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PubMed2025

The influence of 10n and 10n+5 linker lengths on chromatin fiber topologies explored by mesoscale modeling.

The structural organization of chromatin is intricately influenced by the length of linker DNA connecting nucleosomes. Some studies have suggested preferred linker lengths of 10n and 10n+5 base pairs (bp) (n = integer). Because these lengths dictate the rotational orientation of successive nucleosomes in the fiber axis, they can markedly affect chromatin fiber compaction and topology. Using a refined mesoscale chromatin model with 5-bp resolution, we investigate the influence of linker DNA periodicity, linker histone density, salt concentration, and starting fiber topology on chromatin architecture for regular fibers versus "life-like" fibers, the latter with irregular spacing between nucleosomes. Our results reveal that regular fibers with 10n linkers exhibit compact zigzag configurations, whereas 10n+5 linkers generate more open and flexible structures. However, these effects are pronounced only for short linker lengths, as longer linkers are more heterogeneous. Moreover, increased linker histone density further enhances compaction for long linker lengths, and lower salt concentration modifies chromatin topologies, diminishing periodicity-driven effects. In addition, any periodicity effect in tightly packed solenoid configurations is much less pronounced. All these trends for regular fibers are reduced in life-like fibers with irregularly spaced nucleosomes, despite having the same average spacing. Moreover, the trend details depend highly on specific features of the fiber architecture as designed in experiments and simulations. Overall, our study highlights how reported differences depend on modeling details and emphasizes the role of linker DNA length in regulating chromatin fiber architecture and its potential implications for genome accessibility and expression.

Chromatin↗

PubMed2003

Structural rearrangements of the 10-23 DNAzyme to beta 3 integrin subunit mRNA induced by cations and their relations to the catalytic activity.

The intracellular ability of the "10-23" DNAzyme to efficiently inhibit expression of targeted proteins has been evidenced by in vitro and in vivo studies. However, standard conditions for kinetic measurements of the DNAzyme catalytic activity in vitro include 25 mM Mg2+, a concentration that is very unlikely to be achieved intracellularly. To study this discrepancy, we analyzed the folding transitions of the 10-23 DNAzyme induced by Mg2+. For this purpose, spectroscopic analyzes such as fluorescence resonance energy transfer, fluorescence anisotropy, circular dichroism, and surface plasmon resonance measurements were performed. The global geometry of the DNAzyme in the absence of added Mg2+ seems to be essentially extended, has no catalytic activity, and shows a very low binding affinity to its RNA substrate. The folding of the DNAzyme induced by binding of Mg2+ may occur in several distinct stages. The first stage, observed at 0.5 mM Mg2+, corresponds to the formation of a compact structure with limited binding properties and without catalytic activity. Then, at 5 mM Mg2+, flanking arms are projected at right position and angles to bind RNA. In such a state, DNAzyme shows substantial binding to its substrate and significant catalytic activity. Finally, the transition occurring at 15 mM Mg2+ leads to the formation of the catalytic domain, and DNAzyme shows high binding affinity toward substrate and efficient catalytic activity. Under conditions simulating intracellular conditions, the DNAzyme was only partially folded, did not bind to its substrate, and showed only residual catalytic activity, suggesting that it may be inactive in the transfected cells and behave like antisense oligodeoxynucleotide.

Anisotropy↗

PubMed2001

Surface acoustic wave impedance element ISM duplexer: modeling and optical analysis.

Surface acoustic wave (SAW) impedance element antenna duplexers provide compact, high performance, front-end components apt for industrial fabrication. We describe investigations on the design and modeling of a compact ISM antenna duplexer fabricated on a 36 degrees YX-cut LiTaO3 substrate based on SAW impedance elements. In particular, we have performed 3-D modeling of the inductive and capacitive electromagnetic couplings caused by the package parasitics for the duplexer. The use of a 1:3 IDT structure for the reduction of the passband width is discussed. The frequency response of the duplexer is predicted with the help of circuit simulation; the modeling is refined by optimization of the model parameters to improve the fit between the measured and simulated responses. We also report scanning optical imaging of the acoustic field within the resonator structures with the help of laser interferometry; this provides insight into the loss mechanisms beyond that attainable in mere electric measurements.

