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PubMed2001

Linear models of simple cells: correspondence to real cell responses and space spanning properties.

Despite their limitations, linear filter models continue to be used to simulate the receptive field properties of cortical simple cells. For theoreticians interested in large scale models of visual cortex, a family of self-similar filters represents a convenient way in which to characterise simple cells in one basic model. This paper reviews research on the suitability of such models, and goes on to advance biologically motivated reasons for adopting a particular group of models in preference to all others. In particular, the paper describes why the Gabor model, so often used in network simulations, should be dropped in favour of a Cauchy model, both on the grounds of frequency response and mutual filter orthogonality.

Animals↗
PubMed1988

Modelling the 1985 influenza epidemic in France.

The Rvachev-Baroyan-Longini model is a space-time predictive model of the spread of influenza epidemics. It has been applied to 128 cities of the USSR, and more recently, to forecasting the spread of the pandemic of 1968-1969 throughout 52 large cities. It is a deterministic, mass-action, space and time continuous model. The model has been applied to the simulation of the influenza epidemic of 1984-1985 in the 22 French Metropolitan districts and results are presented. Estimates of the parameters of the model were made using the French Communicable Diseases Network data. These parameters are the contact rate, a, (estimate = 0.55) which is the number of people with whom an infectious individual will make contact daily sufficient to pass infection and the infectious period, 1/b, estimated as 2.49 days. The mean annual railroad passenger traffic from district i to district j varies from 0 to 1,991,000 persons depending on the districts. The computer spread of the epidemic is presented on weekly maps. Results are also presented on district charts, giving the size of district epidemics and the time of peak of the epidemic. The precision of the computer fittings was judged satisfactory by the calculated size of peak differing from the real one by less than 100 per cent, in 17 out of 18 districts, and by the calculated time of peak differing from the observed by less than two weeks in 14 out of 18 districts. Although precision could be improved with more detailed information about passenger traffic, the French use of the model has been satisfactory.

Computer Simulation↗
PubMed2003

Thermodynamics of electrolytes on anisotropic lattices.

The phase behavior of ionic fluids on simple cubic and tetragonal (anisotropic) lattices has been studied by grand canonical Monte Carlo simulations. Systems with both the true lattice Coulombic potential and continuous-space 1/r electrostatic interactions have been investigated. At all degrees of anisotropy, only coexistence between a disordered low-density phase and an ordered high-density phase with the structure similar to ionic crystal was found, in contrast to recent theoretical predictions. Tricritical parameters were determined to be increasing functions of anisotropy parameters which is consistent with theoretical calculations based on the Debye-Hückel approach. At large anisotropies a two-dimensional-like behavior is observed, from which we estimated the dimensionless tricritical temperature and density for the two-dimensional square lattice electrolyte to be T*(tri)=0.14 and rho*(tri)=0.70.

Journal Article↗
PubMed2001

Effect of EPS on biofilm structure and function as revealed by an individual-based model of biofilm growth.

We have simulated a nitrifying biofilm with one ammonia and one nitrite oxidising species in order to elucidate the effect of various extracellular polymeric substance (EPS) production scenarios on biofilm structure and function. The individual-based model (IbM) BacSim simulates diffusion of all substrates on a two-dimensional lattice. Each bacterium is individually simulated as a sphere of given size in a continuous, three-dimensional space. EPS production kinetics was described by a growth rate dependent and an independent term (Leudeking-Piret equation). The structure of the biofilm was dramatically influenced by EPS production or capsule formation. EPS production decreased growth of producers and stimulated growth of non-producers because of the energy cost involved. For the same reason, EPS accumulation can fall as its rate of production increases. The patchiness and roughness of the biofilm decreased and the porosity increased due to EPS production. EPS density was maximal in the middle of the vertical profile. Introduction of binding forces between like cells increased clustering.

Ammonia↗
PubMed2004

Calculation of pressure using the virtual-volume-variation method and the virial method from chain conformations obtained by Monte Carlo simulations on the second nearest neighbor diamond lattice.

