The Hinge Region of Human Thyroid-Stimulating Hormone (TSH) Receptor Operates as a Tunable Switch between Hormone Binding and Receptor Activation

The mechanism by which the hinge regions of glycoprotein hormone receptors couple hormone binding to activation of downstream effecters is not clearly understood. In the present study, agonistic (311.62) and antagonistic (311.87) monoclonal antibodies (MAbs) directed against the TSH receptor extracellular domain were used to elucidate role of the hinge region in receptor activation. MAb 311.62 which identifies the LRR/Cb-2 junction (aa 265-275), increased the affinity of TSHR for the hormone while concomitantly decreasing its efficacy, whereas MAb 311.87 recognizing LRR 7-9 (aa 201-259) acted as a non-competitive inhibitor of Thyroid stimulating hormone (TSH) binding. Binding of MAbs was sensitive to the conformational changes caused by the activating and inactivating mutations and exhibited differential effects on hormone binding and response of these mutants. By studying the effects of these MAbs on truncation and chimeric mutants of thyroid stimulating hormone receptor (TSHR), this study confirms the tethered inverse agonistic role played by the hinge region and maps the interactions between TSHR hinge region and exoloops responsible for maintenance of the receptor in its basal state. Mechanistic studies on the antibody-receptor interactions suggest that MAb 311.87 is an allosteric insurmountable antagonist and inhibits initiation of the hormone induced conformational changes in the hinge region, whereas MAb 311.62 acts as a partial agonist that recognizes a conformational epitope critical for coupling of hormone binding to receptor activation. The hinge region, probably in close proximity with the alpha-subunit in the hormone-receptor complex, acts as a tunable switch between hormone binding and receptor activation.

Threshold voltage modeling under size quantization for ultra-thin silicon double-gate metal-oxide-semiconductor field-effect transistor

We report on the threshold voltage modeling of ultra-thin (1 nm-5 nm) silicon body double-gate (DG) MOSFETs using self-consistent Poisson-Schrodinger solver (SCHRED). We define the threshold voltage (V th) of symmetric DG MOSFETs as the gate voltage at which the center potential (Φ c) saturates to Φ c (s a t), and analyze the effects of oxide thickness (t ox) and substrate doping (N A) variations on V th. The validity of this definition is demonstrated by comparing the results with the charge transition (from weak to strong inversion) based model using SCHRED simulations. In addition, it is also shown that the proposed V t h definition, electrically corresponds to a condition where the inversion layer capacitance (C i n v) is equal to the oxide capacitance (C o x) across a wide-range of substrate doping densities. A capacitance based analytical model based on the criteria C i n v C o x is proposed to compute Φ c (s a t), while accounting for band-gap widening. This is validated through comparisons with the Poisson-Schrodinger solution. Further, we show that at the threshold voltage condition, the electron distribution (n(x)) along the depth (x) of the silicon film makes a transition from a strong single peak at the center of the silicon film to the onset of a symmetric double-peak away from the center of the silicon film. © 2012 American Institute of Physics.

Vaporization and collision modeling of liquid fuel sprays in a co-axial fuel and air pre-mixer

Droplet collision occurs frequently in regions where the droplet number density is high. Even for Lean Premixed and Pre-vaporized (LPP) liquid sprays, the collision effects can be very high on the droplet size distributions, which will in turn affect the droplet vaporization process. Hence, in conjunction with vaporization modeling, collision modeling for such spray systems is also essential. The standard O'Rourke's collision model, usually implemented in CFD codes, tends to generate unphysical numerical artifact when simulations are performed on Cartesian grid and the results are not grid independent. Thus, a new collision modeling approach based on no-time-counter method (NTC) proposed by Schmidt and Rutland is implemented to replace O'Rourke's collision algorithm to solve a spray injection problem in a cylindrical coflow premixer. The so called ``four-leaf clover'' numerical artifacts are eliminated by the new collision algorithm and results from a diesel spray show very good grid independence. Next, the dispersion and vaporization processes for liquid fuel sprays are simulated in a coflow premixer. Two liquid fuels under investigation are jet-A and Rapeseed Methyl Esters (RME). Results show very good grid independence in terms of SMD distribution, droplet number distribution and fuel vapor mass flow rate. A baseline test is first established with a spray cone angle of 90 degrees and injection velocity of 3 m/s and jet-A achieves much better vaporization performance than RME due to its higher vapor pressure. To improve the vaporization performance for both fuels, a series of simulations have been done at several different combinations of spray cone angle and injection velocity. At relatively low spray cone angle and injection velocity, the collision effect on the average droplet size and the vaporization performance are very high due to relatively high coalescence rate induced by droplet collisions. Thus, at higher spray cone angle and injection velocity, the results expectedly show improvement in fuel vaporization performance since smaller droplet has a higher vaporization rate. The vaporization performance and the level of homogeneity of fuel-air mixture can be significantly improved when the dispersion level is high, which can be achieved by increasing the spray cone angle and injection velocity. (C) 2012 Elsevier Ltd. All rights reserved.

