920 resultados para intrinsically disordered sequences
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A three-level inverter produces six active vectors, each of normalized magnitudes 1, 0.866, and 0.5, besides a zero vector. The vectors of relative length 0.5 are termed pivot vectors.The three nearest voltage vectors are usually used to synthesize the reference vector. In most continuous pulsewidth-modulation(PWM) schemes, the switching sequence begins from a pivot vector and ends with the same pivot vector. Thus, the pivot vector is applied twice in a subcycle or half-carrier cycle. This paper proposes and investigates alternative switching sequences, which use the pivot vector only once but employ one of the other two vectors twice within the subcycle. The total harmonic distortion(THD) in the fundamental line current pertaining to these novel sequences is studied theoretically as well as experimentally over the whole range of modulation. Compared with centered space vector PWM, two of the proposed sequences lead to reduced THD at high modulation indices at a given average switching frequency.
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Superscalar processors currently have the potential to fetch multiple basic blocks per cycle by employing one of several recently proposed instruction fetch mechanisms. However, this increased fetch bandwidth cannot be exploited unless pipeline stages further downstream correspondingly improve. In particular,register renaming a large number of instructions per cycle is diDcult. A large instruction window, needed to receive multiple basic blocks per cycle, will slow down dependence resolution and instruction issue. This paper addresses these and related issues by proposing (i) partitioning of the instruction window into multiple blocks, each holding a dynamic code sequence; (ii) logical partitioning of the registerjle into a global file and several local jles, the latter holding registers local to a dynamic code sequence; (iii) the dynamic recording and reuse of register renaming information for registers local to a dynamic code sequence. Performance studies show these mechanisms improve performance over traditional superscalar processors by factors ranging from 1.5 to a little over 3 for the SPEC Integer programs. Next, it is observed that several of the loops in the benchmarks display vector-like behavior during execution, even if the static loop bodies are likely complex for compile-time vectorization. A dynamic loop vectorization mechanism that builds on top of the above mechanisms is briefly outlined. The mechanism vectorizes up to 60% of the dynamic instructions for some programs, albeit the average number of iterations per loop is quite small.
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The determination of the crystal and molecular structures of a large number of compounds containing the C(sp(2))-F bond has been investigated in detail in halogenated benzanilides and also in liquids, namely the fluorinated amines. It has been observed that when the fluorine atom is present in the ortho or meta position with respect to the amide functionality in benzanilides or the amino group in fluorinated amines which are liquids at room temperature, the fluorine atom exhibits positional disorder. This is associated with changes in patterns of intermolecular interactions which affect crystal packing. Furthermore, the presence of a fluorine atom on the benzanilide framework, in the presence of a heavier halogen (chloro, bromo and iodo), meta or ortho to the amide group does not eliminate the disorder associated with these molecules. In this article, we highlight the salient features present in halogenated compounds exhibiting disorder in the position of organic fluorine with concomitant changes in crystal packing. This feature is also compared with related compounds exhibiting similarity in electronic features, namely positional disorder.
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In this paper we consider the process of discovering frequent episodes in event sequences. The most computationally intensive part of this process is that of counting the frequencies of a set of candidate episodes. We present two new frequency counting algorithms for speeding up this part. These, referred to as non-overlapping and non-inteleaved frequency counts, are based on directly counting suitable subsets of the occurrences of an episode. Hence they are different from the frequency counts of Mannila et al [1], where they count the number of windows in which the episode occurs. Our new frequency counts offer a speed-up factor of 7 or more on real and synthetic datasets. We also show how the new frequency counts can be used when the events in episodes have time-durations as well.
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Discovering patterns in temporal data is an important task in Data Mining. A successful method for this was proposed by Mannila et al. [1] in 1997. In their framework, mining for temporal patterns in a database of sequences of events is done by discovering the so called frequent episodes. These episodes characterize interesting collections of events occurring relatively close to each other in some partial order. However, in this framework(and in many others for finding patterns in event sequences), the ordering of events in an event sequence is the only allowed temporal information. But there are many applications where the events are not instantaneous; they have time durations. Interesting episodesthat we want to discover may need to contain information regarding event durations etc. In this paper we extend Mannila et al.’s framework to tackle such issues. In our generalized formulation, episodes are defined so that much more temporal information about events can be incorporated into the structure of an episode. This significantly enhances the expressive capability of the rules that can be discovered in the frequent episode framework. We also present algorithms for discovering such generalized frequent episodes.