For a model system of polyethylene of chain lengths 40 and 100 carbon atoms, we calculated the pressure at different densities and compared them with the experimental values. The simulation was conducted on the second nearest neighbor diamond lattice, and the pressure was calculated using the virtual-volume-variation method after the system was reverse mapped to its fully atomistic form in continuous space and energy minimized. In addition, the pressure was also calculated from the virial route by conducting a short molecular dynamics simulation starting from the energy minimized structure. We show that the pressure obtained from our simulations is quite reasonable in the length of simulation time (in Monte Carlo steps) normally employed in our group. These results provide additional evidence for the equilibration of our model systems, and methodology to calculate the pressure in our lattice models.

Journal Article↗
PubMed2005

Rotation or translation of auditory space in neglect? A case study of chronic right-sided neglect.

Egocentric models of neglect explain the lateralised omission of stimuli in neglect patients by an ipsilesional shift of a subjective reference frame. However, they differ in the direction of shift (rotation around the midsagittal plane versus translation in front/back space). We tested this hypothesis in a patient (AJ) with persistent right-sided neglect following a left temporo-parieto-occipital and hypoxic lesion and in six age-matched healthy subjects. AJ showed visual neglect in line bisection, size matching, reading and visual search. Auditory localization was tested by using two different psychophysical techniques based on binaurally simulated stimuli for the horizontal plane in front and back space. Eye position was continuously monitored during stimulus presentation in all subjects. AJ revealed a significant ipsilesional, leftward shift of his auditory subjective median plane (ASMP) in front space (mean: -22.6 degrees), and a rightward shift of the ASMP in back space (+14.5 degrees). This pattern of results was replicated with a different psychophysical technique in a retest 10 months later. The rotational shift of AJ's ASMP contrasted with normal performance in the healthy subjects. Monaural hearing deficits can not account for these differential findings as all subjects (including AJ) performed normally. In conclusion, a rotation of the egocentric spatial reference frame may occur in the auditory modality for right-sided neglect.

Acoustic Stimulation↗
PubMed2001

Model-based administration of inhalation anaesthesia. 1. Developing a system model.

This paper is the first of a series of reports on a system model for the administration of inhalation anaesthesia. We present the development and basic testing of the model. It is a multiple-gas model; it covers fresh-gas flow rates from basal to more than total ventilation and includes an actual, not an idealized, circle-absorber breathing system featuring a standing bellows ventilator. Kinetics of nitrogen, oxygen, carbon dioxide, nitrous oxide, inhaled anaesthetic agents and helium are described. Their partial pressures sum to the total pressure. Ventilation and cardiac output are treated as continuous, not cyclical. The model of the breathing system was empirically matched to the chosen one (a GMS absorber and 7850 ventilator (Datex-Ohmeda)). Predictions for the wash-in of isoflurane and the uptake of desflurane and isoflurane agree well with observed data. The results obtained by continuously checking total gas pressures, calculating mass balances and simulating the measurement of alveolar space by the closed-circuit helium dilution method support the mathematical credibility of the model. It thus merits further exploration.

Algorithms↗
PubMed2001

Temporal frequency analysis of dynamic MRI techniques.

Dynamic imaging strategies often involve updating certain areas of k-space (i.e., the low spatial frequencies) more frequently than others. However, important dynamic signal changes may occur anywhere in k-space. In this study, a dynamic k-space sampling analysis method was developed to determine the energy error associated with specific dynamic sampling strategies. The method uses the temporal power spectrum of k-space signals to determine the level and k-space locations of sampling errors. The proposed method was used to compare two dynamic sampling strategies (full sequential and keyhole) for a dynamic first-pass bolus simulation and a continuous heart imaging study. The error analysis agreed well with the errors in the reconstructed images. The technique can be used to determine the minimum sampling frequency for any location in the k-space, and may ultimately be used to optimize dynamic sampling strategies. Magn Reson Med 45:550-556, 2001.

Computer Simulation↗
PubMed1999

A new Hybrid Monte Carlo algorithm for protein potential function test and structure refinement.

