PURPOSE: To evaluate a computer program to modulate the visual impairment caused by intraocular lens (IOL) misalignment and visualize results obtained by numerical calculations. SETTING: Department of Ophthalmology, Medical Faculty of Charles University, Prague, Czech Republic. METHODS: The optic imagery of a Landolt circle was calculated using a ray-tracing computer program. Visual aberrations resulting from a decentered and/or tilted IOL were studied using this program and compared with theoretical calculations. RESULTS: The IOL decentration and/or tilt shifted the postoperative refractive errors toward myopia and astigmatism (oblique). The combination of IOL decentration and tilt produced a refractive error that depended on the relationship between the geometrical axes of the decentration and tilt. The refractive error can be enhanced or diminished depending on the relationship of these axes. CONCLUSIONS: These findings verify the results calculated by paraxial vergence equations. A ray-tracing program simulated the optic imagery for various kinds of IOL misalignment and IOL optic properties.

• MeSH
• astigmatismus etiologie   MeSH
• biologické modely * MeSH
• lidé MeSH
• migrace cizích těles komplikace   MeSH
• myopie etiologie   MeSH
• nitrooční čočky škodlivé účinky   MeSH
• počítačová simulace * MeSH
• poruchy zraku diagnóza   etiologie   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

A computer-aided stochastic model of the radiolysis of liquid water has been developed. It is based on Monte Carlo simulation of charged-particle tracks, a random-flight method to simulate diffusion of species and the Debye-Smoluchowski theory of reactions between radicals. The model takes into account the formation of ionizations, excitations and subexcitation electrons at the physical stage. The corresponding initial yields at approximately 1 fs were found to be G(ion) = 4.37, G(exc) = 2.81 and G(e-sub) = 4.38. The energy spectrum of subexcitation electrons has been calculated. Autoionizations and dissociations of excited molecules, hole migration, electron thermalization, geminate recombination and the cage effect are considered at the physico-chemical stage. The mean thermalization distance of subexcitation electrons is 24.5 nm. The initial yields of e(aq)-, H+, OH, H, H2 and O are 4.89, 4.86, 5.96, 1.10, 0.15 and 0.15, respectively. The reactions between radicals and products as well as their diffusion are simulated at the chemical stage. The decay kinetics of the most important radicals is reported together with the time evolution of the most important reactions. The yields of the reactive radicals, e(aq)-, H+, OH, H and OH-, at 1 ps are 4.84, 4.85, 5.87, 1.09 and 0.0, respectively. The respective steady-state yields at 10 micros are 2.70, 3.58, 2.89, 1.17 and 0.79. The yields of molecular products, H2O2 and H2, are 0.73 and 0.47 at 10 micros. The concentration-dependent yields of e(aq)-, OH and H2O2 are calculated in three different aqueous solutions. The predictions of the model agree fairly well with experimental data.

• MeSH
• chemické jevy MeSH
• chemické modely MeSH
• elektrony MeSH
• fyzikální chemie MeSH
• ionizující záření MeSH
• ionty MeSH
• počítačová simulace MeSH
• radiochemie MeSH
• stochastické procesy MeSH
• voda * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• ionty MeSH
• voda * MeSH

Impact stress (the impact force divided by the contact area of the vocal folds) has been suspected to be the main traumatizing mechanism in voice production, and the main cause of vocal fold nodules. However, there are also other factors, such as the repetitive acceleration and deceleration, which may traumatize the vocal fold tissues. Using an aeroelastic model of voice production, the present study quantifies the acceleration and impact stress values in relation to lung pressure, fundamental frequency (F0) and prephonatory glottal half-width. Both impact stress and acceleration were found to increase with lung pressure. Compared to impact stress, acceleration was less dependent on prephonatory glottal width and, thus, on voice production type. Maximum acceleration values were about 5-10 times greater for high F0 (approx. 400 Hz) compared to low F0 (approx. 100 Hz), whereas maximum impact stress remained nearly unchanged. This suggests that acceleration, i.e. the inertia forces, may present at high F0 a greater load for the vocal folds, and in addition to the collision forces may contribute to the fact that females develop vocal fold nodules and other vocal fold traumas more frequently than males.

• MeSH
• akustika řeči MeSH
• biologické modely MeSH
• fonace fyziologie   MeSH
• glottis fyziologie   MeSH
• lidé MeSH
• plíce fyziologie   MeSH
• počítačová simulace * MeSH
• pohlavní dimorfismus MeSH
• tlak vzduchu MeSH
• Check Tag
• lidé MeSH
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• srovnávací studie MeSH

The authors present in their paper the possibilities of the application of computer graphics and computer animation for visualization of the electric heart field (EHF). They describe the construction of three-dimensional potential maps by the methods of interpolation, perspective projection, hidden line elimination and text generation. They also present a method for making of animation films showing the electric activity of the heart by using 80 three-dimensional potential maps recorded at different intervals over the entire cardiac cycle.

