Decoding the Design Principles of Amino Acids and the Chemical Logic of Protein Sequences

That only 20 amino acids occur naturally accounting for the structural and functional diversity of proteins remains a mystery. We show here that this is a consequence of the action of a symmetry group, identify the presence of hydrogen bond donor groups, presence of sp3 hybridized [gamma] carbons, absence of [delta] carbons and linearity as properties central to side chain design and quantify the chemical logic of protein sequences

Non-linear Redundancy Calibration

For radio interferometric arrays with a sufficient number of redundant spacings the multiplicity of measurements of the same sky visibility can be used to determine both the antenna gains as well as the true visibilities. Many of the earlier approaches to this problem focused on linearized versions of the relation between the measured and the true visibilities. Here we propose to use a standard non-linear minimization algorithm to solve for both the antenna gains as well as the true visibilities. We show through simulations done in the context of the ongoing upgrade to the Ooty Radio Telescope that the non-linear minimization algorithm is fast compared to the earlier approaches. Further, unlike the most straightforward linearized approach, which works with the logarithms of the visibilities and the gains, the non-linear minimization algorithm leads to unbiased solutions. Finally we present error estimates for the estimated gains and visibilities. Monte-Carlo simulations establish that the estimator is indeed statistically efficient, achieving the Cramer-Rao bound.Comment: 9 pages, 5 figures. Accepted for publication in MNRAS. The definitive version will be available at http://mnras.oxfordjournals.or

ORT observations of the damped Lyman alpha system towards PKS 0201+113

We report a deep radio search with the Ooty Radio Telescope (ORT) for the redshifted 21 cm absorption line from the damped Lyman alpha system seen at redshift 3.388 against the quasar PKS 0201+113. This is currently the most distant system for which a detection of 21 cm absorption has been claimed. The present observations have a sensitivity comparable to the earlier ones and detect no statistically significant absorption. We use the non-detection to place an upper limit of ~ 0.011 on the optical depth of the damped Lyman alpha absorber. This corresponds to a lower limit of ~ 5600 K to the spin temperature of the system. This is considerably higher than the previous upper limit of ~ 1380 K.Comment: 5 pages, 1 figure. Accepted by MNRA

Implications of 21cm observations for damped Ly-α\alpha systems

We present Giant Metrewave Radio Telescope HI 21cm absorption observations, of candidate and confirmed damped Lyman-$\alpha$ systems (DLAS). The derived spin temperatures (T_s) are in all cases $\sim 1000$ K or higher. We have also collated from the literature a list of DLAS for which 21cm observations exist, and discuss their implications for the nature of the absorbers. A cross-comparison of the 21cm profiles with low ionization metal profiles shows that the 21cm absorption coincides in velocity with the deepest metal line feature. This is consistent with models in which the deep metal line features arise from discrete clouds but not with models where the deepest features are the result of velocity crowding. We also find that the typical derived spin temperatures of DLAS are considerably higher than those in the Galaxy or nearby spirals. The only exceptions are DLAS which are known to be associated with the disks of spirals; these do, in fact, show low spin temperatures. In a multi-phase medium,the derived T_s is a weighted average of the temperatures of the individual phases. High derived T_s values are hence to be expected from small, low metallicity objects, since these objects should have a lower fraction of the cold phase in their ISM as compared to large galaxies. The high T_s in DLAS is hence consistent with their observed low metallicities as well as with recent observations that DLAS are also associated with dwarf/LSB galaxies. Finally, we suggest that the following trend may be identified: at low redshift, damped absorption arises from a range of systems, including spiral galaxy disks, while, at high redshift, absorption occurs predominantly in smaller systems. (Abridged)Comment: 7 pages, 2 figure

When are extremely metal-deficient galaxies extremely metal-deficient?