Coalescent Method in Conjunction with Niche Modeling Reveals Cryptic Diversity among Centipedes in the Western Ghats of South India

Background: There has been growing interest in integrative taxonomy that uses data from multiple disciplines for species delimitation. Typically, in such studies, monophyly is taken as a proxy for taxonomic distinctiveness and these units are treated as potential species. However, monophyly could arise due to stochastic processes. Thus here, we have employed a recently developed tool based on coalescent approach to ascertain the taxonomic distinctiveness of various monophyletic units. Subsequently, the species status of these taxonomic units was further tested using corroborative evidence from morphology and ecology. This inter-disciplinary approach was implemented on endemic centipedes of the genus Digitipes (Attems 1930) from the Western Ghats (WG) biodiversity hotspot of India. The species of the genus Digitipes are morphologically conserved, despite their ancient late Cretaceous origin. Principal Findings: Our coalescent analysis based on mitochondrial dataset indicated the presence of nine putative species. The integrative approach, which includes nuclear, morphology, and climate datasets supported distinctiveness of eight putative species, of which three represent described species and five were new species. Among the five new species, three were morphologically cryptic species, emphasizing the effectiveness of this approach in discovering cryptic diversity in less explored areas of the tropics like the WG. In addition, species pairs showed variable divergence along the molecular, morphological and climate axes. Conclusions: A multidisciplinary approach illustrated here is successful in discovering cryptic diversity with an indication that the current estimates of invertebrate species richness for the WG might have been underestimated. Additionally, the importance of measuring multiple secondary properties of species while defining species boundaries was highlighted given variable divergence of each species pair across the disciplines.

State Dependent Attempt Rate modeling of single cell IEEE 802.11 WLANs with homogeneous nodes and Poisson packet arrivals

We study a State Dependent Attempt Rate (SDAR) approximation to model M queues (one queue per node) served by the Carrier Sense Multiple Access with Collision Avoidance (CSMA/CA) protocol as standardized in the IEEE 802.11 Distributed Coordination Function (DCF). The approximation is that, when n of the M queues are non-empty, the (transmission) attempt probability of each of the n non-empty nodes is given by the long-term (transmission) attempt probability of n saturated nodes. With the arrival of packets into the M queues according to independent Poisson processes, the SDAR approximation reduces a single cell with non-saturated nodes to a Markovian coupled queueing system. We provide a sufficient condition under which the joint queue length Markov chain is positive recurrent. For the symmetric case of equal arrival rates and finite and equal buffers, we develop an iterative method which leads to accurate predictions for important performance measures such as collision probability, throughput and mean packet delay. We replace the MAC layer with the SDAR model of contention by modifying the NS-2 source code pertaining to the MAC layer, keeping all other layers unchanged. By this model-based simulation technique at the MAC layer, we achieve speed-ups (w.r.t. MAC layer operations) up to 5.4. Through extensive model-based simulations and numerical results, we show that the SDAR model is an accurate model for the DCF MAC protocol in single cells. (C) 2012 Elsevier B.V. All rights reserved.

Bond Graph Modeling for Energy-Harvesting Wireless Sensor Networks

Researchers can use bond graph modeling, a tool that takes into account the energy conservation principle, to accurately assess the dynamic behavior of wireless sensor networks on a continuous basis.

