Distribution of unselectively bound ligands along DNA.
Lando, Dmitri Y; Nechipurenko, Yury D
2008-10-01
Unselective and reversible adsorption of ligands on DNA for a model of binding proposed by Zasedatelev, Gursky, and Volkenshtein is considered. In this model, the interaction between neighboring ligands located at the distance of i binding centers is characterized by the statistical weight ai. Each ligand covers L binding centers. For this model, expressions for binding averages are represented in a new simple form. This representation is convenient for the calculation of the fraction of inter-ligand distances of i binding centers fd(i) and the fraction of binding centers included in the distances of i binding centers fbc(i) for various types of interaction between bound ligands. It is shown that, for non-cooperative binding, contact cooperativity and long-range cooperativity, the fraction of the zero inter-ligand distance fd(0) is maximal at any relative concentration of bound ligands (r). Calculations demonstrate that, at low r, fd(0) approximately r.ao, and fd(i) approximately r at 11/r-L, then fd(i) rapidly decreases with i at any r for all types of inter-ligand interaction. At high ligand concentration (r is close to rmax=L(-1)), fd(0) is close to unity and fd(i) rapidly decreases with i for any type of inter-ligand interaction. For strong contact cooperativity, fd(0) is close to unity in a much lager r interval ((0.5-1).rmax), and fd(1) approximately ao(-1) at r approximately 0.5.rmax. In the case of long-range interaction between bound ligands, the dependence fd(i) is more complex and has a maximum at i approximately (1/r-L)1/2 for anti-cooperative binding. fbc(i) is maximal at i approximately 1/r-L for all types of binding except the contact cooperativity. A strong asymmetry in the influence of contact cooperativity and anticooperativity on the ligand distribution along DNA is demonstrated.
Optimal bounded control for maximizing reliability of Duhem hysteretic systems
Ming XU; Xiaoling JIN; Yong WANG; Zhilong HUANG
2015-01-01
The optimal bounded control of stochastic-excited systems with Duhem hysteretic components for maximizing system reliability is investigated. The Duhem hysteretic force is transformed to energy-depending damping and stiffness by the energy dissipation balance technique. The controlled system is transformed to the equivalent non-hysteretic system. Stochastic averaging is then implemented to obtain the Itˆo stochastic equation associated with the total energy of the vibrating system, appropriate for eval-uating system responses. Dynamical programming equations for maximizing system re-liability are formulated by the dynamical programming principle. The optimal bounded control is derived from the maximization condition in the dynamical programming equa-tion. Finally, the conditional reliability function and mean time of first-passage failure of the optimal Duhem systems are numerically solved from the Kolmogorov equations. The proposed procedure is illustrated with a representative example.
Dynamics of hydrogen-like atom bounded by maximal acceleration
Friedman, Yaakov
2012-01-01
The existence of a maximal acceleration for massive objects was conjectured by Caianiello 30 years ago based on the Heisenberg uncertainty relations. Many consequences of this hypothesis have been studied, but until now, there has been no evidence that boundedness of the acceleration may lead to quantum behavior. In previous research, we predicted the existence of a universal maximal acceleration and developed a new dynamics for which all admissible solutions have an acceleration bounded by the maximal one. Based on W. K\\"{u}ndig's experiment, as reanalyzed by Kholmetskii et al, we estimated its value to be of the order $10^{19}m/s^2$. We present here a solution of our dynamical equation for a classical hydrogen-like atom and show that this dynamics leads to some aspects of quantum behavior. We show that the position of an electron in a hydrogen-like atom can be described only probabilistically. We also show that in this model, the notion of "center of mass" must be modified. This modification supports the no...
Computational rationality: linking mechanism and behavior through bounded utility maximization.
Lewis, Richard L; Howes, Andrew; Singh, Satinder
2014-04-01
We propose a framework for including information-processing bounds in rational analyses. It is an application of bounded optimality (Russell & Subramanian, 1995) to the challenges of developing theories of mechanism and behavior. The framework is based on the idea that behaviors are generated by cognitive mechanisms that are adapted to the structure of not only the environment but also the mind and brain itself. We call the framework computational rationality to emphasize the incorporation of computational mechanism into the definition of rational action. Theories are specified as optimal program problems, defined by an adaptation environment, a bounded machine, and a utility function. Such theories yield different classes of explanation, depending on the extent to which they emphasize adaptation to bounds, and adaptation to some ecology that differs from the immediate local environment. We illustrate this variation with examples from three domains: visual attention in a linguistic task, manual response ordering, and reasoning. We explore the relation of this framework to existing "levels" approaches to explanation, and to other optimality-based modeling approaches.
Upper Bounds for Maximally Greedy Binary Search Trees
Fox, Kyle
2011-01-01
At SODA 2009, Demaine et al. presented a novel connection between binary search trees (BSTs) and subsets of points on the plane. This connection was independently discovered by Derryberry et al. As part of their results, Demaine et al. considered GreedyFuture, an offline BST algorithm that greedily rearranges the search path to minimize the cost of future searches. They showed that GreedyFuture is actually an online algorithm in their geometric view, and that there is a way to turn GreedyFuture into an online BST algorithm with only a constant factor increase in total search cost. Demaine et al. conjectured this algorithm was dynamically optimal, but no upper bounds were given in their paper. We prove the first non-trivial upper bounds for the cost of search operations using GreedyFuture including giving an access lemma similar to that found in Sleator and Tarjan's classic paper on splay trees.
Online Scheduling of Bounded Length Jobs to Maximize Throughput
Durr, Christoph; Thang, Nguyen Kim
2009-01-01
We consider an online scheduling problem, that is motivated by online auction for regularily produced goods that cannot be stored, and have to be sold immediatly to some customers. More formally we consider the online problem of scheduling with preemptions, where each job j is revealed at release time r_j, has processing time p_j, deadline d_j and weight w_j. The goal is to maximize the total weight of all jobs completed on time. We show that if all jobs have processing time not more than k, then the determinstic competitive ratio of this problem is Theta(k/log k).
Boundedness and unboundedness results for some maximal operators on functions of bounded variation
Aldaz, J. M.; Pérez Lázaro, J.
2008-01-01
We characterize the space BV(I) of functions of bounded variation on an arbitrary interval , in terms of a uniform boundedness condition satisfied by the local uncentered maximal operator MR from BV(I) into the Sobolev space W1,1(I). By restriction, the corresponding characterization holds for W1,1(I). We also show that if U is open in , d>1, then boundedness from BV(U) into W1,1(U) fails for the local directional maximal operator , the local strong maximal operator , and the iterated local directional maximal operator . Nevertheless, if U satisfies a cone condition, then boundedly, and the same happens with , , and MR.
Non-autonomous maximal regularity for forms given by elliptic operators of bounded variation
Fackler, Stephan
2017-09-01
We show maximal Lp-regularity for non-autonomous Cauchy problems provided the trace spaces are stable in some parameterized sense and the time dependence is of bounded variation. In particular on L2 (Ω), for Lipschitz domains Ω and under mixed boundary conditions, we obtain maximal Lp-regularity for all p ∈ (1 , 2 ] for elliptic operators with coefficients aij : Ω → C satisfying aij (ṡ , x) ∈ BV uniformly in x ∈ Ω.
Maximal admissible faces and asymptotic bounds for the normal surface solution space
Burton, Benjamin A
2010-01-01
The enumeration of normal surfaces is a key bottleneck in computational three-dimensional topology. The underlying procedure is the enumeration of admissible vertices of a high-dimensional polytope, where admissibility is a powerful but non-linear and non-convex constraint. The main results of this paper are significant improvements upon the best known asymptotic bounds on the number of admissible vertices, using polytopes in both the standard normal surface coordinate system and the streamlined quadrilateral coordinate system. To achieve these results we examine the layout of admissible points within these polytopes. We show that these points correspond to well-behaved substructures of the face lattice, and we study properties of the corresponding "admissible faces". Key lemmata include upper bounds on the number of maximal admissible faces of each dimension, and a bijection between the maximal admissible faces in the two coordinate systems mentioned above.
A Reward-Maximizing Spiking Neuron as a Bounded Rational Decision Maker.
Leibfried, Felix; Braun, Daniel A
2015-08-01
Rate distortion theory describes how to communicate relevant information most efficiently over a channel with limited capacity. One of the many applications of rate distortion theory is bounded rational decision making, where decision makers are modeled as information channels that transform sensory input into motor output under the constraint that their channel capacity is limited. Such a bounded rational decision maker can be thought to optimize an objective function that trades off the decision maker's utility or cumulative reward against the information processing cost measured by the mutual information between sensory input and motor output. In this study, we interpret a spiking neuron as a bounded rational decision maker that aims to maximize its expected reward under the computational constraint that the mutual information between the neuron's input and output is upper bounded. This abstract computational constraint translates into a penalization of the deviation between the neuron's instantaneous and average firing behavior. We derive a synaptic weight update rule for such a rate distortion optimizing neuron and show in simulations that the neuron efficiently extracts reward-relevant information from the input by trading off its synaptic strengths against the collected reward.
A python-based docking program utilizing a receptor bound ligand shape: PythDock.
Chung, Jae Yoon; Cho, Seung Joo; Hah, Jung-Mi
2011-09-01
PythDock is a heuristic docking program that uses Python programming language with a simple scoring function and a population based search engine. The scoring function considers electrostatic and dispersion/repulsion terms. The search engine utilizes a particle swarm optimization algorithm. A grid potential map is generated using the shape information of a bound ligand within the active site. Therefore, the searching area is more relevant to the ligand binding. To evaluate the docking performance of PythDock, two well-known docking programs (AutoDock and DOCK) were also used with the same data. The accuracy of docked results were measured by the difference of the ligand structure between x-ray structure, and docked pose, i.e., average root mean squared deviation values of the bound ligand were compared for fourteen protein-ligand complexes. Since the number of ligands' rotational flexibility is an important factor affecting the accuracy of a docking, the data set was chosen to have various degrees of flexibility. Although PythDock has a scoring function simpler than those of other programs (AutoDock and DOCK), our results showed that PythDock predicted more accurate poses than both AutoDock4.2 and DOCK6.2. This indicates that PythDock could be a useful tool to study ligand-receptor interactions and could also be beneficial in structure based drug design.
无
2008-01-01
Bit Error Probability (BEP) provides a fundamental performance measure for wireless diversity systems. This paper presents two new exact BEP expressions for Maximal Ratio Combining (MRC) diversity systems. One BEP expression takes a closed form, while the other is derived by treating the squared-sum of Rayleigh random variables as an Erlang variable. Due to the fact that the extant bounds are loose and could not properly characterize the error performance of MRC diversity systems, this paper presents a very tight bound. The numerical analysis shows that the new derived BEP expressions coincide with the extant expressions, and that the new approximation tightly bounds the accurate BEP.
A Review of the N-bound and the Maximal Mass Conjectures Using NUT-Charged dS Spacetimes
Clarkson, R; Mann, R B
2004-01-01
The proposed dS/CFT correspondence remains an intriguing paradigm in the context of string theory. Recently it has motivated two interesting conjectures: the entropic N-bound and the maximal mass conjecture. The former states that there is an upper bound to the entropy in asymptotically de Sitter spacetimes, given by the entropy of pure de Sitter space. The latter states that any asymptotically de Sitter spacetime cannot have a mass larger than the pure de Sitter case without inducing a cosmological singularity. Here we review the status of these conjectures and demonstrate their limitation. We first describe a generalization of gravitational thermodynamics to asymptotically de Sitter spacetimes, and show how to compute conserved quantities and gravitational entropy using this formalism. From this we proceed to a discussion of the N-bound and maximal mass conjectures. We then illustrate that these conjectures are not satisfied for certain asymptotically de Sitter spacetimes with NUT charge. We close with a pr...
Uniqueness of the maximal ideal of the Banach algebra of bounded operators on $C([0,\\omega_1])$
Kania, Tomasz
2011-01-01
Let $\\omega_1$ be the first uncountable ordinal. By a result of Rudin, bounded operators on the Banach space $C([0,\\omega_1])$ have a natural representation as $[0,\\omega_1]\\times 0,\\omega_1]$-matrices. Loy and Willis observed that the set of operators whose final column is continuous when viewed as a scalar-valued function on $[0,\\omega_1]$ defines a maximal ideal of codimension one in the Banach algebra $\\mathscr{B}(C([0,\\omega_1]))$ of bounded operators on $C([0,\\omega_1])$. We give a coordinate-free characterization of this ideal and deduce from it that $\\mathscr{B}(C([0,\\omega_1]))$ contains no other maximal ideals. We then obtain a list of equivalent conditions describing the strictly smaller ideal of operators with separable range, and finally we investigate the structure of the lattice of all closed ideals of $\\mathscr{B}(C([0,\\omega_1]))$.
Arden Perkins
2014-10-01
Full Text Available The aryl hydrocarbon receptor (AHR is a ligand-activated transcription factor that regulates the expression of a diverse group of genes. Exogenous AHR ligands include the environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD, which is a potent agonist, and the synthetic AHR antagonist N-2-(1H-indol-3ylethyl-9-isopropyl-2- (5-methylpyridin-3-yl-9H-purin-6-amine (GNF351. As no experimentally determined structure of the ligand binding domain exists, homology models have been utilized for virtual ligand screening (VLS to search for novel ligands. Here, we have developed an “agonist-optimized” homology model of the human AHR ligand binding domain, and this model aided in the discovery of two human AHR agonists by VLS. In addition, we performed molecular dynamics simulations of an agonist TCDD-bound and antagonist GNF351-bound version of this model in order to gain insights into the mechanics of the AHR ligand-binding pocket. These simulations identified residues 307–329 as a flexible segment of the AHR ligand pocket that adopts discrete conformations upon agonist or antagonist binding. This flexible segment of the AHR may act as a structural switch that determines the agonist or antagonist activity of a given AHR ligand.
Fast Deterministic Distributed Maximal Independent Set Computation on Growth-Bounded Graphs
Kuhn, Fabian; Moscibroda, Thomas; Nieberg, Tim; Wattenhofer, Roger; Fraigniaud, Pierre
2005-01-01
The distributed complexity of computing a maximal independent set in a graph is of both practical and theoretical importance. While there exists an elegant O(log n) time randomized algorithm for general graphs, no deterministic polylogarithmic algorithm is known. In this paper, we study the problem
A nickel tripeptide as a metallodithiolate ligand anchor for resin-bound organometallics.
Green, Kayla N; Jeffery, Stephen P; Reibenspies, Joseph H; Darensbourg, Marcetta Y
2006-05-17
The molecular structure of the acetyl CoA synthase enzyme has clarified the role of individual nickel atoms in the dinickel active site which mediates C-C and C-S coupling reactions. The NiN2S2 portion of the biocatalyst (N2S2 = a cysteine-glycine-cysteine or CGC4- tripeptide ligand) serves as an S-donor ligand comparable to classical bidentate ligands operative in organometallic chemistry, ligating the second nickel which is redox and catalytically active. Inspired by this biological catalyst, the synthesis of NiN2S2 metalloligands, including the solid-phase synthesis of resin-bound Ni(CGC)2-, and sulfur-based derivatization with W(CO)5 and Rh(CO)2+ have been carried out. Through comparison to analogous well-characterized, solution-phase complexes, Attenuated Total Reflectance FTIR spectroscopy establishes the presence of unique heterobimetallic complexes, of the form [Ni(CGC)]M(CO)x, both in solution and immobilized on resin beads. This work provides the initial step toward exploitation of such an evolutionarily optimized nickel peptide as a solid support anchor for hybrid bioinorganic-organometallic catalysts.
Measuring binding of protein to gel-bound ligands using magnetic levitation.
Shapiro, Nathan D; Mirica, Katherine A; Soh, Siowling; Phillips, Scott T; Taran, Olga; Mace, Charles R; Shevkoplyas, Sergey S; Whitesides, George M
2012-03-28
This paper describes the use of magnetic levitation (MagLev) to measure the association of proteins and ligands. The method starts with diamagnetic gel beads that are functionalized covalently with small molecules (putative ligands). Binding of protein to the ligands within the bead causes a change in the density of the bead. When these beads are suspended in a paramagnetic aqueous buffer and placed between the poles of two NbFeB magnets with like poles facing, the changes in the density of the bead on binding of protein result in changes in the levitation height of the bead that can be used to quantify the amount of protein bound. This paper uses a reaction-diffusion model to examine the physical principles that determine the values of rate and equilibrium constants measured by this system, using the well-defined model system of carbonic anhydrase and aryl sulfonamides. By tuning the experimental protocol, the method is capable of quantifying either the concentration of protein in a solution, or the binding affinities of a protein to several resin-bound small molecules simultaneously. Since this method requires no electricity and only a single piece of inexpensive equipment, it may find use in situations where portability and low cost are important, such as in bioanalysis in resource-limited settings, point-of-care diagnosis, veterinary medicine, and plant pathology. It still has several practical disadvantages. Most notably, the method requires relatively long assay times and cannot be applied to large proteins (>70 kDa), including antibodies. The design and synthesis of beads with improved characteristics (e.g., larger pore size) has the potential to resolve these problems.
pMD-Membrane: A Method for Ligand Binding Site Identification in Membrane-Bound Proteins.
Priyanka Prakash
2015-10-01
Full Text Available Probe-based or mixed solvent molecular dynamics simulation is a useful approach for the identification and characterization of druggable sites in drug targets. However, thus far the method has been applied only to soluble proteins. A major reason for this is the potential effect of the probe molecules on membrane structure. We have developed a technique to overcome this limitation that entails modification of force field parameters to reduce a few pairwise non-bonded interactions between selected atoms of the probe molecules and bilayer lipids. We used the resulting technique, termed pMD-membrane, to identify allosteric ligand binding sites on the G12D and G13D oncogenic mutants of the K-Ras protein bound to a negatively charged lipid bilayer. In addition, we show that differences in probe occupancy can be used to quantify changes in the accessibility of druggable sites due to conformational changes induced by membrane binding or mutation.
