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At least 1,675 records · Page 93Linked to original sources
PubMed2002

A maritime navigation display that provides visual feedback to improve conning officers' ship-handling during low visibility environments.

Navigating a ship at night in close proximity to another vessel is a dangerous task. To improve conning officers' night time ship-handling performance, a visual navigation display is proposed that is mounted on the stern of the aircraft carrier that will help shipboard conning officers manoeuvre in a battle group formation. To test the effectiveness of the visual navigation display, the Nimitz-class aircraft and plane guard vessel, a Ticonderoga-class cruiser, were modelled in a virtual environment. A navigation display condition had significantly fewer navigational positional errors than a non-navigation display condition. The navigation display provided immediate feedback as to whether the aircraft carrier had changed bearing or speed, thus enabling the operator to initiate the appropriate input to maintain station astern of the carrier. Actual or potential applications of this research include the deployment of a maritime navigation display to assist conning officers' ship handling.

Computer Graphics↗
PubMed1998

Using leg muscles as shock absorbers: theoretical predictions and experimental results of drop landing performance.

The use of muscles as power dissipators is investigated in this study, both from the modellistic and the experimental points of view. Theoretical predictions of the drop landing manoeuvre for a range of initial conditions have been obtained by accounting for the mechanical characteristics of knee extensor muscles, the limb geometry and assuming maximum neural activation. Resulting dynamics have been represented in the phase plane (vertical displacement versus speed) to better classify the damping performance. Predictions of safe landing in sedentary subjects were associated to dropping from a maximum (feet) height of 1.6-2.0 m (about 11 m on the moon). Athletes can extend up to 2.6-3.0 m, while for obese males (m = 100 kg, standard stature) the limit should reduce to 0.9-1.3 m. These results have been calculated by including in the model the estimated stiffness of the 'global elastic elements' acting below the squat position. Experimental landings from a height of 0.4, 0.7, 1.1 m (sedentary males (SM) and male (AM) and female (AF) athletes from the alpine ski national team) showed dynamics similar to the model predictions. While the peak power (for a drop height of about 0.7 m) was similar in SM and AF (AM shows a +40% increase, about 33 W/kg), AF stopped the downward movement after a time interval (0.219 +/- 0.030 s) from touch-down 20% significantly shorter than SM. Landing strategy and the effect of anatomical constraints are discussed in the paper.

Adult↗
PubMedDate not supplied

Myoelectric control of a computer animated hand: a new concept based on the combined use of a tree-structured artificial neural network and a data glove.

This paper proposes a new learning set-up in the field of control systems for multifunctional hand prostheses. Two male subjects with a traumatic one-hand amputation performed simultaneous symmetric movements with the healthy and the phantom hand. A data glove on the healthy hand was used as a reference to train the system to perform natural movements. Instead of a physical prosthesis with limited degrees of freedom, a virtual (computer-animated) hand was used as the target tool. Both subjects successfully performed seven different motoric actions with the fingers and wrist. To reduce the training time for the system, a tree-structured, self-organizing, artificial neural network was designed. The training time never exceeded 30 seconds for any of the configurations used, which is three to four times faster than most currently used artificial neural network (ANN) architectures.

Amputees↗
PubMed1990

The effects of analogical training models and age on problem-solving in a new domain.

Young and middle-aged adults learned a microcomputer drawing package either with or without an analogical model of the package. Following training, problem-solving flexibility was assessed. Although no age differences were obtained following no-model training, middle-aged subjects performed worse than young subjects following model-based training. These results support the hypothesis that model-based training encourages elaboration and abstraction processes, and that older adults are less likely or less able to engage in such processing.

Adult↗
PubMed1994

Z curves, an intutive tool for visualizing and analyzing the DNA sequences.

