We study the notion of formal duality introduced by Cohn, Kumar, and Sch\"urmann in their computa... more We study the notion of formal duality introduced by Cohn, Kumar, and Sch\"urmann in their computational study of energy-minimizing particle configurations in Euclidean space. In particular, using the Poisson summation formula we reformulate formal duality as a combinatorial phenomenon in finite abelian groups. We give new examples related to Gauss sums and make some progress towards classifying formally dual configurations.
Journal of Computational and Applied Mathematics, May 1, 2005
We propose a triangulation-based partitioning algorithm, TRIOPT, for solving low-dimensional boun... more We propose a triangulation-based partitioning algorithm, TRIOPT, for solving low-dimensional bound-constrained black box global optimization problems. The method starts by forming a Delaunay triangulation of a given set of samples in the feasible domain, and then, it assesses the simplices (partitions) obtained for re-partitioning. Function values at the vertices of each partition are mapped into the zero one interval by a nonlinear transformation function and their aggregate entropy is calculated. Based on this entropy, partitions that hold a promise of containing the global optimum are re-partitioned according to different triangular splitting strategies, forming new partitions. These strategies are efficient in terms of the number of new function evaluations required per new partition.A novelty in the search scheme proposed here is that once a partition narrows down to a small size, its vertices are eliminated from the available sample set. This changes global information on the best solution and triggers a re-calculation of transformed values. Hence, revised entropies change the direction of the search to new areas. The latter scheme leads to a dynamic parallel search policy which is based on an entropy cut. The tree adopts flexible breadth depending on the status of the search. In the experimental results it is demonstrated that TRIOPTs performance is compatible and often better than that of a well-known response surface methodology and two other efficient black box partitioning approaches proposed for global optimization.
We use techniques of Bannai and Sloane to give a new proof that there is a unique (22,891,1/4) sp... more We use techniques of Bannai and Sloane to give a new proof that there is a unique (22,891,1/4) spherical code; this result is implicit in a recent paper by Cuypers. We also correct a minor error in the uniqueness proof given by Bannai and Sloane for the (23,4600,1/3) spherical code.
SsgA-like proteins (SALPs) are a family of homologous cell division-related proteins that occur e... more SsgA-like proteins (SALPs) are a family of homologous cell division-related proteins that occur exclusively in morphologically complex actinomycetes. We show that SsgB, a subfamily of SALPs, is the archetypal SALP that is functionally conserved in all sporulating actinomycetes. Sporulation-specific cell division of Streptomyces coelicolor ssgB mutants is restored by introduction of distant ssgB orthologues from other actinomycetes. Interestingly, the number of septa (and spores) of the complemented null mutants is dictated by the specific ssgB orthologue that is expressed. The crystal structure of the SsgB from Thermobifida fusca was determined at 2.6 A resolution and represents the first structure for this family. The structure revealed similarities to a class of eukaryotic…
Cotton leaf curl disease (CLCuD) is caused by several distinct begomovirus species in association... more Cotton leaf curl disease (CLCuD) is caused by several distinct begomovirus species in association with disease-specific betasatellite essential for induction of disease symptoms. CLCuD is a serious threat for the cultivation of cotton (Gossypium sp.) and several species in the family Malvaceae. In this study, RNAi-based approach was applied to generate transgenic cotton (Gossypium hirsutum) plants resistant to Cotton leaf curl Rajasthan virus (CLCuRV). An intron hairpin (ihp) RNAi construct capable of expressing dsRNA homologous to the intergenic region (IR) of CLCuRV was designed and developed. Following Agrobacterium tumefaciens-mediated transformation of cotton (G. hirsutum cv. Narasimha) plants with the designed ihpRNAi construct, a total of 9 independent lines of transformed cotton were obtained. The presence of the potential stretch of IR in the transformed cotton was confirmed by PCR coupled with Southern hybridization. Upon inoculation with viruliferous whiteflies, the trans...
Proteins Structure Function and Bioinformatics, Jan 11, 2007
BtDyP from Bacteroides thetaiotaomicron (strain VPI-5482) and TyrA from Shewanella oneidensis are... more BtDyP from Bacteroides thetaiotaomicron (strain VPI-5482) and TyrA from Shewanella oneidensis are dye-decolorizing peroxidases (DyPs), members of a new family of heme-dependent peroxidases recently identified in fungi and bacteria. Here, we report the crystal structures of BtDyP and TyrA at 1.6 and 2.7 A, respectively. BtDyP assembles into a hexamer, while TyrA assembles into a dimer; the dimerization interface is conserved between the two proteins. Each monomer exhibits a two-domain, alpha+beta ferredoxin-like fold. A site for heme binding was identified computationally, and modeling of a heme into the proposed active site allowed for identification of residues likely to be functionally important. Structural and sequence comparisons with other DyPs demonstrate a conservation of putative heme-binding residues, including an absolutely conserved histidine. Isothermal titration calorimetry experiments confirm heme binding, but with a stoichiometry of 0.3:1 (heme:protein).(c) 2007 Wiley-Liss, Inc.