The maximal Lyapunov exponent of a co-dimension two-bifurcation system excited by a bounded noise
Sheng-Hong Li; Xian-Bin Liu
2012-01-01
In the present paper,the maximal Lyapunov exponent is investigated for a co-dimension two bifurcation system that is on a three-dimensional central manifold and subjected to parametric excitation by a bounded noise.By using a perturbation method,the expressions of the invariant measure of a one-dimensional phase diffusion process are obtained for three cases,in which different forms of the matrix B,that is included in the noise excitation term,are assumed and then,as a result,all the three kinds of singular boundaries for one-dimensional phase diffusion process are analyzed.Via Monte-Carlo simulation,we find that the analytical expressions of the invariant measures meet well the numerical ones.And furthermore,the P-bifurcation behaviors are investigated for the one-dimensional phase diffusion process.Finally,for the three cases of singular boundaries for one-dimensional phase diffusion process,analytical expressions of the maximal Lyapunov exponent are presented for the stochastic bifurcation system.
Apo and ligand-bound structures of ModA from the archaeon Methanosarcina acetivorans.
Chan, Sum; Giuroiu, Iulia; Chernishof, Irina; Sawaya, Michael R; Chiang, Janet; Gunsalus, Robert P; Arbing, Mark A; Perry, L Jeanne
2010-03-01
The trace-element oxyanion molybdate, which is required for the growth of many bacterial and archaeal species, is transported into the cell by an ATP-binding cassette (ABC) transporter superfamily uptake system called ModABC. ModABC consists of the ModA periplasmic solute-binding protein, the integral membrane-transport protein ModB and the ATP-binding and hydrolysis cassette protein ModC. In this study, X-ray crystal structures of ModA from the archaeon Methanosarcina acetivorans (MaModA) have been determined in the apoprotein conformation at 1.95 and 1.69 A resolution and in the molybdate-bound conformation at 2.25 and 2.45 A resolution. The overall domain structure of MaModA is similar to other ModA proteins in that it has a bilobal structure in which two mixed alpha/beta domains are linked by a hinge region. The apo MaModA is the first unliganded archaeal ModA structure to be determined: it exhibits a deep cleft between the two domains and confirms that upon binding ligand one domain is rotated towards the other by a hinge-bending motion, which is consistent with the 'Venus flytrap' model seen for bacterial-type periplasmic binding proteins. In contrast to the bacterial ModA structures, which have tetrahedral coordination of their metal substrates, molybdate-bound MaModA employs octahedral coordination of its substrate like other archaeal ModA proteins.
Surface-Bound Ligands Modulate Chemoselectivity and Activity of a Bimetallic Nanoparticle Catalyst
Vu, Khanh B.
2015-04-03
"Naked" metal nanoparticles (NPs) are thermodynamically and kinetically unstable in solution. Ligands, surfactants, or polymers, which adsorb at a particle\\'s surface, can be used to stabilize NPs; however, such a mode of stabilization is undesirable for catalytic applications because the adsorbates block the surface active sites. The catalytic activity and the stability of NPs are usually inversely correlated. Here, we describe an example of a bimetallic (PtFe) NP catalyst stabilized by carboxylate surface ligands that bind preferentially to one of the metals (Fe). NPs stabilized by fluorous ligands were found to be remarkably competent in catalyzing the hydrogenation of cinnamaldehyde; NPs stabilized by hydrocarbon ligands were significantly less active. The chain length of the fluorous ligands played a key role in determining the chemoselectivity of the FePt NP catalysts. (Chemical Presented). © 2015 American Chemical Society.
Sato, Nozomi; Ishii, Shoko; Sugimoto, Hiroshi; Hino, Tomoya; Fukumori, Yoshihiro; Sako, Yoshihiko; Shiro, Yoshitsugu; Tosha, Takehiko
2014-07-01
Nitric oxide reductase (NOR) catalyzes the generation of nitrous oxide (N2O) via the reductive coupling of two nitric oxide (NO) molecules at a heme/non-heme Fe center. We report herein on the structures of the reduced and ligand-bound forms of cytochrome c-dependent NOR (cNOR) from Pseudomonas aeruginosa at a resolution of 2.3-2.7 Å, to elucidate structure-function relationships in NOR, and compare them to those of cytochrome c oxidase (CCO) that is evolutionarily related to NOR. Comprehensive crystallographic refinement of the CO-bound form of cNOR suggested that a total of four atoms can be accommodated at the binuclear center. Consistent with this, binding of bulky acetaldoxime (CH3-CH=N-OH) to the binuclear center of cNOR was confirmed by the structural analysis. Active site reduction and ligand binding in cNOR induced only ∼0.5 Å increase in the heme/non-heme Fe distance, but no significant structural change in the protein. The highly localized structural change is consistent with the lack of proton-pumping activity in cNOR, because redox-coupled conformational changes are thought to be crucial for proton pumping in CCO. It also permits the rapid decomposition of cytotoxic NO in denitrification. In addition, the shorter heme/non-heme Fe distance even in the bulky ligand-bound form of cNOR (∼4.5 Å) than the heme/Cu distance in CCO (∼5 Å) suggests the ability of NOR to maintain two NO molecules within a short distance in the confined space of the active site, thereby facilitating N-N coupling to produce a hyponitrite intermediate for the generation of N2O.
Abate, Francesca; Malito, Enrico; Cozzi, Roberta; Lo Surdo, Paola; Maione, Domenico; Bottomley, Matthew J
2014-11-24
The Gram-positive bacterium Staphylococcus pseudintermedius is a leading cause of canine bacterial pyoderma, resulting in worldwide morbidity in dogs. S. pseudintermedius also causes life-threatening human infections. Furthermore, methicillin-resistant S. pseudintermedius is emerging, resembling the human health threat of methicillin-resistant Staphylococcus aureus. Therefore it is increasingly important to characterize targets for intervention strategies to counteract S. pseudintermedius infections. Here we used biophysical methods, mutagenesis, and X-ray crystallography, to define the ligand-binding properties and structure of SitA, an S. pseudintermedius surface lipoprotein. SitA was strongly and specifically stabilized by Mn2+ and Zn2+ ions. Crystal structures of SitA complexed with Mn2+ and Zn2+ revealed a canonical class III solute-binding protein with the metal cation bound in a cavity between N- and C-terminal lobes. Unexpectedly, one crystal contained both apo- and holo-forms of SitA, revealing a large side-chain reorientation of His64, and associated structural differences accompanying ligand binding. Such conformational changes may regulate fruitful engagement of the cognate ABC (ATP-binding cassette) transporter system (SitBC) required for metal uptake. These results provide the first detailed characterization and mechanistic insights for a potential therapeutic target of the major canine pathogen S. pseudintermedius, and also shed light on homologous structures in related staphylococcal pathogens afflicting humans.
Crystal structure of bovine CD1b3 with endogenously bound ligands
Girardi, E.; Wang, J.; Mac, T.T.; Versluis, C.; Bhowruth, V.; Besra, G.; Heck, A.J.R.; van Rhijn, I.; Zajonc, D.M.
2010-01-01
The CD1 family of Ag-presenting molecules is able to display lipids to T cells by binding them within a hydrophobic groove connected to the protein surface. In particular, the CD1b isotype is capable of binding ligands with greatly varying alkyl chain lengths through a complex network of interconnec
Zwitterionic Ligands Bound to CdSe/ZnS Quantum Dots Prevent Adhesion to Mammalian Cells
Ryan F. Landis; Rui TANG; Hou, Singyuk; Yazdani, Mahdieh; Lee, Yiwei; Rotello, Vincent M.
2015-01-01
Zwitterionic materials are useful tools in material science and biology as they provide high water solubility while preventing non-specific interactions. Quantum dots (QDs) functionalized with zwitterionic and quaternary ammonium ligands were synthesized to investigate their interactions with the outer membrane of HeLa cells. Quaternary ammonium functionalized quantum dots adhered strongly to the cell surface while zwitterionic QDs had no cell adhesion. These results demonstrate that future n...
Yuji Tokunaga
2017-09-01
Full Text Available The dynamic property of a ligand in the receptor-bound state is an important metric to characterize the interactions in the ligand–receptor interface, and the development of an experimental strategy to quantify the amplitude of motions in the bound state is of importance to introduce the dynamic aspect into structure-guided drug development (SGDD. Fluorine modifications are frequently introduced at the hit-to-lead optimization stage to enhance the binding potency and other characteristics of a ligand. However, the effects of fluorine modifications are generally difficult to predict, owing to the pleiotropic nature of the interactions. In this study, we report an NMR-based approach to experimentally evaluate the local dynamics of trifluoromethyl (CF3-containing ligands in the receptor-bound states. For this purpose, the forbidden coherence transfer (FCT analysis, which has been used to study the dynamics of methyl moieties in proteins, was extended to the 19F nuclei of CF3-containing ligands. By applying this CF3–FCT analysis to a model interaction system consisting of a ligand, AST-487, and a receptor, p38α, we successfully quantified the amplitude of the CF3 dynamics in the p38α-bound state. The strategy would bring the CF3-containing ligands within the scope of dynamic SGDD to improve the affinity and specificity for the drug-target receptors.
Reinholdt, Marc; Croissant, Jonas; Di Carlo, Lidia; Granier, Dominique; Gaveau, Philippe; Bégu, Sylvie; Devoisselle, Jean-Marie; Mutin, P Hubert; Smith, Mark E; Bonhomme, Christian; Gervais, Christel; van der Lee, Arie; Laurencin, Danielle
2011-08-15
We describe the preparation of the first crystalline compounds based on arylboronate ligands PhB(OH)(3)(-) coordinated to metal cations: [Ca(PhB(OH)(3))(2)], [Sr(PhB(OH)(3))(2)]·H(2)O, and [Ba(PhB(OH)(3))(2)]. The calcium and strontium structures were solved using powder and single-crystal X-ray diffraction, respectively. In both cases, the structures are composed of chains of cations connected through phenylboronate ligands, which interact one with each other to form a 2D lamellar structure. The temperature and pH conditions necessary for the formation of phase-pure compounds were investigated: changes in temperature were found to mainly affect the morphology of the crystallites, whereas strong variations in pH were found to affect the formation of pure phases. All three compounds were characterized using a wide range of analytical techniques (TGA, IR, Raman, XRD, and high resolution (1)H, (11)B, and (13)C solid-state NMR), and the different coordination modes of phenylboronate ligands were analyzed. Two different kinds of hydroxyl groups were identified in the structures: those involved in hydrogen bonds, and those that are effectively "free" and not involved in hydrogen bonds of any significant strength. To position precisely the OH protons within the structures, an NMR-crystallography approach was used: the comparison of experimental and calculated NMR parameters (determined using the Gauge Including Projector Augmented Wave method, GIPAW) allowed the most accurate positions to be identified. In the case of the calcium compound, it was found that it is the (43)Ca NMR data that are critical to help identify the best model of the structure.
Henthorn, Justin T; Lin, Sibo; Agapie, Theodor
2015-02-04
A series of π-bound Mo-quinonoid complexes supported by pendant phosphines have been synthesized. Structural characterization revealed strong metal-arene interactions between Mo and the π system of the quinonoid fragment. The Mo-catechol complex (2a) was found to react within minutes with 0.5 equiv of O(2) to yield a Mo-quinone complex (3), H(2)O, and CO. Si- and B-protected Mo-catecholate complexes also react with O(2) to yield 3 along with (R(2)SiO)n and (ArBO)(3) byproducts, respectively. Formally, the Mo-catecholate fragment provides two electrons, while the elements bound to the catecholate moiety act as acceptors for the O(2) oxygens. Unreactive by itself, the Mo-dimethyl catecholate analogue reduces O(2) in the presence of added Lewis acid, B(C(6)F(5))(3), to generate a Mo(I) species and a bis(borane)-supported peroxide dianion, [[(F(5)C(6))(3)B](2)O(2)(2-)], demonstrating single-electron-transfer chemistry from Mo to the O(2) moiety. The intramolecular combination of a molybdenum center, redox-active ligand, and Lewis acid reduces O(2) with pendant acids weaker than B(C(6)F(5))(3). Overall, the π-bound catecholate moiety acts as a two-electron donor. A mechanism is proposed in which O(2) is reduced through an initial one-electron transfer, coupled with transfer of the Lewis acidic moiety bound to the quinonoid oxygen atoms to the reduced O(2) species.
Optimizing the Readout of Lanthanide-DOTA Complexes for the Detection of Ligand-Bound Copper(I
Jill R. Hanna
2017-05-01
Full Text Available The CuAAC ‘click’ reaction was used to couple alkyne-functionalized lanthanide-DOTA complexes to a range of fluorescent antennae. Screening of the antenna components was aided by comparison of the luminescent output of the resultant sensors using data normalized to account for reaction conversion as assessed by IR. A maximum 82-fold enhanced signal:background luminescence output was achieved using a Eu(III-DOTA complex coupled to a coumarin-azide, in a reaction which is specific to the presence of copper(I. This optimized complex provides a new lead design for lanthanide-DOTA complexes which can act as irreversible ‘turn-on’ catalytic sensors for the detection of ligand-bound copper(I.
Jayalakshmi, V.; Rama Krishna, N.
2004-05-01
We describe an intensity-restrained optimization procedure for refining approximate structures of ligands within the protein binding pockets using STD-NMR intensity data on reversibly forming weak complexes. In this approach, the global minimum for the bound-ligand conformation is obtained by a hybrid structure refinement method involving CORCEMA calculation of intensities and simulated annealing optimization of torsion angles of the bound ligand using STD-NMR intensities as experimental constraints and the NOE R-factor as the pseudo-energy function to be minimized. This method is illustrated using simulated STD data sets for typical carbohydrate and peptide ligands. Our procedure also allows for the optimization of side chain torsion angles of protein residues within the binding pocket. This procedure is useful in refining and improving initial models based on crystallography or computer docking or other algorithms to generate models for the bound ligand (e.g., a lead compound) within the protein binding pocket compatible with solution STD-NMR data. This method may facilitate structure-based drug design efforts.
Dyer, David H.; Vyazunova, Irina; Lorch, Jeffery M.; Forest, Katrina T.; Lan, Que; (UW)
2009-06-12
The sterol carrier protein-2 like 3 gene (AeSCP-2L3), a new member of the SCP-2 protein family, is identified from the yellow fever mosquito, Aedes aegypti. The predicted molecular weight of AeSCP-2L3 is 13.4 kDa with a calculated pI of 4.98. AeSCP-2L3 transcription occurs in the larval feeding stages and the mRNA levels decrease in pupae and adults. The highest levels of AeSCP-2L3 gene expression are found in the body wall, and possibly originated in the fat body. This is the first report of a mosquito SCP-2-like protein with prominent expression in tissue other than the midgut. The X-ray protein crystal structure of AeSCP-2L3 reveals a bound C16 fatty acid whose acyl tail penetrates deeply into a hydrophobic cavity. Interestingly, the ligand-binding cavity is slightly larger than previously described for AeSCP-2 (Dyer et al. J Biol Chem 278:39085-39091, 2003) and AeSCP-2L2 (Dyer et al. J Lipid Res M700460-JLR200, 2007). There are also an additional 10 amino acids in SCP-2L3 that are not present in other characterized mosquito SCP-2s forming an extended loop between {beta}3 and {beta}4. Otherwise, the protein backbone is exceedingly similar to other SCP-2 and SCP-2-like proteins. In contrast to this observed high structural homology of members in the mosquito SCP2 family, the amino acid sequence identity between the members is less than 30%. The results from structural analysis imply that there have been evolutionary constraints that favor the SCP-2 C{alpha} backbone fold while the specificity of ligand binding can be altered.
Hamiaux, C.; Stanley, D.; Greenwood, D.R.; Baker, E.N.; Newcomb, R.D.
2009-05-19
Takeout (To) proteins are found exclusively in insects and have been proposed to have important roles in various aspects of their physiology and behavior. Limited sequence similarity with juvenile hormone-binding proteins (JHBPs), which specifically bind and transport juvenile hormones in Lepidoptera, suggested a role for To proteins in binding hydrophobic ligands. We present the first crystal structure of a To protein, EpTo1 from the light brown apple moth Epiphyas postvittana, solved in-house by the single-wavelength anomalous diffraction technique using sulfur anomalous dispersion, and refined to 1.3 {angstrom} resolution. EpTo1 adopts the unusual {alpha}/{beta}-wrap fold, seen only for JHBP and several mammalian lipid carrier proteins, a scaffold tailored for the binding and/or transport of hydrophobic ligands. EpTo1 has a 45 {angstrom} long, purely hydrophobic, internal tunnel that extends for the full length of the protein and accommodates a bound ligand. The latter was shown by mass spectrometry to be ubiquinone-8 and is probably derived from Escherichia coli. The structure provides the first direct experimental evidence that To proteins are ligand carriers; gives insights into the nature of endogenous ligand(s) of EpTo1; shows, by comparison with JHBP, a basis for different ligand specificities; and suggests a mechanism for the binding/release of ligands.
Suddala, Krishna C.; Rinaldi, Arlie J.; Feng, Jun; Mustoe, Anthony M.; Eichhorn, Catherine D.; Liberman, Joseph A.; Wedekind, Joseph E.; Al-Hashimi, Hashim M.; Brooks, Charles L.; Walter, Nils G.
2013-01-01
Riboswitches are structural elements in the 5′ untranslated regions of many bacterial messenger RNAs that regulate gene expression in response to changing metabolite concentrations by inhibition of either transcription or translation initiation. The preQ1 (7-aminomethyl-7-deazaguanine) riboswitch family comprises some of the smallest metabolite sensing RNAs found in nature. Once ligand-bound, the transcriptional Bacillus subtilis and translational Thermoanaerobacter tengcongensis preQ1 riboswitch aptamers are structurally similar RNA pseudoknots; yet, prior structural studies have characterized their ligand-free conformations as largely unfolded and folded, respectively. In contrast, through single molecule observation, we now show that, at near-physiological Mg2+ concentration and pH, both ligand-free aptamers adopt similar pre-folded state ensembles that differ in their ligand-mediated folding. Structure-based Gō-model simulations of the two aptamers suggest that the ligand binds late (Bacillus subtilis) and early (Thermoanaerobacter tengcongensis) relative to pseudoknot folding, leading to the proposal that the principal distinction between the two riboswitches lies in their relative tendencies to fold via mechanisms of conformational selection and induced fit, respectively. These mechanistic insights are put to the test by rationally designing a single nucleotide swap distal from the ligand binding pocket that we find to predictably control the aptamers′ pre-folded states and their ligand binding affinities. PMID:24003028
Boström, J
2001-12-01
Several programs (Catalyst, Confort, Flo99, MacroModel, and Omega) that are commonly used to generate conformational ensembles have been tested for their ability to reproduce bioactive conformations. The ligands from thirty-two different ligand-protein complexes determined by high-resolution (Confort) performed least well. For the seven ligands in the set having eight or more rotatable bonds, none of the bioactive conformations were ever found, save for one exception (Flo99). These ligands do not bind in a local minimum conformation according to AMBER*\\GB/SA. Taking these last two observations together, it is clear that geometrically similar structures should be collected in order to increase the probability of finding the bioactive conformation among the generated ensembles. Factors influencing bioactive conformational retrieval have been identified and are discussed.
