Solvation dynamics of tryptophan in water-dimethyl sulfoxide binary mixture: In search of molecular origin of composition dependent multiple anomalies

Experimental and simulation studies have uncovered at least two anomalous concentration regimes in water-dimethyl sulfoxide (DMSO) binary mixture whose precise origin has remained a subject of debate. In order to facilitate time domain experimental investigation of the dynamics of such binary mixtures, we explore strength or extent of influence of these anomalies in dipolar solvation dynamics by carrying out long molecular dynamics simulations over a wide range of DMSO concentration. The solvation time correlation function so calculated indeed displays strong composition dependent anomalies, reflected in pronounced non-exponential kinetics and non-monotonous composition dependence of the average solvation time constant. In particular, we find remarkable slow-down in the solvation dynamics around 10%-20% and 35%-50% mole percentage. We investigate microscopic origin of these two anomalies. The population distribution analyses of different structural morphology elucidate that these two slowing down are reflections of intriguing structural transformations in water-DMSO mixture. The structural transformations themselves can be explained in terms of a change in the relative coordination number of DMSO and water molecules, from 1DMSO:2H(2)O to 1H(2)O:1DMSO and 1H(2)O:2DMSO complex formation. Thus, while the emergence of first slow down (at 15% DMSO mole percentage) is due to the percolation among DMSO molecules supported by the water molecules (whose percolating network remains largely unaffected), the 2nd anomaly (centered on 40%-50%) is due to the formation of the network structure where the unit of 1DMSO:1H(2)O and 2DMSO:1H(2)O dominates to give rise to rich dynamical features. Through an analysis of partial solvation dynamics an interesting negative cross-correlation between water and DMSO is observed that makes an important contribution to relaxation at intermediate to longer times.

Feature Search in the Grassmanian in Online Reinforcement Learning

We consider the problem of finding the best features for value function approximation in reinforcement learning and develop an online algorithm to optimize the mean square Bellman error objective. For any given feature value, our algorithm performs gradient search in the parameter space via a residual gradient scheme and, on a slower timescale, also performs gradient search in the Grassman manifold of features. We present a proof of convergence of our algorithm. We show empirical results using our algorithm as well as a similar algorithm that uses temporal difference learning in place of the residual gradient scheme for the faster timescale updates.

Group testing based spectrum hole search using a simple sub-nyquist sampling scheme

In this paper, we consider the problem of finding a spectrum hole of a specified bandwidth in a given wide band of interest. We propose a new, simple and easily implementable sub-Nyquist sampling scheme for signal acquisition and a spectrum hole search algorithm that exploits sparsity in the primary spectral occupancy in the frequency domain by testing a group of adjacent subbands in a single test. The sampling scheme deliberately introduces aliasing during signal acquisition, resulting in a signal that is the sum of signals from adjacent sub-bands. Energy-based hypothesis tests are used to provide an occupancy decision over the group of subbands, and this forms the basis of the proposed algorithm to find contiguous spectrum holes. We extend this framework to a multi-stage sensing algorithm that can be employed in a variety of spectrum sensing scenarios, including non-contiguous spectrum hole search. Further, we provide the analytical means to optimize the hypothesis tests with respect to the detection thresholds, number of samples and group size to minimize the detection delay under a given error rate constraint. Depending on the sparsity and SNR, the proposed algorithms can lead to significantly lower detection delays compared to a conventional bin-by-bin energy detection scheme; the latter is in fact a special case of the group test when the group size is set to 1. We validate our analytical results via Monte Carlo simulations.

Does linear separability really matter? Complex visual search is explained by simple search

Visual search in real life involves complex displays with a target among multiple types of distracters, but in the laboratory, it is often tested using simple displays with identical distracters. Can complex search be understood in terms of simple searches? This link may not be straightforward if complex search has emergent properties. One such property is linear separability, whereby search is hard when a target cannot be separated from its distracters using a single linear boundary. However, evidence in favor of linear separability is based on testing stimulus configurations in an external parametric space that need not be related to their true perceptual representation. We therefore set out to assess whether linear separability influences complex search at all. Our null hypothesis was that complex search performance depends only on classical factors such as target-distracter similarity and distracter homogeneity, which we measured using simple searches. Across three experiments involving a variety of artificial and natural objects, differences between linearly separable and nonseparable searches were explained using target-distracter similarity and distracter heterogeneity. Further, simple searches accurately predicted complex search regardless of linear separability (r = 0.91). Our results show that complex search is explained by simple search, refuting the widely held belief that linear separability influences visual search.

Adaptive selection of search space in look ahead orthogonal matching pursuit

Compressive Sensing theory combines the signal sampling and compression for sparse signals resulting in reduction in sampling rate and computational complexity of the measurement system. In recent years, many recovery algorithms were proposed to reconstruct the signal efficiently. Look Ahead OMP (LAOMP) is a recently proposed method which uses a look ahead strategy and performs significantly better than other greedy methods. In this paper, we propose a modification to the LAOMP algorithm to choose the look ahead parameter L adaptively, thus reducing the complexity of the algorithm, without compromising on the performance. The performance of the algorithm is evaluated through Monte Carlo simulations.

