the study of biological materials at solid-liquid interfaces: Both techniques have excellent resolution levels (Angströms) and they are mature. A stronger interaction between physicists and biologists will allow the use of these two approaches in topics of biological-biomedical interest.

Adsorption↗
PubMed1992

Computer simulation of the pacemaker oscillations of thalamocortical cells.

Computer simulations of the spontaneous pacemaker oscillations observed in thalamocortical (TC) cells were performed using a biophysical model that included the low voltage activated, Ca2+ current, IT, and the mixed Na+/K+, inward rectifying current, Ih. The simulations accurately reproduced the waveform and voltage-dependence of the pacemaker oscillations, hence the transition from tonic firing to burst firing which is a peculiar feature of the electrical activity of TC cells both in vivo and in vitro. The results provide further support to the suggestion that IT and Ih are essential for the presence of the pacemaker oscillations, and indicate that our model is a useful tool for the study of spontaneous, low-frequency oscillatory activities in TC cells.

Animals↗
PubMed2003

Computer simulation studies of the fidelity of DNA polymerases.

Computer simulations can provide in principle quantitative correlation between the structures of DNA polymerases and the replication fidelity. This paper describes our progress in this direction. Using several theoretical approaches, including the free energy perturbation (FEP), linear response approximation (LRA), and the empirical valence bond (EVB) methods, we examined the stability of several mismatched base pairs in DNA duplex in aqueous solution, the contribution of binding energy to the fidelity of DNA polymerases beta and T7, and the mechanism and energetics of the polymerization reaction catalyzed by T7 DNA polymerase.

Computer Simulation↗
PubMed1987

Computer-simulated analysis of in vitro cell migration.

Computer-simulated analysis of cell migration was attempted with the aim of improving the discriminative characterization of the in vitro locomotory behaviour of normal and neoplastic cells and verifying a concept of cell movement regulation proposed earlier. It suggested that cell membrane activity and distribution of resting periods along the cell trajectory could be introduced with advantage among the migration parameters; this appeared to be a promising refinement on the standard methodology. Moreover, it was inferred that setting up critical, instead of optimal, conditions for cells in culture should reveal behavioural differences otherwise hidden.

Cell Membrane↗
PubMed2001

Protein refolding versus aggregation: computer simulations on an intermediate-resolution protein model.

Computer simulations are performed on a system of eight model peptide chains to study how the competition between protein refolding and aggregation affects the optimal conditions for refolding of four-helix bundles. The discontinuous molecular dynamics algorithm is utilized along with an intermediate-resolution protein model that we developed for this work. Physically, the model is much more detailed than any model used to date for simulations of protein aggregation. Each model residue consists of a detailed, three-bead backbone and a simplified, single-bead side-chain. Excluded volume, hydrogen bond, and hydrophobic interactions are modeled with discontinuous (i.e. hard-sphere and square-well) potentials. Simulations efficiently sample conformational space, and complete folding trajectories from random initial configurations to two four-helix bundles are possible within two days on a single processor workstation. Folding of the bundles follows two main pathways, one through a trimeric intermediate and the other through an intermediate with two dimers. The proportion of trajectories that follow each route is significantly different for the eight-peptide system in this work than in a previously studied four-peptide system, which yields one four-helix bundle, suggesting, as our previous simulations have, that protein folding properties are strongly influenced by the presence of other proteins. Folding of the bundles is optimal within a fixed temperature range, with the high-temperature boundary a function of the complexity of the protein (or oligomer) to be folded and the low-temperature boundary a function of the complexity of the protein's environment. Above the optimal temperature range for folding, the model chains tend to unfold; below the optimal range, the model chains tend to aggregate. As has been seen previously, aggregates have substantial levels of native secondary structure, suggesting that aggregates are composed largely of partially folded intermediates, not denatured chains.

Amino Acid Sequence↗
PubMed1989

Integration of distributed cortical systems by reentry: a computer simulation of interactive functionally segregated visual areas.

