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Results for “computational modelling”

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PubMed1999

Computer modelling of the adsorption of proteins on solid surfaces under the influence of double layer and van der Waals energy.

The study of protein interactions with surfaces is important in many branches of biomedical engineering. A computer model has been set up in order to aid the understanding and prediction of the likelihood of protein adsorption at a surface and of coagulation between two proteins. In this model, a protein is represented as a hard sphere, neglecting conformation changes which may occur during the adsorption process. The sphere is assumed to be in a medium whose properties are described by the ionic strength, the pH and the dielectric permittivity. It is considered to interact both with an infinite plane, representing the surface, and with another sphere, representing another protein. The model focuses on the total interaction energy between a protein and a surface and between two proteins. The energy is expressed according to the DLVO theory of colloidal stability, which assumes that the adsorption behaviour of proteins at a surface depends, first, on the van der Waals interactions energy and, second, on the electrostatic double layer interaction energy. The conditions under which adhesion is prevented correspond to the presence of local extremes of the energy function, whereas the conditions under which adhesion is likely to take place correspond to absence of local extremes.

Adsorption↗

PubMed1998

A computer model for the prediction of left epicardial coronary blood flow in normal, stenotic and bypassed coronary arteries, by single or sequential grafting.

This article describes a computer model for calculating left epicardial coronary blood pressure and flow waveforms of a right dominant coronary circulation. Using the geometry of 16 vascular branches and employing the one-dimensional Navier-Stokes equations the model allows for the prediction of blood pressure and flow patterns in normal and stenosed vessels. This model was also used to predict the haemodynamic changes observed after insertion of two single saphenous vein bypass grafts, as compared with the corresponding changes after insertion of a sequential (snake-like) saphenous graft. In normal vessels during systole and diastole, the pressure and the flow waveforms obtained showed patterns that correlate very well with the findings observed by other investigators using intracoronary flowmeter or Doppler velocimeter techniques. In coronary artery disease (90% stenoses in LAD and diagonal branch 1), the authors' main contribution is the reconfirmation of a previously described finding of systolic flow rises in stenotic segments. This finding seems to be an important compensatory mechanism, in contrast to normal coronary vessels, which maintain a mainly diastolic flow pattern. The introduction of single or sequential bypass grafts leads to pressure and flow restoration after graft revascularization. Besides this finding, the general concept of a diastolic flow restoration post-stenotically, in the previously decreased and systolic augmented flow areas, is also observed. The two revascularization methods were also compared with regard to their specific advantages, disadvantages and indications and were also extensively compared with several in vivo studies.

Blood Flow Velocity↗

PubMedDate not supplied

A computational model of the digestive gland epithelial cell of marine mussels and its simulated responses to oil-derived aromatic hydrocarbons.

This paper describes a computational model of digestive gland epithelial cells (digestive cells) of marine mussels. These cells are the major environmental interface for uptake of contaminants, particularly those associated with natural particulates that are filtered from seawater by mussels. Digestive cells show well characterised reactions to exposure to lipophilic xenobiotics, such as oil-derived aromatic hydrocarbons (AHs), which accumulate in these cells with minimal biotransformation. The simulation model is based on processes associated with the flux of carbon through the cell. Physiological parameters such as fluctuating food concentration, cell volume, respiration, secretion/excretion, storage of glycogen and lipid, protein/organelle turnover (autophagy/resynthesis) and export of carbon to other tissues of the mussel are all included in the model. The major response to AHs is induction of increased autophagy in these cells. Simulations indicate that the reactions to AHs and food deprivation correspond well with responses measured in vivo.

Animals↗

PubMed1987

A computer modelling approach to study the mode of binding of L-lyxoflavin-5'-monophosphate to flavodoxin.

The mode of binding of L-lyxoflavin-5'-monophosphate has been studied by a computer modelling method. Energetically preferred conformers of L-lyxoflavin-5'-monophosphate have been obtained using empirical potential energy functions. These minimum energy conformers were used to study the mode of their binding to flavodoxin. The study indicates that L-lyxoflavin-5'-monophosphate can also have coenzymatic activity similar to flavin mononucleotide. But its lower activity compared to flavin mononucleotide is due to the lower conformer population that initiates the binding process. It is also concluded from this study that the inability of L-lyxoflavin to promote growth in some cases is at the phosphorylation level and not at the coenzyme level.

Coenzymes↗

PubMed2004

Computer modelling and visualization of active site of monoamine oxidases.

