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PubMed2001

Interplay between Zeeman coupling and swap action in spin-based quantum computer models: error correction in inhomogeneous magnetic fields.

We consider theoretically the interplay between Zeeman coupling and exchange-induced swap action in spin-based quantum dot quantum computer models in the presence of inhomogeneous magnetic fields, which are invariably present in real systems. We estimate quantitatively swap errors caused by the inhomogeneous field, establishing that error correction would, in principle, be possible in the presence of nonuniform magnetic fields in realistic structures.

Journal Article↗

PubMed2005

Computational modeling suggests that response properties rather than spatial position determine connectivity between olfactory glomeruli.

Olfactory responses require the representation of high-dimensional olfactory stimuli within the constraints of two-dimensional neural networks. We used a computational model of the honeybee antennal lobe to test how inhibitory interactions in the antennal lobe should be organized to best reproduce the experimentally measured input-output function in this structure. Our simulations show that a functionally organized inhibitory network, as opposed to an anatomically or all-to-all organized inhibitory network, best reproduces the input-output function of the antennal lobe observed with calcium imaging. In this network, inhibition between each pair of glomeruli was proportional to the similarity of their odor-response profiles. We conclude that contrast enhancement between odorants in the honeybee antennal lobe is best achieved when interglomerular inhibition is organized based on glomerular odor response profiles rather than on anatomical neighborhood relations.

Animals↗

PubMed1996

A computational model of visual hallucinations in migraine.

Cortical spreading depression is a wave of electrical and biochemical changes that spreads across the cerebral cortex. It has been hypothesized to be an important underlying cause of the visual disturbances occurring during the migraine aura, but this is difficult to test in animals or humans. We created a computational model of cortical spreading depression and found that during the wave of biochemical changes the spatial pattern of neural activity broke up into irregular patterns of lines and small patches of highly activated elements. The corresponding visual disturbances that would be produced by these patterns of neural activity resemble the hallucinations reported during the migraine aura, providing strong support for the cortical spreading depression hypothesis of migraine. The model also makes the testable prediction that these hallucinations move at an exponentially increasing speed across the visual field.

Animals↗

PubMed2004

Using computational modeling to improve patient care unit safety and quality outcomes.

As part of ongoing research to investigate the impact of patient characteristics, organization characteristics and patient unit characteristics on safety and quality outcomes, we are using a computational modeling program, OrgAhead, to model patient care units' achievement of patient safety (medication errors and falls) and quality outcomes. We tuned OrgAhead using data we collected from 16 units in 5 hospitals. Subsequent validation studies demonstrated acceptable levels of correspondence between actual and virtual patient units. In this paper, we report on our initial efforts to use OrgAhead to develop testable hypotheses about the kinds of innovations that nurse managers might realistically implement on their patient care units to improve quality and safety outcomes. Our focus is on unit-level innovations that are likely to be easier for managers to implement. For all but the highest performing unit (for which we encountered a ceiling effect), we were able to generate practical strategies that improved performance of the virtual units by 6-8 percentage points. Nurse Managers have responded enthusiastically to the additional decision support for quality improvement

Accidental Falls↗

PubMed2000

Epidural electrical stimulation of posterior structures of the human lumbosacral cord: 2. quantitative analysis by computer modeling.