Westby, Mike; Smith-Burchnell, Caroline; Mori, Julie; Lewis, Marilyn; Mosley, Michael; Stockdale, Mark; Dorr, Patrick; Ciaramella, Giuseppe; Perros, Manos
2007-03-01
Maraviroc is a CCR5 antagonist in clinical development as one of a new class of antiretrovirals targeting human immunodeficiency virus type 1 (HIV-1) coreceptor binding. We investigated the mechanism of HIV resistance to maraviroc by using in vitro sequential passage and site-directed mutagenesis. Serial passage through increasing maraviroc concentrations failed to select maraviroc-resistant variants from some laboratory-adapted and clinical isolates of HIV-1. However, high-level resistance to maraviroc was selected from three of six primary isolates passaged in peripheral blood lymphocytes (PBL). The SF162 strain acquired resistance to maraviroc in both treated and control cultures; all resistant variants were able to use CXCR4 as a coreceptor. In contrast, maraviroc-resistant virus derived from isolates CC1/85 and RU570 remained CCR5 tropic, as evidenced by susceptibility to the CCR5 antagonist SCH-C, resistance to the CXCR4 antagonist AMD3100, and an inability to replicate in CCR5 Delta32/Delta32 PBL. Strain-specific mutations were identified in the V3 loop of maraviroc-resistant CC1/85 and RU570. The envelope-encoding region of maraviroc-resistant CC1/85 was inserted into an NL4-3 background. This recombinant virus was completely resistant to maraviroc but retained susceptibility to aplaviroc. Reverse mutation of gp120 residues 316 and 323 in the V3 loop (numbering from HXB2) to their original sequence restored wild-type susceptibility to maraviroc, while reversion of either mutation resulted in a partially sensitive virus with reduced maximal inhibition (plateau). The plateaus are consistent with the virus having acquired the ability to utilize maraviroc-bound receptor for entry. This hypothesis was further corroborated by the observation that a high concentration of maraviroc blocks the activity of aplaviroc against maraviroc-resistant virus.
Lin, Chun-Chi; Baek, Kyuwon; Lu, Zhe (UPENN)
2012-05-08
We report the crystal structures of the ligand-binding domain (LBD) of a rat inositol 1,4,5-trisphosphate receptor (InsP{sub 3}R) in its apo and InsP{sub 3}-bound conformations. Comparison of these two conformations reveals that LBD's first {beta}-trefoil fold ({beta}-TF1) and armadillo repeat fold (ARF) move together as a unit relative to its second {beta}-trefoil fold ({beta}-TF2). Whereas apo LBD may spontaneously transition between gating conformations, InsP{sub 3} binding shifts this equilibrium toward the active state.
YU, Ying-Min; FEI, Jin-Hua; ZHANG, Yi-Ping; ZHENG, Xiao-Ming
2006-01-01
The functionalized MCM-41 mesoporous bound ruthenium complex was synthesized and characterized using elemental analysis, atomic absorption spectrophotometer, BET, XRD and FTIR. Hydrogenation of carbon dioxide to formic acid was investigated over these catalysts under supercritical CO2 condition. The effect of reactant gas partial pressure, supports, solvents and ligands on the synthesis of formic acid was studied. These factors could influence the catalyst activity, stability and reuse performance greatly and no byproduct was detected. These promising catalysts also offered the industrial advantages such as easy separation.
Boström, Jonas
2001-12-01
Several programs (Catalyst, Confort, Flo99, MacroModel, and Omega) that are commonly used to generate conformational ensembles have been tested for their ability to reproduce bioactive conformations. The ligands from thirty-two different ligand-protein complexes determined by high-resolution ( le2.0 Å) X-ray crystallography have been analyzed. The Low-Mode Conformational Search method (with AMBER* and the GB/SA hydration model), as implemented in MacroModel, was found to perform better than the other algorithms. The rule-based method Omega, which is orders of magnitude faster than the other methods, also gave reasonable results but were found to be dependent on the input structure. The methods supporting diverse sampling (Catalyst, Confort) performed least well. For the seven ligands in the set having eight or more rotatable bonds, none of the bioactive conformations were ever found, save for one exception (Flo99). These ligands do not bind in a local minimum conformation according to AMBER*GB/SA. Taking these last two observations together, it is clear that geometrically similar structures should be collected in order to increase the probability of finding the bioactive conformation among the generated ensembles. Factors influencing bioactive conformational retrieval have been identified and are discussed.
Liangliang Liu
2016-11-01
Full Text Available Radix astragali is widely used either as a single herb or as a collection of herbs in a complex prescription in China. In this study, bovine serum albumin functionalized magnetic nanoparticles (BSA-MN coupled with high performance liquid chromatography-mass spectrometry (HPLC-MS were used to screen and identify bound ligands from the n-butanol part of a Radix astragali extract. The prepared BSA-MN showed sufficient magnetic response for the separation with an ordinary magnet and satisfied reusability. Fundamental parameters affecting the preparation of BSA-MN and the screening efficiency were studied and optimized. Under the optimum conditions, four bound ligands were screened out from the n-butanol part of a Radix astragali extract and identified as genistin (1, calycosin-7-O-β-d-glucoside (2, ononin (3 and formononetin (4. This effective method could be widely applied for rapid screening and identification of active compounds from complex mixtures without the need for preparative isolation.
Furuya, Fumihiko; Ishii, Toshihisa; Tamura, Shogo; Takahashi, Kazuya; Kobayashi, Hidetoshi; Ichijo, Masashi; Takizawa, Soichi; Kaneshige, Masahiro; Suzuki-Inoue, Katsue; Kitamura, Kenichiro
2017-01-01
In chronic kidney disease (CKD) patients, inflammation plays a pivotal role in the progression of renal fibrosis. Hypothyroidism is associated with an increased occurrence of atherosclerosis and inflammation, suggesting protective roles of thyroid hormones and their receptors against inflammatory processes. The contribution of thyroid hormone receptors to macrophage differentiation has not been well documented. Here, we focused on the endogenous thyroid hormone receptor α (TRα) in macrophages and examined the role of ligand-bound TRα in macrophage polarization-mediated anti-inflammatory effects. TRα-deficient irradiated chimeric mice showed exacerbated tubulointerstitial injury in a unilateral ureteral obstruction model. Compared with wild-type macrophages, macrophages isolated from the obstructed kidneys of mice lacking TRα displayed increased expression of proinflammatory cytokines that was accompanied by enhanced nuclear translocation of p65. Comparison of TRα-deficient bone marrow-derived macrophages with wild-type macrophages confirmed the propensity of the former cells to produce excessive IL-1β levels. Co-culture of these macrophages with renal epithelial cells induced more severe damage to the epithelial cells via the IL-1 receptor. Our findings indicate that ligand-bound TRα on macrophages plays a protective role in kidney inflammation through the inhibition of NF-κB pathways, possibly by affecting the pro- and anti-inflammatory balance that controls the development of CKD. PMID:28272516
Faroongsarng, Damrongsak
2016-04-01
Drug-protein binding may play a role in the thermal energetics of protein denaturation and could lead to the determination of its equilibrium dissociation parameter. The aim of this study was to assess the energetics of a drug that was bound to human serum albumin (HSA) during thermal denaturation. Drugs that were bound at a single high-affinity primary binding site on HSA, including diazepam and ibuprofen, were employed. Commercial HSA was treated with charcoal to remove stabilizers and adjusted to 20% w/v in a pH 7.4 buffered solution. Serial concentrations of individual drugs up to 0.16 mmole/g-protein were added to the cleaned HSA solutions whereas diazepam was added to a commercial HSA solution. Samples were subjected to differential scanning calorimetry (DSC) set to run from 37 to 90°C at 3.0°C/min. Binding of the drug slightly increased the denaturing temperature of the cleaned HSA due to a shift in the equilibrium toward the native protein bound with the drug. Diazepam depressed the denaturing temperature of the commercial HSA by competing with the stabilizers already bound to the primary site of the HSA. This yielded not only the HSA-stabilizer but also the HSA-diazepam type complexes that exhibited a different denaturation process. A rational approximation of the Lumry-Eyring protein denaturation model was used to treat the DSC endotherms. The approximated scheme: [Formula: see text] was successfully fitted to the data. It was used to determine the dissociation parameters for diazepam and ibuprofen bound to the HSA. These results were comparable to those obtained from other methods.
Gautam, Gunjan; Rehman, Syed Arif Abdul; Pandey, Preeti; Gourinath, Samudrala
2017-08-01
The versatility in the recognition of various interacting proteins by the SH3 domain drives a variety of cellular functions. Here, the crystal structure of the C-terminal SH3 domain of myosin IB from Entamoeba histolytica (EhMySH3) is reported at a resolution of 1.7 Å in native and PEG-bound states. Comparisons with other structures indicated that the PEG molecules occupy protein-protein interaction pockets similar to those occupied by the peptides in other peptide-bound SH3-domain structures. Also, analysis of the PEG-bound EhMySH3 structure led to the recognition of two additional pockets, apart from the conventional polyproline and specificity pockets, that are important for ligand interaction. Molecular-docking studies combined with various comparisons revealed structural similarity between EhMySH3 and the SH3 domain of β-Pix, and this similarity led to the prediction that EhMySH3 preferentially binds targets containing type II-like PXXP motifs. These studies expand the understanding of the EhMySH3 domain and provide extensive structural knowledge, which is expected to help in predicting the interacting partners which function together with myosin IB during phagocytosis in E. histolytica infections.
Direct activation of human dendritic cells by particle-bound but not soluble MHC class II ligand.
Renato B Baleeiro
Full Text Available Dendritic cells (DCs are key activators of cellular immune responses through their capacity to induce naïve T cells and sustained effector T cell responses. This capacity is a function of their superior efficiency of antigen presentation via MHC class I and class II molecules, and the expression of co-stimulatory cell surface molecules and cytokines. Maturation of DCs is induced by microbial factors via pattern recognition receptors such as Toll-like receptors, pro-inflammatory cytokines or cognate interaction with CD4(+ T cells. Here we show that, unexpectedly, the PanDR helper T cell epitope PADRE, a generic T helper cell antigen presented by a large fraction of HLA-DR alleles, when delivered in particle-bound form induced maturation of human DCs. The DCs that received the particle-bound PADRE displayed all features of fully mature DCs, such as high expression of the co-stimulatory molecules CD80, CD86, CD83, the MHC-II molecule HLA-DR, secretion of high levels of the biologically active IL-12 (IL-12p70 and induction of vigorous proliferation of naïve CD4(+ T cells. Furthermore, the maturation of DCs induced by particle-bound PADRE was shown to involve sphingosine kinase, calcium signaling from internal sources and downstream signaling through the MAP kinase and the p72syk pathways, and finally activation of the transcription factor NF-κB. Based on our findings, we propose that particle-bound PADRE may be used as a DC activator in DC-based vaccines.
Wang Yan
2010-10-01
Full Text Available Abstract Background Copper nucleases as a famous class of artificial metallonucleases have attracted considerable interest in relation to their diverse potentials not only as therapeutic agents but also in genomic researches. Copper nucleases present high efficient oxidative cleavage of DNA, in which DNA strand scission occurs generally after hydrogen atom abstracted from a sugar moiety. In order to achieve the selective cleavage of DNA sequences by copper nucleases, the DNA specific recognition agents of the Dervan-type hairpin and cyclic polyamides can be considered as proper carriers of copper nucleases. Investigation of the DNA cleavage selectivity of copper nucleases assisted by the hairpin and cyclic polyamides at the molecular level has not yet been elucidated. Results We carried out a series of molecular dynamics simulations for the nuclease [Cu(BPA]2+ or [Cu(IDB]2+ bound to the hairpin/cyclic polyamide and associated with DNA to investigate the selective DNA cleavage properties of Cu(II-based artificial nucleases. The simulated results demonstrate that the DNA cleavage selectivity of the two nucleases assisted by the hairpin polyamide is improved efficiently. The [Cu(BPA]2+ or [Cu(IDB]2+ nuclease with a substrate OOH- bound to the hairpin polyamide can be stably located at the minor groove of DNA, and possibly abstracts H atom from the sugar of DNA. However, the DNA cleavage properties of the two nucleases assisted by the cyclic polyamide are significantly poor due to the rigidity of linking region between the cyclic polyamide and nuclease. With introduction of the flexible linker -CH2CH2CH2NH2, the modified cyclic polyamide can assist the two copper nucleases to improve the selective DNA cleavage properties efficiently. Conclusion A flexible linker and a proper binding site of the polyamide-type recognition agents play an important role in improving the DNA cleavage selectivity of copper nucleases. Current investigations provide an
Christina Koers-Wunrau
Full Text Available BACKGROUND: The matrix metalloproteinases (MMPs and their endogenous regulators, the tissue inhibitor of metalloproteinases (TIMPs 1-4 are responsible for the physiological remodeling of the extracellular matrix (ECM. Among all TIMPs, TIMP3 appears to play a unique role since TIMP3 is a secreted protein and, unlike the other TIMP family members, is tightly bound to the ECM. Moreover TIMP3 has been shown to be able to induce apoptotic cell death. As little is known about the underlying mechanisms, we set out to investigate the pro-apoptotic effect of TIMP3 in human mesenchymal cells. METHODOLOGY/PRINCIPAL FINDINGS: Lentiviral overexpression of TIMP3 in mesenchymal cells led to a strong dose-dependent induction of ligand-independent apoptosis as reflected by a five-fold increase in caspase 3 and 7 activity compared to control (pLenti6/V5-GW/lacZ or uninfected cells, whereas exogenous TIMP3 failed to induce apoptosis. Concordantly, increased cleavage of death substrate PARP and the caspases 3 and 7 was observed in TIMP3 overexpressing cultures. Notably, activation of caspase-8 but not caspase-9 was observed in TIMP3-overexpressing cells, indicating a death receptor-dependent mechanism. Moreover, overexpression of TIMP3 led to a further induction of apoptosis after stimulation with TNF-alpha, FasL and TRAIL. Most interestingly, TIMP3-overexpression was associated with a decrease in phosphorylation of cRaf, extracellular signal-regulated protein kinase (Erk1/2, ribosomal S6 kinase (RSK1 and Akt and serum deprivation of TIMP3-overexpressing cells resulted in a distinct enhancement of apoptosis, pointing to an impaired signaling of serum-derived survival factors. Finally, heparinase treatment of heparan sulfate proteoglycans led to the release of TIMP3 from the surface of overexpressing cells and to a significant decrease in apoptosis indicating that the binding of TIMP3 is necessary for apoptosis induction. CONCLUSION: The results demonstrate that
Stover, Robert J; Murthy, Avinash K; Nie, Golay D; Gourisankar, Sai; Dear, Barton J; Truskett, Thomas M; Sokolov, Konstantin V; Johnston, Keith P
2014-07-03
Gold nanospheres coated with a binary monolayer of bound citrate and cysteine ligands were assembled into nanoclusters, in which the size and near-infrared (NIR) extinction were tuned by varying the pH and concentration of added NaCl. During full evaporation of an aqueous dispersion of 4.5 ± 1.8 nm Au primary particles, the nanoclusters were formed and quenched by the triblock copolymer polylactic acid (PLA)(1K)-b-poly(ethylene glycol) (PEG)(10K)-b-PLA(1K), which also provided steric stabilization. The short-ranged depletion and van der Waals attractive forces were balanced against longer ranged electrostatic repulsion to tune the nanocluster diameter and NIR extinction. Upon lowering the pH from 7 to 5 at a given salinity, the magnitude of the charge on the primary particles decreased, such that the weaker electrostatic repulsion increased the hydrodynamic diameter and, consequently, NIR extinction of the clusters. At a given pH, as the concentration of NaCl was increased, the NIR extinction decreased monotonically. Furthermore, the greater screening of the charges on the nanoclusters weakened the interactions with PLA(1K)-b-PEG(10K)-b-PLA(1K) and thus lowered the amount of adsorbed polymer on the nanocluster surface. The generalization of the concept of self-assembly of small NIR-active nanoclusters to include a strongly bound thiol and the manipulation of the morphologies and NIR extinction by variation of pH and salinity not only is of fundamental interest but also is important for optical biomedical imaging and therapy.
Jennifer L Miller-Gallacher
Full Text Available The β1-adrenoceptor (β1AR is a G protein-coupled receptor (GPCR that is activated by the endogenous agonists adrenaline and noradrenaline. We have determined the structure of an ultra-thermostable β1AR mutant bound to the weak partial agonist cyanopindolol to 2.1 Å resolution. High-quality crystals (100 μm plates were grown in lipidic cubic phase without the assistance of a T4 lysozyme or BRIL fusion in cytoplasmic loop 3, which is commonly employed for GPCR crystallisation. An intramembrane Na+ ion was identified co-ordinated to Asp872.50, Ser1283.39 and 3 water molecules, which is part of a more extensive network of water molecules in a cavity formed between transmembrane helices 1, 2, 3, 6 and 7. Remarkably, this water network and Na+ ion is highly conserved between β1AR and the adenosine A2A receptor (rmsd of 0.3 Å, despite an overall rmsd of 2.4 Å for all Cα atoms and only 23% amino acid identity in the transmembrane regions. The affinity of agonist binding and nanobody Nb80 binding to β1AR is unaffected by Na+ ions, but the stability of the receptor is decreased by 7.5°C in the absence of Na+. Mutation of amino acid side chains that are involved in the co-ordination of either Na+ or water molecules in the network decreases the stability of β1AR by 5-10°C. The data suggest that the intramembrane Na+ and associated water network stabilise the ligand-free state of β1AR, but still permits the receptor to form the activated state which involves the collapse of the Na+ binding pocket on agonist binding.