A new Hybrid Monte Carlo (HMC) algorithm has been developed to test protein potential functions and, ultimately, refine protein structures. The main principle of this algorithm is, in each cycle, a new trial conformation is generated by carrying out a short period of molecular dynamics (MD) iterations with a set of random parameters (including the MD time step, the number of MD steps, the MD temperature, and the seed for initial MD velocity assignment); then to accept or reject the new conformation on the basis of the Metropolis criterion. The novelty in this paper is that the potential in MD iterations is different from that in the MC step. In the former, it is a molecular mechanics potential, in the latter it is a knowledge-based potential (KBP). Directed by the KBP, the MD iteration is used to search conformational space for realistic conformations with low KBP energy. It circumvents the difficulty in using KBP functions directly in MD simulation, as KBP functions are typically incomplete, and do not always have continuous derivatives required for the calculation of the forces. The new algorithm has been tested in explorations of conformational space. In these test calculations the KBP energy was found to drop below the value for the native conformation, and the correlation between the root mean square deviation (RMSD) and the KBP energy was shown to be different from the test results in other references. At the present time, the algorithm is useful for testing new KBP functions. Furthermore, if a KBP function can be found for which the native conformation has the lowest energy and the energy/RMSD correlation is good, then this new algorithm also will be a tool for refinement of the theory-based structural models.

Algorithms↗
PubMed1991

Vector-averaged gravity alters myocyte and neuron properties in cell culture.

To investigate whether changes in the gravitational field of developing neurons and myocytes affect cellular development, we rotated cultures of embryonic spinal neurons and myocytes in a horizontal clinostat. Rotation in the clinostat produces, from the cells' perspective, a "vector-free" gravity environment by continuous averaging of the vector. In this way, rotation in the clinostat simulates the microgravity of space where the gravity vector is substantially reduced. At rotation rates of 1-50 rpm, cellular and nuclear areas of myocytes were significantly enlarged and the number of presumptive nucleoli increased. In neurons, frequent and large swellings appeared along neuritic shafts. Some of these changes were reversible after cessation of rotation. Since our data are generally consistent with findings from other cell types subjected to spaceflight, we suggest that the vector-free gravity environment of the clinostat appears to simulate, at least in part, the microgravity of space. Our data further show that cellular processes are sensitive to altered gravity and suggest that cell development in the microgravity of space may be significantly altered.

Animals↗
PubMed1987

Brownian dynamics simulation of restricted rotational diffusion.

The restricted rotational diffusion of an axially symmetric particle is simulated by the Brownian dynamics technique. In addition to the wobbling-in-a-cone model, several continuous potentials are considered. The particle studied is particularly simple: a sphere anchored to a point fixed in space. However, presenting the results in a convenient, reduced form, they are valid for any axially symmetric particle. From simulated rotational trajectories, we calculate (P2(cos alpha] as a function of t, where alpha is the angle between two orientations separated by time t and P2 is the second Legendre polynomial. This correlation function is closely related to time-resolved electro-optic and spectroscopic properties. Simulated results for the cone model are in excellent agreement with the quasiexact results of Lipari and Szabo (1981, J. Chem. Phys., 75:2971-2976). Thus we confirm the good performance of the simulation technique and the validity of our working conditions. Novel results are presented for continuous restricting potentials, V(theta). The (P2) results for V = 1/2K theta 2 and V = Q(1 - cos theta) are practically the same if K and Q are chosen so tht the long-time (P2) values coincide. Thus, the quadratic potential seems to be a good representation of any monotonically increasing potential. However, for an uniaxial potential such as V = Csin2 theta, the decay is appreciably faster. The (P2) decays simulated for the continuous potentials are analyzed by the monoexponential version of the cone model. We found that such an analysis produces an overestimation of the true rotational diffusion coefficient of approximately 15% only, although for uniaxial potentials the error may be larger.

Biopolymers↗
PubMed1998

Computer simulation of FES standing up in paraplegia: a self-adaptive fuzzy controller with reinforcement learning.