OBJECTIVES: Analysis of the computed recruitment order of an ensemble of ventral and dorsal root fibers should enlighten the relation between the position of a bipolar electrode and the observed order of muscle twitches. MATERIAL AND METHODS: Thresholds of selected spinal root fibers are investigated in a two step procedure. First the electric field generated by the electrodes is computed with the Finite Element Method. In the second step the calculated voltage profile along each target neuron is used as input data for a cable model. For every electrode position the electrical excitability is analyzed for 12 large diameter ventral and dorsal root fibers of the second and fourth lumbar and first sacral segment. The predictions of the neural responses of any target fiber are based on the activating function concept and on the more accurate computer simulations of the electrical behavior of all nodes and internodes in the vicinity of the electrode. RESULTS: For epidural dorsal lumbosacral spinal cord stimulation we found the following rules. (i) The recruitment order of the spinal roots is highly related to the cathode level. (ii) Dorsal root fibers have the lowest threshold values, ventral root fibers are more difficult to excite and dorsal columns are not excitable within the clinical range of 10 V. (iii) For a cathode close to the level of the spinal cord entry of a target fiber thresholds are lowest and spike initiation is expected at the border between cerebrospinal fluid and white matter; excitation of L4 roots is not possible with 210 micros/10 V pulses when cathode is more than 2.2 cm cranial to their entry level (1.5 cm for S1 roots; standard data). (iv) Cathodes positioned (essentially) below the entry level cause spike initiation close to the cathode, in a region where the fibers follow the descending course within the cerebospinal fluid. (v) At rather low stimulation voltage twitches are expected in all investigated lower limb muscles for cathodes below L5 spinal cord level. CONCLUSIONS: Our simulations demonstrate a strong relation between electrode position and the order of muscle twitches which is based on the segmental arrangement of innervation of lower limb muscles. The proposed strategy allows the identification of the position of the electrode relative to spinal cord segments.

Electric Stimulation↗

PubMed2006

Interactions of VEGF isoforms with VEGFR-1, VEGFR-2, and neuropilin in vivo: a computational model of human skeletal muscle.

The vascular endothelial growth factor (VEGF) family of cytokines is involved in the maintenance of existing adult blood vessels as well as in angiogenesis, the sprouting of new vessels. To study the proangiogenic activation of VEGF receptors (VEGFRs) by VEGF family members in skeletal muscle, we develop a computational model of VEGF isoforms (VEGF(121), VEGF(165)), their cell surface receptors, and the extracellular matrix in in vivo tissue. We build upon our validated model of the biochemical interactions between VEGF isoforms and receptor tyrosine kinases (VEGFR-1 and VEGFR-2) and nonsignaling neuropilin-1 coreceptors in vitro. The model is general and could be applied to any tissue; here we apply the model to simulate the transport of VEGF isoforms in human vastus lateralis muscle, which is extensively studied in physiological experiments. The simulations predict the distribution of VEGF isoforms in resting (nonexercising) muscle and the activation of VEGFR signaling. Little of the VEGF protein in muscle is present as free, unbound extracellular cytokine; the majority is bound to the cell surface receptors or to the extracellular matrix. However, interstitial sequestration of VEGF(165) does not affect steady-state receptor binding. In the absence of neuropilin, VEGF(121) and VEGF(165) behave similarly, but neuropilin enhances the binding of VEGF(165) to VEGFR-2. This model is the first to study VEGF tissue distribution and receptor activation in human muscle, and it provides a platform for the design and evaluation of therapeutic approaches.

Computer Simulation↗

PubMed2005

Computational modeling of the propagation of light through liquid crystals containing twist disclinations based on the finite-difference time-domain method.

The finite-difference time-domain (FDTD) method is used to compute propagation of light through textured uniaxial nematic-liquid crystal (NLC) films containing various types of twist disclination (defect) lines. Computational modeling by the FDTD method provides an accurate prediction of the optical response in multidimensional and multiscale heterogeneities in NLC films in which significant spatial optic axis gradients are present. The computations based on the FDTD method are compared with those of the classic Berreman matrix-type method. As expected, significant deviations between predictions from the two methods are observed near the twist disclination line defects because lateral optic axis gradients are ignored in the matrix Berreman method. It is shown that the failure of Berreman's method to take into account lateral optic axis gradient effects leads to significant deviations in optical output. In addition, it is shown that the FDTD method is able to distinguish clearly different types of twist disclination lines. The FDTD optical simulation method can be used for understanding fundamental relationships between optical response and complex NLC defect textures in new liquid-crystal applications including liquid-crystal-based biosensors and rheo-optical characterization of flowing liquid crystals.

Journal Article↗

PubMedDate not supplied

Pressure half-time in aortic regurgitation: evaluation with Doppler in a cardiovascular hydromechanical simulator and in a computer model.