Markov chain modeling of evolution of strains in reinforced concrete flexural beams

From the analysis of experimentally observed variations in surface strains with loading in reinforced concrete beams, it is noted that there is a need to consider the evolution of strains (with loading) as a stochastic process. Use of Markov Chains for modeling stochastic evolution of strains with loading in reinforced concrete flexural beams is studied in this paper. A simple, yet practically useful, bi-level homogeneous Gaussian Markov Chain (BLHGMC) model is proposed for determining the state of strain in reinforced concrete beams. The BLHGMC model will be useful for predicting behavior/response of reinforced concrete beams leading to more rational design.

MODELING HETEROSTRUCTURES WITH SCHRODINGER-POISSON-NAVIER ITERATIVE SCHEMES, EFFECT OF CARRIER CHARGE, AND INFLUENCE OF ELECTROMECHANICAL COUPLING

This paper presents a detailed investigation of the erects of piezoelectricity, spontaneous polarization and charge density on the electronic states and the quasi-Fermi level energy in wurtzite-type semiconductor heterojunctions. This has required a full solution to the coupled Schrodinger-Poisson-Navier model, as a generalization of earlier work on the Schrodinger-Poisson problem. Finite-element-based simulations have been performed on a A1N/GaN quantum well by using both one-step calculation as well as the self-consistent iterative scheme. Results have been provided for field distributions corresponding to cases with zero-displacement boundary conditions and also stress-free boundary conditions. It has been further demonstrated by using four case study examples that a complete self-consistent coupling of electromechanical fields is essential to accurately capture the electromechanical fields and electronic wavefunctions. We have demonstrated that electronic energies can change up to approximately 0.5 eV when comparing partial and complete coupling of electromechanical fields. Similarly, wavefunctions are significantly altered when following a self-consistent procedure as opposed to the partial-coupling case usually considered in literature. Hence, a complete self-consistent procedure is necessary when addressing problems requiring more accurate results on optoelectronic properties of low-dimensional nanostructures compared to those obtainable with conventional methodologies.

Suite of tools for statistical N-gram language modeling for pattern mining in whole genome sequences

Genome sequences contain a number of patterns that have biomedical significance. Repetitive sequences of various kinds are a primary component of most of the genomic sequence patterns. We extended the suffix-array based Biological Language Modeling Toolkit to compute n-gram frequencies as well as n-gram language-model based perplexity in windows over the whole genome sequence to find biologically relevant patterns. We present the suite of tools and their application for analysis on whole human genome sequence.

Premixed flame response to equivalence ratio fluctuations: Comparison between reduced order modeling and detailed computations

Combustion instability events in lean premixed combustion systems can cause spatio-temporal variations in unburnt mixture fuel/air ratio. This provides a driving mechanism for heat-release oscillations when they interact with the flame. Several Reduced Order Modelling (ROM) approaches to predict the characteristics of these oscillations have been developed in the past. The present paper compares results for flame describing function characteristics determined from a ROM approach based on the level-set method, with corresponding results from detailed, fully compressible reacting flow computations for the same two dimensional slot flame configuration. The comparison between these results is seen to be sensitive to small geometric differences in the shape of the nominally steady flame used in the two computations. When the results are corrected to account for these differences, describing function magnitudes are well predicted for frequencies lesser than and greater than a lower and upper cutoff respectively due to amplification of flame surface wrinkling by the convective Darrieus-Landau (DL) instability. However, good agreement in describing function phase predictions is seen as the ROM captures the transit time of wrinkles through the flame correctly. Also, good agreement is seen for both magnitude and phase of the flame response, for large forcing amplitudes, at frequencies where the DL instability has a minimal influence. Thus, the present ROM can predict flame response as long as the DL instability, caused by gas expansion at the flame front, does not significantly alter flame front perturbation amplitudes as they traverse the flame. (C) 2012 The Combustion Institute. Published by Elsevier Inc. All rights reserved.