A computer model based on visual cortex has been constructed to analyze how the operations of multiple, functionally segregated cortical areas can be coordinated and integrated to yield a unified perceptual response. We propose that cortical integration arises through the process of reentry--the ongoing, parallel, recursive signaling between separate maps along ordered anatomical connections. To test the efficacy of this reentrant cortical integration (RCI) model, we have carried out detailed computer simulations of 3 interconnected cortical areas in the striate and extrastriate cortex of the macaque. The simulated networks contained a total of over 222,000 units and 8.5 million connections. The 3 modeled areas, called VOR, VOC, and VMO, incorporate major anatomical and physiological properties of cortical areas V1, V3, and V5 but are vastly simplified compared with monkey visual cortex. Simulated area VOR contains both orientation and directionally selective units; simulated area VMO discriminates the direction of motion of arbitrarily oriented objects; and simulated area VOC responds to both luminance and occlusion boundaries in the stimulus. Area VOC is able to respond to illusory contours (Kanizsa, 1979) by means of the same neural architecture used for the discrimination of occlusion boundaries. This architecture also generates responses to structure-from-motion by virtue of reentrant connections from VMO to VOC. The responses of the simulated networks to these illusions are consistent with the perceptual responses of humans and other species presented with these stimuli. The networks also respond in a consistent manner to a novel illusion that combines illusory contours and structure-from-motion. The response synthesized to this combined illusion provides a strong argument supporting the need for a recursive reentrant process in the cortex. Functional integration of the simulated areas in the RCI model were found to depend upon the combined action of 3 reentrant processes: (1) conflicting responses among segregated areas are competitively eliminated, (2) outputs of each area are used by other areas in their own operations, and (3) outputs of an area are "reentered" back to itself (through lower areas) and can thus be used iteratively to synthesize responses to complex or illusory stimuli. Transection of the reentrant connections selectively abolished these integrative processes and led to failure of figural synthesis. The proposed model of reentry suggests a basis for understanding how multiple visual areas as well as other cortical areas may be integrated within a distributed system.

Animals↗
PubMed1997

The study of the stability of Watson-Crick nucleic acid base pairs in water and dimethyl sulfoxide: computer simulation by the Monte Carlo method.

An extensive computer simulation of nucleic acid bases and Watson-Crick base pairs in a water cluster and DMSO cluster is performed by the Monte Carlo method. It is demonstrated that the unfavorable energetics of pair formation in a water cluster is determined by the significant destabilizing contribution of solvent to the energy of complex formation. It is shown that the formation of coplanar base pairs in a DMSO cluster is favorable. The DMSO cluster stabilizes A-U and A-T base pairs and the insignificant destabilization of the G-C base pair by a DMSO cluster is much less than the stabilization which occurs due to the attraction between bases.

Base Composition↗
PubMed2001

Non-linear computer simulation of brain deformation.

This paper presents realistic computer simulation of deformation of the brain subject to in-vivo indentation. The work presented provides a step towards neurosurgical simulation, with applications to non-rigid registration, virtual reality training and operation planning systems and robotic devices to perform minimally invasive brain surgery. In order to properly analyze experimental data collected in-vivo, a three-dimensional, non-linear finite element model of the brain was developed. Magnetic resonance imaging techniques were used to obtain geometric information needed for the model. The shape of the force-displacement curve obtained using the numerical solution was very similar to the experimental one. The predicted forces were about 31% lower than those recorded during the experiment. Having in mind that the coefficients in the model had been identified based on experimental data obtained in-vitro, and large variability of mechanical properties of biological tissues, such agreement can be considered as very good. By appropriately increasing material parameters describing instantaneous stiffness of the tissue one is able, without changing the structure of the model, to reproduce experimental curve almost perfectly. Numerical studies showed also, that the linear, viscoelastic model of brain tissue is not appropriate for the modeling brain tissue deformation even for moderate strains.

Animals↗
PubMed2007

Integrative metabolomics for characterizing unknown low-abundance metabolites by capillary electrophoresis-mass spectrometry with computer simulations.