Journal Article↗

PubMed2006

On side-chain conformational entropy of proteins.

The role of side-chain entropy (SCE) in protein folding has long been speculated about but is still not fully understood. Utilizing a newly developed Monte Carlo method, we conducted a systematic investigation of how the SCE relates to the size of the protein and how it differs among a protein's X-ray, NMR, and decoy structures. We estimated the SCE for a set of 675 nonhomologous proteins, and observed that there is a significant SCE for both exposed and buried residues for all these proteins-the contribution of buried residues approaches approximately 40% of the overall SCE. Furthermore, the SCE can be quite different for structures with similar compactness or even similar conformations. As a striking example, we found that proteins' X-ray structures appear to pack more "cleverly" than their NMR or decoy counterparts in the sense of retaining higher SCE while achieving comparable compactness, which suggests that the SCE plays an important role in favouring native protein structures. By including a SCE term in a simple free energy function, we can significantly improve the discrimination of native protein structures from decoys.

Algorithms↗

PubMed2002

Compact static Fourier transform spectrometer with a large field of view based on liquid-crystal technology.

We present designs of static Fourier transform spectrometers that are based on a Wollaston prism with a large field of view. Besides the usual advantages of static Fourier spectrometers (large resolving power, large wave-number range, high throughput), these designs also present the advantage of using relatively cheap liquid-crystal technology. The use of twisted liquid-crystal structures gives a large field of view, which in turn gives the ability to collect more light from a divergent light source. Measurements are compared with simulations. Different simulation principles are used. We found new configurations by using twisted structures that show a large field of view.

Journal Article↗

PubMedDate not supplied

A K alpha dual energy x-ray source for coronary angiography.

The use of characteristic-line radiation from rare-earth targets bombarded by high-energy (up to 1 MeV) electron beams has been evaluated as an x-ray source for dual energy K-edge subtraction imaging of the human coronary arteries. Two characteristic-line x-ray sources, one using the split K alpha 1 and K alpha 2 lines of lanthanum excited by a high-energy electron beam and the other using the K alpha lines of barium and cerium, were studied. A Monte Carlo electron-photon simulation was used to calculate x-ray spectra and energy deposition profiles from targets of these elements bombarded by electrons in the energy range 140 keV to 1 MeV. A general dual-energy imaging model was developed that used these calculated source spectra to numerically investigate the dependence of the subtraction image signal-to-noise ratio on such factors as the ratio of K-line to x-ray continuum yield, continuum spectral shape, x-ray filtering, and detector response. A signal averaging technique for enhancing the signal-to-noise ratio was also evaluated. The results of these calculations were used to identify an optimum electron beam, target, filter, and detector configuration. A compact electron accelerator capable of providing the required electron beam parameters was designed. Calculations indicate that under ideal conditions the optimized system would be capable of imaging 2 mg/cm2 of iodine contrast agent in 20 g/cm2 of tissue with a signal-to-noise ratio of 5, a detector pixel size of 0.25 mm2, and a total image acquisition time of 10 ms. These parameters are consistent with those needed to image the human coronary arteries after an intravenous injection of iodine contrast agent. These capabilities, along with the relatively modest hardware requirements of this system, make it attractive as an x-ray source for dual energy transvenous coronary angiography.

Computer Simulation↗

PubMed1999

Simulations of aerosol aggregation including long-range interactions.

Current understanding of solid aerosol particle aggregation is limited to simulation models based on diffusive and ballistic motion of the colliding particles. The role of the long-range van der Waals forces in aggregation phenomena, although important, has never been examined. In an effort to address this issue, a simulation model, based on molecular dynamics techniques, is developed. Using this model to simulate thermal collisions of single spheres with small aggregates of similar spheres, we examine the effects of retardation of the long-range van der Waals forces, particle transport, ambient temperature, and pressure on the collision rates and mass and structure distributions of the aggregated particles. The model calculations were performed at simulated temperatures of 293 and 1500 K and at simulated pressures of 760 and 3040 torr for glassy carbon primary particles in the free molecular regime with diameters of 6 nm, and in the transition regime with diameters of 30 nm. Inclusion of the long-range van der Waals forces resulted in aggregates with relatively open structures and few branches and collision rate constants that were larger than the corresponding hard sphere rate constants, whereas exclusion of the forces resulted in compact structures with more branches and smaller enhancements in the rate constants. The above effects were found to be more pronounced in the free molecular regime than in the transition regime, which is consistent with the observation that the initial conditions and the interparticle forces play a more significant role in particle transport in the free molecular regime than in the transition regime. The effect of retardation of the forces is an increase in the percentage of open aggregates and the collision rate constants over that of the corresponding nonretarded case. An increase in temperature resulted in a collapse of aggregate structure and a decrease in collision rate constants corresponding to the reduced geometrical cross sections. Again, the effects were found to be more pronounced in the free molecular regime than in the transition regime. No significant difference was observed in the structure of the aggregates or in the collision rate constants with a change in pressure, indicating that the pressure effect, if any, is hidden by the much stronger effect of the long-range van der Waals forces.

