RNA-dependent RNA polymerase of Japanese encephalitis virus binds the initiator nucleotide GTP to form a mechanistically important pre-initiation state

Flaviviral RNA-dependent RNA polymerases (RdRps) initiate replication of the single-stranded RNA genome in the absence of a primer. The template sequence 5'-CU-3' at the 3'-end of the flaviviral genome is highly conserved. Surprisingly, flaviviral RdRps require high concentrations of the second incoming nucleotide GTP to catalyze de novo template-dependent RNA synthesis. We show that GTP stimulates de novo RNA synthesis by RdRp from Japanese encephalitis virus (jRdRp) also. Crystal structures of jRdRp complexed with GTP and ATP provide a basis for specific recognition of GTP. Comparison of the jRdRp(GTP) structure with other viral RdRp-GTP structures shows that GTP binds jRdRp in a novel conformation. Apo-jRdRp structure suggests that the conserved motif F of jRdRp occupies multiple conformations in absence of GTP. Motif F becomes ordered on GTP binding and occludes the nucleotide triphosphate entry tunnel. Mutational analysis of key residues that interact with GTP evinces that the jRdRp(GTP) structure represents a novel pre-initiation state. Also, binding studies show that GTP binding reduces affinity of RdRp for RNA, but the presence of the catalytic Mn2+ ion abolishes this inhibition. Collectively, these observations suggest that the observed pre-initiation state may serve as a check-point to prevent erroneous template-independent RNA synthesis by jRdRp during initiation.

Secrecy in the 2-User Symmetric Deterministic Interference Channel with Transmitter Cooperation

This work presents novel achievable schemes for the 2-user symmetric linear deterministic interference channel with limited-rate transmitter cooperation and perfect secrecy constraints at the receivers. The proposed achievable scheme consists of a combination of interference cancelation, relaying of the other user's data bits, time sharing, and transmission of random bits, depending on the rate of the cooperative link and the relative strengths of the signal and the interference. The results show, for example, that the proposed scheme achieves the same rate as the capacity without the secrecy constraints, in the initial part of the weak interference regime. Also, sharing random bits through the cooperative link can achieve a higher secrecy rate compared to sharing data bits, in the very high interference regime. The results highlight the importance of limited transmitter cooperation in facilitating secure communications over 2-user interference channels.

Linear filtering methods for fixed rate quantisation with noisy symmetric error channels

This study considers linear filtering methods for minimising the end-to-end average distortion of a fixed-rate source quantisation system. For the source encoder, both scalar and vector quantisation are considered. The codebook index output by the encoder is sent over a noisy discrete memoryless channel whose statistics could be unknown at the transmitter. At the receiver, the code vector corresponding to the received index is passed through a linear receive filter, whose output is an estimate of the source instantiation. Under this setup, an approximate expression for the average weighted mean-square error (WMSE) between the source instantiation and the reconstructed vector at the receiver is derived using high-resolution quantisation theory. Also, a closed-form expression for the linear receive filter that minimises the approximate average WMSE is derived. The generality of framework developed is further demonstrated by theoretically analysing the performance of other adaptation techniques that can be employed when the channel statistics are available at the transmitter also, such as joint transmit-receive linear filtering and codebook scaling. Monte Carlo simulation results validate the theoretical expressions, and illustrate the improvement in the average distortion that can be obtained using linear filtering techniques.

Nonlinear analysis of a thin pre-twisted and delaminated anisotropic strip

The present work is aimed at the development of an efficient mathematical model to assess the degradation in the stiffness properties of an anisotropic strip due to delamination. In particular, the motive is to capture those nonlinear effects in a strip that arise due to the geometry of the structure, in the presence of delamination. The variational asymptotic method (VAM) is used as a mathematical tool to simplify the original 3D problem to a 1D problem. Further simplification is achieved by modeling the delaminated structure by a sublaminate approach. By VAM, a 2D nonlinear sectional analysis is carried out to determine compact expression for the stiffness terms. The stiffness terms, both linear and nonlinear, are derived as functions of delamination length and location in closed form. In general, the results from the analysis include fully coupled nonlinear 1D stiffness coefficients, 3D strain field, 3D stress field, and in-plane and warping fields. In this work, the utility of the model is demonstrated for a static case, and its capability to capture the trapeze effect in the presence of delamination is investigated and compared with results available in the literature.

