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PubMed2000

Critical behavior of the annihilating random walk of two species with exclusion in one dimension

The A+A-->0, B+B-->0 process, with exclusion between the different kinds, is investigated here numerically. Before treating this model explicitly, we study the generalized Domany-Kinzel cellular automaton model of Hinrichsen on the line of parameter space where only compact clusters can grow. The simplest version is treated with two absorbing phases in addition to the active one. The two kinds of kinks which arise in this case do not react, leading to kinetics differing from the standard annihilating random walk of two species. Time dependent simulations are presented here to illustrate differences caused by exclusion in scaling properties of the usually discussed characteristic quantities. The dependence on the density and composition of the initial state is most apparent. Making use of the parallelism between this process and directed percolation limited by a reflecting parabolic surface, we argue that the two kinds of kinks exert marginal perturbation on each other and lead to deviations from standard annihilating random walk behavior.

Journal Article↗

PubMed2004

Circular photonic crystal resonators.

We study analytically and numerically a new class of circular resonators based on a radial photonic crystal reflector. The Bragg confinement enables the realization of compact resonators exhibiting both large free spectral range and high Q -factor. The dependence of the resonator characteristics on the reflector architecture and dimensions is studied in detail. Good agreement is found between the analytical and the numerical results obtained by finite-difference time-domain simulations.

Journal Article↗

PubMed2002

Near-field diffraction tomography.

We propose an algorithm that deals with broadband ultrasonic signals acquired in the near-field domain using probes close to the skin. This technique is designed for diffraction tomography of compact support objects interrogated by spherical waves (small transducers). It is an approximate inversion procedure in the Born approximation based on elliptical backprojection. Near-field imaging is enhanced by reducing the geometrical distortion observed on standard tomography. Numerical tests based on finite difference time domain (FDTD) simulations of data scattered by a tissue-like phantom are given.

Algorithms↗

PubMed2001

Error rates in a multiple-choice spatial manipulation test.

Error rates in a multiple-choice spatial manipulation test were analyzed post hoc on a number of different test item variables with the intention of building a computational cognitive model that simulates error rates on a spatial manipula tion test. 12 men (Army soldiers), ranging in age from 19 to 38 years, with an average age of 29 yr., participated. The variables included degree of rotation, connectivity, number of blocks in each polygon, types of distractors used, and compactness. Significant effects of connectivity, number of blocks in each polygon. type of distractor, and compactness on error rates were found, with mirror-image distractors being selected more often than nonmirror-image distractors. The amount of rotation of each image was not an influential factor in overall error rate; however, there were indications from verbal protocols that participants were using nonrotational strategies to solve the problems. Our findings suggest that complexity, i.e., connectivity, number of blocks in each polygon, and compactness, may affect error rates for nonrotational manipulation of visual images. Findings also suggest that participants may have difficulty evaluating "handedness" of images while using nonrotational manipulations.

Adult↗

PubMed2005

Denatured proteins and early folding intermediates simulated in a reduced conformational space.

Conformations of globular proteins in the denatured state were studied using a high-resolution lattice model of proteins and Monte Carlo dynamics. The model assumes a united-atom and high-coordination lattice representation of the polypeptide conformational space. The force field of the model mimics the short-range protein-like conformational stiffness, hydrophobic interactions of the side chains and the main-chain hydrogen bonds. Two types of approximations for the short-range interactions were compared: simple statistical potentials and knowledge-based protein-specific potentials derived from the sequence-structure compatibility of short fragments of protein chains. Model proteins in the denatured state are relatively compact, although the majority of the sampled conformations are globally different from the native fold. At the same time short protein fragments are mostly native-like. Thus, the denatured state of the model proteins has several features of the molten globule state observed experimentally. Statistical potentials induce native-like conformational propensities in the denatured state, especially for the fragments located in the core of folded proteins. Knowledge-based protein-specific potentials increase only slightly the level of similarity to the native conformations, in spite of their qualitatively higher specificity in the native structures. For a few cases, where fairly accurate experimental data exist, the simulation results are in semiquantitative agreement with the physical picture revealed by the experiments. This shows that the model studied in this work could be used efficiently in computational studies of protein dynamics in the denatured state, and consequently for studies of protein folding pathways, i.e. not only for the modeling of folded structures, as it was shown in previous studies. The results of the present studies also provide a new insight into the explanation of the Levinthal's paradox.

