Computer simulation of hydraulic flows in the human eye

A two-dimensional computer model was developed to describe hydraulic flows inside the human eye. The flow field was described by coupled Navier-Stokes and Darcy equations. The velocity and pressure profiles in the chambers, the wall, and the vitreous body of the normal eye were obtained using the finite-element method. The model includes filtration of fluid from the retinal capillary and its drainage through the choroid. The applications of this model include estimation of the contribution of convection and diffusion to the transport of drugs and study of the kinetics of biodistribution in the eye.     

Computer simulation of overshoot in saccadic eye movements.

The human horizontal eye movement system produces quick, precise, conjugate eye movements called saccades. These are important in normal vision. For example, reading tasks exclusively utilize saccadic eye movements. The majority of saccades have dynamic overshoot. The amplitude of this overshoot is independent of saccadic amplitude, and is such that it places the image of the stimulus within the retinal region of maximum acuity within a minimum of time. A computer based model of the saccadic mechanisms was used to study the origin of this overshoot. It was discussed that dynamic overshoot cannot be attributed to biomechanism properites of the eye movement mechanism, but must instead be explained by variations in the controlling nervous activity. The form of this neural controller signal is very similar to that required for a time optimal response of an inertial system.     

Computer simulation of human body dynamics

Understanding human body dynamics is important in many situations, such as automobile and aircraft crashes, aircraft ejections, falls, and other acceleration environments. The design of automobile interiors, cockpits, and safety equipment requires knowledge of the forces and accelerations encountered during an emergency. Because of the limited information available from actual events and the various constraints in testing, computer simulations are often the only means of obtaining detailed information. The Armstrong Laboratory (AL) developed the Articulated Total Body (ATB) model to predict the human body dynamics in many of these environments. This model is a three-dimensional rigid body dynamics program in which the human body is modeled as a series of segments. Forces on the body segments are calculated based on their interaction with the surroundings including seat and cockpit surfaces. The model also calculates the internal joint resistive and constraint forces. Because of this capability to predict both internal and external forces acting on the body, the ATB model can be used in investigating injuries. It is also a valuable design tool for evaluating safety of proposed systems before prototypes are built or costly tests conducted. When testing is conducted, the model provides data that cannot be measured, such as forces within the body, and supplementing test data with parameter variation simulations. To validate the model, tests such as those conducted on the AL impact sled are simulated. Test films and instrumentation data are compared with simulation graphics and quantitative output to gain confidence in the simulation results.     

Computer simulation of blood flow in the human arm

This paper considers a finite element method to characterize blood flow in the human arm arteries. A set of different pressure waveforms, which represent normal and diseased heart pulses, is used for the proximal boundary conditions, and a modified Windkessel model is used for the distal arterial boundary conditions. A comparison of the distal pressure and flow waveforms, for each different proximal pressure, is made to determine whether such waveforms are significantly altered from normal waveforms. The results show that the distal pressure and/or flow waveforms in certain cases are sufficiently different to be possibly used as a diagnostic indicator of an abnormal heart condition. Also considered is the effect of stenosis, change of compliance, and dilatation of the distal beds on the pressure and flow waveforms. A stenosis which has an area reduction of greater than approximately 75% is found to significantly alter both the distal pressure and flow waveforms. Changes in arterial compliance, however, do not strongly influence the waveforms. Dilatation of distal vascular beds is simulated by reducing the lumped resistance of these beds, and this reduction increases mean flow and decreases mean distal pressure, but has little effect on the basic shape of either the pressure or flow waveform.     