In spite of significant progress in MAO research culminating in the crystallization of the MAO B, many structure-functional aspects of these enzymes still require better characterization. Computer modelling of the substrate/inhibitory binding region of the active site includes consensus overlay of several series of fully reversible and/or tightly bound inhibitors onto a rigid referent inhibitor(s). The shape of resultant mould obviously reflects spatial characteristic features of the substrate/inhibitor binding region. The comparison of the active site mould of MAO B with its crystal structure revealed correctness of this approach. The resultant moulds may be effectively used for virtual screening of molecular databases for new lead-structures. Using this approach we have found several selective MAO A inhibitors in databases and these compounds have never been tested for MAO inhibitory activity.

Animals↗

PubMed2005

Do cortical maps depend on the timing of sensory input? Experimental evidence and computational model.

Fast adaptations in the functional organization of primary sensory cortex are generally assumed to result from changes of network connectivity. However, the effects of intrinsic neuronal excitability alterations due to the activation of neighboring cortical representational zones, which might as well account for the changes of cortical representative maps, have been paid little attention to. In a recent experiment (Braun et al. 2000b) we showed by neuromagnetic source imaging that random or fixed sequence stimulation of three digits of both hands led to stimulation-timing-induced changes in primary somatosensory (SI) cortical maps. The distance between the cortical representation of thumb and middle finger became significantly shorter during the fixed sequence stimulation. The analysis on the time course of the cortical map changes revealed that these reorganizations occurred within minutes and were fully reversible. The previously reported results were interpreted as the involvement of a superordinate center responsible for detecting and activating the appropriate maps. Here we present an alternative parsimonious explanation that is supported by a computational model. Based on the experimental evidence, we developed a simple model that took intrinsic neuronal excitability together with subthreshold activation into account and assumed partial cortical overlap of the representational zones of neighboring digits. Furthermore, in the model the neuronal excitability decayed slowly with respect to the stimulation frequency. The observed cortical map changes in the experiment could be reproduced by the two-layer feed-forward computational network. Our model thus suggests that the dynamic shifts of cortical maps can be explained by the state and time course of intrinsic neuronal excitability and subthreshold activation, without involving changes in network connectivity.

Adult↗

PubMed1991

Contact combinations in epidural spinal cord stimulation. A comparison by computer modeling.

The geometrical characteristics of longitudinal fiber populations in the dorsal columns (DC), recruited by various contact combinations in epidural spinal cord stimulation (SCS), were compared in a theoretical study. A 3-dimensional computer model was used, representing the geometry and electrical conductivity of the low-thoracic spinal cord and surrounding tissues, in combination with a model representing the electrical properties of a myelinated nerve fiber. It was calculated that, among usual dorsomedial contact combinations, the ratio of mediolateral and dorsoventral extent of the recruited area in DC only varied by 2-5%. The model predicts that in bipolar stimulation the relative lateral extent was smallest at a contact separation of 3-3.5 times the dorsal cerebrospinal-fluid width, which seems to fit the highest ratio of discomfort threshold/paresthesia threshold. It is concluded that the optimal combination varies with distance between cathode and DC and that a unique 'best contact combination' does not exist. When both a decrease of primary afferent diameter in DC and collateral branching near their entrance are considered, the model predicts that recruitment of cutaneous afferents will start in lateral DC and proceed medially at increasing stimulus, which fits clinical observations on the spread of paresthesia. The model predicts that large fibers in the posterior spinocerebellar tract will also be recruited in SCS.

Cerebrospinal Fluid↗

PubMed2003

A computational model for particle size influence on drug absorption during controlled-release colonic delivery.

The effect of particle size on the percent drug absorbed is computationally modeled for controlled-release dosage forms that deliver drug particles to the colon. The relative benefit of reducing particle size is mapped on a diagram of the drug's absorption rate constant (estimated from rat intestinal perfusion, CACO-2 or human intubation permeation rates) versus the drug's solubility. Some drugs fall into a limit of high percentage absorption even with large particles such that particle size reduction has little impact. Another group of drugs is solubility limited such that even with small particles, absorption is negligible. Between the two regions, only drugs with sufficiently high absorption rates are influenced by the drug dissolution rate and thereby the particle size. The size of this region is a function of dosing rate. Comparisons between calculated particle size effects on colon absorption as a function of colon volume suggest caution when using animal models to predict bioavailability from colonic drug delivery. This volume dependence also suggests that the particle size influence will vary as a function of the digestive cycle.

Colon↗

PubMed2003

A computational model as neurodecoder based on synchronous oscillation in the visual cortex.