Animals↗

PubMed1997

Epidermolytic hyperkeratosis in the lower female genital tract: an uncommon simulant of mucocutaneous papillomavirus infection--a report of two cases.

Two examples of epidermolytic hyperkeratosis (EH) involving the female genital tract are described. The first case, an isolated epidermolytic acanthoma, involved the vulva of a 75-year-old woman. The second case involved the vaginal wall of a 40-year-old woman who had similar lesions of the oral mucosa. EH is characterized by epidermal acanthosis, compact papillomatous hyperkeratosis, and dissolution of the suprabasilar epithelium, resulting in perinuclear clear zones. Granular keratohyalin clumping, hypergranulosis, and dyskeratosis resulting in intracellular eosinophilic globules ("cells within a cell" appearance) are additional distinctive findings. Because of the rarity of the lesion in the female genital tract, it may be confused with other lesions that more commonly affect this region. Correct recognition of EH may have significant clinical implications.

Adult↗

PubMed1994

Small-angle scattering study of alpha 1 inhibitor III from rat blood plasma.

The alpha 1 proteinase inhibitor III from rat blood plasma, homologous to the alpha 2-macroglobulin family of proteins, has been studied in solution using small-angle scattering of X-rays and of neutrons: the radius of gyration, Rg, was found to be 4.5 nm, and the largest distance within the molecule, Dmax = 14 nm. When the inhibitor reacts with chymotrypsin or methylamine, the resulting derivatives yield slightly higher Rg-values, 4.7 and 4.85 nm, respectively. The data of the native protein are consistent with a model, the projection of which resembles the letter V and which is formed by the two identical halves of an elliptic cylinder with semi-axes of 2.1 and 5.5 nm and a length of 11 nm. This elliptic cylinder model also explained the scattering from the monomeric complement proteins C3 and C4, as well as that from the monomers of the dimeric and tetrameric alpha 2-macroglobulin family of proteins (Osterberg, R., et al. (1991), Biochemistry 30, 7873-7878). Due to the conformational change occurring when the thiol ester bond is split, the cleft in the V-form seems to be closed; and as a result, the models of the chymotrypsin and methylamine derivatives are more compact than that of the native protein.

Acute-Phase Proteins↗

PubMed2006

Growth of fractal electrodeposited aggregates under action of electric and magnetic fields using a modified diffusion-limited aggregation algorithm.

We have simulated the two-dimensional growth of fractal aggregates produced in electrodeposition experiments with axial symmetry in the presence of electric and magnetic fields. A modified diffusion-limited aggregation algorithm based on the Monte Carlo method is used in order to simulate cluster growth under the action of Coulomb and Lorentz forces, taking into account the thermal energy. The ion-particle movement has each step biased by the resultant force; in the algorithm, it is mediated by the Boltzmann term. The electric voltage between the electrodes tends to compact the aggregates and reduce the effect of screening. The Lorentz force provides a spiral form for aggregates which twists according to the magnetic field direction and intensity. A function was defined to measure the chirality of the system. The fractal dimension was also calculated to measure the influence of the electric and magnetic fields as well as the temperature during the growth process. Good agreement with experimental results was observed.

Journal Article↗

PubMed2006

Molecular dynamics simulation of glycine zwitterion in aqueous solution.

A classical molecular dynamics method was used to study the modifications of the solution structure and the properties of glycine zwitterion in aqueous solution due to the increase of glycine zwitterion concentration and the incorporation of Na(+) and Cl(-) ions to the solution. The glycine zwitterion had fundamentally a hydrophilic behavior at infinite dilution, establishing around six hydrogen bonds with the water molecules that surrounded it, which formed a strong hydration layer. Because of the increase of glycine zwitterion concentration, the hydration structure became more compact and the quantity of water molecules bound to this molecule decreased. The Na(+) ion bound to the CO(2) group of glycine, while the Cl(-) ion bound mainly to the NH(3) group of this molecule. The integration of the ions to the hydration layer of the glycine zwitterion produced modifications in the orientational correlation between atoms of glycine zwitterion and water that surrounded them and an increase of the approaches between the glycine zwitterion molecules. The incorporation of ions to the solution also produced changes in the water-water orientational correlation. Decreases of the water-water hydrogen bonds and diffusion coefficient of all molecules were observed when the glycine zwitterion concentration increased and when the ions were incorporated to the solution.