Doppler echocardiographic determination of pressure half-time has been proposed as a method of assessing the severity of aortic regurgitation. To evaluate this method, we assessed the relation between pressure half-time and simulated aortic regurgitant flow under various conditions in two models of the cardiovascular system. In a hydromechanical model we assessed the influence of total peripheral resistance and arterial compliance on the pressure half-time as measured by continuous wave Doppler echocardiography. In a computer model that used the half-time of the pressure gradient between the aorta and the left ventricle as an expression of pressure half-time, we assessed the influence of total peripheral resistance and arterial compliance and also the influence of left ventricular compliance on pressure half-time. In both models, although we found an inverse relation between regurgitant orifice area and pressure half-time, changing total peripheral resistance and arterial compliance (but not left ventricular compliance) within the physiologic range significantly altered the pressure half-times. We concluded that the influence of total peripheral resistance and arterial compliance limits the usefulness of Doppler echocardiographic determination of pressure half-time as a method of assessing the severity of aortic regurgitation.

Aorta↗

PubMed1998

Representation of object similarity in human vision: psychophysics and a computational model.

We report results from perceptual judgment, delayed matching to sample and long-term memory recall experiments, which indicate that the human visual system can support metrically veridical representations of similarities among 3D objects. In all the experiments, animal-like computer-rendered stimuli formed regular planar configurations in a common 70-dimensional parameter space. These configurations were fully recovered by multidimensional scaling from proximity tables derived from the subject data. We show that such faithful representation of similarity is possible if shapes are encoded by their similarities to a number of reference (prototypical) shapes, as in the computational model that accompanies the psychophysical data.

Computer Simulation↗

PubMed2001

Computational modeling of eukaryotic mRNA turnover.

The process of eukaryotic gene expression involves a diverse number of steps including transcription, RNA processing, transport, translation, and mRNA turnover. A critical step in understanding this process will be the development of mathematical models that quantitatively describe and predict the behavior of this complex system. We have simulated eukaryotic mRNA turnover in a linear multicomponent model based on the known mRNA decay pathways in yeast. Using rate constants based on experimental data for the yeast unstable MFA2 and stable PGK1 transcripts, the computational modeling reproduces experimental observations after minor adjustments. Subsequent analysis and a series of in silico experiments led to several conclusions. First, we demonstrate that mRNA half-life as commonly measured underestimates the average life span of an mRNA. Second, due to the properties of the pathways, the measurement of a half-life can predominantly measure different steps in the decay network. A corollary of this fact is that different mRNAs will be affected differentially by changes in specific rate constants. Third, the way to obtain the largest change of levels of mRNA for the smallest changes in rate is by changing the rate of deadenylation, where a large amount of regulation of mRNA decay occurs. Fourth, the 3'-to-5' degradation of mRNA shows mRNA-specific rates of degradation that are dependent on the 5' structure of the mRNA. These programs can be run over the Web, are adaptable to other eukaryotes, and provide outputs as graphs and virtual northern gels, which can be directly compared to experimental data. Therefore, this model constitutes a useful tool for the quantitative analysis of the process and control of mRNA degradation in eukaryotic cells.

Biological Transport↗

PubMed1995

Computer-models for management of a cardiopulmonary clinic.

To optimize the transition of a cardiopulmonary ward management from a centrally directed (so called "socialist") healthcare system to a free market oriented one, the authors constructed two computer-models: one for the simulation of distribution of the financing and another for the simulation of interventional pathways in an operational flow chart. For parameter estimation specificity, sensitivity, and diagnosis probability, function curves have been defined. After using these models, the effectiveness of ward performance and the quality of care have improved.

Computer Simulation↗

PubMed2006

The development of hypoxaemia during apnoea in children: a computational modelling investigation.