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We report unusual jamming in driven ordered vortex flow in 2H-NbS2. Reinitiating movement in these jammed vortices with a higher driving force and halting it thereafter once again with a reduction in drive leads to a critical behavior centered around the depinning threshold via divergences in the lifetimes of transient states, validating the predictions of a recent simulation study Reichhardt and Olson Reichhardt, Phys. Rev. Lett. 103, 168301 (2009)] which also pointed out a correspondence between plastic depinning in vortex matter and the notion of random organization proposed Corte et al., Nat. Phys. 4, 420 (2008)] in the context of sheared colloids undergoing diffusive motion.
Resumo:
Over the past two decades, many ingenious efforts have been made in protein remote homology detection. Because homologous proteins often diversify extensively in sequence, it is challenging to demonstrate such relatedness through entirely sequence-driven searches. Here, we describe a computational method for the generation of `protein-like' sequences that serves to bridge gaps in protein sequence space. Sequence profile information, as embodied in a position-specific scoring matrix of multiply aligned sequences of bona fide family members, serves as the starting point in this algorithm. The observed amino acid propensity and the selection of a random number dictate the selection of a residue for each position in the sequence. In a systematic manner, and by applying a `roulette-wheel' selection approach at each position, we generate parent family-like sequences and thus facilitate an enlargement of sequence space around the family. When generated for a large number of families, we demonstrate that they expand the utility of natural intermediately related sequences in linking distant proteins. In 91% of the assessed examples, inclusion of designed sequences improved fold coverage by 5-10% over searches made in their absence. Furthermore, with several examples from proteins adopting folds such as TIM, globin, lipocalin and others, we demonstrate that the success of including designed sequences in a database positively sensitized methods such as PSI-BLAST and Cascade PSI-BLAST and is a promising opportunity for enormously improved remote homology recognition using sequence information alone.
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Learning your αβγ's: The diversity of hydrogen-bonding patterns in backbone-expanded hybrid helices is shown by crystal-structure determination of several oligomeric peptides (see scheme; C=gray; H=white; O=red; N=blue). C 12 helices were observed in the αγ peptide series for n=2-8. In comparison, the αα peptide and αβ peptide sequences show C 10 and mixed C 14/C 15 helices, respectively. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Resumo:
Receive antenna selection (AS) has been shown to maintain the diversity benefits of multiple antennas while potentially reducing hardware costs. However, the promised diversity gains of receive AS depend on the assumptions of perfect channel knowledge at the receiver and slowly time-varying fading. By explicitly accounting for practical constraints imposed by the next-generation wireless standards such as training, packetization and antenna switching time, we propose a single receive AS method for time-varying fading channels. The method exploits the low training overhead and accuracy possible from the use of discrete prolate spheroidal (DPS) sequences based reduced rank subspace projection techniques. It only requires knowledge of the Doppler bandwidth, and does not require detailed correlation knowledge. Closed-form expressions for the channel prediction and estimation error as well as symbol error probability (SEP) of M-ary phase-shift keying (MPSK) for symbol-by-symbol receive AS are also derived. It is shown that the proposed AS scheme, after accounting for the practical limitations mentioned above, outperforms the ideal conventional single-input single-output (SISO) system with perfect CSI and no AS at the receiver and AS with conventional estimation based on complex exponential basis functions.
Suite of tools for statistical N-gram language modeling for pattern mining in whole genome sequences
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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.
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A palindrome is a set of characters that reads the same forwards and backwards. Since the discovery of palindromic peptide sequences two decades ago, little effort has been made to understand its structural, functional and evolutionary significance. Therefore, in view of this, an algorithm has been developed to identify all perfect palindromes (excluding the palindromic subset and tandem repeats) in a single protein sequence. The proposed algorithm does not impose any restriction on the number of residues to be given in the input sequence. This avant-garde algorithm will aid in the identification of palindromic peptide sequences of varying lengths in a single protein sequence.
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We present a unified study of the effect of periodic, quasiperiodic, and disordered potentials on topological phases that are characterized by Majorana end modes in one-dimensional p-wave superconducting systems. We define a topological invariant derived from the equations of motion for Majorana modes and, as our first application, employ it to characterize the phase diagram for simple periodic structures. Our general result is a relation between the topological invariant and the normal state localization length. This link allows us to leverage the considerable literature on localization physics and obtain the topological phase diagrams and their salient features for quasiperiodic and disordered systems for the entire region of parameter space. DOI: 10.1103/PhysRevLett.110.146404