Based on synchronized responses of neuronal populations in the visual cortex to external stimuli, we proposed a computational model consisting primarily of a neuronal phase-locked loop (NPLL) and multiscaled operator. The former reveals the function of synchronous oscillations in the visual cortex. Regardless of which of these patterns of the spike trains may be an average firing-rate code, a spike-timing code, or a rate-time code, the NPLL can decode original visual information from neuronal spike trains modulated with patterns of external stimuli, because a voltage-controlled oscillator (VCO), which is included in the NPLL, can precisely track neuronal spike trains and instantaneous variations, that is, VCO can make a copy of an external stimulus pattern. The latter, however, describes multi-scaled properties of visual information processing, but not merely edge and contour detection. In this study, in which we combined NPLL with a multiscaled operator and maximum likelihood estimation, we proved that the model, as a neurodecoder, implements optimum algorithm decoding visual information from neuronal spike trains at the system level. At the same time, the model also obtains increasingly important supports, which come from a series of experimental results of neurobiology on stimulus-specific neuronal oscillations or synchronized responses of the neuronal population in the visual cortex. In addition, the problem of how to describe visual acuity and multiresolution of vision by wavelet transform is also discussed. The results indicate that the model provides a deeper understanding of the role of synchronized responses in decoding visual information.

Action Potentials↗

PubMed2006

Computational modelling of cell spreading and tissue regeneration in porous scaffolds.

Improved biological and mechanical functionality of musculoskeletal tissue-engineered constructs is required for clinical application, which can only be achieved by comprehensive multidisciplinary research. This review focuses on the contribution of computational modelling as a framework for obtaining an integrated understanding of key processes, which include: nutrient transport and utilization, matrix formation, cell population dynamics, cell attachment and migration, and local cell-cell interactions. Such an integrated perspective of these key aspects will be critical to open up new directions in tissue engineering research, as significant progress can be made by combining existing computational and experimental methods. Furthermore, theoretical modelling has enormous potential in applications ranging from the interpretation of experimental results and the identification of the main governing processes, to the optimization of practical tissue engineering protocols with implications therein for an increasing ageing population.

Animals↗

PubMed1995

Learning to ignore: psychophysics and computational modeling of fast learning of direction in noisy motion stimuli.

The effects of practice on the discrimination of direction of motion in briefly presented noisy dynamic random dot patterns are investigated in several forced-choice psychophysical tasks. We found that the percentage of correct responses on any specific task increases linearly with repetition of trials within roughly 200 trials from about chance to a performance of 90% or better. The level of performance remained constant or improved over several days, and in most instances it did not transfer when stimulus parameters changed. We used a modified Radial Basis Function (RBF) representation to model the psychophysical tasks. The performance of the model is functionally similar to the psychophysical results. We propose a Hebbian learning algorithm which deactivates the inputs from neurons responding to motion noise in the stimulus. Our computational model suggests that to solve this task in biological systems, neurons (perhaps in MT) improve their performance by 'learning to ignore' noise in the image.

Acoustic Stimulation↗

PubMed2003

Computer modeling of relationship between critical PvO2, VO2max and blood supply of skeletal muscle at working with a right-shifted blood O2 dissociation curve.

Investigations were performed on a computer model of O2 delivery and O2 consumption in the one working muscle. At working with increasing power and achieving the critical value of VO2 (VO2crit), the muscle VO2 began to lag behind the oxygen demand qO2. The model permits to find critical pO2 in effluent venous blood Pvcrit at VO2crit as well as to calculate VO2max and PvO2 at VO2max under exercise with changing muscle blood flow F and blood pH.Pvcrit was computed from the condition VO2crit = 0.9qO2, and VO2max- from the condition (dVO2/dqO2) = 0.1. VO2max, Pv at VO2max, Pvcrit, and VO2crit were calculated for: 40 < or = F < or = 120 ml/min/100 g; 6.8 < or = pH < or = 7.4. It was shown that the faster is F and the lesser is blood pH, the greater were the Pvcrit and VO2max values. With decreasing F and blood pH, the influence of F on Pvcrit and VO2max increases, whereas the influence of blood pH on these values decreases. With increasing F and, hence, an increasing VO2max, the blood supply efficiency decreases due to the important limiting factor--tissue oxygen diffusion.

Computer Simulation↗

PubMed1995

A computational model of the Simon effect.