Analysis of cracked and un-cracked semicircular rings under symmetric loading

Edge cracked specimens have been widely utilized for fracture testing. Edge cracked semicircular disk (ECSD) specimen has now been well characterized with regard to its form factor and weight function. This paper presents a modified semicircular ring version of this specimen to enhance the form factor in general while retaining other desirable features. The efficacy of the modified design is proved by combining theory of elasticity solutions with finite element results to arrive at the optimum design geometry. New insights emerging from this work are used to theoretically re-examine the arch-tension and the four-point bend specimens. (C) 2014 Elsevier Ltd. All rights reserved.

Symmetric supercapacitor based on partially exfoliated and reduced graphite oxide in neutral aqueous electrolyte

The partially exfoliated and reduced graphite oxide (PE-RGO) is prepared by low temperature thermal exfoliation of graphite oxide under air atmosphere. A symmetric carbon/carbon supercapacitor is studied in a Na2SO4 aqueous electrolyte. The discharge capacitance is 92 F g(-1), when symmetric cell is cycled between the potential ranges from 0 to 1.6 V. This system demonstrates a stable charge/discharge cycle behavior up to 3000 cycles when the cell is operated at a voltage window of 1.6 V. The utilization ratio of potential window is 90% for this system is attributed to the more negative value of electrodes potential when the cell voltage is set to 0 V. The low-temperature exfoliation approach is convenient for mass production of graphenes at low cost and it can be used as electrode material for energy storage applications. (C) 2014 Elsevier Ltd. All rights reserved.

PROPER HOLOMORPHIC MAPS BETWEEN BOUNDED SYMMETRIC DOMAINS REVISITED

We prove that a proper holomorphic map between two nonplanar bounded symmetric domains of the same dimension, one of them being irreducible, is a biholomorphism. Our methods allow us to give a single, all-encompassing argument that unifies the various special cases in which this result is known. We discuss an application of these methods to domains having noncompact automorphism groups that are not assumed to act transitively.

Medium-Voltage Drive for Induction Machine With Multilevel Dodecagonal Voltage Space Vectors With Symmetric Triangles

Multilevel inverters with dodecagonal (12-sided polygon) voltage space vector structure have advantages, such as complete elimination of fifth and seventh harmonics, reduction in electromagnetic interference, reduction in device voltage ratings, reduction of switching frequency, extension of linear modulation range, etc., making it a viable option for high-power medium-voltage drives. This paper proposes two power circuit topologies capable of generating multilevel dodecagonal voltage space vector structure with symmetric triangles (for the first time) with minimum number of dc-link power supplies and floating capacitor H-bridges. The first power topology is composed of two hybrid cascaded five-level inverters connected to either side of an open-end winding induction machine. Each inverter consists of a three-level neutral-point-clamped inverter, which is cascaded with an isolated H-bridge making it a five-level inverter. The second topology is for a normal induction motor. Both of these circuit topologies have inherent capacitor balancing for floating H-bridges for all modulation indexes, including transient operations. The proposed topologies do not require any precharging circuitry for startup. A simple pulsewidth modulation timing calculation method for space vector modulation is also presented in this paper. Due to the symmetric arrangement of congruent triangles within the voltage space vector structure, the timing computation requires only the sampled reference values and does not require any offline computation, lookup tables, or angle computation. Experimental results for steady-state operation and transient operation are also presented to validate the proposed concept.

Directing peptide conformation with centrally positioned pre-organized dipeptide segments: studies of a 12-residue helix and beta-hairpin