Characterization of unknown low-abundance metabolites in biological samples is one the most significant challenges in metabolomic research. In this report, an integrative strategy based on capillary electrophoresis-electrospray ionization-ion trap mass spectrometry (CE-ESI-ITMS) with computer simulations is examined as a multiplexed approach for studying the selective nutrient uptake behavior of E. coli within a complex broth medium. On-line sample preconcentration with desalting by CE-ESI-ITMS was performed directly without off-line sample pretreatment in order to improve detector sensitivity over 50-fold for cationic metabolites with nanomolar detection limits. The migration behavior of charged metabolites were also modeled in CE as a qualitative tool to support MS characterization based on two fundamental analyte physicochemical properties, namely, absolute mobility (muo) and acid dissociation constant (pKa). Computer simulations using Simul 5.0 were used to better understand the dynamics of analyte electromigration, as well as aiding de novo identification of unknown nutrients. There was excellent agreement between computer-simulated and experimental electropherograms for several classes of cationic metabolites as reflected by their relative migration times with an average error of <2.0%. Our studies revealed differential uptake of specific amino acids and nucleoside nutrients associated with distinct stages of bacterial growth. Herein, we demonstrate that CE can serve as an effective preconcentrator, desalter, and separator prior to ESI-MS, while providing additional qualitative information for unambiguous identification among isobaric and isomeric metabolites. The proposed strategy is particularly relevant for characterizing unknown yet biologically relevant metabolites that are not readily synthesized or commercially available.

Biomarkers↗
PubMed1995

A computer simulation of motion in turbo FLASH imaging and echo-planar imaging.

We have experimentally demonstrated motion effects in a turbo FLASH imaging (TFI) using a small cylindrical phantom moving at constant velocity. To further verify these experimental results, image blurring is assessed by using a computer simulation in this study. By applying the same acquisition parameters as phantom experiments, the simulation images are reconstructed to compare with the experimental results. Several kinds of configurations are applied to the simulation of the TFI. A computer simulation of an echo-planar imaging (EPI) is also used to compare the motion effects with TFI.

Computer Simulation↗
PubMed1983

Computer simulation of transport phenomena during dialysis deglycerolization of red blood cells.

A computer simulation model has been developed to aid in the understanding, parameter prediction, and performance optimization of a unique dialysis process where glycerol is removed from cryopreserved red blood cells using a semipermeable membrane pouch fixed in a mildly agitated transport cell. The dynamic system considered here consists of flow channels and the membrane blood pouch which contains the red blood cells, extracellular fluid, and cryopreservatives. Dialysate flows over the membrane surfaces while salt enters the pouch preventing osmotic hemolysis. The glycerol diffuses rapidly from the red cells and plasma across the membrane into the dialysate which carries it out of the transport cell. The system is discretized into completely mixed subdomains. Constituent transport and solvent flux are modeled with the transient convection-diffusion equation and linear equations of nonequilibrium thermodynamics, respectively. The integrated compartment method was used to solve for the principal variables, that is, salt and glycerol concentrations, water flow rates, and pressure in space and time. The computer simulation model, calibrated and verified with in-house data sets, is a reliable, cost-effective and flexible tool for dialysis system investigations, prediction, and optimal design.

Biological Transport↗
PubMedDate not supplied

A computer simulation for teaching critical thinking skills.

Critical thinking is difficult to teach because it is an abstract conceptual skill and there is no standard model. The authors discuss the development and use of a computer simulation that stimulates critical thinking in nursing students. Computer simulations are an efficient method of teaching students content and critical thinking skills without exhausting severely limited clinical time or placing a patient in jeopardy.

Clinical Competence↗
PubMed1992

Computer simulation of neurone pattern processing.

Physiological simulation techniques can provide a very useful additional tool with which to explore the behaviour of neurones, especially for probing those areas that are not easily accessible to experimental monitoring techniques such as activity in the dendrites. This paper explores the information processing capabilities of a cerebral cortical pyramidal neurone using a computer simulation. The computer model simulated two important aspects of pyramidal cell behaviour: the transient distribution of membrane potential over a proportion of the apical dendritic tree of the cell, and the ability of the receptors in the neurones' dendritic spines to undergo plastic changes. The simulation of receptor behaviour modelled the ability of receptor regions to increase their sensitivity if a prior input had occurred when the spine head membrane was depolarized. The model was used to explore the response of the cell to different inputs. It underlined the need for large amounts of local activity before spinal receptors changed their sensitivity. It also demonstrated the ability of pyramidal cells to both recognize patterns of input and to associate one pattern of inputs with another. It is argued that this pattern association property could be a neuronal basis for association learning.

