Simulation of interface states effect on the scanning capacitance microscopy measurement of p-n junctions

A two-dimensional numerical simulation model of interface states in scanning capacitance microscopy (SCM) measurements of p-n junctions is presented-In the model, amphoteric interface states with two transition energies in the Si band gap are represented as fixed charges to account for their behavior in SCM measurements. The interface states are shown to cause a stretch-out-and a parallel shift of the capacitance-voltage characteristics in the depletion. and neutral regions of p-n junctions, respectively. This explains the discrepancy between - the SCM measurement and simulation near p-n junctions, and thus modeling interface states is crucial for SCM dopant profiling of p-n junctions. (C) 2002 American Institute of Physics.

Crystal structures of free, IMP-, and GMP-bound Escherichia coli hypoxanthine phosphoribosyltransferase

Crystal structures have been determined for free Escherichia coli hypoxanthine phosphoribosyltransferase (HPRT) (2.9 Angstrom resolution) and for the enzyme in complex with the reaction products, inosine 5'-monophosphate (IMP) and guanosine 5-monophosphate (GMP) (2.8 Angstrom resolution). Of the known 6-oxopurine phosphoribosyltransferase (PRTase) structures, E. coli HPRT is most similar in structure to that of Tritrichomonas foetus HGXPRT, with a rmsd for 150 Calpha atoms of 1.0 Angstrom. Comparison of the free and product bound structures shows that the side chain of Phe156 and the polypeptide backbone in this vicinity move to bind IMP or GMP. A nonproline cis peptide bond, also found in some other 6-oxopurine PRTases, is observed between Leu46 and Arg47 in both the free and complexed structures. For catalysis to occur, the 6-oxopurine PRTases have a requirement for divalent metal ion, Usually Mg2+ in vivo. In the free structure, a Mg2+, is coordinated to the side chains of Glu103 and Asp104. This interaction may be important for stabilization of the enzyme before catalysis. E. coli HPRT is unique among the known 6-oxopurine PRTases in that it exhibits a marked preference for hypoxanthine as substrate over both xanthine and guanine. The structures suggest that its substrate specificity is due to the modes of binding of the bases. In E. coli HPRT, the carbonyl oxygen of Asp 163 would likely form a hydrogen bond with the 2-exocyclic nitrogen of guanine (in the HPRT-guanine-PRib-PP-Mg2+ complex). However, hypoxanthine does not have a 2-exocyclic atom and the HPRT-IMP structure suggests that hypoxanthine is likely to occupy a different position in the purine-binding pocket.

Free radicals in alcoholic myopathy: Indices of damage and preventive studies

Chronic alcoholic myopathy affects up to two-thirds of all alcohol misusers and is characterized by selective atrophy of Type If (glycolytic, fast-twitch, anaerobic) fibers. In contrast, the Type I fibers (oxidative, slow-twitch, aerobic) are relatively protected. Alcohol increases the concentration of cholesterol hydroperoxides and malondialdehyde-protein adducts, though protein-carbonyl concentration levels do not appear to be overtly increased and may actually decrease in some studies. In alcoholics, plasma concentrations of a-tocopherol may be reduced in myopathic patients. However, a-tocopherol supplementation has failed to prevent either the loss of skeletal muscle protein or the reductions in protein synthesis in alcohol-dosed animals. The evidence for increased oxidative stress in alcohol-exposed skeletal muscle is thus inconsistent. Further work into the role of ROS in alcoholic myopathy is clearly warranted. (C) 2002 Elsevier Science Inc.

Design of microchannel free-space optical interconnects based on vertical-cavity surface-emitting laser arrays

We investigate the design of free-space optical interconnects (FSOIs) based on arrays of vertical-cavity surface-emitting lasers (VCSELs), microlenses, and photodetectors. We explain the effect of the modal structure of a multimodeVCSEL beam on the performance of a FSOI with microchannel architecture. A Gaussian-beam diffraction model is used in combination with the experimentally obtained spectrally resolved VCSEL beam profiles to determine the optical channel crosstalk and the signal-to-noise ratio (SNR) in the system. The dependence of the SNR on the feature parameters of a FSOI is investigated. We found that the presence of higher-order modes reduces the SNR and the maximum feasible interconnect distance. We also found that the positioning of a VCSEL array relative to the transmitter microlens has a significant impact on the SNR and the maximum feasible interconnect distance. Our analysis shows that the departure from the traditional confocal system yields several advantages including the extended interconnect distance and/or improved SNR. The results show that FSOIs based on multimode VCSELs can be efficiently utilized in both chip-level and board-level interconnects. (C) 2002 Optical Society of America.