Secondary structure formation in oligopeptides can be induced by short nucleating segments with a high propensity to form hydrogen bonded turn conformations. Type I/III turns facilitate helical folding while type II'/I' turns favour hairpin formation. This principle is experimentally verified by studies of two designed dodecapeptides, Boc-Val-Phe-Leu-Phe-Val-Aib-Aib-Val-Phe-Leu-Phe-Val-OMe 1 and Boc-Val-Phe-Leu-Phe-Val- (D) Pro- (L) Pro-Val-Phe-Leu-Phe-Val-OMe 2. The N- and C-terminal flanking pentapeptide sequences in both cases are identical. Peptide 1 adopts a largely alpha-helical conformation in crystals, with a small 3(10) helical segment at the N-terminus. The overall helical fold is maintained in methanol solution as evidenced by NMR studies. Peptide 2 adopts an antiparallel beta-hairpin conformation stabilized by 6 interstrand hydrogen bonds. Key nuclear Overhauser effects (NOEs) provide evidence for the antiparallel beta-hairpin structure. Aromatic proton chemical shifts provide a clear distinction between the conformation of peptides 1 (helical) and 2 (beta-hairpin). The proximity of facing aromatic residues positioned at non-hydrogen bonding positions in the hairpin results in extensively ring current shifted proton resonances in peptide 2.

CROSS-SECTIONAL ANALYSIS OF PRE-TWISTED THICK BEAMS USING VARIATIONAL ASYMPTOTIC METHOD

An asymptotically-exact methodology is presented for obtaining the cross-sectional stiffness matrix of a pre-twisted moderately-thick beam having rectangular cross sections and made of transversely isotropic materials. The anisotropic beam is modeled from 3-D elasticity, without any further assumptions. The beam is allowed to have large displacements and rotations, but small strain is assumed. The strain energy of the beam is computed making use of the constitutive law and the kinematical relations derived with the inclusion of geometrical nonlinearities and initial twist. Large displacements and rotations are allowed, but small strain is assumed. The Variational Asymptotic Method is used to minimize the energy functional, thereby reducing the cross section to a point on the reference line with appropriate properties, yielding a 1-D constitutive law. In this method as applied herein, the 2-D cross-sectional analysis is performed asymptotically by taking advantage of a material small parameter and two geometric small parameters. 3-D strain components are derived using kinematics and arranged as orders of the small parameters. Warping functions are obtained by the minimization of strain energy subject to certain set of constraints that renders the 1-D strain measures well-defined. Closed-form expressions are derived for the 3-D non-linear warping and stress fields. The model is capable of predicting interlaminar and transverse shear stresses accurately up to first order.

Analysis of Transverse Shear Strains in Pre-Twisted Thick Beams using Variational Asymptotic Method

The cross-sectional stiffness matrix is derived for a pre-twisted, moderately thick beam made of transversely isotropic materials and having rectangular cross sections. An asymptotically-exact methodology is used to model the anisotropic beam from 3-D elasticity, without any further assumptions. The beam is allowed to have large displacements and rotations, but small strain is assumed. The strain energy is computed making use of the beam constitutive law and kinematical relations derived with the inclusion of geometrical nonlinearities and an initial twist. The energy functional is minimized making use of the Variational Asymptotic Method (VAM), thereby reducing the cross section to a point on the beam reference line with appropriate properties, forming a 1-D constitutive law. VAM is a mathematical technique employed in the current problem to rigorously split the 3-D analysis of beams into two: a 2-D analysis over the beam cross-sectional domain, which provides a compact semi-analytical form of the properties of the cross sections, and a nonlinear 1-D analysis of the beam reference curve. In this method, as applied herein, the cross-sectional analysis is performed asymptotically by taking advantage of a material small parameter and two geometric small parameters. 3-D strain components are derived using kinematics and arranged in orders of the small parameters. Closed-form expressions are derived for the 3-D non-linear warping and stress fields. Warping functions are obtained by the minimization of strain energy subject to certain set of constraints that render the 1-D strain measures well-defined. The zeroth-order 3-D warping field thus yielded is then used to integrate the 3-D strain energy density over the cross section, resulting in the 1-D strain energy density, which in turn helps identify the corresponding cross-sectional stiffness matrix. The model is capable of predicting interlaminar and transverse shear stresses accurately up to first order.

Outer Bounds on the Secrecy Rate of the 2-User Symmetric Deterministic Interference Channel with Transmitter Cooperation

This paper derives outer bounds for the 2-user symmetric linear deterministic interference channel (SLDIC) with limited-rate transmitter cooperation and perfect secrecy constraints at the receivers. Five outer bounds are derived, under different assumptions of providing side information to receivers and partitioning the encoded message/output depending on the relative strength of the signal and the interference. The usefulness of these outer bounds is shown by comparing the bounds with the inner bound on the achievable secrecy rate derived by the authors in a previous work. Also, the outer bounds help to establish that sharing random bits through the cooperative link can achieve the optimal rate in the very high interference regime.