Salvio, Alberto; Strumia, Alessandro; Urbano, Alfredo
2016-01-01
Motivated by the 750 GeV diphoton excess found at LHC, we compute the maximal width into $\\gamma\\gamma$ that a neutral scalar can acquire through a loop of charged fermions or scalars as function of the maximal scale at which the theory holds, taking into account vacuum (meta)stability bounds. We show how an extra gauge symmetry can qualitatively weaken such bounds, and explore collider probes and connections with Dark Matter.
Note on maximal distance separable codes
YANG Jian-sheng; WANG De-xiu; JIN Qing-fang
2009-01-01
In this paper, the maximal length of maximal distance separable(MDS)codes is studied, and a new upper bound formula of the maximal length of MDS codes is obtained. Especially, the exact values of the maximal length of MDS codes in some parameters are given.
Brendle, Joerg
2016-01-01
We show that, consistently, there can be maximal subtrees of P (omega) and P (omega) / fin of arbitrary regular uncountable size below the size of the continuum. We also show that there are no maximal subtrees of P (omega) / fin with countable levels. Our results answer several questions of Campero, Cancino, Hrusak, and Miranda.
BOUNDEDNESS OF MAXIMAL SINGULAR INTEGRALS
CHEN JIECHENG; ZHU XIANGRONG
2005-01-01
The authors study the singular integrals under the Hormander condition and the measure not satisfying the doubling condition. At first, if the corresponding singular integral is bounded from L2 to itseff, it is proved that the maximal singu lar integral is bounded from L∞ to RBMO except that it is infinite μ-a.e. on Rd. A sufficient condition and a necessary condition such that the maximal singular integral is bounded from L2 to itself are also obtained. There is a small gap between the two conditions.
Janusz Brzozowski
2014-05-01
Full Text Available The atoms of a regular language are non-empty intersections of complemented and uncomplemented quotients of the language. Tight upper bounds on the number of atoms of a language and on the quotient complexities of atoms are known. We introduce a new class of regular languages, called the maximally atomic languages, consisting of all languages meeting these bounds. We prove the following result: If L is a regular language of quotient complexity n and G is the subgroup of permutations in the transition semigroup T of the minimal DFA of L, then L is maximally atomic if and only if G is transitive on k-subsets of 1,...,n for 0 <= k <= n and T contains a transformation of rank n-1.
Sampling and Representation Complexity of Revenue Maximization
Dughmi, Shaddin; Han, Li; Nisan, Noam
2014-01-01
We consider (approximate) revenue maximization in auctions where the distribution on input valuations is given via "black box" access to samples from the distribution. We observe that the number of samples required -- the sample complexity -- is tightly related to the representation complexity of an approximately revenue-maximizing auction. Our main results are upper bounds and an exponential lower bound on these complexities.
K B Athreya
2009-09-01
It is shown that (i) every probability density is the unique maximizer of relative entropy in an appropriate class and (ii) in the class of all pdf that satisfy $\\int fh_id_=_i$ for $i=1,2,\\ldots,\\ldots k$ the maximizer of entropy is an $f_0$ that is proportional to $\\exp(\\sum c_i h_i)$ for some choice of $c_i$. An extension of this to a continuum of constraints and many examples are presented.
Nagaraj, Karuppiah; Sakthinathan, Subramanian; Arunachalam, Sankaralingam
2015-08-01
The interaction of two surfactant cobalt(III) complexes, cis-[Co(ip)2(DA)2](ClO4)3 1 and cis-[Co(dpq)2(DA)2](ClO4)3 2 where ip = imidazo[4,5-f][1,10]phenanthroline and dpq = dipyrido[3,2-d:2‧-3‧-f]quinoxaline with yeast tRNA have been explored by using electronic absorption, competitive binding, electrochemical studies and viscosity measurements. The results suggest that these complexes can bind to tRNA by intercalation. The presence of hydrophobic diimine ligand and the long aliphatic double chains of these complexes facilitate its intercalative interaction with the hydrophobic interior of the tRNA. The extent of tRNA binding of complex 2 has greater affinity than that of complex containing imidazo[4,5-f][1,10]phenanthroline ligands.
Nagaraj, Karuppiah; Sakthinathan, Subramanian; Arunachalam, Sankaralingam
2015-08-01
The interaction of two surfactant cobalt(III) complexes, cis-[Co(ip)₂(DA)₂](ClO₄)₃ 1 and cis-[Co(dpq)₂(DA)₂](ClO₄)₃ 2 where ip=imidazo[4,5-f][1,10]phenanthroline and dpq=dipyrido[3,2-d:2'-3'-f]quinoxaline with yeast tRNA have been explored by using electronic absorption, competitive binding, electrochemical studies and viscosity measurements. The results suggest that these complexes can bind to tRNA by intercalation. The presence of hydrophobic diimine ligand and the long aliphatic double chains of these complexes facilitate its intercalative interaction with the hydrophobic interior of the tRNA. The extent of tRNA binding of complex 2 has greater affinity than that of complex containing imidazo[4,5-f][1,10]phenanthroline ligands.
Principles of maximally classical and maximally realistic quantum mechanics
S M Roy
2002-08-01
Recently Auberson, Mahoux, Roy and Singh have proved a long standing conjecture of Roy and Singh: In 2-dimensional phase space, a maximally realistic quantum mechanics can have quantum probabilities of no more than + 1 complete commuting cets (CCS) of observables coexisting as marginals of one positive phase space density. Here I formulate a stationary principle which gives a nonperturbative deﬁnition of a maximally classical as well as maximally realistic phase space density. I show that the maximally classical trajectories are in fact exactly classical in the simple examples of coherent states and bound states of an oscillator and Gaussian free particle states. In contrast, it is known that the de Broglie–Bohm realistic theory gives highly nonclassical trajectories.
Lisonek, Petr
1996-01-01
our classifications confirmthe maximality of previously known sets, the results in E^7 and E^8are new. Their counterpart in dimension larger than 10is a set of unit vectors with only two values of inner products in the Lorentz space R^{d,1}.The maximality of this set again follows from a bound due...
Bound entanglement and entanglement bounds
Sauer, Simeon [Physikalisch-Astronomische Fakultaet, Friedrich-Schiller-Univesitaet Jena (Germany)]|[Physikalisches Institut, Albert-Ludwigs-Universitaet Freiburg, Hermann-Herder-Strasse 3, D-79104 Freiburg (Germany); Melo, Fernando de; Mintert, Florian; Buchleitner, Andreas [Physikalisches Institut, Albert-Ludwigs-Universitaet Freiburg, Hermann-Herder-Strasse 3, D-79104 Freiburg (Germany)]|[Max-Planck-Institut fuer Physik komplexer Systeme, Noethnitzer Str.38, D-01187 Dresden (Germany); Bae, Joonwoo [School of Computational Sciences, Korea Institute for Advanced Study, Seoul 130-012 (Korea); Hiesmayr, Beatrix [Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna (Austria)
2008-07-01
We investigate the separability of Bell-diagonal states of two qutrits. By using lower bounds to algebraically estimate concurrence, we find convex regions of bound entangled states. Some of these regions exactly coincide with the obtained results when employing optimal entanglement witnesses, what shows that the lower bound can serve as a precise detector of entanglement. Some hitherto unknown regions of bound entangled states were discovered with this approach, and delimited efficiently.
Information, Utility & Bounded Rationality
Ortega, Pedro A
2011-01-01
Perfectly rational decision-makers maximize expected utility, but crucially ignore the resource costs incurred when determining optimal actions. Here we employ an axiomatic framework for bounded rational decision-making based on a thermodynamic interpretation of resource costs as information costs. This leads to a variational "free utility" principle akin to thermodynamical free energy that trades off utility and information costs. We show that bounded optimal control solutions can be derived from this variational principle, which leads in general to stochastic policies. Furthermore, we show that risk-sensitive and robust (minimax) control schemes fall out naturally from this framework if the environment is considered as a bounded rational and perfectly rational opponent, respectively. When resource costs are ignored, the maximum expected utility principle is recovered.
Profit maximization mitigates competition
Dierker, Egbert; Grodal, Birgit
1996-01-01
We consider oligopolistic markets in which the notion of shareholders' utility is well-defined and compare the Bertrand-Nash equilibria in case of utility maximization with those under the usual profit maximization hypothesis. Our main result states that profit maximization leads to less price...... competition than utility maximization. Since profit maximization tends to raise prices, it may be regarded as beneficial for the owners as a whole. Moreover, if profit maximization is a good proxy for utility maximization, then there is no need for a general equilibrium analysis that takes the distribution...... of profits among consumers fully into account and partial equilibrium analysis suffices...
Swanepoel, Konrad J
2011-01-01
A subset of a normed space X is called equilateral if the distance between any two points is the same. Let m(X) be the smallest possible size of an equilateral subset of X maximal with respect to inclusion. We first observe that Petty's construction of a d-dimensional X of any finite dimension d >= 4 with m(X)=4 can be generalised to show that m(X\\oplus_1\\R)=4 for any X of dimension at least 2 which has a smooth point on its unit sphere. By a construction involving Hadamard matrices we then show that both m(\\ell_p) and m(\\ell_p^d) are finite and bounded above by a function of p, for all 1 1 such that m(X) <= d+1 for all d-dimensional X with Banach-Mazur distance less than c from \\ell_p^d. Using Brouwer's fixed-point theorem we show that m(X) <= d+1 for all d-\\dimensional X with Banach-Mazur distance less than 3/2 from \\ell_\\infty^d. A graph-theoretical argument furthermore shows that m(\\ell_\\infty^d)=d+1. The above results lead us to conjecture that m(X) <= 1+\\dim X.
Park Jaeok
2012-12-01
Full Text Available Abstract Background Human farnesyl pyrophosphate synthase (FPPS controls intracellular levels of farnesyl pyrophosphate, which is essential for various biological processes. Bisphosphonate inhibitors of human FPPS are valuable therapeutics for the treatment of bone-resorption disorders and have also demonstrated efficacy in multiple tumor types. Inhibition of human FPPS by bisphosphonates in vivo is thought to involve closing of the enzyme’s C-terminal tail induced by the binding of the second substrate isopentenyl pyrophosphate (IPP. This conformational change, which occurs through a yet unclear mechanism, seals off the enzyme’s active site from the solvent environment and is essential for catalysis. The crystal structure of human FPPS in complex with a novel bisphosphonate YS0470 and in the absence of a second substrate showed partial ordering of the tail in the closed conformation. Results We have determined crystal structures of human FPPS in ternary complex with YS0470 and the secondary ligands inorganic phosphate (Pi, inorganic pyrophosphate (PPi, and IPP. Binding of PPi or IPP to the enzyme-inhibitor complex, but not that of Pi, resulted in full ordering of the C-terminal tail, which is most notably characterized by the anchoring of the R351 side chain to the main frame of the enzyme. Isothermal titration calorimetry experiments demonstrated that PPi binds more tightly to the enzyme-inhibitor complex than IPP, and differential scanning fluorometry experiments confirmed that Pi binding does not induce the tail ordering. Structure analysis identified a cascade of conformational changes required for the C-terminal tail rigidification involving Y349, F238, and Q242. The residues K57 and N59 upon PPi/IPP binding undergo subtler conformational changes, which may initiate this cascade. Conclusions In human FPPS, Y349 functions as a safety switch that prevents any futile C-terminal closure and is locked in the “off” position in the
Beeping a Maximal Independent Set
Afek, Yehuda; Alon, Noga; Bar-Joseph, Ziv; Cornejo, Alejandro; Haeupler, Bernhard; Kuhn, Fabian
2012-01-01
We consider the problem of computing a maximal independent set (MIS) in an extremely harsh broadcast model that relies only on carrier sensing. The model consists of an anonymous broadcast network in which nodes have no knowledge about the topology of the network or even an upper bound on its size. Furthermore, it is assumed that an adversary chooses at which time slot each node wakes up. At each time slot a node can either beep, that is, emit a signal, or be silent. At a particular time slot...
Beeping a Maximal Independent Set
Afek, Yehuda; Bar-Joseph, Ziv; Cornejo, Alejandro; Haeupler, Bernhard; Kuhn, Fabian
2012-01-01
We consider the problem of computing a maximal independent set (MIS) in an extremely harsh broadcast model that relies only on carrier sensing. The model consists of an anonymous broadcast network in which nodes have no knowledge about the topology of the network or even an upper bound on its size. Furthermore, it is assumed that an adversary chooses at which time slot each node wakes up. At each time slot a node can either beep, that is, emit a signal, or be silent. At a particular time slot, beeping nodes receive no feedback, while silent nodes can only differentiate between none of its neighbors beeping, or at least one of its neighbors beeping. We start by proving a lower bound that shows that in this model, it is not possible to locally converge to an MIS in sub-polynomial time. We then study four different relaxations of the model which allow us to circumvent the lower bound and find an MIS in polylogarithmic time. First, we show that if a polynomial upper bound on the network size is known, it is possi...
Maximal Hypersurfaces in Spacetimes with Translational Symmetry
Bulawa, Andrew
2016-01-01
We consider four-dimensional vacuum spacetimes which admit a free isometric spacelike R-action. Taking a quotient with respect to the R-action produces a three-dimensional quotient spacetime. We establish several results regarding maximal hypersurfaces (spacelike hypersurfaces of zero mean curvature) in quotient spacetimes. First, we show that complete noncompact maximal hypersurfaces must either be flat cylinders S^1 x R or conformal to the Euclidean plane. Second, we establish a positive mass theorem for certain maximal hypersurfaces. Finally, while it is meaningful to use a bounded lapse when adopting the maximal hypersurface gauge condition in the four-dimensional (asymptotically flat) setting, it is shown here that nontrivial quotient spacetimes admit the maximal hypersurface gauge only with an unbounded lapse.
Maximally incompatible quantum observables
Heinosaari, Teiko, E-mail: teiko.heinosaari@utu.fi [Turku Centre for Quantum Physics, Department of Physics and Astronomy, University of Turku, FI-20014 Turku (Finland); Schultz, Jussi, E-mail: jussi.schultz@gmail.com [Dipartimento di Matematica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano (Italy); Toigo, Alessandro, E-mail: alessandro.toigo@polimi.it [Dipartimento di Matematica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano (Italy); Istituto Nazionale di Fisica Nucleare, Sezione di Milano, Via Celoria 16, I-20133 Milano (Italy); Ziman, Mario, E-mail: ziman@savba.sk [RCQI, Institute of Physics, Slovak Academy of Sciences, Dúbravská cesta 9, 84511 Bratislava (Slovakia); Faculty of Informatics, Masaryk University, Botanická 68a, 60200 Brno (Czech Republic)
2014-05-01
The existence of maximally incompatible quantum observables in the sense of a minimal joint measurability region is investigated. Employing the universal quantum cloning device it is argued that only infinite dimensional quantum systems can accommodate maximal incompatibility. It is then shown that two of the most common pairs of complementary observables (position and momentum; number and phase) are maximally incompatible.
Cycle-maximal triangle-free graphs
Durocher, Stephane; Gunderson, David S.; Li, Pak Ching;
2015-01-01
Abstract We conjecture that the balanced complete bipartite graph K ⌊ n / 2 ⌋ , ⌈ n / 2 ⌉ contains more cycles than any other n -vertex triangle-free graph, and we make some progress toward proving this. We give equivalent conditions for cycle-maximal triangle-free graphs; show bounds...
Francisco de Assis Corrêa
2009-06-01
Full Text Available O Problema Probabilístico de Localização-Alocação de Máxima Cobertura (PPLAMC consiste em localizar facilidades, maximizando a população atendida e fornecendo um bom nível de serviço para toda a população, ou seja, deve-se garantir que um usuário, ao chegar a um centro, não espere mais que um tempo máximo permitido ou não encontre uma fila de atendimento com um número de usuário maior que um valor máximo. Estes dois parâmetros dependem da taxa de chegada dos usuários e do atendimento, ambos probabilísticos. Devido às dificuldades intrínsecas do problema, neste artigo são discutidos limitantes lagrangeanos para o PPLAMC obtidos com a relaxação lagrangeana com clusters (LagClus. Na sua proposição inicial, a LagClus utilizou um grafo de conflitos, porém neste artigo esta relaxação foi aplicada em um grafo especial denominado grafo de cobertura.The Probabilistic Maximal Covering Location-Allocation Problem (PMCLAP aims to locate facilities maximizing the number of people served and providing a good level of service. This means that customers would not have to wait longer than the wait time established or to wait in long lines. These parameters are influenced by the number of the requests for service and service time, both probabilistic. The PMCLAP is NP-Complete and in this paper we study bounds with a Lagrangean Relaxation with Clusters (LagClus. Instead of using a conflict graph to represent a problem, in this paper another strategy for the use of LagClus using a special graph called covering graph is proposed. This approach provides interesting bounds.
Parker, Andrew M.; Wandi Bruine de Bruin; Baruch Fischhoff
2007-01-01
Our previous research suggests that people reporting a stronger desire to maximize obtain worse life outcomes (Bruine de Bruin et al., 2007). Here, we examine whether this finding may be explained by the decision-making styles of self-reported maximizers. Expanding on Schwartz et al. (2002), we find that self-reported maximizers are more likely to show problematic decision-making styles, as evidenced by self-reports of less behavioral coping, greater dependence on others when making decisions...
Ming Yi WANG; Guo ZHAO
2005-01-01
A right R-module E over a ring R is said to be maximally injective in case for any maximal right ideal m of R, every R-homomorphism f : m → E can be extended to an R-homomorphism f' : R → E. In this paper, we first construct an example to show that maximal injectivity is a proper generalization of injectivity. Then we prove that any right R-module over a left perfect ring R is maximally injective if and only if it is injective. We also give a partial affirmative answer to Faith's conjecture by further investigating the property of maximally injective rings. Finally, we get an approximation to Faith's conjecture, which asserts that every injective right R-module over any left perfect right self-injective ring R is the injective hull of a projective submodule.
