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The intrinsic electrophysiological characteristics of fly lobula plate tangential cells: II. Active membrane properties.

The voltage-gated currents in the fly lobula plate tangential cells were examined using the switched electrode voltage clamp technique. In CH cells, two currents were identified (Figs. 1, 2): a slow calcium inward current and a delayed rectifying, noninactivating potassium outward current. HS and VS cells appear to possess similar currents to CH cells, but in addition, exhibit a fast-activating sodium inward current and a sodium-activated potassium outward current (Figs. 3, 4). While the delayed rectifying potassium current in all three cell classes is responsible for the observed outward rectification described previously (Borst and Haag, 1996), the sodium inward current produced the fast and irregular spikelike depolarizations found in HS and VS cells but not in CH cells: When the sodium current is blocked by either. TTX or intracellular QX314, no more action potentials can be elicited in HS cells under current-clamp conditions (Fig. 5). As is demonstrated in HS cells, space clamp conditions are sufficient to suppress synaptically induced action potentials (Fig. 6). The currents described above were incorporated with the appropriate characteristics into compartmental models of the cells (Fig. 7, 8). The anatomical and electrically passive membrane parameters of these cells were determined in a preceding paper (Borst and Haag, 1996). After fitting the current parameters to the voltage-clamp data (Fig. 9), the model cells qualitatively mimicked the fly tangential cells under current clamp conditions in response to current injection (Fig. 10). The simulations demonstrated that the electrical compactness seen in the HS and VS cells, either in passive models or in active models during continuous hyperpolarization, decreased significantly in the active models during continuous depolarization (Fig. 11). Active HS models reproduce the frequency-dependent amplification of current injected into their axon (Fig. 12).

Animals↗

Molecular dynamics simulations of cyclohenicosakis-[(1-->2)-beta-D-gluco-henicosapyranosyl], a cyclic (1-->2)-beta-D-glucan (a 'cyclosophoraose') of DP 21.

We report molecular dynamics simulations of cyclohenicosakis-[(1-->2)-beta-D-gluco-henicosapyranosyl], termed 'cyclosophohenicosamer', a member of a class of cyclic (1-->2)-beta-D-glucans ('cyclosophoraoses'). Our goals were to provide insights into the conformational preferences of these cyclosophoraoses. Simulated annealing and constant-temperature molecular dynamics calculations were performed on the DP 21 cyclosophohenicosamer. The radius of gyration (R(G)) of the molecule and the conformation of glycosidic dihedral angles were used to analyze the result of computational studies. Most glycosidic linkages were concentrated in the lowest-energy region of the phi-psi energy map, and the values of radius of gyration from our simulations were consistent with the reported experimental value. The simulations produced various types of compact and asymmetric conformations within reasonable ranges of the glycosidic linkage conformation and radius of gyration. The results indicate the presence of a high degree of molecular flexibility of cyclosophohenicosamer and suggest the uniqueness of inclusion complexation with other molecules through this molecular flexibility.

Carbohydrate Conformation↗

Monte Carlo simulation of irradiance distribution on the retina after refractive surgery.

PURPOSE: Generation of random wavefronts for ocular wave aberration statistics across the population has been used for various analyses. We propose a more accurate simulation procedure. This simulation technique is not intended to be a perfect representation of an eye, but instead is a tool for those applications where a correct distribution of aberrations across a population is necessary. METHODS: Our technique consists of the generation of coefficients of the wavefront expansion into Zernike modes. The simulation makes use of the variance of every mode measured on a large population by using compact and reliable wavefront sensors. RESULTS: The simulation procedure was verified by reproducing two statistical functions that characterize eye behavior. This tool can be used to predict the performance of sensing techniques and to evaluate the consequences of customized ophthalmic elements and refractive surgery. It may also be useful for deriving both first and second order photon statistics of the point-spread function on the human retina (a key parameter in certain visual perception models). CONCLUSIONS: A new tool for analysis of customized refractive surgery is presented and the evolution of the light intensity probability density function on the retina with compensation attained after customized correction of the eye's aberrations is analyzed.

Humans↗

Hipocrates: a robust system for the control of neuromuscular blockade.