Symmetric Supercapacitor Based on Reduced Graphene Oxide in Non-Aqueous Electrolyte

Reduced graphene oxide (RGO) is prepared by thermal exfoliation of graphite oxide in air. Symmetric RGO/RGO supercapacitors are constructed in a non-aqueous electrolyte and characterized. The values of energy density are 44 Wh kg(-1) and 15 Wh kg(-1), respectively at 0.15 and 8.0 kW kg(-1). The symmetric supercapacitor exhibits stable charge/discharge cycling tested up to 3000 cycles. The low-temperature thermal exfoliation approach is convenient for mass production of RGO at low cost and it can be used as electrode material for energy storage applications. (c) The Author(s) 2015. Published by ECS. All rights reserved.

Inner Bound on the GDOF of the K-User MIMO Gaussian Symmetric Interference Channel

The K-user multiple input multiple output (MIMO) Gaussian symmetric interference channel where each transmitter has M antennas and each receiver has N antennas is studied from a generalized degrees of freedom (GDOF) perspective. An inner bound on the GDOF is derived using a combination of techniques such as treating interference as noise, zero forcing (ZF) at the receivers, interference alignment (IA), and extending the Han-Kobayashi (HK) scheme to K users, as a function of the number of antennas and the log INR/log SNR level. Several interesting conclusions are drawn from the derived bounds. It is shown that when K > N/M + 1, a combination of the HK and IA schemes performs the best among the schemes considered. When N/M < K <= N/M + 1, the HK-scheme outperforms other schemes and is found to be GDOF optimal in many cases. In addition, when the SNR and INR are at the same level, ZF-receiving and the HK-scheme have the same GDOF performance.

Design of symmetric TIM barrel proteins from first principles

Background: Computational protein design is a rapidly maturing field within structural biology, with the goal of designing proteins with custom structures and functions. Such proteins could find widespread medical and industrial applications. Here, we have adapted algorithms from the Rosetta software suite to design much larger proteins, based on ideal geometric and topological criteria. Furthermore, we have developed techniques to incorporate symmetry into designed structures. For our first design attempt, we targeted the (alpha/beta)(8) TIM barrel scaffold. We gained novel insights into TIM barrel folding mechanisms from studying natural TIM barrel structures, and from analyzing previous TIM barrel design attempts. Methods: Computational protein design and analysis was performed using the Rosetta software suite and custom scripts. Genes encoding all designed proteins were synthesized and cloned on the pET20-b vector. Standard circular dichroism and gel chromatographic experiments were performed to determine protein biophysical characteristics. 1D NMR and 2D HSQC experiments were performed to determine protein structural characteristics. Results: Extensive protein design simulations coupled with ab initio modeling yielded several all-atom models of ideal, 4-fold symmetric TIM barrels. Four such models were experimentally characterized. The best designed structure (Symmetrin-1) contained a polar, histidine-rich pore, forming an extensive hydrogen bonding network. Symmetrin-1 was easily expressed and readily soluble. It showed circular dichroism spectra characteristic of well-folded alpha/beta proteins. Temperature melting experiments revealed cooperative and reversible unfolding, with a T-m of 44 degrees C and a Gibbs free energy of unfolding (Delta G degrees) of 8.0 kJ/mol. Urea denaturing experiments confirmed these observations, revealing a C-m of 1.6 M and a Delta G degrees of 8.3 kJ/mol. Symmetrin-1 adopted a monomeric conformation, with an apparent molecular weight of 32.12 kDa, and displayed well resolved 1D-NMR spectra. However, the HSQC spectrum revealed somewhat molten characteristics. Conclusions: Despite the detection of molten characteristics, the creation of a soluble, cooperatively folding protein represents an advancement over previous attempts at TIM barrel design. Strategies to further improve Symmetrin-1 are elaborated. Our techniques may be used to create other large, internally symmetric proteins.