Computer Simulation↗
PubMed1977

On the mechanism of sodium- and potassium-activated adenosine triphosphatase. Time course of intermediary steps examined by computer simulation of transient kinetics.

In order to learn whether the kinetics of transient phosphorylation of sodium plus potassium ion transport adenosine triphosphatase was compatible with the hydrolysis of ATP, computer simulation of experimental data was studied. The enzyme mechanism was described in terms of first order and pseudo-first order reactions. The resulting system of linear first order differential equations was solved by a Runge-Kutta method. Phosphorylation kinetics was studied by means of a rapid mixing apparatus at 21 degrees in the presence of 100 micron ATP, 3 mM MgCl2, 120 mM NaCl, and 10 mM KCl. Computer simulation gave a close fit to experimental data with a model of the reaction mechanism which included a sequence of two dephospho forms and two phospho forms of the enzyme. With this model, rate constants obtained by computer simulation were in agreement with constants which had been determined in separate phosphorylation and dephosphorylation experiments. Within experimental limits, the net flux of reaction in each partial step was compatible with the (Na+,K+)-stimulated hydrolysis of ATP (about 324 and 300 nmol-mg-1-min-1, respectively).

Adenosine Triphosphatases↗
PubMedDate not supplied

Computer simulation of rapidly responding forced exponential systems.

Two common problems in computer simulations are the decisions to ignore or include a particular element of a system under study in a model and the choice of an appropriate integration algorithm. To examine aspects of these problems, a simple exponential system is considered in which a large simulation error is induced by a rather small truncation error. The effect of computational precision, step size and hardware selection on this error is examined at standard and extended precisions over a range of step sizes and on a variety of computers. For this model, simulation accuracy is an exponential function of the number of bits in the mantissa of the computer word. Optimal step size is a function of accuracy required and precision used; a trade-off between truncation and round-off errors becomes important as accuracy requirements increase. Machine selection is important primarily in economic terms if the required precision is available. We conclude that the effect on a simulation of small terms such as truncation errors can be unexpectedly large, that solutions should always be checked, and that high precision and wide dynamic range are important to the successful computer simulation of models such as that examined.

Computers↗
PubMed2005

A computer simulation model of diabetes progression, quality of life, and cost.

OBJECTIVE: To develop and validate a comprehensive computer simulation model to assess the impact of screening, prevention, and treatment strategies on type 2 diabetes and its complications, comorbidities, quality of life, and cost. RESEARCH DESIGN AND METHODS: The incidence of type 2 diabetes and its complications and comorbidities were derived from population-based epidemiologic studies and randomized, controlled clinical trials. Health utility scores were derived for patients with type 2 diabetes using the Quality of Well Being-Self-Administered. Direct medical costs were derived for managed care patients with type 2 diabetes using paid insurance claims. Monte Carlo techniques were used to implement a semi-Markov model. Performance of the model was assessed using baseline and 4- and 10-year follow-up data from the older-onset diabetic population studied in the Wisconsin Epidemiologic Study of Diabetic Retinopathy (WESDR). RESULTS: Applying the model to the baseline WESDR population with type 2 diabetes, we predicted mortality to be 51% at 10 years. The prevalences of stroke and myocardial infarction were predicted to be 18 and 19% at 10 years. The prevalences of nonproliferative diabetic retinopathy, proliferative retinopathy, and macular edema were predicted to be 45, 16, and 18%, respectively; the prevalences of microalbuminuria, proteinuria, and end-stage renal disease were predicted to be 19, 39, and 3%, respectively; and the prevalences of clinical neuropathy and amputation were predicted to be 52 and 5%, respectively, at 10 years. Over 10 years, average undiscounted total direct medical costs were estimated to be USD $53,000 per person. Among survivors, the average utility score was estimated to be 0.56 at 10 years. CONCLUSIONS: Our computer simulation model accurately predicted survival and the cardiovascular, microvascular, and neuropathic complications observed in the WESDR cohort with type 2 diabetes over 10 years. The model can be used to predict the progression of diabetes and its complications, comorbidities, quality of life, and cost and to assess the relative effectiveness, cost-effectiveness, and cost-utility of alternative strategies for the prevention and treatment of type 2 diabetes.

Computer Simulation↗