Computer simulation of polypeptides in a confinement

A coarse-grained model of polypeptide chains confined in a slit formed by two parallel impenetrable surfaces was studied. The chains were flexible heteropolymers (polypeptides) built of two kinds of united atoms—hydrophobic and hydrophilic. The positions of the united atoms were restricted to the vertices of a [310] lattice. The force field consisted of a rigorous excluded volume, a long-distance potential between a pair of amino-acid residues and a local preference for forming secondary structure (helices). The properties of the chains were studied at a wide range of temperatures from good to bad solvent conditions. Monte-Carlo simulations were carried out using the algorithm based on the chain’s local changes of conformation and employing the Replica Exchange technique. The influence of the chain length, the distances between the confining surfaces, the temperature and the force field on the dimension and the structure of chains were studied. It was shown that the presence of the confinement chain complicates the process of the chain collapse to low-temperature structures. For some conditions, one can find a rapid decrease of chain size and a second transition indicated by the rapid decrease of the total energy of the system. Figure A scheme of a polypeptide chain built on a [310] lattice and confined to a slit formed by a pair of parallel impenetrable surfaces Proceedings of “Modeling Interactions in Biomolecules II,” Prague, September 5th–9th, 2005.     

Computer simulation of the geometry of the human bronchial tree

Some morphological features of the human bronchial tree were simulated by computergenerated trees. The trees were ordered by the methods of Horsfield and Strahler. Delta, the difference between the Horsfield orders of the two branches at a bifurcation, was determined by pseudorandom numbers generated according to a distribution of probabilities defined on input. By trial and error a distribution was found which resulted in trees being generated with average Strahler order branching ratios of 2.82, similar to a real bronchial tree. Branching angles and length ratio could also be defined on input. By varying these input parameters it was found that the form of the tree was quite sensitive to them, and that by a suitable choice the intrasegmental part of the bronchial tree could be simulated. It is concluded that branching ratio, length ratio, mean branching angles and distribution of delta are controlled within tight limits in the bronchial tree, and this may support the concept of optimal design.     

Computer simulation of a cerebellar cortex compartment

Computer simulation experiments are described regarding information storage and retrieval at a network consisting of one Purkinje cell and 20,000 granule cells. The information content depends on a scheme type and the properties of Purkinje cells. It is shown that a practically attainable information record efficiency is of the order 0.6 bit per binary memorising synapse. Associative information recall is demonstrated for the Marr's memory unit and expressions are derived for an information-content estimation based on parameter values obtained by simulation. The consequences of this computer simulation for physiological experiments are extensively discussed.     

Computer simulation of a cerebellar cortex compartment

Here, Marr's theory of the cerebellum is elaborated at a detailed cellular level. The experimental grounds for the theory are briefly reviewed and problems related to (mossy-fibres) - (granule cell) coding are formulated. The properties of several particular types of (mossy-fibres) - (granule cell) connection matrices are illustrated through computer simulation.     

Computer simulation of Gd(III) speciation in human interstitial fluid

The speciation and distribution of Gd(III) in human interstitial fluid was studied by computer simulation. The results show that at the background concentration, all the Gd(III) species are soluble and no precipitates appear. However as the total concentration of Gd(III) rises above 2.610 × 10^–9 mol/l,the insoluble species become predominant. GdPO₄ is formed first as a precipitate and then Gd₂(CO₃)₃. Among soluble species, free Gd(III), [Gd(HSA)], [Gd(Ox)] and the ternary complexes of Gd(III) with citrate as the primary ligand are main species when the total concentration of Gd(III) is below 2.074 × 10^–2 mol/l. With the total concentration of Gd(III) further rising, [Gd₃(OH)₄] begins to appear and gradually becomes a predominant species.     

Computer simulation of the neural discharge carried by the abducens nerve during eye fixation in the cat

The neural signal carried by the abducens nerve during eye fixations was simulated. The neural discharge was defined by the number of spikes carried by the abducens nerve within each ms. Calculations were based on real neurophysiological data. The computed neural signal showed frequency histograms and variance/mean ratios typical of Poisson distribution. A peak was obtained in the power spectral density function of the simulated neural signal. This peak appeared in the frequency range corresponding to the firing rate of single motoneurons for each eye position. It remained as a broad spectral peak after filtering by a second-order differential equation simulating the ocular mechanics. The obtained spectra are similar to the described power spectral density function of eye position recordings. Present results add evidence of a possible neural basis for ocular tremor.     