OBJECTIVE: Development of an automatic system (software package Hipocrates) for the control of neuromuscular blockade by continuous infusion of the non-depolarising types of muscle relaxant drugs presently used in anaesthesia, namely atracurium, cisatracurium, vecuronium and rocuronium. METHODS: Hipocrates incorporates control strategies based upon classical, adaptive and robust control, as well as a wide range of noise reduction techniques and on-line adaptation to patient-specific characteristics. Therefore, the system provides strong robustness to inter- and intra-individual variability of the patients responses or unexpected circumstances and adaptation to the individual requirements. RESULTS: The control system is easy to set up and to use in a clinical environment. It consists of a portable PC computer, a Datex AS/3 NMT sensor and a B/Braun compact perfusion pump. In the simulation mode the software package incorporates sophisticated generation of pharmacokinetic/pharmacodynamic models driven by simulated drug administration regimes (bolus, continuous infusion and a combination of both). CONCLUSIONS: Hipocrates is an advanced standalone application for the control of neuromuscular blockade with a friendly graphic interface. It has been extensively validated, and it can be used on patients undergoing surgery as well as for simulation studies. Therefore Hipocrates also provides an excellent environment for education and training purposes.

Anesthesia, General↗

Temperature dependence of NMR order parameters and protein dynamics.

The helical subdomain, HP36, of the F-actin-binding headpiece domain of chicken villin, is the smallest naturally occurring polypeptide that folds to a thermostable compact structure. Unconstrained molecular dynamics simulations and constrained molecular dynamics simulations using umbrella sampling are used to study the temperature dependence of internal motions of the backbone amide moieties of HP36. The potential of mean force (PMF) for the N-H bond vector, determined from the constrained simulations, is found to be temperature dependent. A simple analytical expression is derived that describes the temperature dependence of the PMF. The parameters of this model are obtained from the PMF, from the unconstrained molecular dynamics simulations, or from experimental values of the generalized order parameter. The results provide a linkage between experimental and theoretical measures of the temperature dependence of protein motions.

Computer Simulation↗

Powder densification. 1. Particle-particle basis for incorporation of viscoelastic material properties.

The present investigation was undertaken to examine the basic unit of densification: the particle-particle indentation. The true interparticle contact area that is established during densification ultimately determines the quality of the tablet compact. By examining the interfacial contact between mutually indenting viscoelastic particles, the process of contact evolution may be represented in mathematical form through extension of the classical Hertzian elastic contact description to encompass material viscoelastic terms. In this way, the time-dependent response of materials to applied loads may be addressed explicitly. The effects of rates of applied loading and maximum load levels were also considered. This analysis was based on viscoelastic stress data collected using an instrumented Instron analyzer during the densification of PMMA/coMMA, a pharmaceutical polymeric coating material. A crossed cylinder matrix compaction geometry was used to simulate the geometry of two mutually indenting spherical particles. Numerical and graphical solutions delineating the relationship between contact area evolution and the prescribed loading force are presented. This particle-particle description of the contacting interface serves as a unit basis for describing the entire powder bed. The powder bed may ultimately be modeled as a collection of these particles in contact.

Algorithms↗

Silicon synaptic conductances.

We have developed compact analog integrated circuits that simulate two synaptic excitatory conductances. A four-transistor circuit captures the dynamics of an excitatory postsynaptic current caused by a real AMPA conductance. A six-transistor circuit simulates the effects of a real voltage-dependent NMDA conductance. The postsynaptic current dynamics are modeled by a current mirror integrator with adjustable gain. The voltage dependence of the silicon NMDA conductance is realized by a differential pair. We show the operation of these silicon synaptic conductances and their integration with the silicon neuron (Mahowald and Douglas, 1991).

Action Potentials↗

Application of evolutionary algorithm methods to polypeptide folding: comparison with experimental results for unsolvated Ac-(Ala-Gly-Gly)5-LysH+.

We present an evolutionary method for finding the low-energy conformations of polypeptides. The application, called FOLDAWAY,is based on a generic framework and uses several evolutionary operators as well as local optimization to navigate the complex energy landscape of polypeptides. It maintains two complementary representations of the structures and uses the CHARMM force field for evaluating the energies. The method is applied to unsolvated Met-enkephalin and Ac-(Ala-Gly-Gly)(5)-Lys(+)H(+). Unsolvated Ac-(Ala-Gly-Gly)(5)-Lys(+)H(+) has been the object of recent experimental studies using ion mobility measurements. It has a flat energy landscape where helical and globular conformations have similar energies. FOLDAWAY locates several large groups of structures not found in previous molecular dynamics simulations for this peptide, including compact globular conformations, which are probably present in the experiments. However, the relative energies of the different conformations found by FOLDAWAY do not accurately match the relative energies expected from the experimental observations.

Algorithms↗

Application of constraint programming techniques for structure prediction of lattice proteins with extended alphabets.

MOTIVATION: Predicting the ground state of biopolymers is a notoriously hard problem in biocomputing. Model systems, such as lattice proteins, are simple tools and valuable to test and improve new methods. Best known are models with sequences composed from a binary (hydrophobic and polar) alphabet. The major drawback is the degeneracy, i.e. the number of different ground state conformations. RESULTS: We show how recently developed constraint programming techniques can be used to solve the structure prediction problem efficiently for a higher order alphabet. To our knowledge it is the first report of an exact and computationally feasible solution to model proteins of length up to 36 and without resorting to maximally compact states. We further show that degeneracy is reduced by more than one order of magnitude and that ground state conformations are not necessarily compact. Therefore, more realistic protein simulations become feasible with our model.