We study the notion of formal duality introduced by Cohn, Kumar, and Sch\"urmann in their computa... more We study the notion of formal duality introduced by Cohn, Kumar, and Sch\"urmann in their computational study of energy-minimizing particle configurations in Euclidean space. In particular, using the Poisson summation formula we reformulate formal duality as a combinatorial phenomenon in finite abelian groups. We give new examples related to Gauss sums and make some progress towards classifying formally dual configurations.
Journal of Computational and Applied Mathematics, May 1, 2005
We propose a triangulation-based partitioning algorithm, TRIOPT, for solving low-dimensional boun... more We propose a triangulation-based partitioning algorithm, TRIOPT, for solving low-dimensional bound-constrained black box global optimization problems. The method starts by forming a Delaunay triangulation of a given set of samples in the feasible domain, and then, it assesses the simplices (partitions) obtained for re-partitioning. Function values at the vertices of each partition are mapped into the zero one interval by a nonlinear transformation function and their aggregate entropy is calculated. Based on this entropy, partitions that hold a promise of containing the global optimum are re-partitioned according to different triangular splitting strategies, forming new partitions. These strategies are efficient in terms of the number of new function evaluations required per new partition.A novelty in the search scheme proposed here is that once a partition narrows down to a small size, its vertices are eliminated from the available sample set. This changes global information on the best solution and triggers a re-calculation of transformed values. Hence, revised entropies change the direction of the search to new areas. The latter scheme leads to a dynamic parallel search policy which is based on an entropy cut. The tree adopts flexible breadth depending on the status of the search. In the experimental results it is demonstrated that TRIOPTs performance is compatible and often better than that of a well-known response surface methodology and two other efficient black box partitioning approaches proposed for global optimization.
We use techniques of Bannai and Sloane to give a new proof that there is a unique (22,891,1/4) sp... more We use techniques of Bannai and Sloane to give a new proof that there is a unique (22,891,1/4) spherical code; this result is implicit in a recent paper by Cuypers. We also correct a minor error in the uniqueness proof given by Bannai and Sloane for the (23,4600,1/3) spherical code.
SsgA-like proteins (SALPs) are a family of homologous cell division-related proteins that occur e... more SsgA-like proteins (SALPs) are a family of homologous cell division-related proteins that occur exclusively in morphologically complex actinomycetes. We show that SsgB, a subfamily of SALPs, is the archetypal SALP that is functionally conserved in all sporulating actinomycetes. Sporulation-specific cell division of Streptomyces coelicolor ssgB mutants is restored by introduction of distant ssgB orthologues from other actinomycetes. Interestingly, the number of septa (and spores) of the complemented null mutants is dictated by the specific ssgB orthologue that is expressed. The crystal structure of the SsgB from Thermobifida fusca was determined at 2.6 A resolution and represents the first structure for this family. The structure revealed similarities to a class of eukaryotic…
Cotton leaf curl disease (CLCuD) is caused by several distinct begomovirus species in association... more Cotton leaf curl disease (CLCuD) is caused by several distinct begomovirus species in association with disease-specific betasatellite essential for induction of disease symptoms. CLCuD is a serious threat for the cultivation of cotton (Gossypium sp.) and several species in the family Malvaceae. In this study, RNAi-based approach was applied to generate transgenic cotton (Gossypium hirsutum) plants resistant to Cotton leaf curl Rajasthan virus (CLCuRV). An intron hairpin (ihp) RNAi construct capable of expressing dsRNA homologous to the intergenic region (IR) of CLCuRV was designed and developed. Following Agrobacterium tumefaciens-mediated transformation of cotton (G. hirsutum cv. Narasimha) plants with the designed ihpRNAi construct, a total of 9 independent lines of transformed cotton were obtained. The presence of the potential stretch of IR in the transformed cotton was confirmed by PCR coupled with Southern hybridization. Upon inoculation with viruliferous whiteflies, the trans...
Proteins Structure Function and Bioinformatics, Jan 11, 2007
BtDyP from Bacteroides thetaiotaomicron (strain VPI-5482) and TyrA from Shewanella oneidensis are... more BtDyP from Bacteroides thetaiotaomicron (strain VPI-5482) and TyrA from Shewanella oneidensis are dye-decolorizing peroxidases (DyPs), members of a new family of heme-dependent peroxidases recently identified in fungi and bacteria. Here, we report the crystal structures of BtDyP and TyrA at 1.6 and 2.7 A, respectively. BtDyP assembles into a hexamer, while TyrA assembles into a dimer; the dimerization interface is conserved between the two proteins. Each monomer exhibits a two-domain, alpha+beta ferredoxin-like fold. A site for heme binding was identified computationally, and modeling of a heme into the proposed active site allowed for identification of residues likely to be functionally important. Structural and sequence comparisons with other DyPs demonstrate a conservation of putative heme-binding residues, including an absolutely conserved histidine. Isothermal titration calorimetry experiments confirm heme binding, but with a stoichiometry of 0.3:1 (heme:protein).(c) 2007 Wiley-Liss, Inc.
Uploads
Papers by Abhinav Kumar