Journal Article↗

PubMed2001

Conformational analysis of the eight-membered ring of the oxidized cysteinyl-cysteine unit implicated in nicotinic acetylcholine receptor ligand recognition.

Nicotinic acetylcholine receptors (nAChRs) are membrane-bound, pentameric ligand-gated ion channels associated with a variety of human disorders such as Alzheimer's disease, Parkinson's disease, schizophrenia, and pain. Most known nAChRs contain an unusual eight-membered disulfide-containing cysteinyl-cysteine ring, ox-[Cys-Cys], as does the soluble acetylcholine binding protein (AChBP) found in the snail Lymnaea stagnalis. The cysteinyl-cysteine ring is located in a region implicated in ligand binding, and conformational changes involving this ring may be important for modulation of nAChR function. We have studied the preferred conformations of Ac-ox-[Cys-Cys]-NH2 by NMR in water and computationally by Monte Carlo simulations using the OPLS-AA force field and GB/SA water model. ox-[Cys-Cys] adopts four distinct low-energy conformers at slightly above 0 degrees C in water. Two populations are dependent on the peptide omega2 dihedral angle, with the trans amide favored over the cis amide by a ratio of ca. 60:40. Two ox-[Cys-Cys] conformers with a cis amide bond (C+ and C-) differ from each other primarily by variation of the chi3 dihedral angle, which defines the orientation of the helicity about the S-S bond (+/- 90 degrees ). Two trans amide conformers have the same S-S helicity (chi3 approximately -90 degrees ), but are distinguished by a backbone rotation about phi2 and psi1 (T- and T'-). The ratio of T-/T'-/C+/C- is 47:15:29:9. The orientation of the pendant moieties from the eight-membered ring is more compact for the major trans conformer (T-) than for the extended conformations adopted by T'-, C+, and C-. These conformational preferences are also observed in tetrapeptide and undecapeptide fragments of the human alpha7 subtype of the nAChR that contains the ox-[Cys-Cys] unit. Conformer T- is nearly identical to the conformation seen in the X-ray structure of ox-[Cys(187)-Cys(188)] found in the unliganded AChBP, and is a Type VIII beta-turn.

Computer Simulation↗

PubMed1993

Microcystic adnexal carcinoma of the skin. A reappraisal of the differentiation and differential diagnosis of an underrecognized neoplasm.

BACKGROUND: Microcystic adnexal carcinoma (MAC) is a locally aggressive adnexal neoplasm whose histogenesis is disputed. Many cases referred to us had been misdiagnosed. OBJECTIVE: Our purpose was to clarify the differential diagnosis and differentiation of MAC. METHODS: We sought follow-up data and examined routinely stained sections from 17 cases. We performed immunoperoxidase stains for carcinoembryonic antigen, pilar keratin (AE13), proliferating cell nuclear antigen (PCNA), type IV collagen, p53, and CD34 on selected cases. RESULTS: Nine biopsy specimens had initially been misinterpreted. Cysts containing compact keratin or shadow cells were present in 11 cases, which we interpret as evidence of follicular differentiation. Sebaceous gland and duct as well as inner root sheath structures were seen in one case each. CD34 did not mark the clear cells as it does those of the outer root sheath. Staining for PCNA, type IV collagen, and p53 did not distinguish MAC from benign adnexal neoplasms. CONCLUSION: MAC can be distinguished from its simulants in adequate biopsy specimens. Incompletely excised lesions usually recur. Both follicular and sudoriforous differentiation is present. Type IV collagen, PCNA, and p53 antisera were not useful in differential diagnosis.