Andrew M. Parker
2007-12-01
Full Text Available Our previous research suggests that people reporting a stronger desire to maximize obtain worse life outcomes (Bruine de Bruin et al., 2007. Here, we examine whether this finding may be explained by the decision-making styles of self-reported maximizers. Expanding on Schwartz et al. (2002, we find that self-reported maximizers are more likely to show problematic decision-making styles, as evidenced by self-reports of less behavioral coping, greater dependence on others when making decisions, more avoidance of decision making, and greater tendency to experience regret. Contrary to predictions, self-reported maximizers were more likely to report spontaneous decision making. However, the relationship between self-reported maximizing and worse life outcomes is largely unaffected by controls for measures of other decision-making styles, decision-making competence, and demographic variables.
Brüstle, Thomas; Pérotin, Matthieu
2012-01-01
Maximal green sequences are particular sequences of quiver mutations which were introduced by Keller in the context of quantum dilogarithm identities and independently by Cecotti-Cordova-Vafa in the context of supersymmetric gauge theory. Our aim is to initiate a systematic study of these sequences from a combinatorial point of view. Interpreting maximal green sequences as paths in various natural posets arising in representation theory, we prove the finiteness of the number of maximal green sequences for cluster finite quivers, affine quivers and acyclic quivers with at most three vertices. We also give results concerning the possible numbers and lengths of these maximal green sequences. Finally we describe an algorithm for computing maximal green sequences for arbitrary valued quivers which we used to obtain numerous explicit examples that we present.
Positive Root Bounds and Root Separation Bounds
Herman, Aaron Paul
In this thesis, we study two classes of bounds on the roots of a polynomial (or polynomial system). A positive root bound of a polynomial is an upper bound on the largest positive root. A root separation bound of a polynomial is a lower bound on the distance between the roots. Both classes of bounds are fundamental tools in computer algebra and computational real algebraic geometry, with numerous applications. In the first part of the thesis, we study the quality of positive root bounds. Higher quality means that the relative over-estimation (the ratio of the bound and the largest positive root) is smaller. We find that all known positive root bounds can be arbitrarily bad. We then show that a particular positive root bound is tight for certain important classes of polynomials. In the remainder of the thesis, we turn to root separation bounds. We observe that known root separation bounds are usually very pessimistic. To our surprise, we also find that known root separation bounds are not compatible with the geometry of the roots (unlike positive root bounds). This motivates us to derive new root separation bounds. In the second part of this thesis, we derive a new root separation for univariate polynomials by transforming a known bound into a new improved bound. In the third part of this thesis, we use a similar strategy to derive a new improved root separation bound for polynomial systems.
Utility maximization under solvency constraints and unhedgeable risks
T. Kleinow; A. Pelsser
2008-01-01
We consider the utility maximization problem for an investor who faces a solvency or risk constraint in addition to a budget constraint. The investor wishes to maximize her expected utility from terminal wealth subject to a bound on her expected solvency at maturity. We measure solvency using a solv
On a discrete version of Tanaka's theorem for maximal functions
Bober, Jonathan; Hughes, Kevin; Pierce, Lillian B
2010-01-01
In this paper we prove a discrete version of Tanaka's Theorem \\cite{Ta} for the Hardy-Littlewood maximal operator in dimension $n=1$, both in the non-centered and centered cases. For the discrete non-centered maximal operator $\\wM $ we prove that, given a function $f: \\Z \\to \\R$ of bounded variation,
Predicting the accuracy of ligand overlay methods with Random Forest models.
Nandigam, Ravi K; Evans, David A; Erickson, Jon A; Kim, Sangtae; Sutherland, Jeffrey J
2008-12-01
The accuracy of binding mode prediction using standard molecular overlay methods (ROCS, FlexS, Phase, and FieldCompare) is studied. Previous work has shown that simple decision tree modeling can be used to improve accuracy by selection of the best overlay template. This concept is extended to the use of Random Forest (RF) modeling for template and algorithm selection. An extensive data set of 815 ligand-bound X-ray structures representing 5 gene families was used for generating ca. 70,000 overlays using four programs. RF models, trained using standard measures of ligand and protein similarity and Lipinski-related descriptors, are used for automatically selecting the reference ligand and overlay method maximizing the probability of reproducing the overlay deduced from X-ray structures (i.e., using rmsd overlay accuracy, and their use in template and method selection produces correct overlays in 57% of cases for 349 overlay ligands not used for training RF models. The inclusion in the models of protein sequence similarity enables the use of templates bound to related protein structures, yielding useful results even for proteins having no available X-ray structures.
Ballester Pla, Coralio
2012-03-01
Full Text Available The observation of the actual behavior by economic decision makers in the lab and in the field justifies that bounded rationality has been a generally accepted assumption in many socio-economic models. The goal of this paper is to illustrate the difficulties involved in providing a correct definition of what a rational (or irrational agent is. In this paper we describe two frameworks that employ different approaches for analyzing bounded rationality. The first is a spatial segregation set-up that encompasses two optimization methodologies: backward induction and forward induction. The main result is that, even under the same state of knowledge, rational and non-rational agents may match their actions. The second framework elaborates on the relationship between irrationality and informational restrictions. We use the beauty contest (Nagel, 1995 as a device to explain this relationship.
La observación del comportamiento de los agentes económicos tanto en el laboratorio como en la vida real justifica que la racionalidad acotada sea un supuesto aceptado en numerosos modelos socio-económicos. El objetivo de este artículo es ilustrar las dificultades que conlleva una correcta definición de qué es un agente racional (irracional. En este artículo se describen dos marcos que emplean diferentes metodologías para analizar la racionalidad acotada. El primero es un modelo de segregación espacial donde se contrastan dos metodologías de optimización: inducción hacia atrás y hacia adelante. El resultado principal es que, incluso con el mismo nivel de conocimiento, tanto agentes racionales como irracionales podrían coincidir en sus acciones. El segundo marco trabaja sobre la relación entre irracionalidad y restricción de información. Se utiliza el juego llamado “beauty contest” (Nagel 1995 como mecanismo para explicar dicha relación.
Cycle-maximal triangle-free graphs
Durocher, Stephane; Gunderson, David S.; Li, Pak Ching
2015-01-01
Abstract We conjecture that the balanced complete bipartite graph K ⌊ n / 2 ⌋ , ⌈ n / 2 ⌉ contains more cycles than any other n -vertex triangle-free graph, and we make some progress toward proving this. We give equivalent conditions for cycle-maximal triangle-free graphs; show bounds...... on the numbers of cycles in graphs depending on numbers of vertices and edges, girth, and homomorphisms to small fixed graphs; and use the bounds to show that among regular graphs, the conjecture holds. We also consider graphs that are close to being regular, with the minimum and maximum degrees differing...
Upper bounds on the solution of coupled algebraic riccati equation
Czornik Adam
2001-01-01
Full Text Available Upper bounds for eigenvalues of a solution to continuous time coupled algebraic Riccati equation (CCARE and discrete time coupled algebraic Riccati equation (DCARE are developed as special cases of bounds for the unified coupled algebraic Riccati equation (UCARE. They include bounds of the maximal eigenvalues, the sums of the eigenvalues and the trace.
Ligand placement based on prior structures: the guided ligand-replacement method
Klei, Herbert E. [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Bristol-Myers Squibb, Princeton, NJ 08543-4000 (United States); Moriarty, Nigel W., E-mail: nwmoriarty@lbl.gov; Echols, Nathaniel [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Terwilliger, Thomas C. [Los Alamos National Laboratory, Los Alamos, NM 87545-0001 (United States); Baldwin, Eric T. [Bristol-Myers Squibb, Princeton, NJ 08543-4000 (United States); Natural Discovery LLC, Princeton, NJ 08542-0096 (United States); Pokross, Matt; Posy, Shana [Bristol-Myers Squibb, Princeton, NJ 08543-4000 (United States); Adams, Paul D. [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); University of California at Berkeley, Berkeley, CA 94720-1762 (United States)
2014-01-01
A new module, Guided Ligand Replacement (GLR), has been developed in Phenix to increase the ease and success rate of ligand placement when prior protein-ligand complexes are available. The process of iterative structure-based drug design involves the X-ray crystal structure determination of upwards of 100 ligands with the same general scaffold (i.e. chemotype) complexed with very similar, if not identical, protein targets. In conjunction with insights from computational models and assays, this collection of crystal structures is analyzed to improve potency, to achieve better selectivity and to reduce liabilities such as absorption, distribution, metabolism, excretion and toxicology. Current methods for modeling ligands into electron-density maps typically do not utilize information on how similar ligands bound in related structures. Even if the electron density is of sufficient quality and resolution to allow de novo placement, the process can take considerable time as the size, complexity and torsional degrees of freedom of the ligands increase. A new module, Guided Ligand Replacement (GLR), was developed in Phenix to increase the ease and success rate of ligand placement when prior protein–ligand complexes are available. At the heart of GLR is an algorithm based on graph theory that associates atoms in the target ligand with analogous atoms in the reference ligand. Based on this correspondence, a set of coordinates is generated for the target ligand. GLR is especially useful in two situations: (i) modeling a series of large, flexible, complicated or macrocyclic ligands in successive structures and (ii) modeling ligands as part of a refinement pipeline that can automatically select a reference structure. Even in those cases for which no reference structure is available, if there are multiple copies of the bound ligand per asymmetric unit GLR offers an efficient way to complete the model after the first ligand has been placed. In all of these applications, GLR
Ligand-modified metal clusters for gas separation and purification
Okrut, Alexander; Ouyang, Xiaoying; Runnebaum, Ron; Gates, Bruce C.; Katz, Alexander
2017-02-21
Provided is an organic ligand-bound metal surface that selects one gaseous species over another. The species can be closely sized molecular species having less than 1 Angstrom difference in kinetic diameter. In one embodiment, the species comprise carbon monoxide and ethylene. Such organic ligand-bound metal surfaces can be successfully used in gas phase separations or purifications, sensing, and in catalysis.
Rudiger Bubner
1998-12-01
Full Text Available Even though the maxims' theory is not at thecenter of Kant's ethics, it is the unavoidable basis of the categoric imperative's formulation. Kant leanson the transmitted representations of modem moral theory. During the last decades, the notion of maxims has deserved more attention, due to the philosophy of language's debates on rules, and due to action theory's interest in this notion. I here by brietly expound my views in these discussions.
On the reflection of magnon bound states
MacKay, Niall
2010-01-01
We investigate the reflection of two-particle bound states of a free open string in the light-cone AdS_5 x S^5 string sigma model, for large angular momentum J=J_56 and ending on a D7 brane which wraps the entire AdS_5 and a maximal S^3 of S^5. We use the superspace formalism to analyse fundamental and two-particle bound states in the cases of supersymmetry-preserving and broken-supersymmetry boundaries. We find the boundary S-matrices corresponding to bound states both in the bulk and on the boundary.
Andersen, Klaus Ejner
1985-01-01
Guinea pig maximization tests (GPMT) with chlorocresol were performed to ascertain whether the sensitization rate was affected by minor changes in the Freund's complete adjuvant (FCA) emulsion used. Three types of emulsion were evaluated: the oil phase was mixed with propylene glycol, saline with...... to the saline/oil emulsion. Placing of the challenge patches affected the response, as simultaneous chlorocresol challenge on the flank located 2 cm closer to the abdomen than the usual challenge site gave decreased reactions....
Zak, Michail
2008-01-01
A report discusses an algorithm for a new kind of dynamics based on a quantum- classical hybrid-quantum-inspired maximizer. The model is represented by a modified Madelung equation in which the quantum potential is replaced by different, specially chosen 'computational' potential. As a result, the dynamics attains both quantum and classical properties: it preserves superposition and entanglement of random solutions, while allowing one to measure its state variables, using classical methods. Such optimal combination of characteristics is a perfect match for quantum-inspired computing. As an application, an algorithm for global maximum of an arbitrary integrable function is proposed. The idea of the proposed algorithm is very simple: based upon the Quantum-inspired Maximizer (QIM), introduce a positive function to be maximized as the probability density to which the solution is attracted. Then the larger value of this function will have the higher probability to appear. Special attention is paid to simulation of integer programming and NP-complete problems. It is demonstrated that the problem of global maximum of an integrable function can be found in polynomial time by using the proposed quantum- classical hybrid. The result is extended to a constrained maximum with applications to integer programming and TSP (Traveling Salesman Problem).
Bounds on localisable information via semidefinite programming
Synak, B; Horodecki, M; Synak, Barbara; Horodecki, Karol; Horodecki, Michal
2004-01-01
We investigate so-called localisable information of bipartite states and a parallel notion of information deficit. Localisable information is defined as the amount of information that can be concentrated by means of classical communication and local operations where only maximally mixed states can be added for free. The information deficit is defined as difference between total information contents of the state and localisable information. We consider a larger class of operations: the so called PPT operations, which in addition preserve maximally mixed state (PPT-PMM operations). We formulate the related optimization problem as sedmidefnite program with suitable constraints. We then provide bound for fidelity of transition of a given state into product pure state on Hilbert space of dimension d. This allows to obtain general upper bound for localisable information (and also for information deficit). We calculated the bounds exactly for Werner states and isotropic states in any dimension. Surprisingly it turns...
Social group utility maximization
Gong, Xiaowen; Yang, Lei; Zhang, Junshan
2014-01-01
This SpringerBrief explains how to leverage mobile users' social relationships to improve the interactions of mobile devices in mobile networks. It develops a social group utility maximization (SGUM) framework that captures diverse social ties of mobile users and diverse physical coupling of mobile devices. Key topics include random access control, power control, spectrum access, and location privacy.This brief also investigates SGUM-based power control game and random access control game, for which it establishes the socially-aware Nash equilibrium (SNE). It then examines the critical SGUM-b
Brandes, U; Gaertler, M; Goerke, R; Hoefer, M; Nikoloski, Z; Wagner, D
2006-01-01
Several algorithms have been proposed to compute partitions of networks into communities that score high on a graph clustering index called modularity. While publications on these algorithms typically contain experimental evaluations to emphasize the plausibility of results, none of these algorithms has been shown to actually compute optimal partitions. We here settle the unknown complexity status of modularity maximization by showing that the corresponding decision version is NP-complete in the strong sense. As a consequence, any efficient, i.e. polynomial-time, algorithm is only heuristic and yields suboptimal partitions on many instances.
Measurable Maximal Energy and Minimal Time Interval
Dahab, Eiman Abou El
2014-01-01
The possibility of finding the measurable maximal energy and the minimal time interval is discussed in different quantum aspects. It is found that the linear generalized uncertainty principle (GUP) approach gives a non-physical result. Based on large scale Schwarzshild solution, the quadratic GUP approach is utilized. The calculations are performed at the shortest distance, at which the general relativity is assumed to be a good approximation for the quantum gravity and at larger distances, as well. It is found that both maximal energy and minimal time have the order of the Planck time. Then, the uncertainties in both quantities are accordingly bounded. Some physical insights are addressed. Also, the implications on the physics of early Universe and on quantized mass are outlined. The results are related to the existence of finite cosmological constant and minimum mass (mass quanta).
SnapShot: GPCR-Ligand Interactions.
Ghosh, Eshan; Nidhi, Kumari; Shukla, Arun K
2014-12-18
G-protein-coupled receptors enable cells to recognize numerous external stimuli and to transmit corresponding signals across the plasma membrane to trigger appropriate cellular responses. Crystal structures of a number of these receptors have now been determined in inactive and active conformations bound to chemically and functionally distinct ligands. These crystal structures illustrate overall receptor organization and atomic details of ligand-receptor interactions. Copyright © 2014 Elsevier Inc. All rights reserved.
Greedy Maximal Scheduling in Wireless Networks
Li, Qiao
2010-01-01
In this paper we consider greedy scheduling algorithms in wireless networks, i.e., the schedules are computed by adding links greedily based on some priority vector. Two special cases are considered: 1) Longest Queue First (LQF) scheduling, where the priorities are computed using queue lengths, and 2) Static Priority (SP) scheduling, where the priorities are pre-assigned. We first propose a closed-form lower bound stability region for LQF scheduling, and discuss the tightness result in some scenarios. We then propose an lower bound stability region for SP scheduling with multiple priority vectors, as well as a heuristic priority assignment algorithm, which is related to the well-known Expectation-Maximization (EM) algorithm. The performance gain of the proposed heuristic algorithm is finally confirmed by simulations.
Maximizing without difficulty: A modified maximizing scale and its correlates
Linda Lai
2010-01-01
This article presents several studies that replicate and extend previous research on maximizing. A modified scale for measuring individual maximizing tendency is introduced. The scale has adequate psychometric properties and reflects maximizers' aspirations for high standards and their preference for extensive alternative search, but not the decision difficulty aspect included in several previous studies. Based on this scale, maximizing is positively correlated with optimism, need for cogniti...
Challenging the Lieb-Oxford Bound in a systematic way
Seidl, Michael
2015-01-01
The Lieb-Oxford bound, a nontrivial inequality for the indirect part of the many-body Coulomb repulsion in an electronic system, plays an important role in the construction of approximate exchange-correlation energy functionals in density functional theory. Writing the original Lieb-Oxford bound as the supremum of another density functional $\\Lambda[\\rho]$, we challenge the bound systematically by investigating the functional gradient $\\delta\\Lambda[\\rho]/\\delta\\rho({\\bf r})$. We prove that a maximizing density for the bound does not exist (as it would violate $N$-representability), but the use of the gradient allows us to find $N$-representable densities that maximally challenge the bound for a given number of electrons. With our construction we are able to improve the bound for $N=2$ electrons that was originally found by Lieb and Oxford.
HEMI: Hyperedge Majority Influence Maximization
Gangal, Varun; Narayanam, Ramasuri
2016-01-01
In this work, we consider the problem of influence maximization on a hypergraph. We first extend the Independent Cascade (IC) model to hypergraphs, and prove that the traditional influence maximization problem remains submodular. We then present a variant of the influence maximization problem (HEMI) where one seeks to maximize the number of hyperedges, a majority of whose nodes are influenced. We prove that HEMI is non-submodular under the diffusion model proposed.