Chlorine↗

PubMed2005

Evaluation of hydrodynamics in the basket dissolution apparatus using computational fluid dynamics--dissolution rate implications.

The aim of this work was to simulate the fluid flow in the basket dissolution apparatus using computational fluid dynamics (CFD) and to use the resulting velocity data (in combination with velocity data from simulated flow fields of the paddle dissolution apparatus) to relate velocities in the vicinity of a dissolving surface to dissolution rate. A further objective of the work was to compare fluid velocities between the basket and paddle dissolution apparatuses. CFD simulations of the basket apparatus were carried out using Fluent software. Flow field solutions were compared with results from flow visualisation techniques and with published ultrasound-pulse-echo velocity data. Velocity data from the flow field solution revealed velocities within the basket to be of the same order as those at the base of the paddle apparatus at the same rotation speed, supporting equivalent dissolution rate data from these locations. Dissolution rates were obtained for compacts of benzoic acid dissolved in 0.1 M HCl at 37 degrees C in the basket apparatus at 50 rpm. The relationship between maximum velocity in the vicinity of a dissolving surface and dissolution rate data from both the paddle and basket apparatuses was in good agreement with theoretical predictions. Analysis of the dissolution rates suggests a significant contribution from free convection in regions of low velocity at the base of the vessel of the basket apparatus.

Benzoic Acid↗

PubMed1999

The solution structure of the Sac7d/DNA complex: a small-angle X-ray scattering study.

Small-angle X-ray scattering has been used to study the structure of the multimeric complexes that form between double-stranded DNA and the archaeal chromatin protein Sac7d from Sulfolobus acidocaldarius. Scattering data from complexes of Sac7d with a defined 32-mer oligonucleotide, with poly[d(GC)], and with E. coli DNA indicate that the protein binds along the surface of an extended DNA structure. Molecular models of fully saturated Sac7d/DNA complexes were constructed using constraints from crystal structure and solution binding data. Conformational space was searched systematically by varying the parameters of the models within the constrained set to find the best fits between the X-ray scattering data and simulated scattering curves. The best fits were obtained for models composed of repeating segments of B-DNA with sharp kinks at contiguous protein binding sites. The results are consistent with extrapolation of the X-ray crystal structure of a 1:1 Sac7d/octanucleotide complex [Robinson, H., et al. (1998) Nature 392, 202-205] to polymeric DNA. The DNA conformation in our multimeric Sac7d/DNA model has the base pairs tilted by about 35 degrees and displaced 3 A from the helix axis. There is a large roll between two base pairs at the protein-induced kink site, resulting in an overall bending angle of about 70 degrees for Sac7d binding. Regularly repeating bends in the fully saturated complex result in a zigzag structure with negligible compaction of DNA. The Sac7d molecules in the model form a unique structure with two left-handed helical ribbons winding around the outside of the right-handed duplex DNA.

Archaeal Proteins↗

PubMed2005

Sorption and desorption of radioselenium on calcareous soil and its solid components studied by batch and column experiments.

The effect of different calcareous soil solid components on the sorption and desorption of radioselenium was investigated by using a selective extraction method. The distribution coefficients, the breakthrough curves and the displacement curves were experimentally determined by batch and column experiments. The experiments were carried out at pH 7.8 +/- 0.2, T=20 +/- 1 degrees C and in the presence of 0.001 M CaCl2. It is found that all sorption isotherms are linear, the sorption-desorption hysteresis for untreated and treated soils to remove organic matter, CaCO3 and organic matter plus CaCO3 is obvious; and the retention of radioselenium can probably be attributed to clay and oxides. The contributions of organic matter and CaCO3 to the sorption of radioselenium are significant, and the interaction effects among organic matter, CaCO3 and other components play an important role in the sorption of radioselenium in calcareous soil. The content of interlaminary space of compacted soil plays an important role in the sorption of radioselenium in compacted soil. The presence of CaCO3 retards the transport of radioselenium in soils, CaCO3 is an important trap of radioselenium. It is very difficult for the effluent concentration to reach the influent concentration, although radioselenium is very quickly detected in the effluent solution. The breakthrough curves (BTCs) can be simulated by a one-dimensional convection-dispersion transport model.

