Conflict-Free Coloring for Rectangle Ranges Using O(n.382) Colors

Given a set of points P ⊆ R2, a conflict-free coloring of P w.r.t. rectangle ranges is an assignment of colors to points of P, such that each nonempty axisparallel rectangle T in the plane contains a point whose color is distinct from all other points in P ∩ T . This notion has been the subject of recent interest and is motivated by frequency assignment in wireless cellular networks: one naturally would like to minimize the number of frequencies (colors) assigned to base stations (points) such that within any range (for instance, rectangle), there is no interference. We show that any set of n points in R2 can be conflict-free colored with O(nβ∗+o(1)) colors in expected polynomial time, where β∗ = 3−√5 2 < 0.382.

Confinement and viscoelastic effects on chain closure dynamics

Chemical reactions inside cells are typically subject to the effects both of the cell's confining surfaces and of the viscoelastic behavior of its contents. In this paper, we show how the outcome of one particular reaction of relevance to cellular biochemistry - the diffusion-limited cyclization of long chain polymers - is influenced by such confinement and crowding effects. More specifically, starting from the Rouse model of polymer dynamics, and invoking the Wilemski-Fixman approximation, we determine the scaling relationship between the mean closure time t(c) of a flexible chain (no excluded volume or hydrodynamic interactions) and the length N of its contour under the following separate conditions: (a) confinement of the chain to a sphere of radius d and (b) modulation of its dynamics by colored Gaussian noise. Among other results, we find that in case (a) when d is much smaller than the size of the chain, t(c) similar to Nd-2, and that in case (b), t(c) similar to N-2/(2 (2H)), H being a number between 1/2 and 1 that characterizes the decay of the noise correlations. H is not known a priori, but values of about 0.7 have been used in the successful characterization of protein conformational dynamics. At this value of H (selected for purposes of illustration), t(c) similar to N-3.4, the high scaling exponent reflecting the slow relaxation of the chain in a viscoelastic medium. (C) 2012 American Institute of Physics. http://dx.doi.org/10.1063/1.4729041]

Rainbow connection number and connected dominating sets

The rainbow connection number of a connected graph is the minimum number of colors needed to color its edges, so that every pair of its vertices is connected by at least one path in which no two edges are colored the same. In this article we show that for every connected graph on n vertices with minimum degree delta, the rainbow connection number is upper bounded by 3n/(delta + 1) + 3. This solves an open problem from Schiermeyer (Combinatorial Algorithms, Springer, Berlin/Hiedelberg, 2009, pp. 432437), improving the previously best known bound of 20n/delta (J Graph Theory 63 (2010), 185191). This bound is tight up to additive factors by a construction mentioned in Caro et al. (Electr J Combin 15(R57) (2008), 1). As an intermediate step we obtain an upper bound of 3n/(delta + 1) - 2 on the size of a connected two-step dominating set in a connected graph of order n and minimum degree d. This bound is tight up to an additive constant of 2. This result may be of independent interest. We also show that for every connected graph G with minimum degree at least 2, the rainbow connection number, rc(G), is upper bounded by Gc(G) + 2, where Gc(G) is the connected domination number of G. Bounds of the form diameter(G)?rc(G)?diameter(G) + c, 1?c?4, for many special graph classes follow as easy corollaries from this result. This includes interval graphs, asteroidal triple-free graphs, circular arc graphs, threshold graphs, and chain graphs all with minimum degree delta at least 2 and connected. We also show that every bridge-less chordal graph G has rc(G)?3.radius(G). In most of these cases, we also demonstrate the tightness of the bounds.

Rainbow connectivity: hardness and tractability

A path in an edge colored graph is said to be a rainbow path if no two edges on the path have the same color. An edge colored graph is (strongly) rainbow connected if there exists a (geodesic) rainbow path between every pair of vertices. The (strong) rainbow connectivity of a graph G, denoted by (src(G), respectively) rc(G) is the smallest number of colors required to edge color the graph such that G is (strongly) rainbow connected. In this paper we study the rainbow connectivity problem and the strong rainbow connectivity problem from a computational point of view. Our main results can be summarised as below: 1) For every fixed k >= 3, it is NP-Complete to decide whether src(G) <= k even when the graph G is bipartite. 2) For every fixed odd k >= 3, it is NP-Complete to decide whether rc(G) <= k. This resolves one of the open problems posed by Chakraborty et al. (J. Comb. Opt., 2011) where they prove the hardness for the even case. 3) The following problem is fixed parameter tractable: Given a graph G, determine the maximum number of pairs of vertices that can be rainbow connected using two colors. 4) For a directed graph G, it is NP-Complete to decide whether rc(G) <= 2.