Functional characterization, homology modeling and docking studies of beta-glucosidase responsible for bioactivation of cyanogenic hydroxynitrile glucosides from Leucaena leucocephala (subabul)

Glycosyl hydrolase family 1 beta-glucosidases are important enzymes that serve many diverse functions in plants including defense, whereby hydrolyzing the defensive compounds such as hydroxynitrile glucosides. A hydroxynitrile glucoside cleaving beta-glucosidase gene (Llbglu1) was isolated from Leucaena leucocephala, cloned into pET-28a (+) and expressed in E. coli BL21 (DE3) cells. The recombinant enzyme was purified by Ni-NTA affinity chromatography. The optimal temperature and pH for this beta-glucosidase were found to be 45 A degrees C and 4.8, respectively. The purified Llbglu1 enzyme hydrolyzed the synthetic glycosides, pNPGlucoside (pNPGlc) and pNPGalactoside (pNPGal). Also, the enzyme hydrolyzed amygdalin, a hydroxynitrile glycoside and a few of the tested flavonoid and isoflavonoid glucosides. The kinetic parameters K (m) and V (max) were found to be 38.59 mu M and 0.8237 mu M/mg/min for pNPGlc, whereas for pNPGal the values were observed as 1845 mu M and 0.1037 mu M/mg/min. In the present study, a three dimensional (3D) model of the Llbglu1 was built by MODELLER software to find out the substrate binding sites and the quality of the model was examined using the program PROCHEK. Docking studies indicated that conserved active site residues are Glu 199, Glu 413, His 153, Asn 198, Val 270, Asn 340, and Trp 462. Docking of rhodiocyanoside A with the modeled Llbglu1 resulted in a binding with free energy change (Delta G) of -5.52 kcal/mol on which basis rhodiocyanoside A could be considered as a potential substrate.

Petri net based performance modeling for effective DVFS for multithreaded programs

Dynamic Voltage and Frequency Scaling (DVFS) is a very effective tool for designing trade-offs between energy and performance. In this paper, we use a formal Petri net based program performance model that directly captures both the application and system properties, to find energy efficient DVFS settings for CMP systems, that satisfy a given performance constraint, for SPMD multithreaded programs. Experimental evaluation shows that we achieve significant energy savings, while meeting the performance constraints.

Device oriented statistical modeling method for process variability in 45nm analog CMOS technology

With the rapid scaling down of the semiconductor process technology, the process variation aware circuit design has become essential today. Several statistical models have been proposed to deal with the process variation. We propose an accurate BSIM model for handling variability in 45nm CMOS technology. The MOSFET is designed to meet the specification of low standby power technology of International Technology Roadmap for Semiconductors (ITRS).The process parameters variation of annealing temperature, oxide thickness, halo dose and title angle of halo implant are considered for the model development. One parameter variation at a time is considered for developing the model. The model validation is done by performance matching with device simulation results and reported error is less than 10%.© (2012) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only.

Modeling the effect of transmission errors on TCP controlled transfers over infrastructure 802.11 wireless LANs

There have been several studies on the performance of TCP controlled transfers over an infrastructure IEEE 802.11 WLAN, assuming perfect channel conditions. In this paper, we develop an analytical model for the throughput of TCP controlled file transfers over the IEEE 802.11 DCF with different packet error probabilities for the stations, accounting for the effect of packet drops on the TCP window. Our analysis proceeds by combining two models: one is an extension of the usual TCP-over-DCF model for an infrastructure WLAN, where the throughput of a station depends on the probability that the head-of-the-line packet at the Access Point belongs to that station; the second is a model for the TCP window process for connections with different drop probabilities. Iterative calculations between these models yields the head-of-the-line probabilities, and then, performance measures such as the throughputs and packet failure probabilities can be derived. We find that, due to MAC layer retransmissions, packet losses are rare even with high channel error probabilities and the stations obtain fair throughputs even when some of them have packet error probabilities as high as 0.1 or 0.2. For some restricted settings we are also able to model tail-drop loss at the AP. Although involving many approximations, the model captures the system behavior quite accurately, as compared with simulations.

Multi-port network modeling for fractal shape microstrip antenna

In this paper we demonstrate the use of multi-port network modeling to analyze one such antenna with fractal shaped parts. Based on simulation and experimental studies, it has been demonstrated that model can accurately predict the input characteristics of antennas with Minkowski geometry replacing a side micro strip square ring.