Using computer simulation, the theoretical feasibility of functional electrical stimulation (FES) assisted standing up is demonstrated using a closed-loop self-adaptive fuzzy logic controller based on reinforcement machine learning (FLC-RL). The control goal was to minimize upper limb forces and the terminal velocity of the knee joint. The reinforcement learning (RL) technique was extended to multicontroller problems in continuous state and action spaces. The validated algorithms were used to synthesize FES controllers for the knee and hip joints in simulated paraplegic standing up. The FLC-RL controller was able to achieve the maneuver with only 22% of the upper limb force required to stand-up without FES and to simultaneously reduce the terminal velocity of the knee joint close to zero. The FLC-RL controller demonstrated, as expected, the closed loop fuzzy logic control and on-line self-adaptation capability of the RL was able to accommodate for simulated disturbances due to voluntary arm forces, FES induced muscle fatigue and anthropometric differences between individuals. A method of incorporating a priori heuristic rule based knowledge is described that could reduce the number of the learning trials required to establish a usable control strategy. We also discuss how such heuristics may also be incorporated into the initial FLC-RL controller to ensure safe operation from the onset.

Arm↗
PubMed2004

Sensitivity of finite helical axis parameters to temporally varying realistic motion utilizing an idealized knee model.

Various uses of the screw or helical axis have previously been reported in the literature in an attempt to quantify the complex displacements and coupled rotations of in vivo human knee kinematics. Multiple methods have been used by previous authors to calculate the axis parameters, and it has been theorized that the mathematical stability and accuracy of the finite helical axis (FHA) is highly dependent on experimental variability and rotation increment spacing between axis calculations. Previous research has not addressed the sensitivity of the FHA for true in vivo data collection, as required for gait laboratory analysis. This research presents a controlled series of experiments simulating continuous data collection as utilized in gait analysis to investigate the sensitivity of the three-dimensional finite screw axis parameters of rotation, displacement, orientation and location with regard to time step increment spacing, utilizing two different methods for spatial location. Six-degree-of-freedom motion parameters are measured for an idealized rigid body knee model that is constrained to a planar motion profile for the purposes of error analysis. The kinematic data are collected using a multicamera optoelectronic system combined with an error minimization algorithm known as the point cluster method. Rotation about the screw axis is seen to be repeatable, accurate and time step increment insensitive. Displacement along the axis is highly dependent on time step increment sizing, with smaller rotation angles between calculations producing more accuracy. Orientation of the axis in space is accurate with only a slight filtering effect noticed during motion reversal. Locating the screw axis by a projected point onto the screw axis from the mid-point of the finite displacement is found to be less sensitive to motion reversal than finding the intersection of the axis with a reference plane. A filtering effect of the spatial location parameters was noted for larger time step increments during periods of little or no rotation.

Algorithms↗
PubMed1975

Renal effects of continuous negative pressure breathing.

Continuous negative pressure breathing (CNPB) was utilized to simulate the thoracic vascular distension of zero G or Space, in 11 anesthetized rats. The animals underwent renal clearance and micropuncture renal nephron studies before, during, and after CNPB. Four rats were pretreated with a high salt diet and I-M desoxycorticosterone (DOCA) in excess. None of these rats diuresed with CNPB. In contrast, five of the seven remaining rats increased the fraction of the filtered sodium excreted (CNa/GFR, p less than 0.05) and their urinary flow rate (V, p less than 0.05). Potassium excretion increased (UK V, p less than 0.05). End proximal tubular fluid specimen's TF/P inulin ratios were unchanged. Whole kidney and single nephron glomerular filtration rates fell 10%. CNPB, a mechanism for atrial distension, appears to cause in the rat a decrease in distal tubular sodium and water reabsorption. Exogenous mineral-corticoid prevents the diuresis, saluresis, and kaluresis. In a separate group of five rats, the CNPB was prolonged or excessive (CNPB greater than 3.5 cm H2O negative pressure); in these, the diuresis ceased and/or antidiuresis occurred. This confirmed the adequacy of other nonatrial volume control mechanisms in regulating renal salt and water conservation in opposition to the studied atrial-renal (Henry-Gauer) reflex of thoracic vascular distension. It encourages us to suggest that the atrial distension reflex diuresis that occurs with shifts of blood to the thorax in assuming a weightless condition, if comparable to the thoracic vascular distension of this model, will not progressively impair the circulation or the mammal but will be minor and short-lived.