Andersen, Klaus Ejner
1985-01-01
Guinea pig maximization tests (GPMT) with chlorocresol were performed to ascertain whether the sensitization rate was affected by minor changes in the Freund's complete adjuvant (FCA) emulsion used. Three types of emulsion were evaluated: the oil phase was mixed with propylene glycol, saline...... with 30% (v/v) ethanol or saline, respectively. Relative viscosity was used as one measure of physical properties of the emulsion. Higher degrees of sensitization (but not rates) were obtained at the 48 h challenge reading with the oil/propylene glycol and oil/saline + ethanol emulsions compared...... to the saline/oil emulsion. Placing of the challenge patches affected the response, as simultaneous chlorocresol challenge on the flank located 2 cm closer to the abdomen than the usual challenge site gave decreased reactions....
Viscosity bound versus the universal relaxation bound
Hod, Shahar
2017-10-01
For gauge theories with an Einstein gravity dual, the AdS/CFT correspondence predicts a universal value for the ratio of the shear viscosity to the entropy density, η / s = 1 / 4 π. The holographic calculations have motivated the formulation of the celebrated KSS conjecture, according to which all fluids conform to the lower bound η / s ≥ 1 / 4 π. The bound on η / s may be regarded as a lower bound on the relaxation properties of perturbed fluids and it has been the focus of much recent attention. In particular, it was argued that for a class of field theories with Gauss-Bonnet gravity dual, the shear viscosity to entropy density ratio, η / s, could violate the conjectured KSS bound. In the present paper we argue that the proposed violations of the KSS bound are strongly constrained by Bekenstein's generalized second law (GSL) of thermodynamics. In particular, it is shown that physical consistency of the Gauss-Bonnet theory with the GSL requires its coupling constant to be bounded by λGB ≲ 0 . 063. We further argue that the genuine physical bound on the relaxation properties of physically consistent fluids is ℑω(k > 2 πT) > πT, where ω and k are respectively the proper frequency and the wavenumber of a perturbation mode in the fluid.
Entangled states close to the maximally mixed state
Hildebrand, Roland
2009-01-01
We give improved upper bounds on the radius of the largest ball of separable states of an m-qubit system around the maximally mixed state. The ratio between the upper bound and the best known lower bound (Hildebrand, quant.ph/0601201) thus shrinks to a constant c = \\sqrt{34/27} ~ 1.122, as opposed to a term of order \\sqrt{m\\log m} for the best upper bound known previously (Aubrun and Szarek, quant.ph/0503221). We give concrete examples of separable states on the boundary to entanglement which realize these upper bounds. As a by-product, we compute the radii of the largest balls that fit into the projective tensor product of four unit balls in R^3 and in the projective tensor product of an arbitrary number of unit balls in R^n for n = 2,4,8.
Functions of bounded variation
Lind, Martin
2006-01-01
The paper begins with a short survey of monotone functions. The functions of bounded variation are introduced and some basic properties of these functions are given. Finally the jump function of a function of bounded variation is defined.
Felker, Susan B.
2005-01-01
Robert Cobb Jr., of Greensboro, N.C., a 1986-89 participant in the Virginia Tech Upward Bound program, was recently named Virginia's TRIO Achiever for 2004. Federal TRIO programs include Upward Bound and Educational Talent Search.
MAXIMS VIOLATIONS IN LITERARY WORK
Widya Hanum Sari Pertiwi
2015-12-01
Full Text Available This study was qualitative research action that focuses to find out the flouting of Gricean maxims and the functions of the flouting in the tales which are included in collection of children literature entitled My Giant Treasury of Stories and Rhymes. The objective of the study is generally to identify the violation of maxims of quantity, quality, relevance, and manner in the data sources and also to analyze the use of the flouting in the tales which are included in the book. Qualitative design using categorizing strategies, specifically coding strategy, was applied. Thus, the researcher as the instrument in this investigation was selecting the tales, reading them, and gathering every item which reflects the violation of Gricean maxims based on some conditions of flouting maxims. On the basis of the data analysis, it was found that the some utterances in the tales, both narration and conversation, flouting the four maxims of conversation, namely maxim of quality, maxim of quantity, maxim of relevance, and maxim of manner. The researcher has also found that the flouting of maxims has one basic function that is to encourage the readers’ imagination toward the tales. This one basic function is developed by six others functions: (1 generating specific situation, (2 developing the plot, (3 enlivening the characters’ utterance, (4 implicating message, (5 indirectly characterizing characters, and (6 creating ambiguous setting. Keywords: children literature, tales, flouting maxims
Ligand binding mechanics of maltose binding protein.
Bertz, Morten; Rief, Matthias
2009-11-13
In the past decade, single-molecule force spectroscopy has provided new insights into the key interactions stabilizing folded proteins. A few recent studies probing the effects of ligand binding on mechanical protein stability have come to quite different conclusions. While some proteins seem to be stabilized considerably by a bound ligand, others appear to be unaffected. Since force acts as a vector in space, it is conceivable that mechanical stabilization by ligand binding is dependent on the direction of force application. In this study, we vary the direction of the force to investigate the effect of ligand binding on the stability of maltose binding protein (MBP). MBP consists of two lobes connected by a hinge region that move from an open to a closed conformation when the ligand maltose binds. Previous mechanical experiments, where load was applied to the N and C termini, have demonstrated that MBP is built up of four building blocks (unfoldons) that sequentially detach from the folded structure. In this study, we design the pulling direction so that force application moves the two MBP lobes apart along the hinge axis. Mechanical unfolding in this geometry proceeds via an intermediate state whose boundaries coincide with previously reported MBP unfoldons. We find that in contrast to N-C-terminal pulling experiments, the mechanical stability of MBP is increased by ligand binding when load is applied to the two lobes and force breaks the protein-ligand interactions directly. Contour length measurements indicate that MBP is forced into an open conformation before unfolding even if ligand is bound. Using mutagenesis experiments, we demonstrate that the mechanical stabilization effect is due to only a few key interactions of the protein with its ligand. This work illustrates how varying the direction of the applied force allows revealing important details about the ligand binding mechanics of a large protein.
The Automorphism Groups of a Family of Maximal Curves
Guralnick, Robert; Pries, Rachel
2011-01-01
The Hasse Weil bound restricts the number of points of a curve which are defined over a finite field; if the number of points meets this bound, the curve is called maximal. Giulietti and Korchmaros introduced a curve C_3 which is maximal over F_{q^6} and determined its automorphism group. Garcia, Guneri, and Stichtenoth generalized this construction to a family of curves C_n, indexed by an odd integer n greater than or equal to 3, such that C_n is maximal over F_{q^{2n}}. In this paper, we determine the automorphism group Aut(C_n) when n > 3; in contrast with the case n=3, it fixes the point at infinity on C_n. The proof requires a new structural result about automorphism groups of curves in characteristic p such that each Sylow p-subgroup has exactly one fixed point. MSC:11G20, 14H37.
Unified Maximally Natural Supersymmetry
Huang, Junwu
2016-01-01
Maximally Natural Supersymmetry, an unusual weak-scale supersymmetric extension of the Standard Model based upon the inherently higher-dimensional mechanism of Scherk-Schwarz supersymmetry breaking (SSSB), possesses remarkably good fine tuning given present LHC limits. Here we construct a version with precision $SU(2)_{\\rm L} \\times U(1)_{\\rm Y} $ unification: $\\sin^2 \\theta_W(M_Z) \\simeq 0.231$ is predicted to $\\pm 2\\%$ by unifying $SU(2)_{\\rm L} \\times U(1)_{\\rm Y} $ into a 5D $SU(3)_{\\rm EW}$ theory at a Kaluza-Klein scale of $1/R_5 \\sim 4.4\\,{\\rm TeV}$, where SSSB is simultaneously realised. Full unification with $SU(3)_{\\rm C}$ is accommodated by extending the 5D theory to a $N=4$ supersymmetric $SU(6)$ gauge theory on a 6D rectangular orbifold at $1/R_6 \\sim 40 \\,{\\rm TeV}$. TeV-scale states beyond the SM include exotic charged fermions implied by $SU(3)_{\\rm EW}$ with masses lighter than $\\sim 1.2\\,{\\rm TeV}$, and squarks in the mass range $1.4\\,{\\rm TeV} - 2.3\\,{\\rm TeV}$, providing distinct signature...
Maximal subgroups of finite groups
S. Srinivasan
1990-01-01
Full Text Available In finite groups maximal subgroups play a very important role. Results in the literature show that if the maximal subgroup has a very small index in the whole group then it influences the structure of the group itself. In this paper we study the case when the index of the maximal subgroups of the groups have a special type of relation with the Fitting subgroup of the group.
Finding Maximal Quasiperiodicities in Strings
Brodal, Gerth Stølting; Pedersen, Christian N. S.
2000-01-01
of length n in time O(n log n) and space O(n). Our algorithm uses the suffix tree as the fundamental data structure combined with efficient methods for merging and performing multiple searches in search trees. Besides finding all maximal quasiperiodic substrings, our algorithm also marks the nodes......Apostolico and Ehrenfeucht defined the notion of a maximal quasiperiodic substring and gave an algorithm that finds all maximal quasiperiodic substrings in a string of length n in time O(n log2 n). In this paper we give an algorithm that finds all maximal quasiperiodic substrings in a string...
Maximizing Entropy over Markov Processes
Biondi, Fabrizio; Legay, Axel; Nielsen, Bo Friis
2013-01-01
computation reduces to finding a model of a specification with highest entropy. Entropy maximization for probabilistic process specifications has not been studied before, even though it is well known in Bayesian inference for discrete distributions. We give a characterization of global entropy of a process...... as a reward function, a polynomial algorithm to verify the existence of an system maximizing entropy among those respecting a specification, a procedure for the maximization of reward functions over Interval Markov Chains and its application to synthesize an implementation maximizing entropy. We show how...
Maximizing entropy over Markov processes
Biondi, Fabrizio; Legay, Axel; Nielsen, Bo Friis
2014-01-01
computation reduces to finding a model of a specification with highest entropy. Entropy maximization for probabilistic process specifications has not been studied before, even though it is well known in Bayesian inference for discrete distributions. We give a characterization of global entropy of a process...... as a reward function, a polynomial algorithm to verify the existence of a system maximizing entropy among those respecting a specification, a procedure for the maximization of reward functions over Interval Markov Chains and its application to synthesize an implementation maximizing entropy. We show how...
Shedding of cell membrane-bound proteoglycans.
Nam, Eon Jeong; Park, Pyong Woo
2012-01-01
Membrane-bound proteoglycans function primarily as coreceptors for many glycosaminoglycan (GAG)-binding ligands at the cell surface. The majority of membrane-bound proteoglycans can also function as soluble autocrine or paracrine effectors as their extracellular domains, replete with all GAG chains, are enzymatically cleaved and released from the cell surface by ectodomain shedding. In particular, the ectodomain shedding of syndecans, a major family of cell surface heparan sulfate proteoglycans, is an important posttranslational mechanism that modulates diverse pathophysiological processes. Syndecan shedding is a tightly controlled process that regulates the onset, progression, and resolution of various infectious and noninfectious inflammatory diseases. This review describes methods to induce and measure the shedding of cell membrane-bound proteoglycans, focusing on syndecan shedding as a prototypic example.
Physical Uncertainty Bounds (PUB)
Vaughan, Diane Elizabeth [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Preston, Dean L. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
2015-03-19
This paper introduces and motivates the need for a new methodology for determining upper bounds on the uncertainties in simulations of engineered systems due to limited fidelity in the composite continuum-level physics models needed to simulate the systems. We show that traditional uncertainty quantification methods provide, at best, a lower bound on this uncertainty. We propose to obtain bounds on the simulation uncertainties by first determining bounds on the physical quantities or processes relevant to system performance. By bounding these physics processes, as opposed to carrying out statistical analyses of the parameter sets of specific physics models or simply switching out the available physics models, one can obtain upper bounds on the uncertainties in simulated quantities of interest.
Riding the Wave of Monodentate Ligand Revival: From the A/B Concept to Noncovalent Interactions.
Pignataro, Luca; Gennari, Cesare
2016-12-01
The rediscovery of chiral monodentate ligands made in the period 1999-2003 had important consequences in enantioselective transition-metal catalysis, such as the introduction of the A/B concept (i.e., use of monodentate ligand mixtures) and, later, a renewed interest in supramolecular ligands capable of ligand-ligand and ligand-substrate interactions. This Personal Account summarizes the contributions made by our research group in this area in the period 2004-2015, which reflect the abovementioned developments. Within this area, we introduced some original concepts, such as 1) the use of chiral tropos ligand mixtures; 2) the development of new strategies to maximize heterocomplex formation from combinations of simple monodentate ligands; 3) the investigation of new ligand-ligand interactions to achieve selective heterocomplex formation; and 4) the development of highly efficient and synthetically accessible supramolecular ligands. © 2016 The Chemical Society of Japan & Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
Gonzalez-Sanchez, Jon
2010-01-01
Let $w = w(x_1,..., x_n)$ be a word, i.e. an element of the free group $F =$ on $n$ generators $x_1,..., x_n$. The verbal subgroup $w(G)$ of a group $G$ is the subgroup generated by the set $\\{w (g_1,...,g_n)^{\\pm 1} | g_i \\in G, 1\\leq i\\leq n \\}$ of all $w$-values in $G$. We say that a (finite) group $G$ is $w$-maximal if $|G:w(G)|> |H:w(H)|$ for all proper subgroups $H$ of $G$ and that $G$ is hereditarily $w$-maximal if every subgroup of $G$ is $w$-maximal. In this text we study $w$-maximal and hereditarily $w$-maximal (finite) groups.
Endurance bounds of aerial systems
Harrington, Aaron M.; Kroninger, Christopher M.
2014-06-01
Within the past few years micro aerial vehicles (MAVs) have received much more attention and are starting to proliferate into military as well as civilian roles. However, one of the major drawbacks for this technology currently, has been their poor endurance, usually below 10 minutes. This is a direct result of the inefficiencies inherent in their design. Often times, designers do not consider the various components in the vehicle design and match their performance to the desired mission for the vehicle. These vehicles lack a prescribed set of design guidelines or empirically derived design equations which often limits their design to selection of commercial off-the-shelf components without proper consideration of their affect on vehicle performance. In the current study, the design space for different vehicle configurations has been examined including insect flapping, avian flapping, rotary wing, and fixed wing, and their performance bounds are established. The propulsion system typical of a rotary wing vehicle is analyzed to establish current baselines for efficiency of vehicles at this scale. The power draw from communications is analyzed to determine its impact on vehicle performance. Finally, a representative fixed wing MAV is examined and the effects of adaptive structures as a means for increasing vehicle endurance and range are examined. This paper seeks to establish the performance bounds for micro air vehicles and establish a path forward for future designs so that efficiency may be maximized.
de Rham, Claudia; Tolley, Andrew J; Zhou, Shuang-Yong
2016-01-01
Recently, aLIGO has announced the first direct detections of gravitational waves, a direct manifestation of the propagating degrees of freedom of gravity. The detected signals GW150914 and GW151226 have been used to examine the basic properties of these gravitational degrees of freedom, particularly setting an upper bound on their mass. It is timely to review what the mass of these gravitational degrees of freedom means from the theoretical point of view, particularly taking into account the recent developments in constructing consistent massive gravity theories. Apart from the GW150914 mass bound, a few other observational bounds have been established from the effects of the Yukawa potential, modified dispersion relation and fifth force that are all induced when the fundamental gravitational degrees of freedom are massive. We review these different mass bounds and examine how they stand in the wake of recent theoretical developments and how they compare to the bound from GW150914.
Bounding species distribution models
Thomas J. STOHLGREN, Catherine S. JARNEVICH, Wayne E. ESAIAS,Jeffrey T. MORISETTE
2011-10-01
Full Text Available Species distribution models are increasing in popularity for mapping suitable habitat for species of management concern. Many investigators now recognize that extrapolations of these models with geographic information systems (GIS might be sensitive to the environmental bounds of the data used in their development, yet there is no recommended best practice for “clamping” model extrapolations. We relied on two commonly used modeling approaches: classification and regression tree (CART and maximum entropy (Maxent models, and we tested a simple alteration of the model extrapolations, bounding extrapolations to the maximum and minimum values of primary environmental predictors, to provide a more realistic map of suitable habitat of hybridized Africanized honey bees in the southwestern United States. Findings suggest that multiple models of bounding, and the most conservative bounding of species distribution models, like those presented here, should probably replace the unbounded or loosely bounded techniques currently used [Current Zoology 57 (5: 642–647, 2011].
Bounding Species Distribution Models
Stohlgren, Thomas J.; Jarnevich, Cahterine S.; Morisette, Jeffrey T.; Esaias, Wayne E.
2011-01-01
Species distribution models are increasing in popularity for mapping suitable habitat for species of management concern. Many investigators now recognize that extrapolations of these models with geographic information systems (GIS) might be sensitive to the environmental bounds of the data used in their development, yet there is no recommended best practice for "clamping" model extrapolations. We relied on two commonly used modeling approaches: classification and regression tree (CART) and maximum entropy (Maxent) models, and we tested a simple alteration of the model extrapolations, bounding extrapolations to the maximum and minimum values of primary environmental predictors, to provide a more realistic map of suitable habitat of hybridized Africanized honey bees in the southwestern United States. Findings suggest that multiple models of bounding, and the most conservative bounding of species distribution models, like those presented here, should probably replace the unbounded or loosely bounded techniques currently used [Current Zoology 57 (5): 642-647, 2011].
Maximal energy extraction under discrete diffusive exchange
Hay, M. J., E-mail: hay@princeton.edu [Department of Astrophysical Sciences, Princeton University, Princeton, New Jersey 08544 (United States); Schiff, J. [Department of Mathematics, Bar-Ilan University, Ramat Gan 52900 (Israel); Fisch, N. J. [Department of Astrophysical Sciences, Princeton University, Princeton, New Jersey 08544 (United States); Princeton Plasma Physics Laboratory, Princeton, New Jersey 08543 (United States)
2015-10-15
Waves propagating through a bounded plasma can rearrange the densities of states in the six-dimensional velocity-configuration phase space. Depending on the rearrangement, the wave energy can either increase or decrease, with the difference taken up by the total plasma energy. In the case where the rearrangement is diffusive, only certain plasma states can be reached. It turns out that the set of reachable states through such diffusive rearrangements has been described in very different contexts. Building upon those descriptions, and making use of the fact that the plasma energy is a linear functional of the state densities, the maximal extractable energy under diffusive rearrangement can then be addressed through linear programming.