A novel method mapping the DNA or RNA sequence into a folding curve in three dimensional space, the Z curve, has been proposed based on the symmetry of the regular tetrahedrons. There exists a unique Z curve for a given DNA sequence, on the contrary, the DNA sequence can be uniquely determined by the given Z curve. The properties of the Z curves have been studied in great details. The symmetry, the periodicity, the local motif, and the global feather of the distribution of bases of the DNA sequences are reflected by the rich folding structures of the Z curves. The Z curves may be smoothed by the B-spline functions of different orders. Therefore, the Z curves may have any resolution by choosing the suitable spline functions. The higher the order of the B-spline function chosen, the lower the resolution of the Z curve. So, the Z curves are suitable for visualizing and analyzing the DNA sequences with any length. The study of the Z curves develops further a new area to visualizing and analyzing the DNA sequences by a geometrical approach. The method of the Z curves may be strengthened by using the ripe mathematical tools of geometry on the one hand; and by using the powerful technique of the computer graphics on the other hand.

Algorithms↗
PubMed1994

Molecular dynamics simulations of a r(GA12G).d(CT12C) hybrid duplex.

RNA.DNA hybrid duplexes are relevant in various biological mechanisms like transcription and replication. Enzymes like RNase H cleave specifically the RNA strand in RNA.DNA duplexes. In antisense technology the complexation of mRNA with "modified" oligo(deoxy)-nucleotides leads to new hybrid duplexes. The knowledge about structure and dynamical behavior on an atomic level is fundamental for the understanding of any process involving hybrid duplexes. Therefore, molecular dynamics studies (200 picoseconds of trajectory) on a hybrid duplex structure r(GA12G).d(CT12C) were performed. During the stimulations, the deoxyribose residues assumed a puckering state between C2'-endo and C3'-endo, with an average mode around O4'-endo-C1'-exo, whereas the riboses of the RNA strand remained in the C3'-endo puckering domain. The results are compared to those obtained for the DNA.DNA duplex d(GA12G).d(CT12C) under identical simulation conditions. The DNA strand in the hybrid duplex behaves similar to that in a standard B-type DNA duplex. The helical parameters of the hybrid duplex however are closer to A- than to B-type. These observations suggest that RNA.DNA hybrid double helices are neither clearly A-form nor B-form. The furanoses in both strands can assume different puckering modes without the appearance of major geometrical constraints. The simulation results are in excellent agreement with recent experimental data.

Base Sequence↗
PubMed1994

Molecular modelling study of DNA-Troeger's bases interactions.

The two enantiomeric forms: 1R,5R (R) and 1S,5S (S) of the Troeger's base analog, 9,19-methano-9,10,19,20-tetrahydrodiacridino-[b,f]-[1,5]- diazocine which possess a C2 axis of symmetry, are susceptible to interact differently with DNA. This paper reports the results of molecular modelling calculations on B DNA-Troeger's base complexes. Two interaction modes have been examined: intercalation and binding in the grooves. Into the limits of accuracy of such a kind of calculations, some tendencies seem to appear. In the intercalation mode, the R and S enantiomers exhibit a selectivity for alternating dinucleotidic sequences and the minor groove is enantioselective for S. Binding in the major groove is selective for S with G-C sequences, and in the minor groove the stereoselectivity appears for R with A-T sequences. The S-(dG-dC)5.(dG-dC)5 complex in the major groove seems to be the most favoured.

Azocines↗
PubMed1995

Molecular dynamics simulation of anesthetic-phospholipid bilayer interactions.

To probe the hypothesis of a lipid-mediated mechanism of general anesthetic action on a molecular level, and to help elucidate the nature of the interactions of bioactive compounds with membranes, the effects of trichloroethylene (TCE), an inhalational general anesthetic, on a dioleoylphosphatidylcholine (DOPC) lipid bilayer have been investigated by molecular dynamics (MD) simulations at 37 degrees C and 1 atm and the results compared with 31P and 2H NMR experimental studies (Ref 1). The model used included a single TCE molecule embedded in a lipid bilayer consisting of 24 DOPC molecules and an 8 A layer of explicit water of solvation in each polar head group region of the bilayer, together with constant-pressure periodic boundary conditions in three dimensions. A comparison of the bilayer properties calculated in the presence and absence of the anesthetic led to the detection of three major perturbations of the bilayer caused by the anesthetic at 1 atm: i) an increase in the ratio of the effective areas of hydrocarbon tails and the head group per lipid, predicting the tendency of lipids near the anesthetic site of action to form a hexagonal phase (HII); ii) a slight increase in the frequency of chain dihedral angles found in the gauche conformation; and iii) a significant increase in the lateral mean-square displacement of lipid molecules, an indication of increased lipid lateral diffusion and membrane fluidity. The pressure antagonism of these effects was also studied by MD simulations at pressures of 200 and 400 atm. The study of the pressure reversibility of these effects at 200 and 400 atm indicated that they were partially prevented at 200 atm and essentially blocked at 400 atm, suggesting their probable relevance to the pressure reversal effect seen with general anesthesia. These results may thus provide insights into the interaction between general anesthetics and similar small organic molecules with membranes.