Adult↗

PubMed2006

Predicted performance of clay-barrier landfill covers in arid and semi-arid environments.

Conventional landfill cover systems for municipal solid waste include low-permeability compacted clay barriers to minimize infiltration into the landfilled waste. Such layers are vulnerable in climates where arid to semi-arid conditions prevail, whereby the clay cover tends to desiccate and crack, resulting in drastically higher infiltration, i.e., lower cover efficiency. To date, this phenomenon, which has been reported in field observations, has not been adequately assessed. In this paper, the performance of a cover system solely relying on a clay barrier was simulated using a numerical finite element formulation to capture changes in the clay layer and the corresponding modified hydraulic characteristics. The cover system was guided by USEPA Subtitle-D minimum requirements and consisted of a clay layer underlying a protective vegetated soil. The intrinsic characteristics of the clay barrier and vegetative soil cover, including their saturated hydraulic conductivities and their soil-water characteristic curves, were varied as warranted to simulate intact or "cracked" conditions as determined through the numerical analyses within the proposed methodology. The results indicate that the levels of percolation through the compromised or cracked cover were up to two times greater than those obtained for intact covers, starting with an intact clay hydraulic conductivity of 10(-5)cm/s.

Aluminum Silicates↗

PubMed2003

Environmentally mediated synergy between perception and behaviour in mobile robots.

The notion that behaviour influences perception seems self-evident, but the mechanism of their interaction is not known. Perception and behaviour are usually considered to be separate processes. In this view, perceptual learning constructs compact representations of sensory events, reflecting their statistical properties, independently of behavioural relevance. Behavioural learning, however, forms associations between perception and action, organized by reinforcement, without regard for the construction of perception. It is generally assumed that the interaction between these two processes is internal to the agent, and can be explained solely in terms of the neuronal substrate. Here we show, instead, that perception and behaviour can interact synergistically via the environment. Using simulated and real mobile robots, we demonstrate that perceptual learning directly supports behavioural learning and so promotes a progressive structuring of behaviour. This structuring leads to a systematic bias in input sampling, which directly affects the organization of the perceptual system. This external, environmentally mediated feedback matches the perceptual system to the emerging behavioural structure, so that the behaviour is stabilized.

Adaptation, Physiological↗

PubMed2005

Self-organization in protein folding and the hydrophobic interaction.

Self-organization is a critical aspect of living systems. During the folding of protein molecules, the hydrophobic interaction plays an important role in the collapse of the peptide chain to a compact shape. As the hydrophobic core tightens and excludes water, not only does the number of hydrophobic side chain contacts increase, but stabilization is further enhanced by an increase in strength of each hydrophobic interaction between side chains in the core. Thus, the self-organization of the protein folding process augments itself by enhancing the stability of the core against large-scale motions that would unfold the protein. Through calculations and computer simulations on a model four-helix bundle protein, we show how the strengthening of the hydrophobic interaction is crucial for stabilizing the core long enough for completion of the folding process and quantitatively manifests self-organizing dynamical behavior.

Algorithms↗

PubMed2002

Generalized contact process on random environments.

Spreading from a seed is studied by Monte Carlo simulation on a square lattice with two types of sites affecting the rates of birth and death. These systems exhibit a critical transition between survival and extinction. For time-dependent background, this transition is equivalent to those found in homogeneous systems (i.e., to directed percolation). For frozen backgrounds, the appearance of the Griffiths phase prevents the accurate analysis of this transition. For long times in the subcritical region, the spreading remains localized in compact (rather than ramified) patches, and the average number of occupied sites increases logarithmically in the surviving trials.

Journal Article↗

PubMed2002

Complex formation in systems of oppositely charged polyelectrolytes: a molecular dynamics simulation study.

Results of molecular dynamics simulations for systems with two flexible, oppositely charged polymer chains are presented. The lengths N and interaction strength lambda of the chains are varied. We find that the chains remain separated for small values of lambda. For large interaction strengths, i.e., large Bjerrum lengths, we find glasslike structures and order on the length scale of a few monomer diameters. Between these two limits of the interaction strengths, the chains of various lengths collapse into compact complexes that exhibit self-similar structures. The scaling behavior of the radius of gyration is discussed as a function of chain length and interaction strength. In addition, the local structure of the collapsed systems is analyzed and the dependence of the density of the aggregate on the interaction strength is discussed.