Maximal energy extraction under discrete diffusive exchange
Hay, Michael J; Fisch, Nathaniel J
2015-01-01
Waves propagating through a bounded plasma can rearrange the densities of states in the six-dimensional velocity-configuration phase space. Depending on the rearrangement, the wave energy can either increase or decrease, with the difference taken up by the total plasma energy. In the case where the rearrangement is diffusive, only certain plasma states can be reached. It turns out that the set of reachable states through such diffusive rearrangements has been described in very different contexts. Building upon those descriptions, and making use of the fact that the plasma energy is a linear functional of the state densities, the maximal extractable energy under diffusive rearrangement can then be addressed through linear programming.
Maximizing without difficulty: A modified maximizing scale and its correlates
Lai, Linda
2010-01-01
... included in several previous studies. Based on this scale, maximizing is positively correlated with optimism, need for cognition, desire for consistency, risk aversion, intrinsic motivation, self-efficacy and perceived workload, whereas...
Maximizing and customer loyalty: Are maximizers less loyal?
Linda Lai
2011-06-01
Full Text Available Despite their efforts to choose the best of all available solutions, maximizers seem to be more inclined than satisficers to regret their choices and to experience post-decisional dissonance. Maximizers may therefore be expected to change their decisions more frequently and hence exhibit lower customer loyalty to providers of products and services compared to satisficers. Findings from the study reported here (N = 1978 support this prediction. Maximizers reported significantly higher intentions to switch to another service provider (television provider than satisficers. Maximizers' intentions to switch appear to be intensified and mediated by higher proneness to regret, increased desire to discuss relevant choices with others, higher levels of perceived knowledge of alternatives, and higher ego involvement in the end product, compared to satisficers. Opportunities for future research are suggested.
Are maximizers really unhappy? The measurement of maximizing tendency,
Dalia L. Diab
2008-06-01
Full Text Available Recent research suggesting that people who maximize are less happy than those who satisfice has received considerable fanfare. The current study investigates whether this conclusion reflects the construct itself or rather how it is measured. We developed an alternative measure of maximizing tendency that is theory-based, has good psychometric properties, and predicts behavioral outcomes. In contrast to the existing maximization measure, our new measure did not correlate with life (dissatisfaction, nor with most maladaptive personality and decision-making traits. We conclude that the interpretation of maximizers as unhappy may be due to poor measurement of the construct. We present a more reliable and valid measure for future researchers to use.
Kakeya sets and directional maximal operators in the plane
Bateman, Michael
2009-01-01
We completely characterize the boundedness of planar directional maximal operators on $L^p$ . More precisely, if $\\Omega$ is a set of directions, we show that $M_{\\Omega}$ , the maximal operator associated to line segments in the directions $\\Omega$ , is unbounded on $L^p$ for all $p \\lt \\infty$ precisely when $\\Omega$ admits Kakeya-type sets. In fact, we show that if $\\Omega$ does not admit Kakeya sets, then $\\Omega$ is a generalized lacunary set, and hence, $M_{\\Omega}$ is bounded on $L^p$ ...
Weighted Inequalities for the Generalized Maximal Operator in Martingale Spaces
Wei CHEN; Peide LIU
2011-01-01
The generalized maximal operator M in martingale spaces is considered.For 1 ＜ p ≤ q ＜ ∞,the authors give a necessary and sufficient condition on the pair (（μ),v)for M to be a bounded operator from martingale space LP(v) into Lq(（μ）) or weak-Lq(（μ）),where （μ） is a measure on Ω× N and v a weight on Ω.Moreover,the similar inequalities for usual maximal operator are discussed.
Vukovic, Sinisa; Brennan, Paul E.; Huggins, David J.
2016-09-01
The interaction between any two biological molecules must compete with their interaction with water molecules. This makes water the most important molecule in medicine, as it controls the interactions of every therapeutic with its target. A small molecule binding to a protein is able to recognize a unique binding site on a protein by displacing bound water molecules from specific hydration sites. Quantifying the interactions of these water molecules allows us to estimate the potential of the protein to bind a small molecule. This is referred to as ligandability. In the study, we describe a method to predict ligandability by performing a search of all possible combinations of hydration sites on protein surfaces. We predict ligandability as the summed binding free energy for each of the constituent hydration sites, computed using inhomogeneous fluid solvation theory. We compared the predicted ligandability with the maximum observed binding affinity for 20 proteins in the human bromodomain family. Based on this comparison, it was determined that effective inhibitors have been developed for the majority of bromodomains, in the range from 10 to 100 nM. However, we predict that more potent inhibitors can be developed for the bromodomains BPTF and BRD7 with relative ease, but that further efforts to develop inhibitors for ATAD2 will be extremely challenging. We have also made predictions for the 14 bromodomains with no reported small molecule K d values by isothermal titration calorimetry. The calculations predict that PBRM1(1) will be a challenging target, while others such as TAF1L(2), PBRM1(4) and TAF1(2), should be highly ligandable. As an outcome of this work, we assembled a database of experimental maximal K d that can serve as a community resource assisting medicinal chemistry efforts focused on BRDs. Effective prediction of ligandability would be a very useful tool in the drug discovery process.
Amino Acids in Nine Ligand-Prefer Ramachandran Regions
Chen Cao
2015-01-01
Full Text Available Several secondary structures, such as π-helix and left-handed helix, have been frequently identified at protein ligand-binding sites. A secondary structure is considered to be constrained to a specific region of dihedral angles. However, a comprehensive analysis of the correlation between main chain dihedral angles and ligand-binding sites has not been performed. We undertook an extensive analysis of the relationship between dihedral angles in proteins and their distance to ligand-binding sites, frequency of occurrence, molecular potential energy, amino acid composition, van der Waals contacts, and hydrogen bonds with ligands. The results showed that the values of dihedral angles have a strong preference for ligand-binding sites at certain regions in the Ramachandran plot. We discovered that amino acids preceding the ligand-prefer ϕ/ψ box residues are exposed more to solvents, whereas amino acids following ligand-prefer ϕ/ψ box residues form more hydrogen bonds and van der Waals contacts with ligands. Our method exhibited a similar performance compared with the program Ligsite-csc for both ligand-bound structures and ligand-free structures when just one ligand-binding site was predicted. These results should be useful for the prediction of protein ligand-binding sites and for analysing the relationship between structure and function.
On entire f-maximal graphs in the Lorentzian product Gn ×R1
An, H. V. Q.; Cuong, D. V.; Duyen, N. T. M.; Hieu, D. T.; Nam, T. L.
2017-04-01
In the Lorentzian product Gn ×R1, we give a comparison theorem between the f-volume of an entire f-maximal graph and the f-volume of the hyperbolic Hr+ under the condition that the gradient of the function defining the graph is bounded away from 1. This condition comes from an example of non-planar entire f-maximal graph in Gn ×R1 and is equivalent to the hyperbolic angle function of the graph being bounded. As a consequence, we obtain a Calabi-Bernstein type theorem for f-maximal graphs in Gn ×R1.
Maximizing ROI with yield management
Neil Snyder
2001-01-01
.... the technology is based on the concept of yield management, which aims to sell the right product to the right customer at the right price and the right time therefore maximizing revenue, or yield...
Multicolor Bound Soliton Molecule
Luo, Rui; Lin, Qiang
2015-01-01
We show a new class of bound soliton molecule that exists in a parametrically driven nonlinear optical cavity with appropriate dispersion characteristics. The composed solitons exhibit distinctive colors but coincide in time and share a common phase, bound together via strong inter-soliton four-wave mixing and Cherenkov radiation. The multicolor bound soliton molecule shows intriguing spectral locking characteristics and remarkable capability of spectrum management to tailor soliton frequencies, which may open up a great avenue towards versatile generation and manipulation of multi-octave spanning phase-locked Kerr frequency combs, with great potential for applications in frequency metrology, optical frequency synthesis, and spectroscopy.
Are CEOs Expected Utility Maximizers?
John List; Charles Mason
2009-01-01
Are individuals expected utility maximizers? This question represents much more than academic curiosity. In a normative sense, at stake are the fundamental underpinnings of the bulk of the last half-century's models of choice under uncertainty. From a positive perspective, the ubiquitous use of benefit-cost analysis across government agencies renders the expected utility maximization paradigm literally the only game in town. In this study, we advance the literature by exploring CEO's preferen...
Gaussian maximally multipartite entangled states
Facchi, Paolo; Lupo, Cosmo; Mancini, Stefano; Pascazio, Saverio
2009-01-01
We introduce the notion of maximally multipartite entangled states (MMES) in the context of Gaussian continuous variable quantum systems. These are bosonic multipartite states that are maximally entangled over all possible bipartitions of the system. By considering multimode Gaussian states with constrained energy, we show that perfect MMESs, which exhibit the maximum amount of bipartite entanglement for all bipartitions, only exist for systems containing n=2 or 3 modes. We further numerically investigate the structure of MMESs and their frustration for n <= 7.
All maximally entangling unitary operators
Cohen, Scott M. [Department of Physics, Duquesne University, Pittsburgh, Pennsylvania 15282 (United States); Department of Physics, Carnegie-Mellon University, Pittsburgh, Pennsylvania 15213 (United States)
2011-11-15
We characterize all maximally entangling bipartite unitary operators, acting on systems A and B of arbitrary finite dimensions d{sub A}{<=}d{sub B}, when ancillary systems are available to both parties. Several useful and interesting consequences of this characterization are discussed, including an understanding of why the entangling and disentangling capacities of a given (maximally entangling) unitary can differ and a proof that these capacities must be equal when d{sub A}=d{sub B}.
On the maximal sum of exponents of runs in a string
Crochemore, Maxime; Radoszewski, Jakub; Rytter, Wojciech; Walen, Tomasz
2010-01-01
A run is an inclusion maximal occurrence in a string (as a subinterval) of a repetition $v$ with a period $p$ such that $2p \\le |v|$. The exponent of a run is defined as $|v|/p$ and is $\\ge 2$. We show new bounds on the maximal sum of exponents of runs in a string of length $n$. Our upper bound of $4.1n$ is better than the best previously known proven bound of $5.6n$ by Crochemore & Ilie (2008). The lower bound of $2.035n$, obtained using a family of binary words, contradicts the conjecture of Kolpakov & Kucherov (1999) that the maximal sum of exponents of runs in a string of length $n$ is smaller than $2n$
The Recognition of Identical Ligands by Unrelated Proteins.
Barelier, Sarah; Sterling, Teague; O'Meara, Matthew J; Shoichet, Brian K
2015-12-18
The binding of drugs and reagents to off-targets is well-known. Whereas many off-targets are related to the primary target by sequence and fold, many ligands bind to unrelated pairs of proteins, and these are harder to anticipate. If the binding site in the off-target can be related to that of the primary target, this challenge resolves into aligning the two pockets. However, other cases are possible: the ligand might interact with entirely different residues and environments in the off-target, or wholly different ligand atoms may be implicated in the two complexes. To investigate these scenarios at atomic resolution, the structures of 59 ligands in 116 complexes (62 pairs in total), where the protein pairs were unrelated by fold but bound an identical ligand, were examined. In almost half of the pairs, the ligand interacted with unrelated residues in the two proteins (29 pairs), and in 14 of the pairs wholly different ligand moieties were implicated in each complex. Even in those 19 pairs of complexes that presented similar environments to the ligand, ligand superposition rarely resulted in the overlap of related residues. There appears to be no single pattern-matching "code" for identifying binding sites in unrelated proteins that bind identical ligands, though modeling suggests that there might be a limited number of different patterns that suffice to recognize different ligand functional groups.
Shadle, S. E.
1994-08-01
Ligand K-edge X-ray absorption spectroscopy (XAS) has been developed as a technique for the investigation of ligand-metal bonding and has been applied to the study of electronic structure in organic model complexes and metalloprotein active sites. Ligand K-edge XAS has been measured at the chloride K-edge for a series of complexes containing chloride ligands bound to open shell d(sup 9) copper ions. The intensity of the pre-edge feature in these spectra reflects the covalency in the half-occupied d(sub x)2(sub -y)2-derived molecular orbital (HOMO) of the complex. The energy of the pre-edge feature is related to both the charge on the ligand and the HOMO energy. An analysis of the intensity and energy of the pre-edge feature as well as the energy of the rising edge absorption provides quantitative information about the covalency of the ligand-metal interaction, the charge donated by the chloride, and the energy of the copper d-manifold. The results demonstrate that ligand K-edge XAS features can be used to obtain quantitative information about ligand-metal bonding. The results also identify the chemical basis for trends in the XAS data for the complexes: D(sub 4h)CuCl4(sup 2-), D(sub 2d)CuCl4(sup 2-), planar, trans-CuCl2(pdmp)(sub 2) (pdmp=N-phenyl-3,5-dimethylpyrazole), square pyramidal CuCl5(sup 3-), the planar dimer KCuCl3, the distorted tetrahedral dimer (Ph4P)CuCl3, and two dimers with mixed ligation, one containing a bridging chloride, and the other, terminally bound chloride. A geometric distortion from square planar to distorted tetrahedral results in a decrease in the chloride-copper HOMO covalency but an increase in the total charge donation by the chlorides. Thus, while the geometry can maximize the overlap for a highly covalent HOMO, this does not necessarily reflect the overall charge donation. The Cl-Cu(II) bonding interactions are dependent on the nature of the other coordinating ligands.
A. Garmroodi Asil
2017-09-01
To further reduce the sulfur dioxide emission of the entire refining process, two scenarios of acid gas or air preheats are investigated when either of them is used simultaneously with the third enrichment scheme. The maximum overall sulfur recovery efficiency and highest combustion chamber temperature is slightly higher for acid gas preheats but air preheat is more favorable because it is more benign. To the best of our knowledge, optimization of the entire GTU + enrichment section and SRU processes has not been addressed previously.
Increased accuracy of ligand sensing by receptor internalization
Aquino, Gerardo
2010-01-01
Many types of cells can sense external ligand concentrations with cell-surface receptors at extremely high accuracy. Interestingly, ligand-bound receptors are often internalized, a process also known as receptor-mediated endocytosis. While internalization is involved in a vast number of important functions for the life of a cell, it was recently also suggested to increase the accuracy of sensing ligand as the overcounting of the same ligand molecules is reduced. Here we show, by extending simple ligand-receptor models to out-of-equilibrium thermodynamics, that internalization increases the accuracy with which cells can measure ligand concentrations in the external environment. Comparison with experimental rates of real receptors demonstrates that our model has indeed biological significance.
Algebraic curves of maximal cyclicity
Caubergh, Magdalena; Dumortier, Freddy
2006-01-01
The paper deals with analytic families of planar vector fields, studying methods to detect the cyclicity of a non-isolated closed orbit, i.e. the maximum number of limit cycles that can locally bifurcate from it. It is known that this multi-parameter problem can be reduced to a single-parameter one, in the sense that there exist analytic curves in parameter space along which the maximal cyclicity can be attained. In that case one speaks about a maximal cyclicity curve (mcc) in case only the number is considered and of a maximal multiplicity curve (mmc) in case the multiplicity is also taken into account. In view of obtaining efficient algorithms for detecting the cyclicity, we investigate whether such mcc or mmc can be algebraic or even linear depending on certain general properties of the families or of their associated Bautin ideal. In any case by well chosen examples we show that prudence is appropriate.
Maximal annuli with parallel planar boundaries in the 3-dimensional Lorentz-Minkowski space
Pyo, Juncheol
2009-01-01
We prove that maximal annuli in $\\mathbb{L}^{3}$ bounded by circles, straight lines or cone points in a pair of parallel spacelike planes are part of either a Lorentzian catenoid or a Lorentzian Riemann's example. We show that under the same boundary condition, the same conclusion holds even when the maximal annuli have a planar end. Moreover, we extend Shiffman's convexity result to maximal annuli but by using Perron's method we construct a maximal annulus with a planar end where Shiffman type result fails.
Hoyer, Paul
2016-01-01
Even a first approximation of bound states requires contributions of all powers in the coupling. This means that the concept of "lowest order bound state" needs to be defined. In these lectures I discuss the "Born" (no loop, lowest order in $\\hbar$) approximation. Born level states are bound by gauge fields which satisfy the classical field equations. As a check of the method, Positronium states of any momentum are determined as eigenstates of the QED Hamiltonian, quantized at equal time. Analogously, states bound by a strong external field $A^\\mu(\\xv)$ are found as eigenstates of the Dirac Hamiltonian. Their Fock states have dynamically created $e^+e^-$ pairs, whose distribution is determined by the Dirac wave function. The linear potential of $D=1+1$ dimensions confines electrons but repels positrons. As a result, the mass spectrum is continuous and the wave functions have features of both bound states and plane waves. The classical solutions of Gauss' law are explored for hadrons in QCD. A non-vanishing bo...
Bounding species distribution models
Thomas J. STOHLGREN; Catherine S. JARNEVICH; Wayne E. ESAIAS; Jeffrey T. MORISETTE
2011-01-01
Species distribution models are increasing in popularity for mapping suitable habitat for species of management concern.Many investigators now recognize that extrapolations of these models with geographic information systems (GIS) might be sensitive to the environmental bounds of the data used in their development,yet there is no recommended best practice for “clamping” model extrapolations.We relied on two commonly used modeling approaches:classification and regression tree (CART) and maximum entropy (Maxent) models,and we tested a simple alteration of the model extrapolations,bounding extrapolations to the maximum and minimum values of primary environmental predictors,to provide a more realistic map of suitable habitat of hybridized Africanized honey bees in the southwestern United States.Findings suggest that multiple models of bounding,and the most conservative bounding of species distribution models,like those presented here,should probably replace the unbounded or loosely bounded techniques currently used [Current Zoology 57 (5):642-647,2011].
