A Deterministic Optimization Approach to Protein Sequence Design Using Continuous Models

Determining the sequence of amino acid residues in a heteropolymer chain of a protein with a given conformation is a discrete combinatorial problem that is not generally amenable for gradient-based continuous optimization algorithms. In this paper we present a new approach to this problem using continuous models. In this modeling, continuous "state functions" are proposed to designate the type of each residue in the chain. Such a continuous model helps define a continuous sequence space in which a chosen criterion is optimized to find the most appropriate sequence. Searching a continuous sequence space using a deterministic optimization algorithm makes it possible to find the optimal sequences with much less computation than many other approaches. The computational efficiency of this method is further improved by combining it with a graph spectral method, which explicitly takes into account the topology of the desired conformation and also helps make the combined method more robust. The continuous modeling used here appears to have additional advantages in mimicking the folding pathways and in creating the energy landscapes that help find sequences with high stability and kinetic accessibility. To illustrate the new approach, a widely used simplifying assumption is made by considering only two types of residues: hydrophobic (H) and polar (P). Self-avoiding compact lattice models are used to validate the method with known results in the literature and data that can be practically obtained by exhaustive enumeration on a desktop computer. We also present examples of sequence design for the HP models of some real proteins, which are solved in less than five minutes on a single-processor desktop computer Some open issues and future extensions are noted.

Coherence and Localization in 2D Luttinger Liquids

Recent measurements on the resistivity of (La-Sr)(2)CuO4 are shown to tit within the general framework of Luttinger liquid transport theory. They exhibit a crossover from the spin-charge separated ''holon nondrag regime'' usually observed, with rho(ab) similar to T, to a ''localizing'' regime dominated by impurity scattering at low temperature. The proportionality of rho(c) and rho(ab) and the giant anisotropy follow directly from the theory.

Analytical And Experimental Aeroacoustic Studies Of Open-Ended 3-Duct Perforated Elements Used In Mufflers

Perforated element mufflers have been known to have good acousticp erformancew, henu sedo n automotive xhausst ystemsIn. thel astd ecadea nda half, plugm ufflersc, oncentrihc oler esonators, and three-ductc losed-endp erforatede lementsh ave been studied.T he presenti nvestigation concernso pen-endedt,h ree-ducpt erforatede lementsw, hich are knownt o combineh igh acoustic transmissiolno ss with low back pressuresT. he governinge quationsh ave been solved in the frequencyd omain,u singt he recouplinga pproacha longw ith appropriatbe oundaryc onditionst,o derivet he transferm atrixa ndt hent o calculaten oiser eductiona ndt ransmissiolno ss.T he predicted noiser eductionv aluesh aveb eens hownt o corroboratew ell with experimentallyo bservedv alues. Finally,p arametrics tudiesh aveb eend onet o draw designc urvesf or suchm ufflers.

CCD: Connected Component Descriptor for Robust Mosaicing of Camera-Captured Document Images

We propose a robust method for mosaicing of document images using features derived from connected components. Each connected component is described using the Angular Radial Tran. form (ART). To ensure geometric consistency during feature matching, the ART coefficients of a connected component are augmented with those of its two nearest neighbors. The proposed method addresses two critical issues often encountered in correspondence matching: (i) The stability of features and (ii) Robustness against false matches due to the multiple instances of characters in a document image. The use of connected components guarantees a stable localization across images. The augmented features ensure a successful correspondence matching even in the presence of multiple similar regions within the page. We illustrate the effectiveness of the proposed method on camera captured document images exhibiting large variations in viewpoint, illumination and scale.

Complexes of lanthanide perchlorates with the open-chain pentadentate ligand n,n,$n^{'},n^{'}$-tetramethyl-3,6,9-trioxaundecane diamide

Complexes of lanthanide perchlorates with the ligand N,N,N,N-tetra-methyl-3,6,9-trioxaundecane diamide (TUD) of the composition Ln(TUD)2-(ClO4)3 (Ln triple bond; length as m-dash La, Nd, Ho, Er, Y) were isolated. Electrical conductivity values indicate that all the perchlorate groups are ionic. IR and nuclear magnetic resonance (1H and 13C) data prove that the ligand coordinates to the metal via the three ether oxygens and the two carbonyl oxygens. A probable coordination number of ten can be assigned for all the complexes.

Instability of laminated composite thin-walled open-section beams

Instability of thin-walled open-section laminated composite beams is studied using the finite element method. A two-noded, 8 df per node thin-walled open-section laminated composite beam finite element has been used. The displacements of the element reference axis are expressed in terms of one-dimensional first order Hermite interpolation polynomials, and line member assumptions are invoked in formulation of the elastic stiffness matrix and geometric stiffness matrix. The nonlinear expressions for the strains occurring in thin-walled open-section beams, when subjected to axial, flexural and torsional loads, are incorporated in a general instability analysis. Several problems for which continuum solutions (exact/approximate) are possible have been solved in order to evaluate the performance of finite element. Next its applicability is demonstrated by predicting the buckling loads for the following problems of laminated composites: (i) two layer (45°/−45°) composite Z section cantilever beam and (ii) three layer (0°/45°/0°) composite Z section cantilever beam.