Experimental study of drop-interface coalescence in the presence of polymer stabilisers

An experimental study has been carried out to characterise the performance of polymer stabilisers, partially hydrolysed polyvinyl acetate (PVAc), used in suspension polymerisation processes. The stabilisers are ranked by their ability to stabilise the dispersion characterised by the median coalescence time of a single drop with its homophase at a planar liquid/liquid interface. Results show that the stability of the dispersion relates closely to the molecular properties of the PVAcs. Other conditions being equal, PVAcs with higher molecular weights or lower degrees of hydrolysis can better stabilise a liquid-liquid dispersion. The stability of the dispersion also depends strongly on where the PVAc resides. The presence of a PVAc in the dispersed phase significantly reduces stability. Consistent with results reported in the literature, considerable scatter has been observed on the coalescence times of identical drops under the same conditions. An explanation for the scatter is also proposed in the paper, based on the classical Reynolds model for film thinning. (C) 2002 Elsevier Science B.V. All rights reserved.

On learning context-free and context-sensitive languages

The long short-term memory (LSTM) is not the only neural network which learns a context sensitive language. Second-order sequential cascaded networks (SCNs) are able to induce means from a finite fragment of a context-sensitive language for processing strings outside the training set. The dynamical behavior of the SCN is qualitatively distinct from that observed in LSTM networks. Differences in performance and dynamics are discussed.

Characterization of the retinoid orphan-related receptor-alpha coactivator binding interface: A structural basis for ligand-independent transcription

The retinoid orphan-related receptor-alpha (RORalpha) is a member of the ROR subfamily of orphan receptors and acts as a constitutive activator of transcription in the absence of exogenous ligands. To understand the basis of this activity, we constructed a homology model of Rill using the closely related TRbeta as a template. Molecular modeling suggested that bulky hydrophobic side chains occupy the RORa ligand cavity leaving a small but distinct cavity that may be involved in receptor stabilization. This model was subject to docking simulation with a receptor-interacting peptide from the steroid receptor coactivator, GR-interacting protein-1, which delineated a coactivator binding surface consisting of the signature motif spanning helices 3-5 and helix 12 [activation function 2 (AF2)]. Probing this surface with scanning alanine mutagenesis showed structural and functional equivalence between homologous residues of RORalpha and TRbeta. This was surprising (given that Rill is a ligand-independent activator, whereas TRbeta has an absolute requirement for ligand) and prompted us to use molecular modeling to identify differences between Rill and TRbeta in the way that the All helix interacts with the rest of the receptor. Modeling highlighted a nonconserved amino acid in helix 11 of RORa (Phe491) and a short-length of 3.10 helix at the N terminus of AF2 which we suggest i) ensures that AF2 is locked permanently in the holoconformation described for other liganded receptors and thus 2) enables ligand-independent recruitment of coactivators. Consistent with this, mutation of RORa Phe491 to either methionine or alanine (methionine is the homologous residue in TRbeta), reduced and ablated transcriptional activation and recruitment of coactivators, respectively. Furthermore, we were able to reconstitute transcriptional activity for both a deletion mutant of Ill lacking All and Phe491 Met, by overexpression of a GAL-AF2 fusion protein, demonstrating ligand-independent recruitment of AF2 and a role for Phe491 in recruiting AF2.

Modeling of phase equilibrium and vapor adsorption on carbon black based on a combination of a lattice theory and equation of state

A thermodynamic approach is developed in this paper to describe the behavior of a subcritical fluid in the neighborhood of vapor-liquid interface and close to a graphite surface. The fluid is modeled as a system of parallel molecular layers. The Helmholtz free energy of the fluid is expressed as the sum of the intrinsic Helmholtz free energies of separate layers and the potential energy of their mutual interactions calculated by the 10-4 potential. This Helmholtz free energy is described by an equation of state (such as the Bender or Peng-Robinson equation), which allows us a convenient means to obtain the intrinsic Helmholtz free energy of each molecular layer as a function of its two-dimensional density. All molecular layers of the bulk fluid are in mechanical equilibrium corresponding to the minimum of the total potential energy. In the case of adsorption the external potential exerted by the graphite layers is added to the free energy. The state of the interface zone between the liquid and the vapor phases or the state of the adsorbed phase is determined by the minimum of the grand potential. In the case of phase equilibrium the approach leads to the distribution of density and pressure over the transition zone. The interrelation between the collision diameter and the potential well depth was determined by the surface tension. It was shown that the distance between neighboring molecular layers substantially changes in the vapor-liquid transition zone and in the adsorbed phase with loading. The approach is considered in this paper for the case of adsorption of argon and nitrogen on carbon black. In both cases an excellent agreement with the experimental data was achieved without additional assumptions and fitting parameters, except for the fluid-solid potential well depth. The approach has far-reaching consequences and can be readily extended to the model of adsorption in slit pores of carbonaceous materials and to the analysis of multicomponent adsorption systems. (C) 2002 Elsevier Science (USA).

