Progressive structure-based alignment of homologous proteins: Adopting sequence comparison strategies

Comparison of multiple protein structures has a broad range of applications in the analysis of protein structure, function and evolution. Multiple structure alignment tools (MSTAs) are necessary to obtain a simultaneous comparison of a family of related folds. In this study, we have developed a method for multiple structure comparison largely based on sequence alignment techniques. A widely used Structural Alphabet named Protein Blocks (PBs) was used to transform the information on 3D protein backbone conformation as a ID sequence string. A progressive alignment strategy similar to CLUSTALW was adopted for multiple PB sequence alignment (mulPBA). Highly similar stretches identified by the pairwise alignments are given higher weights during the alignment. The residue equivalences from PB based alignments are used to obtain a three dimensional fit of the structures followed by an iterative refinement of the structural superposition. Systematic comparisons using benchmark datasets of MSTAs underlines that the alignment quality is better than MULTIPROT, MUSTANG and the alignments in HOMSTRAD, in more than 85% of the cases. Comparison with other rigid-body and flexible MSTAs also indicate that mulPBA alignments are superior to most of the rigid-body MSTAs and highly comparable to the flexible alignment methods. (C) 2012 Elsevier Masson SAS. All rights reserved.

Analogy Between Rotating Euler-Bernoulli and Timoshenko Beams and Stiff Strings

The governing differential equation of a rotating beam becomes the stiff-string equation if we assume uniform tension. We find the tension in the stiff string which yields the same frequency as a rotating cantilever beam with a prescribed rotating speed and identical uniform mass and stiffness. This tension varies for different modes and are found by solving a transcendental equation using bisection method. We also find the location along the rotating beam where equivalent constant tension for the stiff string acts for a given mode. Both Euler-Bernoulli and Timoshenko beams are considered for numerical results. The results provide physical insight into relation between rotating beams and stiff string which are useful for creating basis functions for approximate methods in vibration analysis of rotating beams.

Reuse, recycle to de-bloat software

Most Java programmers would agree that Java is a language that promotes a philosophy of “create and go forth”. By design, temporary objects are meant to be created on the heap, possibly used and then abandoned to be collected by the garbage collector. Excessive generation of temporary objects is termed “object churn” and is a form of software bloat that often leads to performance and memory problems. To mitigate this problem, many compiler optimizations aim at identifying objects that may be allocated on the stack. However, most such optimizations miss large opportunities for memory reuse when dealing with objects inside loops or when dealing with container objects. In this paper, we describe a novel algorithm that detects bloat caused by the creation of temporary container and String objects within a loop. Our analysis determines which objects created within a loop can be reused. Then we describe a source-to-source transformation that efficiently reuses such objects. Empirical evaluation indicates that our solution can reduce upto 40% of temporary object allocations in large programs, resulting in a performance improvement that can be as high as a 20% reduction in the run time, specifically when a program has a high churn rate or when the program is memory intensive and needs to run the GC often.

Efficient Regular Expression Pattern Matching for Network Intrusion Detection Systems using Modified Word-based Automata

Network Intrusion Detection Systems (NIDS) intercept the traffic at an organization's network periphery to thwart intrusion attempts. Signature-based NIDS compares the intercepted packets against its database of known vulnerabilities and malware signatures to detect such cyber attacks. These signatures are represented using Regular Expressions (REs) and strings. Regular Expressions, because of their higher expressive power, are preferred over simple strings to write these signatures. We present Cascaded Automata Architecture to perform memory efficient Regular Expression pattern matching using existing string matching solutions. The proposed architecture performs two stage Regular Expression pattern matching. We replace the substring and character class components of the Regular Expression with new symbols. We address the challenges involved in this approach. We augment the Word-based Automata, obtained from the re-written Regular Expressions, with counter-based states and length bound transitions to perform Regular Expression pattern matching. We evaluated our architecture on Regular Expressions taken from Snort rulesets. We were able to reduce the number of automata states between 50% to 85%. Additionally, we could reduce the number of transitions by a factor of 3 leading to further reduction in the memory requirements.

Black hole formation in fuzzy sphere collapse

We study the collapse of a fuzzy sphere, that is a spherical membrane built out of D0-branes, in the Banks-Fischler-Shenker-Susskind model. At weak coupling, as the sphere shrinks, open strings are produced. If the initial radius is large then open string production is not important and the sphere behaves classically. At intermediate initial radius the backreaction from open string production is important but the fuzzy sphere retains its identity. At small initial radius the sphere collapses to form a black hole. The crossover between the later two regimes is smooth and occurs at the correspondence point of Horowitz and Polchinski.