• MeSH
• elektrofyziologie MeSH
• elektrokardiografie MeSH
• modely kardiovaskulární * MeSH
• počítačová grafika * MeSH
• počítačová simulace * MeSH
• srdce fyziologie   MeSH
• Publikační typ
• časopisecké články MeSH

This study aimed to reveal interactions of the stress response sigma subunits (factors) σD and σH of RNA polymerase and promoters in Gram-positive bacterium Corynebacterium glutamicum by combining wet-lab obtained data and in silico modeling. Computer modeling-guided point mutagenesis of C. glutamicum σH subunit led to the creation of a panel of σH variants. Their ability to initiate transcription from naturally occurring hybrid σD/σH-dependent promoter Pcg0441 and two control canonical promoters (σD-dependent PrsdA and σH-dependent PuvrD3) was measured and interpreted using molecular dynamics simulations of homology models of all complexes. The results led us to design the artificial hybrid promoter PD35H10 combining the -10 element of the PuvrD3 promoter and the -35 element of the PrsdA promoter. This artificial hybrid promoter PD35-rsdAH10-uvrD3 showed almost optimal properties needed for the bio-orthogonal transcription (not interfering with the native biological processes).

• Klíčová slova
• Bio-orthogonal transcription, Corynebacterium, Promoter, Sigma factor,
• MeSH
• bakteriální proteiny * genetika   metabolismus   chemie   MeSH
• bodová mutace * MeSH
• Corynebacterium glutamicum * genetika   MeSH
• DNA řízené RNA-polymerasy genetika   metabolismus   chemie   MeSH
• fyziologický stres genetika   MeSH
• genetická transkripce MeSH
• počítačová simulace MeSH
• promotorové oblasti (genetika) * MeSH
• regulace genové exprese u bakterií MeSH
• sigma faktor * genetika   metabolismus   chemie   MeSH
• simulace molekulární dynamiky * MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• bakteriální proteiny * MeSH
• DNA řízené RNA-polymerasy MeSH
• sigma faktor * MeSH

For the modeling of systems, the computers are more and more used while the other "media" (including the human intellect) carrying the models are abandoned. For the modeling of knowledges, i.e. of more or less general concepts (possibly used to model systems composed of instances of such concepts), the object-oriented programming is nowadays widely used. For the modeling of processes existing and developing in the time, computer simulation is used, the results of which are often presented by means of animation (graphical pictures moving and changing in time). Unfortunately, the object-oriented programming tools are commonly not designed to be of a great use for simulation while the programming tools for simulation do not enable their users to apply the advantages of the object-oriented programming. Nevertheless, there are exclusions enabling to use general concepts represented at a computer, for constructing simulation models and for their easy modification. They are described in the present paper, together with true definitions of modeling, simulation and object-oriented programming (including cases that do not satisfy the definitions but are dangerous to introduce misunderstanding), an outline of their applications and of their further development. In relation to the fact that computing systems are being introduced to be control components into a large spectrum of (technological, social and biological) systems, the attention is oriented to models of systems containing modeling components.

• MeSH
• počítačová simulace * MeSH
• programovací jazyk MeSH
• teoretické modely * MeSH
• Publikační typ
• časopisecké články MeSH

This paper describes a design process for a universal development kit based on an analog computer concept that can model the dynamics of an arbitrarily complex dynamical system up to the fourth order. The constructed development kit contains digital blocks and associated analog-to-digital and digital-to-analog converters (ADCs and DAC), such that multiple-segmented piecewise-linear input-output characteristics can be used for the synthesis of the prescribed mathematical model. Polynomial input-output curves can be implemented easily by four-quadrant analog multipliers. The proposed kit was verified through several experimental scenarios, starting with simple sinusoidal oscillators and ending with generators of continuous-time robust chaotic attractors. The description of each individual part of the development kit is accompanied by links to technical documentation, allowing skilled readers in the construction of electronic systems to replicate the proposed functional example. For this purpose, the electrical scheme of the hybrid analog computer and all important source codes are available online.

• Klíčová slova
• analog computer, chaotic system, circuit synthesis, strange attractor, transfer function,
• Publikační typ
• časopisecké články MeSH

Capillary electrophoresis hyphenated with electrospray mass spectrometry (CE-ESI-MS) has emerged in the past decade as one of the most powerful bioanalytical techniques. As the sensitivity and efficiency of new CE-ESI-MS interface designs are continuously improving, numerical modeling can play important role during their development. In this review, different aspects of computer modeling and simulation of CE-ESI-MS interfaces are comprehensively discussed. Relevant essentials of hydrodynamics as well as state-of-the-art modeling techniques are critically evaluated. Sheath liquid-, sheathless-, and liquid-junction interfaces are reviewed from the viewpoint of multidisciplinary numerical modeling along with details of single and multiphase models together with electric field mediated flows, electrohydrodynamics, and free fluid-surface methods. Practical examples are given to help non-specialists to understand the basic principles and applications. Finally, alternative approaches like air amplifiers are also included. © 2014 Wiley Periodicals, Inc. Mass Spec Rev 34: 558-569, 2015.