A scaled unscented transformation based directed Gaussian sum filter for nonlinear dynamic system identification

Impoverishment of particles, i.e. the discretely simulated sample paths of the process dynamics, poses a major obstacle in employing the particle filters for large dimensional nonlinear system identification. A known route of alleviating this impoverishment, i.e. of using an exponentially increasing ensemble size vis-a-vis the system dimension, remains computationally infeasible in most cases of practical importance. In this work, we explore the possibility of unscented transformation on Gaussian random variables, as incorporated within a scaled Gaussian sum stochastic filter, as a means of applying the nonlinear stochastic filtering theory to higher dimensional structural system identification problems. As an additional strategy to reconcile the evolving process dynamics with the observation history, the proposed filtering scheme also modifies the process model via the incorporation of gain-weighted innovation terms. The reported numerical work on the identification of structural dynamic models of dimension up to 100 is indicative of the potential of the proposed filter in realizing the stated aim of successfully treating relatively larger dimensional filtering problems. (C) 2013 Elsevier Ltd. All rights reserved.

The exploration of Kemp's triacid (KTA) as the core for the synthesis of 3-fold symmetric 2(3)-cyclophane, 2(2)-cyclophane and novel linker directed designs

For the first time, two units of KTA have been linked to three units of cyst-di-OMe. The reaction is noteworthy since it involves the formation of six amide bonds leading to a three-fold symmetric 23-cyclophane (3) harboring a cluster of three S-S bridges. The major product is a di-imide (4), arising from the interaction of a cystine NH with a neighbouring activated ester. A third reaction of tethering KTA with a single cyst-di-OMe unit afforded the flexible compound 6 and, with benzidine, the novel linker directed 7 with orthogonally disposed anchor modules.

Filling-in Void and Sparse Regions in Protein Sequence Space by Protein-Like Artificial Sequences Enables Remarkable Enhancement in Remote Homology Detection Capability

Protein functional annotation relies on the identification of accurate relationships, sequence divergence being a key factor. This is especially evident when distant protein relationships are demonstrated only with three-dimensional structures. To address this challenge, we describe a computational approach to purposefully bridge gaps between related protein families through directed design of protein-like ``linker'' sequences. For this, we represented SCOP domain families, integrated with sequence homologues, as multiple profiles and performed HMM-HMM alignments between related domain families. Where convincing alignments were achieved, we applied a roulette wheel-based method to design 3,611,010 protein-like sequences corresponding to 374 SCOP folds. To analyze their ability to link proteins in homology searches, we used 3024 queries to search two databases, one containing only natural sequences and another one additionally containing designed sequences. Our results showed that augmented database searches showed up to 30% improvement in fold coverage for over 74% of the folds, with 52 folds achieving all theoretically possible connections. Although sequences could not be designed between some families, the availability of designed sequences between other families within the fold established the sequence continuum to demonstrate 373 difficult relationships. Ultimately, as a practical and realistic extension, we demonstrate that such protein-like sequences can be ``plugged-into'' routine and generic sequence database searches to empower not only remote homology detection but also fold recognition. Our richly statistically supported findings show that complementary searches in both databases will increase the effectiveness of sequence-based searches in recognizing all homologues sharing a common fold. (C) 2013 Elsevier Ltd. All rights reserved.

Diffraction tomography from intensity measurements: an evolutionary stochastic search to invert experimental data

We develop iterative diffraction tomography algorithms, which are similar to the distorted Born algorithms, for inverting scattered intensity data. Within the Born approximation, the unknown scattered field is expressed as a multiplicative perturbation to the incident field. With this, the forward equation becomes stable, which helps us compute nearly oscillation-free solutions that have immediate bearing on the accuracy of the Jacobian computed for use in a deterministic Gauss-Newton (GN) reconstruction. However, since the data are inherently noisy and the sensitivity of measurement to refractive index away from the detectors is poor, we report a derivative-free evolutionary stochastic scheme, providing strictly additive updates in order to bridge the measurement-prediction misfit, to arrive at the refractive index distribution from intensity transport data. The superiority of the stochastic algorithm over the GN scheme for similar settings is demonstrated by the reconstruction of the refractive index profile from simulated and experimentally acquired intensity data. (C) 2014 Optical Society of America

Progress in tuberculosis vaccine development and host-directed therapies-a state of the art review