Adsorption↗

PubMed2005

Multidimensional detection of nitroorganic explosives by gas chromatography-pyrolysis-ultraviolet detection.

We describe a new methodology for the trace detection of organic explosives containing nitro functionalities. Conventional gas chromatography separates the components of an explosive mixture. Effluent from the gas chromatograph is pyrolyzed by passage over a heated Nichrome wire. Nitric oxide produced on pyrolysis of a nitroorganic compound is then detected by ultraviolet absorption spectroscopy between 180 and 240 nm, using a deuterium lamp as the light source. Nitric oxide exhibits a sharply banded, characteristic spectrum in this region, enabling detection of nitroorganics. The system is tested using the explosive simulants nitrobenzene and 2,4-dinitrotoluene, and with the nitramine explosive tetryl. Detection limits are 25 ng for nitrobenzene and 50 ng for 2,4-dinitrotoluene. Tetryl is detected with a detection limit of 50 ng. The system is both easy to implement and could be built as a compact, low-power device.

Journal Article↗

PubMed2006

Coarse-grained modeling of proline rich protein 1 (PRP-1) in bulk solution and adsorbed to a negatively charged surface.

Structural properties of the acidic proline rich protein PRP-1 of salivary origin in bulk solution and adsorbed onto a negatively charged surface have been studied by Monte Carlo simulations. A simple model system with focus on electrostatic interactions and short-ranged attractions among the uncharged amino acids has been used. In addition to PRP-1, some mutants were considered to assess the role of the interactions in the systems. Contrary to polyelectrolytes, the protein has a compact structure in salt-free bulk solutions, whereas at high salt concentration the protein becomes more extended. The protein adsorbs to a negatively charged surface, although its net charge is negative. The adsorbed protein displays an extended structure, which becomes more compact upon addition of salt. Hence, the conformational response upon salt addition in the adsorbed state is the opposite as compared to that in bulk solution. The conformational behavior of PRP-1 in bulk solution and at charged surfaces as well as its propensity to adsorb to surfaces with the same net charge are rationalized by the block polyampholytic character of the protein. The presence of a triad of positively charged amino acids in the C-terminal was found to be important for the adsorption of the protein.

Adsorption↗

PubMed2002

PvuII-endonuclease induces structural alterations at the scissile phosphate group of its cognate DNA.

We investigated the PvuII endonuclease with its cognate DNA by means of molecular dynamics simulations. Comparing the complexed DNA with a reference simulation of free DNA, we saw structural changes at the scissile phosphodiester bond. At this GpC step, the enzyme induces the highest twist and axial rise, inclination is increased and the minor groove widened. The distance between the scissile phosphate group and the phosphate group of the following thymine base is shortened significantly, indicating a substrate-assisted catalysis. A feasible reason for this vicinity is the catalytically important amino acid residue lysine 70, which bridges the free oxygen atoms of the successive phosphate groups. Due to this geometry, a compact reaction pocket is formed where a water molecule can be held, thus bringing the reaction partners for hydrolysis into contact. The O1-P-O2 angle of the scissile nucleotide is decreased, probably due to a complexation of the negative oxygen atoms through protein and solvent contacts.

Binding Sites↗

PubMed2003

Morphology transitions induced by chemotherapy in carcinomas in situ.