BACKGROUND: Hypoxaemia during apnoea develops earlier and progresses faster in children than in adults. Ethical and practical considerations prevent detailed investigation of the issue. METHODS: We used the Nottingham Physiology Simulator, an integrated, computational model of the respiratory and cardiovascular systems, to model four healthy virtual children (ages: 1 month, 1, 8 and 18 yr) and exposed them to apnoea after a variety of preoxygenation periods (0, 1 and 3 min) and with open and obstructed airways during apnoea. RESULTS: The rate of oxygen desaturation of haemoglobin from 90 to 40% was similar across the ages studied, being approximately 30% min(-1). The greatest difference between ages was found in the speed of early desaturation (i.e. between the onset of apnoea and the acceleration of haemoglobin desaturation); in the absence of preoxygenation and with an open airway, this time was 6.6 s in the 1-month-old and 33.6 s in the 8-yr-old. CONCLUSIONS: Preoxygenation had a substantial effect on the speed of early desaturation, but less effect on the time for SaO2 to decrease from 90 to 40%. Preoxygenation substantially delayed dangerous desaturation in all age groups, although the rapidity of denitrogenation in the very young (caused by the large ratio of minute ventilation to functional residual capacity) resulted in lengthy preoxygenation having little benefit over brief preoxygenation. Airway obstruction during apnoea accelerated every child's hypoxaemia through prevention of mass flow addition to oxygen stores and through intrathoracic depressurization. On average, haemoglobin desaturation from SaO2 90 to 40% was 33% min(-1) with an obstructed airway and 26% min(-1) with an open airway; all ages were similarly susceptible to this effect.

Adolescent↗

PubMed2005

Computational modeling of mechanical anisotropy in the cornea and sclera.

PURPOSE: To determine the biomechanical deformation of the cornea resulting from tissue cutting and removal by use of a new computational model and to investigate the effect of mechanical anisotrophy resulting from the fibrillar architecture. SETTING: Department of Mechanical Engineering, Stanford University, Stanford, California, USA. METHODS: A mathematical model for a typical lamella that explicitly accounts for the strain energy of the collagen fibrils, extrafibrillar matrix, and proteoglycan cross-linking was developed. A stromal model was then obtained by generalized averaging of the lamella properties through the stromal thickness, taking into account the preferred orientations of the collagen fibrils, which were obtained from x-ray scattering data. RESULTS: The model was used to predict astigmatism induced by a tunnel incision in the sclera, such as is used for cataract extraction and intraocular lens implantation. The amount of induced cylinder was in good agreement with published clinical data. Results show it is important for the model to incorporate preexisting corneal physiological stress caused by intraocular pressure. CONCLUSIONS: The mathematical model described appears to provide a framework for further development, capturing the essential features of mechanical anisotropy of the cornea. The tunnel incision simulation indicated the importance of the anisotropy in this case.

Anisotropy↗

PubMed1990

A neural and computational model for the chromatic control of accommodation.

Accommodation is more accurate with polychromatic stimuli than with narrowband or monochromatic stimuli. The aim of this paper is to develop a computational model for how the visual system uses the extra information in polychromatic stimuli to increase the accuracy of accommodation responses. The proposed model is developed within the context of both trichromacy and also the organization of spatial and chromatic processing within the visual cortex. The refractive error present in the retinal image can be estimated by comparing image quality with and without small additional changes in refractive state. In polychromatic light, the chromatic aberration of the eye results in differences in ocular refractive power for light of different wavelengths. As a result, the refractive state of the eye can be estimated by comparing image quality in the three types of cone photoreceptor. The ability of cortical neurons to perform such comparisons on image quality with a crude form of spatial-frequency analysis is examined theoretically. It is found that spatially band-pass chromatically opponent neurons (that may correspond to double opponent neurons) can perform such calculations and that chromatic cues to accommodation are extracted most effectively by neurons responding to spatial frequencies of between 2 and 8 cycles/deg.

Accommodation, Ocular↗

PubMed1987

The conformation of glycans of the oligo-D-mannosidic type, and their interaction with concanavalin A: a computer-modelling study.