Biochemical characterization of C4 protein of cotton leaf curl Kokhran virus-Dabawali

Background: Cotton leaf curl Kokhran Virus-Dabawali (CLCuKV-Dab) is a monopartite begomovirus encoding two proteins V1 and V2 in the virion sense and four proteins Cl, C2, C3 and C4 in the complementary sense. The C4 protein of monopartite begomoviruses has been implicated to play a role in symptom determination and virus movement. The present work aims at the biochemical characterization of this protein. Methods: The C4 protein of CLCuKV-Dab was purified in fusion with GST and tested for the ability to hydrolyze ATP and other phosphate containing compounds. ATPase activity was assayed by using radiolabeled gamma-32P]-ATP and separating the product of reaction by thin layer chromatography. The hydrolysis of other compounds was monitored by the formation of a blue colored phosphomolybdate complex which was estimated by measuring the absorbance at 655 nm. Results: The purified GST-C4 protein exhibited metal ion dependent ATPase and inorganic pyrophosphatase activities. Deletion of a sequence resembling the catalytic motif present in phosphotyrosine phosphatases resulted in 70% reduction in both the activities. Mutational analysis suggested arginine 13 to be catalytically important for the ATPase and cysteine 8 for the pyrophosphatase activity of GST-C4. Interaction of V2 with GST-C4 resulted in an increase in both the enzymatic activities of GST-C4. Conclusions: The residues important for the enzymatic activities of GST-C4 are present in a motif different from the classical Walker motifs and the non-classical ATP binding motifs reported so far. General significance: The C4 protein of CLCuKV-Dab, a putative natively unfolded protein, exhibits enzymatic activities.

Quantum entropic ambiguities: Ethylene

In a quantum system, there may be many density matrices associated with a state on an algebra of observables. For each density matrix, one can compute its entropy. These are, in general, different. Therefore, one reaches the remarkable possibility that there may be many entropies for a given state R. Sorkin (private communication)]. This ambiguity in entropy can often be traced to a gauge symmetry emergent from the nontrivial topological character of the configuration space of the underlying system. It can also happen in finite-dimensional matrix models. In the present work, we discuss this entropy ambiguity and its consequences for an ethylene molecule. This is a very simple and well-known system, where these notions can be put to tests. Of particular interest in this discussion is the fact that the change of the density matrix with the corresponding entropy increase drives the system towards the maximally disordered state with maximum entropy, where Boltzman's formula applies. Besides its intrinsic conceptual interest, the simplicity of this model can serve as an introduction to a similar discussion of systems such as colored monopoles and the breaking of color symmetry.

Two new atom centered fragment descriptors and scoring function enhance classification of antibacterial activity

Classification of pharmacologic activity of a chemical compound is an essential step in any drug discovery process. We develop two new atom-centered fragment descriptors (vertex indices) - one based solely on topological considerations without discriminating atomor bond types, and another based on topological and electronic features. We also assess their usefulness by devising a method to rank and classify molecules with regard to their antibacterial activity. Classification performances of our method are found to be superior compared to two previous studies on large heterogeneous data sets for hit finding and hit-to-lead studies even though we use much fewer parameters. It is found that for hit finding studies topological features (simple graph) alone provide significant discriminating power, and for hit-to-lead process small but consistent improvement can be made by additionally including electronic features (colored graph). Our approach is simple, interpretable, and suitable for design of molecules as we do not use any physicochemical properties. The singular use of vertex index as descriptor, novel range based feature extraction, and rigorous statistical validation are the key elements of this study.