A Dual Seven-Level Inverter Supply for an Open-End Winding Induction Motor Drive

This paper develops a seven-level inverter structure for open-end winding induction motor drives. The inverter supply is realized by cascading four two-level and two three-level neutral-point-clamped inverters. The inverter control is designed in such a way that the common-mode voltage (CMV) is eliminated. DC-link capacitor voltage balancing is also achieved by using only the switching-state redundancies. The proposed power circuit structure is modular and therefore suitable for fault-tolerant applications. By appropriately isolating some of the inverters, the drive can be operated during fault conditions in a five-level or a three-level inverter mode, with preserved CMV elimination and DC-link capacitor voltage balancing, within a reduced modulation range.

A reply to a discussion by D.J. Cook of the paper a reaction product of lime and silica from rice husk asha star, open

Abstract is not available.

Spectral Sensing for Cognitive Radio: Estimation of Adaptive Frequency Hopping Signal

The issue of dynamic spectrum scene analysis in any cognitive radio network becomes extremely complex when low probability of intercept, spread spectrum systems are present in environment. The detection and estimation become more complex if frequency hopping spread spectrum is adaptive in nature. In this paper, we propose two phase approach for detection and estimation of frequency hoping signals. Polyphase filter bank has been proposed as the architecture of choice for detection phase to efficiently detect the presence of frequency hopping signal. Based on the modeling of frequency hopping signal it can be shown that parametric methods of line spectral analysis are well suited for estimation of frequency hopping signals if the issues of order estimation and time localization are resolved. An algorithm using line spectra parameter estimation and wavelet based transient detection has been proposed which resolves above issues in computationally efficient manner suitable for implementation in cognitive radio. The simulations show promising results proving that adaptive frequency hopping signals can be detected and demodulated in a non cooperative context, even at a very low signal to noise ratio in real time.

Localization of testis-variant histones in rat testis chromatin

Nucleosome core particles and oligonucleosomes were isolated by digesting rat testis nuclei with micrococcal nuclease to 20% acid-solubility, followed by fractionation of the digest on a Bio-Gel A-5m column. The core particles thus isolated were characterized on the basis of their DNA length of 151 +/- 5 base-pairs and sedimentation coefficient of 11.4S. Analysis of the acid-soluble proteins of the core particles indicated that histones TH2B and X2 are constituents of the core particles, in addition to the somatic histones H2A, H2B, H3 and H4. The acid-soluble proteins of the oligonucleosomes comprised all the histones, including both the somatic (H1, H2A, H2B, H3, H4 and X2) and the testis-specific ones (TH1 and TH2B). It was also observed that histones TH1 and H1 are absent from the core particles and were readily extracted from the chromatin by 0.6 M-NaCl, which indicated that both of them are bound to the linker DNA.

TlCaBa2Cu2O7: The 1122 (90 K) superconductor in the new Tl(Ca,Ba)n+1CunO2n+3 seriesstar, open

The 1122 (n=2) member of the Tl(Ca,Ba)n+1CunO2n+3 series containing a single Tl-O layer is shown to be associated with a Tc of 90 K. This value of Tc is significantly lower than that of the 2122 phase (Tcnot, vert, similar110 K) with two Tl-O layers.

Microstructural study of rapidly solidified titanium eutectoid alloysstar, open

Rapid solidification of Ti-7.3wt.%Cu (near-eutectoid composition), Ti-36.2wt.%Ni and Ti-34.3wt.% Ni-5.8wt.%Si alloys has been carried out by electron beam melting and splat quenching on a water-cooled rotating copper disc. The product obtained was in the form of thin ribbons 60–100 μm thick. Transmission electron microscopy studies of Ti---Cu alloy splats showed that the microstructure consisted of a mixture of martensite and a lamellar eutectoid product. The formation of the intermetallic compound Ti2Cu involved a diffusionless ω transformation and spinodal clustering. In the case of Ti---Ni alloy the as-quenched microstructure is complex, consisting of α, transformed β and intermetallic phases. This could have arisen possibly as a result of local variation in cooling rates. Rapid solidification of Ti---Ni---Si alloy resulted in partial quenching of an amorphous phase. The amorphous phase was seen to be extremely hard (a Vickers hardness of about 800 HV).

5-Methyl-2-Thiouridine in the tRNA of Candida tropicalis and Its Localization in Lysine tRNA

35S incorporation studies showed that Candida tropicalis tRNA contained two thionucleosides, one of which was identified as 5-methyl-2-thiouridine. The other thionucleoside was alkali labile, and it appeared to be an ester. Pulse-chase experiments suggested that the two thionucleosides were structurally related. 5-Methyl-2-thiouridine was present in one of the lysine tRNAs. This is the first report of the presence of this nucleoside in a yeast tRNA.

Finite element analysis of laminated anisotropic thin-walled open-section beams

A finite element analysis of thin-walled open-section laminated anisotropic beams is presented herein. A two-noded, 8 degrees of freedom per node thin-walled open-section laminated anisotropic beam finite element has been developed and used. The displacements of the element reference axes are expressed in terms of one-dimensional first order Hermite interpolation polynomials and line member assumptions are invoked in the formulation of the stiffness matrix. The problems of: 1. (a) an isotropic material Z section straight cantilever beam, and 2. (b) a single-layer (0°) composite Z section straight cantilever beam, for which continuum solutions (exact/approximate) are possible, have been solved in order to evaluate the performance of the finite element. Its applicability has been shown by solving the following problems: 3. (c) a two-layer (45°/−45°) composite Z section straight cantilever beam, 4. (d) a three-layer (0°/45°/0°) composite Z section straight cantilever beam.