Computer Graphics↗
PubMed1995

Conformational properties of the Arg-Leu-Gly tripeptide--DMSO--water clusters with the combined use of molecular dynamics and energy minimization studies.

The Arg-Leu-Gly tripeptide is the repeating fragment of sequential arginine-rich polypeptides capable of interacting with DNA. The conformational influence of solvent molecules (DMSO/H2O) were investigated with the combined use of molecular dynamics and energy minimization. It was found that water molecules greatly contribute to the peptide structure by solvating all its hydrophylic sites even in the presence of DMSO excess, whereas one water molecule links the ammonium and carboxylic ends of the Arg-Leu-Gly. The persistence of residual water, which was confirmed by varying the computer simulation parameters, indicates that pretreatment of peptide segments in aqueous solutions should greatly affect their conformational properties in organic media. A satisfactory agreement between experimental data (1H-NMR and IR spectroscopy) and the presented computational study deserves also to be noted.

Amino Acid Sequence↗
PubMed1995

Interaction with DNA of photoactive viologens based on the 6-(2- pyridinium)phenanthridinium structure.

A new type of DNA-interacting violgens derived from the N,N'-dialkyl 6-(2-pyridinium)-phenanthridinium structure (in which dialkyl is -CH2CH2-,-CH2CH2CH2-, or (-CH3)2) have been synthesized. Electronic spectroscopy, steady-state and time-resolved fluorescence, cyclic voltammetry, binding isotherms, viscosity titrations, and molecular modeling techniques were employed to characterize the structural, photophysical and redox properties of the novel drugs as well as the corresponding drug-DNA complexes. The viologens display significant visible absorption (up to ca. 490 nm), and a rather intense luminescence (phi cm from 0.06 to 0.20 at 491-565 nm wavelength maxima) which is efficiently quenched by DNA. The calculated redox potentials of these drugs in their singlet excited state (+2.1 V vs. SHE) predict a large driving force for a photoelectron transfer reaction from the nucleobases to the drugs. Photochemical measurements of the viologens in the presence of mononucleotides, nucleosides, and deoxyribose indicate that the observed fluorescence quenching occurs indeed by electron transfer from the DNA bases rather than the sugar phosphate backbone. Large association constants to double helical DNA (in the order of 10(5) M-1) have been evaluated from the absorbance-based binding isotherms. Viscosimetry supports intercalation of the drugs into the DNA helix. Computer simulations (molecular mechanics of d(CGCGCG)2-drug complexes) confirm the intercalative nature of the binding and provide finer details about the geometry of the different viologen-DNA complexes. Molecular modeling has also revealed a stereoselective interaction of the enantiomeric drug conformers with the chiral DNA helix. A DNA-targeted drug design of future generations of these ligands in order to improve and/or modulate their photochemical, redox, and nucleic acid binding properties appears to be possible by a careful selection of the N,N'-dialkylating chain and/or the substituents on the azaheterocyclic moieties.

Base Sequence↗
PubMed1995

Interaction of an amphiphilic peptide with a phospholipid bilayer surface by molecular dynamics simulation study.