Extremely metal-deficient (XMD) galaxies, by definition, have oxygen abundances \le 1/10 solar, and form a very small fraction of the local gas-rich, star-forming dwarf galaxy population. We examine their positions in the luminousity-metallicity (L-Z) and mass-metallicity (M-Z) planes, with respect to the L-Z and M-Z relations of other gas-rich, star-forming dwarf galaxies, viz., blue compact galaxies (BCGs) and dwarf irregular (dI) galaxies. We find that while the metallicities of some low-luminousity XMD galaxies are consistent with those expected from the L-Z relation, other XMD galaxies are deviant. We determine the 95 per cent confidence interval around the L-Z relation for BCGs, and find that its lower boundary is given by 12 + log(O/H) = -0.177 M_{B} + 4.87. We suggest that a galaxy should be regarded as XMD, in a statistically significant manner, only if it lies below this boundary in the L-Z plane. Of our sample of XMD galaxies, we find that more than half are XMD by this criterion. We also determine the gas mass fractions and chemical yields of galaxies in all three samples. We find that the effective chemical yield increases with increasing baryonic mass, consistent with what is expected if outflows of metal-enriched gas are important in determining the effective yield. XMD galaxies have lower effective yield than BCG/dI galaxies of similar baryonic mass. Motivated by the fact that interactions are common in XMD galaxies, we suggest that improved (tidally-driven) mixing of the interstellar media (ISM) in XMD galaxies leads to a lowering of both, the measured metallicity and the calculated effective yield. We suggest that XMD galaxies are deviant from the L-Z relation because of a combination of being gas-rich (i.e., having processed less gas into stars) and having more uniform mixing of metals in their ISM.Comment: Accepted for publication in MNRA

Variable 21cm absorption at z=0.3127

We report multi-epoch GMRT HI observations of the z = 0.3127 damped absorber towards the quasar PKS 1127-145, which reveal variability in both the absorption profile and the flux of the background source, over a time-scale of a few days. The observed variations cannot be explained by simple inter-stellar scintillation (ISS) models where there are only one or two scintillating components and all of the ISS occurs in the Galaxy. More complicated models where there are either more scintillating components or some of the ISS occurs in the ISM of the z=0.3127 absorber may be acceptable. However, the variability can probably best be explained in models incorporating motion (on sub-VLBI scales) of a component of the background continuum source, with or without some ISS. All models for producing the variable 21cm absorption profile require small scale variations in the 21cm optical depth of the absorber. The length scale for the opacity variations is $\sim 0.1$ pc in pure super-luminal motion models, and $\sim$ 10 pc in pure ISS models. Models involving sub-luminal motion, combined with scintillation of the moving component, require opacity variations on far smaller scales, $\sim$ 10 - 100 AU.Comment: 5 pages, 2 figures. Accepted for publication in MNRA

Towards Optimal Moment Estimation in Streaming and Distributed Models

One of the oldest problems in the data stream model is to approximate the p-th moment ||X||_p^p = sum_{i=1}^n X_i^p of an underlying non-negative vector X in R^n, which is presented as a sequence of poly(n) updates to its coordinates. Of particular interest is when p in (0,2]. Although a tight space bound of Theta(epsilon^-2 log n) bits is known for this problem when both positive and negative updates are allowed, surprisingly there is still a gap in the space complexity of this problem when all updates are positive. Specifically, the upper bound is O(epsilon^-2 log n) bits, while the lower bound is only Omega(epsilon^-2 + log n) bits. Recently, an upper bound of O~(epsilon^-2 + log n) bits was obtained under the assumption that the updates arrive in a random order. We show that for p in (0, 1], the random order assumption is not needed. Namely, we give an upper bound for worst-case streams of O~(epsilon^-2 + log n) bits for estimating |X |_p^p. Our techniques also give new upper bounds for estimating the empirical entropy in a stream. On the other hand, we show that for p in (1,2], in the natural coordinator and blackboard distributed communication topologies, there is an O~(epsilon^-2) bit max-communication upper bound based on a randomized rounding scheme. Our protocols also give rise to protocols for heavy hitters and approximate matrix product. We generalize our results to arbitrary communication topologies G, obtaining an O~(epsilon^2 log d) max-communication upper bound, where d is the diameter of G. Interestingly, our upper bound rules out natural communication complexity-based approaches for proving an Omega(epsilon^-2 log n) bit lower bound for p in (1,2] for streaming algorithms. In particular, any such lower bound must come from a topology with large diameter