Journal Article↗

PubMed2003

Comments on selected aspects of nucleic acid electrostatics.

Recent experimental, theoretical, and computational developments in the field of nucleic acid electrostatics have brought interesting concepts to the fore. The phosphate charge on the double helix apparently influences its structure. When the charge is neutralized asymmetrically, the resulting force imbalance drives bending toward the neutralized side. When the charge is uniformly neutralized, the force imbalance acts to buckle the helical axis, resulting in a compact tertiary conformation. Sharing of condensed counterions by single strands is a stabilizing factor for formation of the double helix. Sharing of condensed counterions by two double helices causes clustering of DNA and may be a factor in RNA folding. Support for these statements is reviewed.

Computer Simulation↗

PubMed1988

A nonlinear finite element analysis of interface conditions in porous coated hip endoprostheses.

We used a geometrically simplified finite element model to investigate load transfer between a porous coated hip endoprosthesis and a femur. Assuming both rigidly bonded and nonlinear interfaces, we analyzed fully and partially coated stems that had coatings of different elastic moduli. Our results indicate that maximum values for relative motion in the interface between bone and implant occur for implants with the same elastic modulus as compact bone. By comparison, interface motion is reduced by about half for Co-Cr-Mo alloy stems. We also showed that the elastic modulus of the porous coating had only a small influence on bone stresses.

Biomechanical Phenomena↗

PubMed1997

Pyrene excimer fluorescence as a proximity probe for investigation of residual structure in the unfolded state of human carbonic anhydrase II.

The excimer fluorescence from two pyrenyl moieties attached to cysteines in human carbonic anhydrase II has been monitored to characterize residual structure retained under strong denaturing conditions. A position in beta-strand 3, N67C, together with the single naturally occurring cysteine 206 in beta-strand 7, were used as attachment sites. The eximer formation by the pyrenyls, requiring proximity of the probes, revealed an unfolding transition at a GuHCl concentration significantly higher than that required to induce unfolding of the molten globule state as monitored by CD. These results indicate that the excimer transition monitors the unfolding of a residual compact structure that spans beta-strands 3-7. This region constitutes the central and the most hydrophobic part of the molecule, emphasizing the importance of hydrophobic interaction in maintaining residual structure under strong unfolding conditions.

Carbonic Anhydrases↗

PubMed1998

The effect of stiffness on the localization of tensile stress at the surface of bonded posterior restorations.

OBJECTIVES: The aim of this study is to assess the distribution of tensile stress under the conditions representative of tooth-food contact in a restored posterior tooth. The ideal stiffness for a bonded restoration will be predicted. METHODS: A two-dimensional plane-strain finite element representation of a restored first maxillary molar is created. The restoration with Class I/II bucco-lingual geometry is assigned a range of Young's moduli (E = 10-80 GPa), representative of the range of materials available. In addition, a hypothetical multi-phase model, in which stiffness is gradually increased from the intercuspal concavity to the adjacent enamel, is also created. A food particle is modeled and pushed close to the interface onto the site of (1) intact enamel and (2) restored surface. RESULTS: For all single-phase models tested, the magnitude of tensile stress at the surface is far greater than that present elsewhere in the tooth. However, the exact position and magnitude of the maximum tensile stress varied according to the modulus assigned to the restoration and the position of load. The results of the model imply that interfacial problems are likely in low-modulus restorations (E = 10-20 GPa), whereas stress-related problems could occur in the intercuspal concavity of high-modulus restorations (E = 40-80 GPa). Of all the single-phase models, tensile stresses are lowest when the Young's modulus assigned to the restoration is 30 GPa. These tensile stresses are reduced in the multi-phase model. SIGNIFICANCE: Given the limitations of the model, the results indicate that the most suitable modulus for a single-phase posterior bonded restoration is around 30 GPa. Such a modulus is approached in compact-filled composites. In addition, the highly desirable dissipation of load in the multi-phase model should warrant further investigation. It is suggested that the use of an incremental filling technique with region-specific proportions of hard-filler could be one way forward.

Computer Simulation↗