Even though stimulus location is task irrelevant, reaction times are faster when the location of the stimulus corresponds with the location of the response than when it does not. This phenomenon is called the Simon effect. Most accounts of the Simon effect are based on the assumption that it arises from a conflict between the spatial code of the stimulus and that of the response. In this paper a computational model of this hypothesis is presented. It provides a computationally explicit mechanism of the Simon effect. Consistent with human performance, the model provides reaction times that indicate both an advantage for the ipsilateral, corresponding response (i.e., facilitation) and a disadvantage of the contralateral, noncorresponding response (i.e., inhibition). In addition, the model accounts for the fact that the size for the effect depends on task difficulty.

Attention↗

PubMed2006

New computing model helps Hamilton Health Sciences address changing business requirements.

This case study presents the impetus, business case, chronology and benefits of implementing a new server-based computing model at Hamilton Health Sciences that solved a critical desktop management problem while reducing IT costs. The new approach also provided a robust, flexible and scalable technology platform that is helping the hospital address business requirements driven by the emerging virtual healthcare community.

Cost Control↗

PubMed1998

A computer model of cardiac electrical activity for the simulation of arrhythmias.

Modern computer power allows development of models of the heart that may be helpful for the understanding of arrhythmia mechanisms if, based on realistic physiological parameters, such models can display phenomena difficult to study in nature. Therefore, a two-dimensional model of the cardiac tissue has been implemented, where the modeling of each cell is based on membrane ionic channels (Beeler-Reuter and Luo-Rudy models). In addition, an ECG was computed based on the ionic currents simulated. This model allows us to observe the propagation of the action potentials Vm across the cardiac tissue, the evolution of Vm for any of the cardiac cells, and the underlying ionic currents. The computation of the ECG makes it possible to relate this information with an often-used diagnostic tool. Simulations of normal and pathological phenomena such as functional and anatomic reentry have been performed. Our simulation results show that the applied computer model based on ionic currents seems accurate and realistic when compared with biological models and offers a new approach to study the origin, prevention, and termination of arrhythmias.

Action Potentials↗

PubMed2001

Novel approach to computer modeling of seven-helical transmembrane proteins: current progress in the test case of bacteriorhodopsin.

G-protein coupled receptors (GPCRs) are thought to be proteins with 7-membered transmembrane helical bundles (7TM proteins). Recently, the X-ray structures have been solved for two such proteins, namely for bacteriorhodopsin (BR) and rhodopsin (Rh), the latter being a GPCR. Despite similarities, the structures are different enough to suggest that 3D models for different GPCRs cannot be obtained directly employing 3D structures of BR or Rh as a unique template. The approach to computer modeling of 7TM proteins developed in this work was capable of reproducing the experimental X-ray structure of BR with great accuracy. A combination of helical packing and low-energy conformers for loops most close to the X-ray structure possesses the r.m.s.d. value of 3.13 A. Such a level of accuracy for the 3D-structure prediction for a 216-residue protein has not been achieved, so far, by any available ab initio procedure of protein folding. The approach may produce also other energetically consistent combinations of helical bundles and loop conformers, creating a variety of possible templates for 3D structures of 7TM proteins, including GPCRs. These templates may provide experimentalists with various plausible options for 3D structure of a given GPCR; in our view, only experiments will determine the final choice of the most reasonable 3D template.

Bacteriorhodopsins↗

PubMedDate not supplied

Unidirectional block in a computer model of partially coupled segments of cardiac Purkinje tissue.

The initiation of a reentrant circuit requires a zone of slow conduction and a zone of unidirectional block. This study used computer model conditions under which partial coupling between segments of cardiac Purkinje tissue resulted in unidirectional block. The structure used was one-dimensional and divided into three segments: a middle segment of variable length coupled to two long (semi-infinite in concept) segments. The DiFrancesco-Noble equations represented the ionic currents of the membrane. The results show that the possibility of unidirectional block depends on the size of the middle segment and the coupling resistances between the segments. No combination of coupling resistances allowed unidirectional block for middle segments with a length of two space constants (4 mm) or longer. Unidirectional block occurred for many combinations of coupling resistances as the length of the middle segment decreased to around half a space constant (1 mm). The number of length combinations that caused unidirectional block decreased again as segment length further decreased. These results provide a possible mechanism of unidirectional block for situations where islands of viable tissue are connected through nonviable tissue, such as in a healed myocardial infarction.

Animals↗

PubMed1996

A computer model to assess continuity of care.

The implementation of continuity of care recommended in Changing Childbirth has not been easy and in practice varies from hospital to hospital. A computer model being developed at St Thomas' Hospital, allows users to consider the implications of different scenarios, for example: -different midwives' rotas -different caseloads per midwife -size of the team if team midwifery is being implemented. This model can be used to identify the benefits and disadvantages of different policies for both the midwives and the women in their care.

Computer Simulation↗