Computer simulation of inhibition-dependent binding in a neural network

Reverberating dynamics of neural network is modeled on PC in order to illustrate possible role of inhibition as binding controller in the network. The network is composed of binding neurons. In the binding neuron model [BioSystems 48 (1998) 263], the degree of temporal coherence between synaptic inputs is decisive for triggering, and slow inhibition is expressed in terms of the degree, which is necessary for triggering. Two learning mechanisms are implemented in the network, namely, adjusting synaptic strength and/or propagation delays. By means of forced playing of external pattern, the network is taught to support dynamics with disconnected and bound patterns of activity. By choosing either high, or low inhibition, one can switch between the disconnected and bound patterns, respectively. This is interpreted as inhibition-controlled binding in the network.     

Computer simulation of selection in a hypothetical crop species

A computer simulation model demonstrating the effect of directionalselection upon a simplified quantitative genetic character,is presented. Complementary homozygous parents were crossedto generate a filly heterozygous F₁ population. Phenolypic truncationselection was effected upon the F₂ and subsequent generations,and genotypic and phenolypic response to selection, as wellas the change in population heterozygosizy, was monitored togeneration F₉ The model simulates selection for alternativebreeding regimes, modes of allelic interaction, selection pressure,population size and levels of environmental variation. Threealternative methods for the simulation of the environmentalcomponent of phenozypic variance are incorporated, and mechanismsand relative merits of the rival methods are discussed. Datagenerated by the model confonned closely to theoretical expectation,lending support to the use of the model as a platform for developmentof more comprehensive simulation models. Potential improvementsto the model are discussed.     

Computer analysis of rapid eye movements

Simulation of the saccadic eye movement mechanism and, more recently, diagnosis of neuromuscular disorders associated with saccades rely on accurate recording and analysis of saccade characteristics. Traditionally, eye movements are monitored objectively by registering a transduced voltage correlate of eye position on a pen or cathode ray oscillograph. Analysis of the record obtained is tedious and often inaccurate. The advent of small digital computers with analog-to-digital capability permits more efficient recording. However, computer programs reviewed are limited to the analysis of specific saccade parameters or partly depend on manual operations. The computer program described stores the entire saccadic event of each eye between pre-defined limits including the pre- and post-saccade intervals. Preliminary operations including artifact identification, location of onset, elimination of RC decay, DC offset and amplitude scaling prepare the data for display and subsequent analysis. The program also includes a subroutine to derive the mean and standard deviation of successive saccades.     

Computer simulation of polypeptide translocation through a nanopore

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

Computer simulation of DNA supercoiling in a simple elastomechanical approximation

DNA supercoiling is both an interesting problem from the theoretical point of view and an important phenomenon affecting DNA functions in vivo. Experimentally, however, hardly more than the overall hydrodynamic shape, superhelical density, and enzymic or chemical reactivity of the parameters that are in some way related to DNA secondary and tertiary structure in the superhelical state can be determined. Consequently, it is highly desirable to build up models of DNA supercoiling that, on the one hand, match the above type of global data and, on the other, take advantage of the knowledge about DNA structure at lower levels of complexity, i.e., with linear DNA molecules and its synthetic models. One possible approach, presented here, deals with an extension of Fuller's and Benham's general ideas concerning an elastomechanical model of DNA supercoiling. We extend their model with an algorithm suitable for numerical calculations and construct a fast computer program, ROPASE , that displays the rod shapes as dependent on its elastic properties and applied stress. Development of this program made inevitable a detailed analysis of the input parameters found to be degenerate in the sense that not all of them should be considered variable to generate the whole set of possible solutions of the model. Many calculations were performed using ROPASE to test its properties and the properties of the elastomechanical model. Representative DNA shapes are presented.     

Computer simulation of mutagenesis

A FORTRAN program is described which simulates point-substitution mutations in the DNA strands of typical organisms. Its objective is to help students to understand the significance and structure of the genetic code, and the mechanisms and effects of mutagenesis. The program is intended to be used as part of an elementary course in genetics at degree level.