Algorithms↗

Traveling length and minimal traveling time for flow through percolation networks with long-range spatial correlations.

We study the distributions of traveling length l and minimal traveling time t(min) through two-dimensional percolation porous media characterized by long-range spatial correlations. We model the dynamics of fluid displacement by the convective movement of tracer particles driven by a pressure difference between two fixed sites ("wells") separated by Euclidean distance r. For strongly correlated pore networks at criticality, we find that the probability distribution functions P(l) and P(t(min)) follow the same scaling ansatz originally proposed for the uncorrelated case, but with quite different scaling exponents. We relate these changes in dynamical behavior to the main morphological difference between correlated and uncorrelated clusters, namely, the compactness of their backbones. Our simulations reveal that the dynamical scaling exponents d(l) and d(t) for correlated geometries take values intermediate between the uncorrelated and homogeneous limiting cases, where l(*) approximately r(d(l)) and t(*)(min) approximately r(d(t)), and l(*) and t(*)(min) are the most probable values of l and t(min), respectively.

Journal Article↗

An anthropomorphic phantom for periodontal radiography.

OBJECTIVE: To construct an anthropomorphic phantom for periodontal radiography. METHODS: The phantom material for the spongiosa was produced by melting polyethylene with calcium hydroxyapatite. Compact bone and teeth were simulated by mixing silicone rubber with calcium hydroxyapatite and calcium carbonate respectively. RESULTS: Radiographs of the phantom show nearly all the structures relevant for periodontal radiography. Measurements of X-ray attenuation and optical density correspond to those of the human mandible. Any defect in the periodontal bone can be reproduced. CONCLUSION: The new phantom will be useful for research and education.

Alveolar Bone Loss↗

A fast, compact approximation of the exponential function.

Neural network simulations often spend a large proportion of their time computing exponential functions. Since the exponentiation routines of typical math libraries are rather slow, their replacement with a fast approximation can greatly reduce the overall computation time. This article describes how exponentiation can be approximated by manipulating the components of a standard (IEEE-754) floating-point representation. This models the exponential function as well as a lookup table with linear interpolation, but is significantly faster and more compact.

Algorithms↗

Molecular dynamics simulations of the rehydration of folded and unfolded cytochrome C ions in the vapor phase.

Molecular dynamics (MD) simulations have been performed to study the rehydration of compact and unfolded cytochrome c ions in the vapor phase. Experimental studies have shown that the compact conformations adsorb many more water molecules than unfolded ones when exposed to water vapor. MD simulations performed with up to 150 water molecules reproduce the key experimental observations, including a partial refolding caused by hydration. According to the calculations it is more energetically favorable to hydrate the compact conformation in the initial stages of hydration, because it is easier for a water molecule to interact simultaneously with several polar groups (due to their proximity). The protonated side chains are not favored hydration sites in the simulations because they have "self-solvation" shells which must be disrupted for the water to penetrate. For both conformations, the adsorbed water molecules are mainly located in surface crevices.

Computer Simulation↗

Neutron and X-ray solution-scattering studies of the ternary complex between proteoglycan-binding region, link protein and hyaluronan.

Proteoglycan aggregates of cartilage are stabilized by the formation of a ternary complex between the G1 domain at the N-terminus of the proteoglycan monomer (aggrecan), link protein and hyaluronan polysaccharide. Both the G1 domain and link protein contain similar three-domain structures formed from an immunoglobulin fold and two proteoglycan tandem repeats, the arrangement of which had been investigated by neutron and synchrotron X-ray scattering [Perkins, Nealis, Dunham, Hardingham & Muir (1991) Biochemistry 30, 10708-10716]. Here, solution scattering was used to investigate the ternary complexes formed between a proteolytic fragment of proteoglycan monomer containing G1 (termed binding region), link protein and hyaluronan oligosaccharides containing either 34 or 450 saccharide units (HA34 and HA450). The ternary complex with HA34 had a neutron radius of gyration, RG, at infinite contrast not exceeding 5.5 nm. The ternary complex with HA34 had an X-ray cross-sectional radius of gyration Rxs of 2.4 nm and a neutron Rxs at infinite contrast of 2.00 nm. Since both were similar or larger than the Rxs for binding region (X-rays, 2.04 nm; neutrons, 1.84 nm) and link protein (neutrons, 0.8 nm), analyses showed that the cross-sectional mean width of the ternary complex is greater than those in each of the free proteins, i.e. the two proteins associated side-by-side. Similar results were obtained with HA450 complexed with binding region and with both binding region and link protein. This structural model was verified by hydrodynamic simulations of the experimental sedimentation coefficient of 5.5 S, which showed that a compact ternary-complex structure was formed. Although scattering curve simulations using small spheres were limited for the ternary complex with HA34 because of its approximate RG value, the scattering data were compatible with the formation of a compact complex formed by side-by-side contacts between G1 and link protein.