Structure constants of beta deformed super Yang-Mills

We study the structure constants of the N = 1 beta deformed theory perturbatively and at strong coupling. We show that the planar one loop corrections to the structure constants of single trace gauge invariant operators in the scalar sector is determined by the anomalous dimension Hamiltonian. This result implies that 3 point functions of the chiral primaries of the theory do not receive corrections at one loop. We then study the structure constants at strong coupling using the Lunin-Maldacena geometry. We explicitly construct the supergravity mode dual to the chiral primary with three equal U(1) R-charges in the Lunin-Maldacena geometry. We show that the 3 point function of this supergravity mode with semi-classical states representing two other similar chiral primary states but with large U(1) charges to be independent of the beta deformation and identical to that found in the AdS(5) x S-5 geometry. This together with the one-loop result indicate that these structure constants are protected by a non-renormalization theorem. We also show that three point function of U(1) R-currents with classical massive strings is proportional to the R-charge carried by the string solution. This is in accordance with the prediction of the R-symmetry Ward identity.

CFT(4) partition functions and the heat kernel on AdS(5)

We consider four-dimensional CFTs which admit a large-N expansion, and whose spectrum contains states whose conformal dimensions do not scale with N. We explicitly reorganise the partition function obtained by exponentiating the one-particle partition function of these states into a heat kernel form for the dual string spectrum on AdS(5). On very general grounds, the heat kernel answer can be expressed in terms of a convolution of the one-particle partition function of the light states in the four-dimensional CFT. (C) 2013 Elsevier B.V. All rights reserved.

Packaging of Polyvinylidene fluoride nasal sensor for biomedical applications

This paper presents the design technique that has been adopted for packaging of Polyvinylidene fluoride (PVDF) nasal sensor for biomedical applications. The PVDF film with the dimension of length 10mm, width 5mm and thickness 28 mu m was firmly adhered on one end of plastic base (8mmx5mmx30 mu m) in such a way that it forms a cantilever configuration leaving the other end free for deflection. Now with the leads attached on the surface of the PVDF film, the cantilever configuration becomes the PVDF nasal sensor. For mounting a PVDF nasal sensor, a special headphone was designed, that can fit most of the human head sizes. Two flexible strings are soldered on either side of the headphone. Two identical PVDF nasal sensors were then connected to either side of flexible string of the headphone in such a way that they are placed below the right and left nostrils respectively without disturbing the normal breathing. When a subject wares headphone along with PVDF nasal sensors, two voltage signals due to the piezoelectric property of the PVDF film were generated corresponding to his/her nasal airflow from right and left nostril. The entire design was made compact, so that PVDF nasal sensors along with headphone can be made portable. No special equipment or machines are needed for mounting the PVDF nasal sensors. The time required for packaging of PVDF nasal sensors was less and the approximate cost of the entire assembly (PVDF nasal sensors + headphone) was very nominal.

Desingularization of the Milne Universe

Resolution of cosmological singularities is an important problem in any full theory of quantum gravity. The Milne orbifold is a cosmology with a big-bang/big-crunch singularity, but being a quotient of flat space it holds potential for resolution in string theory. It is known, however, that some perturbative string amplitudes diverge in the Milne geometry. Here we show that flat space higher spin theories can effect a simple resolution of the Milne singularity when one embeds the latter in 2 + 1 dimensions. We explain how to reconcile this with the expectation that non-perturbative string effects are required for resolving Milne. Along the way, we introduce a Grassmann realization of the inonfi-Wigner contraction to export much of the AdS technology to -our flat space computation. (C) 2014 The Authors. Published by Elsevier BAT.

Growing dynamical facilitation on approaching the random pinning colloidal glass transition

Despite decades of research, it remains to be established whether the transformation of a liquid into a glass is fundamentally thermodynamic or dynamic in origin. Although observations of growing length scales are consistent with thermodynamic perspectives, the purely dynamic approach of the Dynamical Facilitation (DF) theory lacks experimental support. Further, for vitrification induced by randomly freezing a subset of particles in the liquid phase, simulations support the existence of an underlying thermodynamic phase transition, whereas the DF theory remains unexplored. Here, using video microscopy and holographic optical tweezers, we show that DF in a colloidal glass-forming liquid grows with density as well as the fraction of pinned particles. In addition, we observe that heterogeneous dynamics in the form of string-like cooperative motion emerges naturally within the framework of facilitation. Our findings suggest that a deeper understanding of the glass transition necessitates an amalgamation of existing theoretical approaches.