• Klíčová slova
• CE-ESI-MS, CFD, interface design, modeling, simulation,
• MeSH
• algoritmy MeSH
• chemické modely MeSH
• elektroforéza kapilární přístrojové vybavení   metody   MeSH
• elektromagnetická pole MeSH
• hmotnostní spektrometrie s elektrosprejovou ionizací přístrojové vybavení   metody   MeSH
• hydrodynamika MeSH
• lidé MeSH
• počítačová simulace MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH

Phonation into a glass tube is a voice training and therapy method that leads to beneficial effects in voice production. It has not been known, however, what changes occur in the vocal tract during and after the phonation into a tube. This pilot study examined the vocal tract shape in a female subject before, during, and after phonation into a tube using computer tomography (CT). Three-dimensional finite-element models (FEMs) of the vocal tract were derived from the CT images and used to study changes in vocal tract input impedance. When phonating on vowel [a:] the data showed tightened velopharyngeal closure and enlarged cross-sectional areas of the oropharyngeal and oral cavities during and after the tube-phonation. FEM calculations revealed an increased input inertance of the vocal tract and an increased acoustic energy radiated out of the vocal tract after the tube-phonation. The results indicate that the phonation into a tube causes changes in the vocal tract which remain also when the tube is removed. These effects may help improving voice production in patients and voice professionals.

• MeSH
• akustika řeči * MeSH
• analýza metodou konečných prvků * MeSH
• biologické modely * MeSH
• fonace * MeSH
• hlasové řasy diagnostické zobrazování   fyziologie   MeSH
• kvalita hlasu MeSH
• larynx diagnostické zobrazování   fyziologie   MeSH
• lidé středního věku MeSH
• lidé MeSH
• pilotní projekty MeSH
• počítačová rentgenová tomografie * MeSH
• rentgenový obraz - interpretace počítačová MeSH
• zobrazování trojrozměrné MeSH
• Check Tag
• lidé středního věku MeSH
• lidé MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

BACKGROUND: Fungal beta-N-acetylhexosaminidases catalyze the hydrolysis of chitobiose into its constituent monosaccharides. These enzymes are physiologically important during the life cycle of the fungus for the formation of septa, germ tubes and fruit-bodies. Crystal structures are known for two monomeric bacterial enzymes and the dimeric human lysosomal beta-N-acetylhexosaminidase. The fungal beta-N-acetylhexosaminidases are robust enzymes commonly used in chemoenzymatic syntheses of oligosaccharides. The enzyme from Aspergillus oryzae was purified and its sequence was determined. RESULTS: The complete primary structure of the fungal beta-N-acetylhexosaminidase from Aspergillus oryzae CCF1066 was used to construct molecular models of the catalytic subunit of the enzyme, the enzyme dimer, and the N-glycosylated dimer. Experimental data were obtained from infrared and Raman spectroscopy, and biochemical studies of the native and deglycosylated enzyme, and are in good agreement with the models. Enzyme deglycosylated under native conditions displays identical kinetic parameters but is significantly less stable in acidic conditions, consistent with model predictions. The molecular model of the deglycosylated enzyme was solvated and a molecular dynamics simulation was run over 20 ns. The molecular model is able to bind the natural substrate - chitobiose with a stable value of binding energy during the molecular dynamics simulation. CONCLUSION: Whereas the intracellular bacterial beta-N-acetylhexosaminidases are monomeric, the extracellular secreted enzymes of fungi and humans occur as dimers. Dimerization of the fungal beta-N-acetylhexosaminidase appears to be a reversible process that is strictly pH dependent. Oligosaccharide moieties may also participate in the dimerization process that might represent a unique feature of the exclusively extracellular enzymes. Deglycosylation had only limited effect on enzyme activity, but it significantly affected enzyme stability in acidic conditions. Dimerization and N-glycosylation are the enzyme's strategy for catalytic subunit stabilization. The disulfide bridge that connects Cys448 with Cys483 stabilizes a hinge region in a flexible loop close to the active site, which is an exclusive feature of the fungal enzymes, neither present in bacterial nor mammalian structures. This loop may play the role of a substrate binding site lid, anchored by a disulphide bridge that prevents the substrate binding site from being influenced by the flexible motion of the loop.

• MeSH
• Aspergillus oryzae enzymologie   MeSH
• beta-N-acetylhexosaminidasy chemie   izolace a purifikace   metabolismus   MeSH
• dimerizace MeSH
• glykosylace MeSH
• koncentrace vodíkových iontů MeSH
• konformace proteinů MeSH
• molekulární modely MeSH
• počítačová simulace * MeSH
• Ramanova spektroskopie metody   MeSH
• spektroskopie infračervená s Fourierovou transformací metody   MeSH
• stabilita enzymů MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• beta-N-acetylhexosaminidasy MeSH