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Search Results: 1 - 10 of 130426 matches for " V. Gadagkar "
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Evidence for a Superglass State in Solid 4He
B. Hunt,E. Pratt,V. Gadagkar,M. Yamashita,A. V. Balatsky,J. C. Davis
Physics , 2009, DOI: 10.1126/science.1169512
Abstract: Although solid helium-4 (4He) may be a supersolid it also exhibits many phenomena unexpected in that context. We studied relaxation dynamics in the resonance frequency f(T) and dissipation D(T) of a torsional oscillator containing solid 4He. With the appearance of the "supersolid" state, the relaxation times within f(T) and D(T) began to increase rapidly together. More importantly, the relaxation processes in both D(T) and a component of f(T) exhibited a complex synchronized ultraslow evolution towards equilibrium. Analysis using a generalized rotational susceptibility revealed that, while exhibiting these apparently glassy dynamics, the phenomena were quantitatively inconsistent with a simple excitation freeze-out transition because the variation in f was far too large. One possibility is that amorphous solid 4He represents a new form of supersolid in which dynamical excitations within the solid control the superfluid phase stiffness.
Interplay of Rotational, Relaxational, and Shear Dynamics in Solid 4He
E. J. Pratt,B. Hunt,V. Gadagkar,M. Yamashita,M. J. Graf,A. V. Balatsky,J. C. Davis
Physics , 2011, DOI: 10.1126/science.1203080
Abstract: Using a high-sensitivity torsional oscillator technique, we mapped the rotational and relaxational dynamics of solid helium-4 throughout the parameter range of the proposed supersolidity. We found evidence that the same microscopic excitations controlling the torsional oscillator motions are generated independently by thermal and mechanical stimulation. Moreover, a measure for the relaxation times of these excitations diverges smoothly without any indication for a critical temperature or critical velocity of a supersolid transition. Finally, we demonstrated that the combined temperature-velocity dependence of the TO response is indistinguishable from the combined temperature-strain dependence of the solid's shear modulus. This implies that the rotational responses of solid helium-4 attributed to supersolidity are associated with generation of the same microscopic excitations as those produced by direct shear strain.
Phylogenetic inference under varying proportions of indel-induced alignment gaps
Bhakti Dwivedi, Sudhindra R Gadagkar
BMC Evolutionary Biology , 2009, DOI: 10.1186/1471-2148-9-211
Abstract: (1) In general, there was a strong – almost deterministic – relationship between the amount of gap in the data and the level of phylogenetic accuracy when the alignments were very "gappy", (2) gaps resulting from deletions (as opposed to insertions) contributed more to the inaccuracy of phylogenetic inference, (3) the probabilistic methods (Bayesian, PhyML & "MLε, " a method implemented in DNAML in PHYLIP) performed better at most levels of gap percentage when compared to parsimony (MP) and distance (NJ) methods, with Bayesian analysis being clearly the best, (4) methods that treat gapped sites as missing data yielded less accurate trees when compared to those that attribute phylogenetic signal to the gapped sites (by coding them as binary character data – presence/absence, or as in the MLε method), and (5) in general, the accuracy of phylogenetic inference depended upon the amount of available data when the gaps resulted from mainly deletion events, and the amount of missing data when insertion events were equally likely to have caused the alignment gaps.When gaps in an alignment are a consequence of indel events in the evolution of the sequences, the accuracy of phylogenetic analysis is likely to improve if: (1) alignment gaps are categorized as arising from insertion events or deletion events and then treated separately in the analysis, (2) the evolutionary signal provided by indels is harnessed in the phylogenetic analysis, and (3) methods that utilize the phylogenetic signal in indels are developed for distance methods too. When the true homology is known and the amount of gaps is 20 percent of the alignment length or less, the methods used in this study are likely to yield trees with 90–100 percent accuracy.DNA sequences are used routinely to infer phylogenies [1-3]. The sequences within lineages (branches of the phylogenetic tree) evolve independently over time by means of several evolutionary processes, including point replacements of nucleotides (base subst
The impact of sequence parameter values on phylogenetic accuracy
Bhakti Dwivedi,Sudhindra R Gadagkar
Biology and Medicine , 2009,
Abstract: An accurately inferred phylogeny is important to the study of molecular evolution. Factors affecting the accuracy of aphylogenetic tree can be traced to several sequential steps leading to the inference of the phylogeny. I examine herethe features of the sequences in the alignment which impact phylogenetic (topological) accuracy rather than anysource of error during the process of sequence alignment or choice of the method of inference. Specifically, I studythe implications of the following five parameters, individually and in combination: sequence length, substitution rate,nucleotide base composition, the transition-transversion rate ratio and the rate heterogeneity among the sites. It isfound that the transition-transversion rate ratio or kappa has a significant impact on phylogenetic accuracy, with astrong positive interaction with accuracy at high substitution rates, contrary to general belief. This work on knownexpected tree has implications for the researcher in field and would enable them to choose from among the multiplegenes typically available today for an accurate phylogenetic inference. In addition, the increased accuracy withincrease in kappa suggest that the phylogenetic signal may be strong in the nucleotide sites that have experiencedconsiderable number of transversion than transition substitutions and thus can be useful in inference of a meaningfulphylogeny.