Corticotropin-releasing factor (CRF) is the principal neuroregulator of adrenocorticotropic hormone (ACTH) secretion. Previous experiments have demonstrated that CRF binds avidly to the surface of single egg phosphatidylcholine vesicles and its amphiphilic secondary structure might play an important role in the function. In this study, the interaction of the residues 13-41 in human CRF with the surface of a DOPC bilayer was investigated by molecular dynamics (MD) simulation in order to understand the role of the membrane surface in the formation of the amphiphilic alpha helix as well as to determine the effects of the peptide on the lipid bilayer. The model used included 60 DOPC molecules, 1 helical peptide (CRF13-41) on the bilayer surface, and explicit waters of solvation in the lipid polar head group regions, together with constant-volume periodic boundary conditions in three dimensions. The MD simulation was carried out for 510 ps. In addition, CRF13-41, initially in a helical form, was simulated in vacuo as a control. The results indicate that while it was completely unstable in vacuo, the peptide helical form was generally maintained on the bilayer surface, but with distortions near the terminal ends. The peptide was confined to the bilayer headgroup/water region, similar to that reported from neutron diffraction measurement of tripeptides bound to the phosphatidylcholine bilayer surface (Ref 1). The amphiphilicity of the peptide matched that of the bilayer headgroup environment, with the hydrophilic side oriented toward water and the hydrophobic side making contact with the bilayer hydrocarbon core. These results support the hypothesis that the amphiphilic environment of a membrane surface is important in the induction of peptide amphiphilic alpha-helical secondary structure. Two major effects of the peptide on the lipids were found: the first CH2 segment in the lipid chains was significantly disordered and the lipid headgroup distribution was broadened towards the water region.

Amino Acid Sequence↗
PubMed1995

Calculations of the phi-psi conformational contour maps for N-acetyl alanine N'-methyl amide and of the characteristic ratios of poly-L-alanine using various molecular mechanics forcefields.

We generated phi- psi conformational energy contour maps for the N-acetyl alanine N'-methyl amide using the molecular mechanics forcefields AMBER, AMBER3, BIO85, CFF91, CVFF, MM2, MM3, MM+, AND SYBYL. With MM2, MM3, and MM+ we used a dielectric constant of epsilon = 1.5, the default effective value for these forcefields. With the other forcefields we used epsilon = 1 and 4, except with SYBYL, which, in Spartan 3.1, has no electrostatic term. All forcefields yielded the C7eq conformation as a low-energy minimum or the global minimum. Most of the forcefields also yielded a minimum-energy conformation in the C5, alpha R, and alpha L regions of the phi-psi contour map. Fewer of the forcefields yielded a minimum in the C7ax region; however, adiabatic relaxation frequently lowered the relative energy of this region. Based on the appearance of the phi-psi maps, the following pairs of forcefields were broadly similar (but not identical) to each other but dissimilar to the other pairs: AMBER3 and AMBER, BIO85 and CHARMM, MM+ and MM2, SYBYL and ECEPP, and CFF91 and MM3. We used the data from the phi-psi contour maps to compute the characteristic ratio of poly-L-alanine. Most of the computed values deviated significantly from the experimental value. Only the computed characteristic ratio of CFF91 without adiabatic relaxation at epsilon = 4 and MM3 without adiabatic relaxation at epsilon = 1.5 agreed with the experimental value.

Alanine↗
PubMed1996

Molecular modelling study of the netropsin complexation with a nucleic acid triple helix.

A detailed molecular mechanical study has been made on the complexes of netropsin with the double stranded oligonucleotide (dA)12.(dT)12 and with the triple helix (dA)12.(dT)12.(dT)12. The complexes were built using computer graphics and energy refined using JUMNA program. In agreement with circular dichroism experiments we have shown that 3 netropsins can bind the minor grooves of the triple helix and of the double helix. The groove geometry in the duplex and in the triplex is very similar. However a detailed analysis of the energetic terms shows, in agreement with thermal denaturation studies, that the affinity of netropsin toward the double helices is larger than towards triple helices.

DNA↗
PubMed2005

Computer system for definition of the quantitative geometry of musculature from CT images.

The computer system for quantitative determination of musculoskeletal geometry from computer tomography (CT) images has been developed. The computer system processes series of CT images to obtain three-dimensional (3D) model of bony structures where the effective muscle fibres can be interactively defined. Presented computer system has flexible modular structure and is suitable also for educational purposes.