The favored conformations of glycans of the oligo-D-mannosidic type have been determined by using empirical energy calculations. An interesting aspect is that the alpha-(1----3)-linked terminal D-mannose residue of the outer trimannosidic core fragment, in all the conformations which fall within 5 kcal.mol-1 of the global minimum, always lies close to the chitobiose core. These models are in general agreement with the available n.m.r. data. The probable modes of binding of these glycans to concanavalin A (Con A) were determined, by using a computer-modelling technique which identifies the positions for the different conformers of the carbohydrate in the binding site of Con A, based on stereochemical considerations. These studies showed that Con A can bind only to two of the three terminal D-mannose residues in these glycans, because the D-mannose residue which lies close to the chitobiose core is inaccessible for the binding of Con A. Of these two terminal D-mannose residues, the alpha-(1----6)-linked D-mannose may bind the more strongly. Furthermore, it is shown that the internal D-mannose residue will, at best, interact very weakly with the carbohydrate-binding site of Con A. These results rationalize well the available data on the binding affinity of these glycans to Con A. They further support the conclusion that the binding affinity of a glycan to Con A does not depend on the number in the glycan, of D-mannose residues which possess free 3-, 4-, and 6-hydroxyl groups, but, rather, on the accessibility of these residues to Con A.

Carbohydrate Conformation↗

PubMed1995

A computer model of dorsal cochlear nucleus pyramidal cells: intrinsic membrane properties.

Manis [P. B. Manis, J. Neurosci. 10, 2338-2351 (1990)] studied "simple spiking," pyramidal cells of the dorsal cochlear nucleus (DCN) maintained in vitro. Response profiles to hyperpolarizing and depolarizing current pulses were generated. Hyperpolarization of the cell membrane followed by depolarization produced markedly different response profiles from those generated when no prehyperpolarization was imposed. By manipulating the magnitude of the hyperpolarizing and depolarizing pulses, "chopper," "pauser" and "build-up" response patterns, similar to those in vivo, could be generated by individual cells. Manis concluded that the different response profiles resulted from the modulation of intrinsic membrane conductances by the prehyperpolarizing pulses. Here a computer model is used to show that (a) steady-state hyperpolarization can influence cell responding to subsequent depolarization in a manner consistent with the data reported by Manis; and (b) the effects reported can be generated by the addition of a modeled transient potassium conductance to the standard Hodgkin-Huxley model of spike generation [A. L. Hodgkin and A. F. Huxley, J. Physiol. 117, 500-544 (1952)]. The model will be of use to those who wish to consider the role of various excitatory and inhibitory inputs to pyramidal cells and to establish their functional role within the DCN.

Cochlear Nucleus↗

PubMed2005

Computational modeling of a dynamic knee simulator for reproduction of knee loading.

As a first step towards reproducing desired three-dimensional joint loading and motion on a dynamic knee simulator, the goal of this study was to develop and verify a three-dimensional computational model that generated control profiles for the simulator using desired knee loading and motion as model inputs. The developed model was verified by predicting tibio-femoral loading on an instrumented analog knee for given actuator forces and the ability to generate simulator control profiles was demonstrated using a three-dimensional walking profile. The model predicted axial tibia loading for a sagittal-plane dual-limb squat within 1% of measured peak loading. Adding out-of-sagittal-plane forces decreased the accuracy of load prediction. The model generated control profiles to the simulator that produced axial tibia loading within 16% of desired for walking. Discrepancies in predicted and measured quadriceps forces influenced the accuracy of the generated control profiles. Future work will replace the analog knee in both the model and machine with a prosthetic knee.

Biomimetics↗

PubMed1998

Computer models of hippocampal circuit changes of the kindling model of epilepsy.

Abnormalities in the organization of brain circuits may underlie many types of epilepsy. This hypothesis can best be evaluated in the case of temporal lobe epilepsy, where evidence of rewiring (synaptic reorganization) can be found in the dentate gyrus. Computer modeling of normal and reorganized dentate gyrus was used to understand the functional consequences of these structural changes. Hyperexcitability appeared to be largely limited by the powerful intrinsic adaptation characteristic of granule cells, the principal cells in this area. Combining disinhibition with new recurrent excitatory circuitry was necessary to produce repeated firing of these cells. Paradoxically, continuing regenerative activity was only seen with a large reduction in the strength of the inciting stimulus. Validation of these findings will require further physiological correlation.

Computer Simulation↗