Spinning strings and minimal surfaces in AdS(3) with mixed 3-form fluxes

Motivated by the recent proposal for the S-matrix in AdS(3) x S-3 with mixed three form fluxes, we study classical folded string spinning in AdS(3) with both Ramond and Neveu-Schwarz three form fluxes. We solve the equations of motion of these strings and obtain their dispersion relation to the leading order in the Neveu-Schwarz flux b. We show that dispersion relation for the spinning strings with large spin S acquires a term given by -root lambda/2 pi b(2) log(2) S in addition to the usual root lambda/pi log S term where root lambda is proportional to the square of the radius of AdS(3). Using SO(2, 2) transformations and re-parmetrizations we show that these spinning strings can be related to light like Wilson loops in AdS(3) with Neveu-Schwarz flux b. We observe that the logarithmic divergence in the area of the light like Wilson loop is also deformed by precisely the same coefficient of the b(2) log(2) S term in the dispersion relation of the spinning string. This result indicates that the coefficient of b(2) log(2) S has a property similar to the coefficient of the log S term, known as cusp-anomalous dimension, and can possibly be determined to all orders in the coupling lambda using the recent proposal for the S-matrix.

Logarithmic corrections to twisted indices from the quantum entropy function

We compute logarithmic corrections to the twisted index B-6(g) in four-dimensional N = 4 and N = 8 string theories using the framework of the Quantum Entropy Function. We find that these vanish, matching perfectly with the large-charge expansion of the corresponding microscopic expressions.

Low tension strings on a cosmological singularity

It has recently been argued that the singularity of the Milne orbifold can be resolved in higher spin theories. In string theory scattering amplitudes, however, the Milne singularity gives rise to ultraviolet divergences that signal uncontrolled backreaction. Since string theory in the low tension limit is expected to be a higher spin theory (although precise proposals only exist in special cases), we investigate what happens to these scattering amplitudes in the low tension limit. We point out that the known problematic ultraviolet divergences disappear in this limit. In addition we systematically identify all divergences of the simplest 2-to-2 tree-level string scattering amplitude on the Milne orbifold, and argue that the divergences that survive in the low tension limit have sensible infrared interpretations.

Strings vs. spins on the null orbifold

We study the null orbifold singularity in 2+1 d flat space higher spin theory as well as string theory. Using the Chern-Simons formulation of 2+1 d Einstein gravity, we first observe that despite the singular nature of this geometry, the eigenvalues of its Chern-Simons holonomy are trivial. Next, we construct a resolution of the singularity in higher spin theory: a Kundt spacetime with vanishing scalar curvature invariants. We also point out that the UV divergences previously observed in the 2-to-2 tachyon tree level string amplitude on the null orbifold do not arise in the at alpha' -> infinity limit. We find all the divergences of the amplitude and demonstrate that the ones remaining in the tensionless limit are physical IR-type divergences. We conclude with a discussion on the meaning and limitations of higher spin (cosmological) singularity resolution and its potential connection to string theory.

Non-uniform beams and stiff strings isospectral to axially loaded uniform beams and piano strings

In this paper, we derive analytical expressions for mass and stiffness functions of transversely vibrating clamped-clamped non-uniform beams under no axial loads, which are isospectral to a given uniform axially loaded beam. Examples of such axially loaded beams are beam columns (compressive axial load) and piano strings (tensile axial load). The Barcilon-Gottlieb transformation is invoked to transform the non-uniform beam equation into the axially loaded uniform beam equation. The coupled ODEs involved in this transformation are solved for two specific cases (pq (z) = k (0) and q = q (0)), and analytical solutions for mass and stiffness are obtained. Examples of beams having a rectangular cross section are shown as a practical application of the analysis. Some non-uniform beams are found whose frequencies are known exactly since uniform axially loaded beams with clamped ends have closed-form solutions. In addition, we show that the tension required in a stiff piano string with hinged ends can be adjusted by changing the mass and stiffness functions of a stiff string, retaining its natural frequencies.