Recently, we have proposed a nutrient-limited model for the avascular growth of tumors including cell proliferation, motility, and death [S. C. Ferreira, Jr., M. L. Martins, and M. J. Vilela, Phys. Rev. E 65, 021907 (2002)], which qualitatively reproduces commonly observed morphologies for carcinomas in situ. In the present work, we analyze the effects of distinct chemotherapeutic strategies on the patterns, scaling, and growth laws obtained for the nutrient-limited model. Two kinds of chemotherapeutic strategies were considered, namely, those that kill cancer cells and those that block cell mitosis but allow the cell to survive for some time. Depending on the chemotherapeutic schedule used, the tumors are completely eliminated, reach a stationary size, or grow following power laws. The model suggests that the scaling properties of the tumors are not affected by the mild cytotoxic treatments, although a reduction in growth rates and an increase in invasiveness are observed. For the strategies based on antimitotic drugs, a morphological transition in which compact tumors become more fractal under aggressive treatments was seen.

Antineoplastic Agents↗

PubMed1995

Numerical instabilities in bone remodeling simulations: the advantages of a node-based finite element approach.

Long bone structure occurs in two distinct forms. The bone mass near the joint is primarily found in a distributed, porous trabecular structure, while in the diaphyses a tubular cortical structure is formed. It seems likely that these two observed morphologies come about, at least in part, as a mechanical adaptation to the different mechanical demands in the two regions. Mathematical formulations of this dependency have been proposed, thus facilitating numerical simulations of bone adaptation. Recently two types of discontinuities have been observed in these simulations. The first type (near-field) appears in areas near distributed load application and is characterized by a 'checkerboard' pattern of density wherein adjacent remodeled elements alternate between low and high density. The second type of discontinuity (far-field) appears remote from the load application and is characterized by strut or column-like regions of elements which become fully compact bone while adjacent regions are fully resorbed. In fact, the far-field discontinuity is an accurate representation of bone physiology and morphology since it is consistent with the appearance of cortical bone in the diaphysis. On the other hand, the near-field discontinuity, appears in a region where continuous distributions of intermediate apparent densities (trabecular bone) are expected. This finding may cause some to question whether a single continuum formulation of bone remodeling can predict both discontinuous far-field behavior and continuous near-field behavior. We describe a node-based implementation of current continuum bone remodeling theories which eliminates the spurious near-field discontinuities and preserves the anatomically correct far-field discontinuities, thus indicating that a single biological process may be at work in forming and maintaining both far-field and near-field morphologies.

Algorithms↗

PubMed2004

HIV Rev self-assembly is linked to a molten-globule to compact structural transition.

By regulating the differential expression of proviral pre mRNA in the host cell, Rev plays a crucial role in the HIV-1 life cycle. The capacity of Rev to function is intimately linked to its ability to self-associate. Nevertheless, little is known about the exact role of self-association in the molecular mechanism defining its biological activity. A prerequisite knowledge is a definition of the molecular events undertaken by Rev during the process of self-assembly. Thus, this study was initiated to monitor the structure of Rev as a function of protein concentration. Rev undergoes a structural transition as a consequence of self-assembly. This structural transition was monitored by three spectroscopic methods. The accessibility of the single tryptophan in Rev monomer to acrylamide quenching increases with decreasing protein concentration. At very low concentration of Rev, the tryptophan accessibility is close to that of an unfolded Rev. As evaluated by circular dichroism, the secondary structure of Rev is protein concentration dependent as evidenced by an increase in the magnitude of ellipticity with increasing protein concentration. Further, results from ANS binding studies indicate that the ANS binding sites in Rev experience an apparent increase in hydrophobicity as the Rev concentration was increased. These concentration dependent changes seem to reach a maximum above 5 microM Rev monomer concentration. In order to define the mode of Rev self-association sedimentation velocity and equilibrium experiments were conducted. There are evidently two consecutive progressive association processes. At protein concentrations below 0.5 mg/ml, the data from sedimentation studies can be fitted to a single isodesmic model. Simulation of velocity sedimentation profile indicates that free Rev monomer that has not entered into the association processes can best be described to exhibit a value of S(20,w) that is substantially smaller than 1.4 S, a value needed to fit the rest of the data. The latter value is consistent for a Rev monomer with the expected molecules weight and if it were to assume a compact globular shape. These spectroscopic and hydrodynamic results imply that monomeric Rev is in a molten globule state, which becomes more compact upon self-association.

Acrylamide↗