Arthrography↗
PubMed2006

A proposed computational biomechanics cyber-infrastructure for multi-phase and multi-scale problems: delivering biomechanics to the surgeon.

This paper presents a new direction for practitioners of computational biomechanics. It provides a description of three prototype software platforms, which demonstrate how the cyber-infrastructure can be used to integrate the algorithms of computational biomechanics to solve multi-phase and multi-scale problems. Then, a development platform is presented. This platform can also deliver integrated biomechanics into the surgical ward for surgical planning. This platform performs these tasks without the need for advanced network software tools: an appendix provides all the simple and fundamental open source and CI technologies that are required. The overarching goal of this paper is to make the potential of the emerging cyber-infrastructure comprehensible and accessible to practitioners of computational biomechanics.

Biomechanical Phenomena↗
PubMedDate not supplied

Sharing digital micrographs and other data files between computers.

It ought to be easy to exchange digital micrographs and other computer data files with a colleague even on another continent. In practice, this often is not the case. The advantages and disadvantages of various methods that are available for exchanging data files between computers are discussed. When possible, data should be transferred through computer networking. When data are to be exchanged locally between computers with similar operating systems, the use of a local area network is recommended. For computers in commercial or academic environments that have dissimilar operating systems or are more widely spaced, the use of FTPs is recommended. Failing this, posting the data on a website and transferring by hypertext transfer protocol is suggested. If peer to peer exchange between computers in domestic environments is needed, the use of Messenger services such as Microsoft Messenger or Yahoo Messenger is the method of choice. When it is not possible to transfer the data files over the internet, single use, writable CD ROMs are the best media for transferring data. If for some reason this is not possible, DVD-R/RW, DVD+R/RW, 100 MB ZIP disks and USB flash media are potentially useful media for exchanging data files.

Computer Communication Networks↗
PubMed1994

Integration of graph theory and quantum chemistry for structure-activity relationships.

The objective of this article is to outline both graph-theoretically based and quantum chemically based structural indices of potential use in quantitative structure activity correlations. We consider graph-theoretical indices such as the connectivity index, topological index, Wiener index and molecular ID indices. Several structural and geometry-dependent indices can be derived from semiempirical and ab initio quantum calculations based on the charge densities, overlap matrices, frontier orbitals, molecular hardness, free valence, density matrices, quantum spectral difference indices, quantum spectral indices and bond matrices. Finally, the use of electrostatic potentials and charge densities for the prediction of reactive sites will be discussed.

Butadienes↗
PubMed1985

Rod cells dissociated from mature salamander retina: ultrastructure and uptake of horseradish peroxidase.

To test the effects of isolation on adult neurons, we investigated the fine structure and synaptic activity of rod cells dissociated from the mature salamander retina and maintained in vitro. First, freshly isolated rod cells appeared remarkably similar to their counterparts in the intact retina: the outer segment retained its stack of membranous disks and the inner segment contained its normal complements of organelles. Some reorganization of the cell surface, however, was observed: (a) radial fins, present at the level of the cell body, were lost; and (b) the apical and distal surfaces of the inner and outer segments, respectively became broadly fused. Second, the synaptic endings or pedicles retained their presynaptic active zones: reconstruction of serially sectioned pedicles by using three-dimensional computer graphics revealed that 73% of the synaptic ribbons remained attached to the plasmalemma either at the cell surface or along its invaginations. Finally, tracer experiments that used horseradish peroxidase demonstrated that dissociated rod cells recycled synaptic vesicle membrane in the dark and thus probably released transmitter by exocytosis. Under optimal conditions, a maximum of 40% of the synaptic vesicles within the pedicle were labeled. As in the intact retina, uptake of horseradish peroxidase was suppressed by light. Thus, freshly dissociated receptor neurons retained many of their adult morphological and physiological characteristics. In long-term culture, the photoreceptors tended to round up; however, active zones were present even 2 wk after removal of the postsynaptic processes.

Ambystoma↗