Initial effects of elbow taping on pain-free grip strength and pressure pain threshold

Study design: Single-blind, placebo control, randomized, crossover, experimental Study with repeated measures, Objective: To determine the initial effects of a taping technique on grip strength and pain in individuals with lateral epicondylalgia. Background: Taping techniques are advocated for chronic musculoskeletal conditions such as lateral epicondylalgia, a prevalent disorder with significant impact on the individual and community. Little evidence exists supporting the effects of taping techniques on musculoskeletal pain. Methods and Measures: Sixteen participants (mean age +/- SD, 45.8 +/- 10.2 years) with chronic lateral epicondylalgia (rnean duration +/- SD, 13.1 +/- 9.9 months) participated in a placebo control study of an elbow taping technique. Outcome measures were pain-free grip strength and pressure pain threshold taken before, immediately after, and 30 minutes after application of tape. Results: The taping technique significantly improved pain-free grip strength by 24% from baseline (P = .028). The treatment effect was greater than that for placebo and control conditions. Changes in pressure pain threshold (19%), although positive, were not statistically significant. Conclusion: This preliminary study demonstrated an initial ameliorative effect of a taping technique for lateral epicondylalgia and suggests that it should be considered as an adjunct in the management of this condition.

The first strand transfer reaction of HIV-1 reverse transcription is more efficient in infected cells than in cell-free natural endogenous reverse transcription reactions

Background: In the presence of dNTPs, intact HIV-1 virions are capable of reverse transcribing at least part of their genome, a process known as natural endogenous reverse transcription (NERT). PCR analysis of virion DNA produced by NERT revealed that the first strand transfer reaction (1stST) was inefficient in intact virions, with minus strand (-) strong stop DNA (ssDNA) copy numbers up to 200 times higher than post-1stST products measured using primers in U3 and U5. This was in marked contrast to the efficiency of 1stST observed in single-round cell infection assays, in which (-) ssDNA and U3-U5 copy numbers were indistinguishable. Objectives: To investigate the reasons for the discrepancy in first strand transfer efficiency between intact cell-free virus and the infection process. Study design: Alterations of both NERT reactions and the conditions of cell infection were used to test whether uncoating and/or entry play a role in the discrepancy in first strand transfer efficiency. Results and Conclusions: The difference in 1stST efficiency could not be attributed simply to viral uncoating, since addition of very low concentrations of detergent to NERT reactions removed the viral envelope without disrupting the reverse transcription complex, and these conditions resulted in no improvement in 1stST efficiency. Virus pseudotyped with surface glycoproteins from either vesicular stomatitis virus or amphotrophic murine leukaemia virus also showed low levels of 1stST in low detergent NERT assays and equivalent levels of (-) ssDNA and 1stST in single-round infections of cells, demonstrating that the gp120-mediated infection process did not select for virions capable of carrying out 1stST. These data indicate that a post-entry event or factor may be involved in efficient HIV-1 reverse transcription in vivo. (C) 2002 Elsevier Science B.V. All rights reserved.

Modeling diffraction in free-space optical interconnects by the mode expansion method

Free-space optical interconnects (FSOIs), made up of dense arrays of vertical-cavity surface-emitting lasers, photodetectors and microlenses can be used for implementing high-speed and high-density communication links, and hence replace the inferior electrical interconnects. A major concern in the design of FSOIs is minimization of the optical channel cross talk arising from laser beam diffraction. In this article we introduce modifications to the mode expansion method of Tanaka et al. [IEEE Trans. Microwave Theory Tech. MTT-20, 749 (1972)] to make it an efficient tool for modelling and design of FSOIs in the presence of diffraction. We demonstrate that our modified mode expansion method has accuracy similar to the exact solution of the Huygens-Kirchhoff diffraction integral in cases of both weak and strong beam clipping, and that it is much more accurate than the existing approximations. The strength of the method is twofold: first, it is applicable in the region of pronounced diffraction (strong beam clipping) where all other approximations fail and, second, unlike the exact-solution method, it can be efficiently used for modelling diffraction on multiple apertures. These features make the mode expansion method useful for design and optimization of free-space architectures containing multiple optical elements inclusive of optical interconnects and optical clock distribution systems. (C) 2003 Optical Society of America.