Rainbow Connection Number of Graph Power and Graph Products

Rainbow connection number, rc(G), of a connected graph G is the minimum number of colors needed to color its edges so that every pair of vertices is connected by at least one path in which no two edges are colored the same (note that the coloring need not be proper). In this paper we study the rainbow connection number with respect to three important graph product operations (namely the Cartesian product, the lexicographic product and the strong product) and the operation of taking the power of a graph. In this direction, we show that if G is a graph obtained by applying any of the operations mentioned above on non-trivial graphs, then rc(G) a parts per thousand currency sign 2r(G) + c, where r(G) denotes the radius of G and . In general the rainbow connection number of a bridgeless graph can be as high as the square of its radius 1]. This is an attempt to identify some graph classes which have rainbow connection number very close to the obvious lower bound of diameter (and thus the radius). The bounds reported are tight up to additive constants. The proofs are constructive and hence yield polynomial time -factor approximation algorithms.

A matrix model for QCD: QCD color is mixed

We use general arguments to show that colored QCD states when restricted to gauge invariant local observables are mixed. This result has important implications for confinement: a pure colorless state can never evolve into two colored states by unitary evolution. Furthermore, the mean energy in such a mixed colored state is infinite. Our arguments are confirmed in a matrix model for QCD that we have developed using the work of Narasimhan and Ramadas(3) and Singer.(2) This model, a (0 + 1)-dimensional quantum mechanical model for gluons free of divergences and capturing important topological aspects of QCD, is adapted to analytical and numerical work. It is also suitable to work on large N QCD. As applications, we show that the gluon spectrum is gapped and also estimate some low-lying levels for N = 2 and 3 (colors). Incidentally the considerations here are generic and apply to any non-Abelian gauge theory.

A matrix model for QCD

Gribov's observation that global gauge fixing is impossible has led to suggestions that there may be a deep connection between gauge fixing and confinement. We find an unexpected relation between the topological nontriviality of the gauge bundle and colored states in SU(N) Yang-Mills theory, and show that such states are necessarily impure. We approximate QCD by a rectangular matrix model that captures the essential topological features of the gauge bundle, and demonstrate the impure nature of colored states explicitly. Our matrix model also allows the inclusion of the QCD theta-term, as well as to perform explicit computations of low-lying glueball masses. This mass spectrum is gapped. Since an impure state cannot evolve to a pure one by a unitary transformation, our result shows that the solution to the confinement problem in pure QCD is fundamentally quantum information-theoretic.

A simplified model for dark matter interacting primarily with gluons

We consider a simple renormalizable model providing a UV completion for dark matter whose interactions with the Standard Model are primarily via the gluons. The model consists of scalar dark matter interacting with scalar colored mediator particles. A novel feature is the fact that (in contrast to more typical models containing dark matter whose interactions are mediated via colored scalars) the colored scalars typically decay into multi-quark final states, with no associated missing energy. We construct this class of models and examine associated phenomena related to dark matter annihilation, scattering with nuclei, and production at colliders.

Looking for BSM physics using top-quark polarization and decay-lepton kinematic asymmetries

We explore beyond-standard-model (BSM) physics signatures in the l + jets channel of the t (t) over bar pair production process at the Tevatron and the LHC. We study the effects of BSM physics scenarios on the top-quark polarization and on the kinematics of the decay leptons. To this end, we construct asymmetries using the lepton energy and angular distributions. Further, we find their correlations with the top polarization, net charge asymmetry and top forward-backward asymmetry. We show that when used together, these observables can help discriminate effectively between SM and different BSM scenarios, which can lead to varying degrees of top polarization at the Tevatron as well as the LHC. We use two types of colored mediator models to demonstrate the effectiveness of proposed observables, an s-channel axigluon and a u-channel diquark.

Two-Dimensional Noise-Predictive Maximum Likelihood Method for Magnetic Recording Channels

Noise-predictive maximum likelihood (NPML) is a well known signal detection technique used in partial response maximum likelihood (PRML) scheme in 1D magnetic recording channels. The noise samples colored by the partial response (PR) equalizer are predicted/ whitened during the signal detection using a Viterbi detector. In this paper, we propose an extension of the NPML technique for signal detection in 2D ISI channels. The impact of noise prediction during signal detection is studied in PRML scheme for a particular choice of 2D ISI channel and PR targets.