Genome-wide analysis of primate and rodent protein-coding and associated non-coding nucleotide sequences
Gadagkar Sudhindra R,Rond Luke A
BMC Proceedings , 2012, DOI: 10.1186/1753-6561-6-s6-p9
Abstract:
Tubulin evolution in insects: gene duplication and subfunctionalization provide specialized isoforms in a functionally constrained gene family
Mark G Nielsen, Sudhindra R Gadagkar, Lisa Gutzwiller
BMC Evolutionary Biology , 2010, DOI: 10.1186/1471-2148-10-113
Abstract: Sixty-six alpha tubulins and eighty-six beta tubulin gene copies were retrieved and subjected to molecular evolutionary analyses. Four ancient clades of alpha and beta tubulins are found in insects, a major isoform clade (alpha 1, beta 1) and three minor, tissue-specific clades (alpha 2-4, beta 2-4). Based on a Homarus americanus (lobster) outgroup, these were generated through gene duplication events on major beta and alpha tubulin ancestors, followed by subfunctionalization in expression domain. Strong purifying selection acts on all tubulins, yet maximum pairwise amino acid distances between tubulin paralogs are large (0.464 substitutions/site beta tubulins, 0.707 alpha tubulins). Conversely orthologs, with the exception of reproductive tissue isoforms, show little sequence variation except in the last 15 carboxy terminus tail (CTT) residues, which serve as sites for post-translational modifications (PTMs) and interactions with microtubule-associated proteins. CTT residues overwhelming comprise the co-evolving residues between Drosophila alpha 2 and beta 3 tubulin proteins, indicating CTT specializations can be mediated at the level of the tubulin dimer. Gene duplications post-dating separation of the insect orders are unevenly distributed, most often appearing in major alpha 1 and minor beta 2 clades. More than 40 introns are found in tubulins. Their distribution among tubulins reveals that insertion and deletion events are common, surprising given their potential for disrupting tubulin coding sequence. Compensatory evolution is found in Drosophila beta 2 tubulin cis-regulation, and reveals selective pressures acting to maintain testis expression without the use of previously identified testis cis-regulatory elements.Tubulins have stringent structure/function relationships, indicated by strong purifying selection, the loss of many gene duplication products, alpha-beta co-evolution in the tubulin dimer, and compensatory evolution in beta 2 tubulin cis-regulation.
ALFRED: An Allele Frequency Database for Microevolutionary Studies
Haseena Rajeevan,Kei-Hoi Cheung,Rohit Gadagkar,Shannon Stein
Evolutionary Bioinformatics , 2005,
Abstract: Many kinds of microevolutionary studies require data on multiple polymorphisms in multiple populations. Increasingly, and especially for human populations, multiple research groups collect relevant data and those data are dispersed widely in the literature. ALFRED has been designed to hold data from many sources and make them available over the web. Data are assembled from multiple sources, curated, and entered into the database. Multiple links to other resources are also established by the curators. A variety of search options are available and additional geographic based interfaces are being developed. The database can serve the human anthropologic genetic community by identifying what loci are already typed on many populations thereby helping to focus efforts on a common set of markers. The database can also serve as a model for databases handling similar DNA polymorphism data for other species.