Extracellular Matrix Proteins↗

Safe immobilization of Cr(III) in heat-treated zeolite tuff compacts.

The possibility to remove chromium ions from a simulated electroplating wastewater by a discontinuous ion-exchange process based on phillipsite-rich Neapolitan yellow tuff (NYT) has been investigated. The immobilization of the pollutant cation in the resulting sludge through a heat-treatment has been realized, demonstrating that compacts made of Cr-loaded NYT powder, fired at temperatures of 1000 degrees C or over, are safe materials with negligible Cr3+ leaching. The set up overall process allows, in addition, a volume reduction of the waste with associated lower disposal costs or, better, the obtainment of a ceramic material, whose physical and mechanical properties are comparable to those of similar ordinary ceramics, such as bricks. In summary, the proposed strategy looks at the polluted sludge as a resource to be exploited, instead of a dangerous material to safely dispose of.

Cations↗

A new cardiac auscultation simulator.

We have successfully developed a new cardiac auscultation simulator by applying recently developed digital and computer technology, which digitally records, stores, modifies, and plays back heart sounds and murmurs characteristic of various heart diseases. The simulator is capable of playing back different heart sounds or murmurs at each auscultatory site (aortic, pulmonic, tricuspid, and mitral) of a human chest-sized mannequin (made of urethane foam), through four built-in speakers. We were able to listen to accurate reproductions of heart sounds and murmurs at the same timing as in real patients by any type of stethoscope used in routine medical practice. This compact and portable educational apparatus, which simulates realistic auscultatory sounds, will impact greatly on the medical training of cardiac auscultation for physicians, medical students, nurses, and paramedicals.

Computer Simulation↗

Analysis of fragments induced by simulated lattice protein folding.

The folding process of a set of 42 proteins, representative of the various folds, has been simulated by means of a Monte Carlo method on a discrete lattice, using two different potentials of mean force. Multiple compact fragments of contiguous residues are formed in the simulation, stable in composition, but not in geometry. During time, the number of fragments decreases until one final compact globular state is reached. We focused on the early steps of the folding in order to evidence the maximum number of fragments, provided they are sufficiently stable in sequence. A correlation has been established between these proto fragments and regular secondary-structure elements, whatever their nature, alpha helices or beta strands. Quantitatively, this is revealed by an overall mean one-residue quality factor of nearly 60%, which is better for proteins mainly composed of alpha helices. The correspondence between the number of fragments and the number of secondary-structure elements is of 77% and the regions separating successive fragments are mainly located in loops. Besides, hydrophobic clusters deduced from HCA correspond to fragments with an equivalent accuracy. These results suggest that folding pathways do not contain structurally static intermediate. However, since the beginning of folding, most residues that will later form one given secondary structure are kept close in space by being involved in the same fragment. This aggregation may be a way to accelerate the formation of the native state and enforces the key role played by hydrophobic residues in the formation of the fragments, thus in the folding process itself.

Computer Simulation↗

Monte Carlo simulation of LNCaP human prostate cancer cell aggregation in liquid-overlay culture.

Neoplastic cells self-assemble in liquid-overlay cultures into multicellular spheroids that resemble micrometastases and avascular regions of larger tumors. A Monte Carlo simulation based on Meakin's cluster-cluster aggregation model resolved the physical mechanisms by which LNCaP human prostate cancer cells aggregate in this environment. The best-fit solution suggests that LNCaP cells aggregate with an adhesion probability of 0.5% when they migrate within a radius of influence between cell centers of 180 microm, 10 times the cell diameter. The sweeping radius of influence is indicative of cell tethering and/or chemotaxis and results in an intrinsic rate of self-aggregation that increases from k(11) = 1.5 h(-1) for single cells to k(1010) = 17.5 h(-1) for 10-mers. Similar rates are predicted by Smoluchowski's collision theory (1), suggesting that they are inherent properties of LNCaP liquid-overlay culture. Aggregates form more compact structures in culture than during simulation as measured by the fractal dimension: D(F) = 1.74 +/- 0.04 for 10-mers in culture vs D(F) = 1.25 +/- 0.10 for simulated 10-mers. Additional restructuring would further extend the radius of influence and diminish adhesion. Applications of this work include the production of highly viable spheroids for drug testing and basic oncological research.

Cell Adhesion↗