Animals↗
PubMed2003

Combining endogenous and exogenous spatial variability in analytical population models.

Analytically tractable models of dynamics in continuous space rarely incorporate both endogenous and exogenous spatial heterogeneity. We use spatial moment equations in combination with simulation models to analyze the combined effects of endogenous and exogenous variability on population viability in a simple single-population model where landscape heterogeneity and local population density both affect mortality rate. The equations partition the effects of heterogeneity into an effect of local crowding and an effect of habitat association caused by differential mortality. Exogenous heterogeneity in mortality rate increases population viability through habitat association and decreases it through increased crowding; the net effect of exogenous heterogeneity is generally to improve population viability. This result is contrary to some (but not all) conclusions in the literature, which usually focus on the effects of fragmentation rather than the benefits of refuges to short-dispersing individuals.

Algorithms↗
PubMed2005

Hysteresis multicycles in nanomagnet arrays.

We predict two physical effects in arrays of single-domain nanomagnets by performing simulations using a realistic model Hamiltonian and physical parameters. First, we find hysteretic multicycles for such nanomagnets. The simulation uses continuous spin dynamics through the Landau-Lifshitz-Gilbert (LLG) equation. In some regions of parameter space, the probability of finding a multicycle is as high as approximately 0.6 . We find that systems with larger and more anisotropic nanomagnets tend to display more multicycles. Our results also demonstrate the importance of disorder and frustration for multicycle behavior. Second, we show that there is a fundamental difference between the more realistic vector LLG equation and scalar models of hysteresis, such as Ising models. In the latter case spin and external field inversion symmetry is obeyed, but in the former it is destroyed by the dynamics, with important experimental implications.

Journal Article↗
PubMed2004

Retinal glutamate transporter activity persists under simulated ischemic conditions.

Elevated extracellular concentrations of the neurotransmitter glutamate are neurotoxic and directly contribute to CNS damage as a result of ischemic pathologies. However, the main contributors to this uncontrolled rise in glutamate are still unconfirmed. It has been reported that the reversal of high-affinity glutamate transporters is a significant contributing factor. Conversely, it has also been observed that these transporters continue to take up glutamate, albeit at a reduced saturation concentration, under ischemic conditions. We sought to determine whether glutamate transporters continue to remove glutamate from the extracellular space under ischemic conditions by pharmacologically modulating the activity of high-affinity retinal glutamate transporters during simulated ischemia in vitro. Retinal glutamate transporter activity was significantly reduced under these ischemic conditions. The suppression of retinal glutamate transporter activity, with the protein kinase C inhibitor chelerythrine, significantly reduced ischemic glutamate uptake and enhanced retinal neurodegeneration. These findings imply a limited but protective role for retinal glutamate transporters under certain ischemic conditions, suggesting that pharmacological enhancement of high-affinity glutamate transporter activity may reduce tissue damage and loss of function resulting from toxic extracellular glutamate concentrations.

Amino Acid Transport System X-AG↗
PubMed2000

Three-dimensional attenuation map reconstruction using geometrical models and free-form deformations.

We address the issue of using deformable models to reconstruct an unknown attenuation map of the torso from a set of transmission scans. We assume the three-dimensional (3-D) distribution of attenuation coefficients to be piecewise uniform. We represent the unknown distribution by a set of closed surfaces defining regions having the same attenuating properties. The methods of reconstruction published so far tend to directly deform the surfaces, the parameters being the surface elements. Rather than deforming the surfaces, we explore the possibility of deforming the space in which the geometrical primitives are contained. We focus on the use of free-form deformations (FFD's) to describe the continuous transformation of space used to match a set of transmission measurements. We illustrate this approach by reconstructing realistically simulated transmission scans of the torso with various noise levels and compare the results to standard reconstruction methods.

Algorithms↗