Collapse of Double-Walled Carbon Nanotube Bundles under Hydrostatic Pressure
Vikram Gadagkar,Prabal K. Maiti,Yves Lansac,A. Jagota,A. K. Sood
Physics , 2006, DOI: 10.1103/PhysRevB.73.085402
Abstract: We use classical molecular dynamics simulations to study the collapse of single (SWNT) and double-walled (DWNT) carbon nanotube bundles under hydrostatic pressure. The collapse pressure (pc) varies as 1/R^3, where R is the SWNT radius or the DWNT effective radius. The bundles show ~ 30% hysteresis and the hexagonally close packed lattice is completely restored on decompression. The pc of DWNT is found to be close to the sum of its values for the inner and the outer tubes considered separately as SWNT, demonstrating that the inner tube supports the outer tube and that the effective bending stiffness of DWNT, D(DWNT) ~ 2D(SWNT) . We use an elastica formulation to derive the scaling and the collapse behavior of DWNT and multi-walled carbon nanotubes.
The Evolution of Complexity in Social Organization - A Model Using Dominance-Subordinate Behaviour in Two Social Wasp Species
Anjan K. Nandi,Anindita Bhadra,Annagiri Sumana,Sujata A. Deshpande,Raghavendra Gadagkar
Quantitative Biology , 2014, DOI: 10.1016/j.jtbi.2013.01.010
Abstract: Dominance and subordinate behaviours are important ingredients in the social organizations of group living animals. Behavioural observations on the two eusocial species \textit{Ropalidia marginata} and \textit{Ropalidia cyathiformis} suggest varying complexities in their social systems. The queen of R. cyathiformis is an aggressive individual who usually holds the top position in the dominance hierarchy although she does not necessarily show the maximum number of acts of dominance, while the R. marginata queen rarely shows aggression and usually does not hold the top position in the dominance hierarchy of her colony. These differences are reflected in the distribution of dominance-subordinate interactions among the hierarchically ranked individuals in both the species. The percentage of dominance interactions decrease gradually with hierarchical ranks in R. marginata while in R. cyathiformis it first increases and then decreases. We use an agent-based model to investigate the underlying mechanism that could give rise to the observed patterns for both the species. The model assumes, besides some non-interacting individuals, that the interaction probabilities of the agents depend on their pre-differentiated winning abilities. Our simulations show that if the queen takes up a strategy of being involved in a moderate number of dominance interactions, one could get the pattern similar to R. cyathiformis, while taking up the strategy of very low interactions by the queen could lead to the pattern of R. marginata. We infer that both the species follow a common interaction pattern, while the differences in their social organization are due to the slight changes in queen as well as worker strategies. These changes in strategies are expected to accompany the evolution of more complex societies from simpler ones.
Sexual selection studies: A NESCent catalyst meeting
Joan Roughgarden,Elizabeth Adkins-Regan,Erol Akay,Jeremy Chase Crawford,Raghavendra Gadagkar,Simon C. Griffith,Camilla A Hinde,Thierry Hoquet,Cailin O’Connor,Zofia M. Prokop,Richard O. Prum,Sharoni Shafir,Samuel S. Snow,Daniel Taylor,Jeremy Van Cleve,Michael Weisberg
PeerJ , 2015, DOI: 10.7287/peerj.preprints.680v2
Abstract: A catalyst meeting on sexual selection studies was held in July 2013 at the facilities of the National Evolutionary Synthesis Center (NESCent) in Durham, NC. This article by a subcommittee of the participants foregrounds some of the topics discussed at the meeting. Topics mentioned here include the relevance of heritability estimates to assessing the presence of sexual selection, whether sexual selection is distinct from natural selection, and the utility of distinguishing sexual selection from fecundity selection. A possible definition of sexual selection is offered based on a distinction between sexual selection as a frequency-dependent process and fecundity selection as a density-dependent process. Another topic highlighted is a deep disagreement among participants in the reality of good-genes, sexy-sons, and run-away processes. Finally, the status of conflict in political-economic theory is contrasted with the status accorded to conflict in evolutionary behavioral theory, and the professional responsibility of sexual-selection workers to consider the ethical dimension of their research is underscored.
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