Tuberculosis continues to kill 1.4 million people annually. During the past 5 years, an alarming increase in the number of patients with multidrug-resistant tuberculosis and extensively drug-resistant tuberculosis has been noted, particularly in eastern Europe, Asia, and southern Africa. Treatment outcomes with available treatment regimens for drug-resistant tuberculosis are poor. Although substantial progress in drug development for tuberculosis has been made, scientific progress towards development of interventions for prevention and improvement of drug treatment outcomes have lagged behind. Innovative interventions are therefore needed to combat the growing pandemic of multidrug-resistant and extensively drug-resistant tuberculosis. Novel adjunct treatments are needed to accomplish improved cure rates for multidrug-resistant and extensively drug-resistant tuberculosis. A novel, safe, widely applicable, and more effective vaccine against tuberculosis is also desperately sought to achieve disease control. The quest to develop a universally protective vaccine for tuberculosis continues. So far, research and development of tuberculosis vaccines has resulted in almost 20 candidates at different stages of the clinical trial pipeline. Host-directed therapies are now being developed to refocus the anti-Mycobacterium tuberculosis-directed immune responses towards the host; a strategy that could be especially beneficial for patients with multidrug-resistant tuberculosis or extensively drug-resistant tuberculosis. As we are running short of canonical tuberculosis drugs, more attention should be given to host-directed preventive and therapeutic intervention measures.

Features in visual search combine linearly

Single features such as line orientation and length are known to guide visual search, but relatively little is known about how multiple features combine in search. To address this question, we investigated how search for targets differing in multiple features ( intensity, length, orientation) from the distracters is related to searches for targets differing in each of the individual features. We tested race models (based on reaction times) and coactivation models ( based on reciprocal of reaction times) for their ability to predict multiple feature searches. Multiple feature searches were best accounted for by a co-activation model in which feature information combined linearly (r = 0.95). This result agrees with the classic finding that these features are separable i.e., subjective dissimilarity ratings sum linearly. We then replicated the classical finding that the length and width of a rectangle are integral features-in other words, they combine nonlinearly in visual search. However, to our surprise, upon including aspect ratio as an additional feature, length and width combined linearly and this model outperformed all other models. Thus, length and width of a rectangle became separable when considered together with aspect ratio. This finding predicts that searches involving shapes with identical aspect ratio should be more difficult than searches where shapes differ in aspect ratio. We confirmed this prediction on a variety of shapes. We conclude that features in visual search co-activate linearly and demonstrate for the first time that aspect ratio is a novel feature that guides visual search.

Group Testing-Based Spectrum Hole Search for Cognitive Radios

This paper investigates the use of adaptive group testing to find a spectrum hole of a specified bandwidth in a given wideband of interest. We propose a group testing-based spectrum hole search algorithm that exploits sparsity in the primary spectral occupancy by testing a group of adjacent subbands in a single test. This is enabled by a simple and easily implementable sub-Nyquist sampling scheme for signal acquisition by the cognitive radios (CRs). The sampling scheme deliberately introduces aliasing during signal acquisition, resulting in a signal that is the sum of signals from adjacent subbands. Energy-based hypothesis tests are used to provide an occupancy decision over the group of subbands, and this forms the basis of the proposed algorithm to find contiguous spectrum holes of a specified bandwidth. We extend this framework to a multistage sensing algorithm that can be employed in a variety of spectrum sensing scenarios, including noncontiguous spectrum hole search. Furthermore, we provide the analytical means to optimize the group tests with respect to the detection thresholds, number of samples, group size, and number of stages to minimize the detection delay under a given error probability constraint. Our analysis allows one to identify the sparsity and SNR regimes where group testing can lead to significantly lower detection delays compared with a conventional bin-by-bin energy detection scheme; the latter is, in fact, a special case of the group test when the group size is set to 1 bin. We validate our analytical results via Monte Carlo simulations.

Shape and size directed self-selection in organic cage formation

The selective formation of a single isomer of a 3+2] self-assembled organic cage from a reaction mixture of an unsymmetrical aldehyde and a flexible amine is discussed. The experimental and theoretical findings suggest that in such a process, the geometric features of the aldehyde play a key role.

Directed Nonabelian Sandpile Models on Trees

We define two general classes of nonabelian sandpile models on directed trees (or arborescences), as models of nonequilibrium statistical physics. Unlike usual applications of the well-known abelian sandpile model, these models have the property that sand grains can enter only through specified reservoirs. In the Trickle-down sandpile model, sand grains are allowed to move one at a time. For this model, we show that the stationary distribution is of product form. In the Landslide sandpile model, all the grains at a vertex topple at once, and here we prove formulas for all eigenvalues, their multiplicities, and the rate of convergence to stationarity. The proofs use wreath products and the representation theory of monoids.

A search for chaos in the optical light curve of a blazar: W2R 1926+42

Aims. In this work we search for the signatures of low-dimensional chaos in the temporal behavior of the Kepler-field blazar W2R 1946+42. Methods. We use a publicly available, similar to 160 000-point-long and mostly equally spaced light curve of W2R 1946+42. We apply the correlation integral method to both real datasets and phase randomized surrogates. Results. We are not able to confirm the presence of low-dimensional chaos in the light curve. This result, however, still leads to some important implications for blazar emission mechanisms, which are discussed.