ESTIMATING ERROR BOUNDS FOR TERNARY SUBDIVISION CURVES/SURFACES
Ghulam Mustafa; Jiansong Deng
2007-01-01
We estimate error bounds between ternary subdivision curves/surfaces and their control polygons after k-fold subdivision in terms of the maximal differences of the initial control point sequences and constants that depend on the subdivision mask. The bound is independent of the process of subdivision and can be evaluated without recursive subdivision.Our technique is independent of parametrization therefore it can be easily and efficiently implemented. This is useful and important for pre-computing the error bounds of subdivision curves/surfaces in advance in many engineering applications such as surface/surface intersection, mesh generation, NC machining, surface rendering and so on.
Bounded Computational Capacity Equilibrium
Hernandez, Penelope
2010-01-01
We study repeated games played by players with bounded computational power, where, in contrast to Abreu and Rubisntein (1988), the memory is costly. We prove a folk theorem: the limit set of equilibrium payoffs in mixed strategies, as the cost of memory goes to 0, includes the set of feasible and individually rational payoffs. This result stands in sharp contrast to Abreu and Rubisntein (1988), who proved that when memory is free, the set of equilibrium payoffs in repeated games played by players with bounded computational power is a strict subset of the set of feasible and individually rational payoffs. Our result emphasizes the role of memory cost and of mixing when players have bounded computational power.
Bachoc, Christine; Cohen, Gerard; Sole, Patrick; Tchamkerten, Aslan
2010-01-01
The maximum size of a binary code is studied as a function of its length N, minimum distance D, and minimum codeword weight W. This function B(N,D,W) is first characterized in terms of its exponential growth rate in the limit as N tends to infinity for fixed d=D/N and w=W/N. The exponential growth rate of B(N,D,W) is shown to be equal to the exponential growth rate of A(N,D) for w <= 1/2, and equal to the exponential growth rate of A(N,D,W) for 1/2< w <= 1. Second, analytic and numerical upper bounds on B(N,D,W) are derived using the semidefinite programming (SDP) method. These bounds yield a non-asymptotic improvement of the second Johnson bound and are tight for certain values of the parameters.
Carlson, C E; Lebed, R F; Carlson, Carl E.; Carone, Christopher D.; Lebed, Richard F.
2001-01-01
Jurco, Moller, Schraml, Schupp, and Wess have shown how to construct noncommutative SU(N) gauge theories from a consistency relation. Within this framework, we present the Feynman rules for noncommutative QCD and compute explicitly the most dangerous Lorentz-violating operator generated through radiative corrections. We find that interesting effects appear at the one-loop level, in contrast to conventional noncommutative U(N) gauge theories, leading to a stringent bound. Our results are consistent with others appearing recently in the literature that suggest collider limits are not competitive with low-energy tests of Lorentz violation for bounding the scale of spacetime noncommutativity.
Understanding maximal repetitions in strings
Crochemore, Maxime
2008-01-01
The cornerstone of any algorithm computing all repetitions in a string of length n in O(n) time is the fact that the number of runs (or maximal repetitions) is O(n). We give a simple proof of this result. As a consequence of our approach, the stronger result concerning the linearity of the sum of exponents of all runs follows easily.
Reinforcement Learning with Bounded Information Loss
Peters, Jan; Mülling, Katharina; Seldin, Yevgeny; Altun, Yasemin
2011-03-01
Policy search is a successful approach to reinforcement learning. However, policy improvements often result in the loss of information. Hence, it has been marred by premature convergence and implausible solutions. As first suggested in the context of covariant or natural policy gradients, many of these problems may be addressed by constraining the information loss. In this paper, we continue this path of reasoning and suggest two reinforcement learning methods, i.e., a model-based and a model free algorithm that bound the loss in relative entropy while maximizing their return. The resulting methods differ significantly from previous policy gradient approaches and yields an exact update step. It works well on typical reinforcement learning benchmark problems as well as novel evaluations in robotics. We also show a Bayesian bound motivation of this new approach [8].
Empirical processes with bounded \\psi_1 diameter
Mendelson, Shahar
2010-01-01
We study the empirical process indexed by F^2=\\{f^2 : f \\in F\\}, where F is a class of mean-zero functions on a probability space. We present a sharp bound on the supremum of that process which depends on the \\psi_1 diameter of the class F (rather than on the \\psi_2 one) and on the complexity parameter \\gamma_2(F,\\psi_2). In addition, we present optimal bounds on the random diameters \\sup_{f \\in F} \\max_{|I|=m} (\\sum_{i \\in I} f^2(X_i))^{1/2} using the same parameters. As applications, we extend several well known results in Asymptotic Geometric Analysis to any isotropic, log-concave ensemble on R^n.
High accuracy semidefinite programming bounds for kissing numbers
Mittelmann, H.D.; Vallentin, F.
2009-01-01
The kissing number in n-dimensional Euclidean space is the maximal number of non-overlapping unit spheres which simultaneously can touch a central unit sphere. Bachoc and Vallentin developed a method to find upper bounds for the kissing number based on semidefinite programming. This paper is a repor
High accuracy semidefinite programming bounds for kissing numbers
H.D. Mittelmann; F. Vallentin (Frank)
2010-01-01
htmlabstractThe kissing number in n-dimensional Euclidean space is the maximal number of non-overlapping unit spheres which simultaneously can touch a central unit sphere. Bachoc and Vallentin developed a method to find upper bounds for the kissing number based on semidefinite programming. This
High accuracy semidefinite programming bounds for kissing numbers
H.D. Mittelmann; F. Vallentin (Frank)
2009-01-01
htmlabstractThe kissing number in n-dimensional Euclidean space is the maximal number of non-overlapping unit spheres which simultaneously can touch a central unit sphere. Bachoc and Vallentin developed a method to find upper bounds for the kissing number based on semidefinite programming. This
Disney, Matthew D. (Inventor); Childs-Disney, Jessica L. (Inventor)
2017-01-01
Disclosed are methods for identifying a nucleic acid (e.g., RNA, DNA, etc.) motif which interacts with a ligand. The method includes providing a plurality of ligands immobilized on a support, wherein each particular ligand is immobilized at a discrete location on the support; contacting the plurality of immobilized ligands with a nucleic acid motif library under conditions effective for one or more members of the nucleic acid motif library to bind with the immobilized ligands; and identifying members of the nucleic acid motif library that are bound to a particular immobilized ligand. Also disclosed are methods for selecting, from a plurality of candidate ligands, one or more ligands that have increased likelihood of binding to a nucleic acid molecule comprising a particular nucleic acid motif, as well as methods for identifying a nucleic acid which interacts with a ligand.
Covariant Entropy Bound and Padmanabhan's Emergent Paradigm
Hadi, H; Darabi, F
2016-01-01
The covariant entropy conjecture is invariant under time reversal and consequently its origin must be statistical rather than thermodynamical. This may impose a fundamental constraint on the number of degrees of freedom in nature. Indeed, the covariant entropy bound imposes an upper entropy bound for any physical system. Considering a cosmological system, we show that Padmanabhan's emergent paradigm, which indicates that the emergence of cosmic space is due to the discrepancy between the surface and bulk degrees of freedom, leads to a lower entropy bound. The lower and upper entropy bounds may coincide on the apparent horizon for the radiation field and dark energy with the equations of state $\\omega=\\frac{1}{3}$ and $\\omega=-1$, respectively. Moreover, the maximal entropy inside the apparent horizon occurs when it is filled completely by the radiation field or dark energy. It turns out that for dark energy case (pure de Sitter space)\\ the holographic principle is satisfied in the sense that the number of deg...
Maximally reliable Markov chains under energy constraints.
Escola, Sean; Eisele, Michael; Miller, Kenneth; Paninski, Liam
2009-07-01
Signal-to-noise ratios in physical systems can be significantly degraded if the outputs of the systems are highly variable. Biological processes for which highly stereotyped signal generations are necessary features appear to have reduced their signal variabilities by employing multiple processing steps. To better understand why this multistep cascade structure might be desirable, we prove that the reliability of a signal generated by a multistate system with no memory (i.e., a Markov chain) is maximal if and only if the system topology is such that the process steps irreversibly through each state, with transition rates chosen such that an equal fraction of the total signal is generated in each state. Furthermore, our result indicates that by increasing the number of states, it is possible to arbitrarily increase the reliability of the system. In a physical system, however, an energy cost is associated with maintaining irreversible transitions, and this cost increases with the number of such transitions (i.e., the number of states). Thus, an infinite-length chain, which would be perfectly reliable, is infeasible. To model the effects of energy demands on the maximally reliable solution, we numerically optimize the topology under two distinct energy functions that penalize either irreversible transitions or incommunicability between states, respectively. In both cases, the solutions are essentially irreversible linear chains, but with upper bounds on the number of states set by the amount of available energy. We therefore conclude that a physical system for which signal reliability is important should employ a linear architecture, with the number of states (and thus the reliability) determined by the intrinsic energy constraints of the system.
Appell, Jürgen; Merentes Díaz, Nelson José
2013-01-01
This monographis a self-contained exposition of the definition and properties of functionsof bounded variation and their various generalizations; the analytical properties of nonlinear composition operators in spaces of such functions; applications to Fourier analysis, nonlinear integral equations, and boundary value problems. The book is written for non-specialists. Every chapter closes with a list of exercises and open problems.
Emiris, Ioannis Z.; Mourrain, Bernard; Tsigaridas, Elias
2010-01-01
of variables. One application is to the bitsize of the eigenvalues and eigenvectors of an integer matrix, which also yields a new proof that the problem is polynomial. We also compare against recent lower bounds on the absolute value of the root coordinates by Brownawell and Yap [5], obtained under...
Wirmer-Bartoschek, Julia; Bendel, Lars Erik; Jonker, Hendrik R A; Grün, J Tassilo; Papi, Francesco; Bazzicalupi, Carla; Messori, Luigi; Gratteri, Paola; Schwalbe, Harald
2017-06-12
Telomeric G-quadruplexes have recently emerged as drug targets in cancer research. Herein, we present the first NMR structure of a telomeric DNA G-quadruplex that adopts the biologically relevant hybrid-2 conformation in a ligand-bound state. We solved the complex with a metalorganic gold(III) ligand that stabilizes G-quadruplexes. Analysis of the free and bound structures reveals structural changes in the capping region of the G-quadruplex. The ligand is sandwiched between one terminal G-tetrad and a flanking nucleotide. This complex structure involves a major structural rearrangement compared to the free G-quadruplex structure as observed for other G-quadruplexes in different conformations, invalidating simple docking approaches to ligand-G-quadruplex structure determination. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
Tsujikawa, Hiroto; Sato, Kenta; Wei, Cao; Saad, Gul; Sumikoshi, Kazuya; Nakamura, Shugo; Terada, Tohru; Shimizu, Kentaro
2016-09-01
We present a new method for predicting protein-ligand-binding sites based on protein three-dimensional structure and amino acid conservation. This method involves calculation of the van der Waals interaction energy between a protein and many probes placed on the protein surface and subsequent clustering of the probes with low interaction energies to identify the most energetically favorable locus. In addition, it uses amino acid conservation among homologous proteins. Ligand-binding sites were predicted by combining the interaction energy and the amino acid conservation score. The performance of our prediction method was evaluated using a non-redundant dataset of 348 ligand-bound and ligand-unbound protein structure pairs, constructed by filtering entries in a ligand-binding site structure database, LigASite. Ligand-bound structure prediction (bound prediction) indicated that 74.0 % of predicted ligand-binding sites overlapped with real ligand-binding sites by over 25 % of their volume. Ligand-unbound structure prediction (unbound prediction) indicated that 73.9 % of predicted ligand-binding residues overlapped with real ligand-binding residues. The amino acid conservation score improved the average prediction accuracy by 17.0 and 17.6 points for the bound and unbound predictions, respectively. These results demonstrate the effectiveness of the combined use of the interaction energy and amino acid conservation in the ligand-binding site prediction.
Modeling RNA-ligand interactions: the Rev-binding element RNA-aminoglycoside complex.
Leclerc, F; Cedergren, R
1998-01-15
An approach to the modeling of ligand-RNA complexes has been developed by combining three-dimensional structure-activity relationship (3D-SAR) computations with a docking protocol. The ability of 3D-SAR to predict bound conformations of flexible ligands was first assessed by attempting to reconstruct the known, bound conformations of phenyloxazolines complexed with human rhinovirus 14 (HRV14) RNA. Subsequently, the same 3D-SAR analysis was applied to the identification of bound conformations of aminoglycosides which associate with the Rev-binding element (RBE) RNA. Bound conformations were identified by parsing ligand conformational data sets with pharmacophores determined by the 3D-SAR analysis. These "bioactive" structures were docked to the receptor RNA, and optimization of the complex was undertaken by extensive searching of ligand conformational space coupled with molecular dynamics computations. The similarity between the bound conformations of the ligand from the 3D-SAR analysis and those found in the docking protocol suggests that this methodology is valid for the prediction of bound ligand conformations and the modeling of the structure of the ligand-RNA complexes.
Bounds on quantum entanglement from Random Matrix Theory
Bandyopadhyay, J N; Bandyopadhyay, Jayendra N.; Lakshminarayan, Arul
2002-01-01
Recent results [A. Lakshminarayan, Phys. Rev. E, vol.64, Page no. 036207 (2001)] indicate that it is not easy to dynamically create maximally entangled states. Chaos can lead to substantial entropy production thereby maximizing dynamical entanglement, which still falls short of maximality. We show that this dynamical bound is universal and depends only on the dimensions of the Hilbert spaces involved. This entails pointing out the universal distribution of the eigenvalues of the reduced density matrices that one can expect from a Random Matrix Theory (RMT) modeling of composite quantum chaotic systems. This distribution provides a statistical upper bound for the entanglement of formation of arbitrary time evolving and stationary states. We substantiate these conclusions with the help of a quantized chaotic coupled kicked top model.
On Entropy Bounds and Holography
Halyo, Edi
2009-01-01
We show that the holographic entropy bound for gravitational systems and the Bekenstein entropy bound for nongravitational systems are holographically related. Using the AdS/CFT correspondence, we find that the Bekenstein bound on the boundary is obtained from the holographic bound in the bulk by minimizing the boundary energy with respect the AdS radius or the cosmological constant. This relation may also ameliorate some problems associated with the Bekenstein bound.
Zhang, Yixuan; Deng, Lu; Kitova, Elena N.; Klassen, John S.
2013-10-01
The results of collision-induced dissociation (CID) experiments performed on gaseous protonated and deprotonated ions of complexes of cholera toxin B subunit homopentamer (CTB5) with the pentasaccharide (β-D-Gal p-(1→3)-β-D-Gal pNAc-(1→4)[α-D-Neu5Ac-(2→3)]-β-D-Gal p-(1→4)-β-D-Glc p (GM1)) and corresponding glycosphingolipid (β-D-Gal p-(1→3)-β-D-Gal pNAc-(1→4)[α-D-Neu5Ac-(2→3)]-β-D-Gal p-(1→4)-β-D-Glc p-Cer (GM1-Cer)) ligands, and the homotetramer streptavidin (S4) with biotin (B) and 1,2-dipalmitoyl- sn-glycero-3-phosphoethanolamine-N-(biotinyl) (Btl), are reported. The protonated (CTB5 + 5GM1)n+ ions dissociated predominantly by the loss of a single subunit, with the concomitant migration of ligand to another subunit. The simultaneous loss of ligand and subunit was observed as a minor pathway. In contrast, the deprotonated (CTB5 + 5GM1)n- ions dissociated preferentially by the loss of deprotonated ligand; the loss of ligand-bound and ligand-free subunit were minor pathways. The presence of ceramide (Cer) promoted ligand migration and the loss of subunit. The main dissociation pathway for the protonated and deprotonated (S4 + 4B)n+/- ions, as well as for deprotonated (S4 + 4Btl)n- ions, was loss of the ligand. However, subunit loss from the (S4 + 4B)n+ ions was observed as a minor pathway. The (S4 + 4Btl)n+ ions dissociated predominantly by the loss of free and ligand-bound subunit. The charge state of the complex and the collision energy were found to have little effect on the relative contribution of the different dissociation channels. Thermally-driven ligand migration between subunits was captured in the results of molecular dynamics simulations performed on protonated (CTB5 + 5GM1)15+ ions (with a range of charge configurations) at 800 K. Notably, the migration pathway was found to be highly dependent on the charge configuration of the ion. The main conclusion of this study is that the dissociation pathways of multisubunit protein-ligand
Maximization, learning, and economic behavior.
Erev, Ido; Roth, Alvin E
2014-07-22
The rationality assumption that underlies mainstream economic theory has proved to be a useful approximation, despite the fact that systematic violations to its predictions can be found. That is, the assumption of rational behavior is useful in understanding the ways in which many successful economic institutions function, although it is also true that actual human behavior falls systematically short of perfect rationality. We consider a possible explanation of this apparent inconsistency, suggesting that mechanisms that rest on the rationality assumption are likely to be successful when they create an environment in which the behavior they try to facilitate leads to the best payoff for all agents on average, and most of the time. Review of basic learning research suggests that, under these conditions, people quickly learn to maximize expected return. This review also shows that there are many situations in which experience does not increase maximization. In many cases, experience leads people to underweight rare events. In addition, the current paper suggests that it is convenient to distinguish between two behavioral approaches to improve economic analyses. The first, and more conventional approach among behavioral economists and psychologists interested in judgment and decision making, highlights violations of the rational model and proposes descriptive models that capture these violations. The second approach studies human learning to clarify the conditions under which people quickly learn to maximize expected return. The current review highlights one set of conditions of this type and shows how the understanding of these conditions can facilitate market design.
Coarse-grained molecular dynamics simulations of protein-ligand binding.
Negami, Tatsuki; Shimizu, Kentaro; Terada, Tohru
2014-09-30
Coarse-grained molecular dynamics (CGMD) simulations with the MARTINI force field were performed to reproduce the protein-ligand binding processes. We chose two protein-ligand systems, the levansucrase-sugar (glucose or sucrose), and LinB-1,2-dichloroethane systems, as target systems that differ in terms of the size and shape of the ligand-binding pocket and the physicochemical properties of the pocket and the ligand. Spatial distributions of the Coarse-grained (CG) ligand molecules revealed potential ligand-binding sites on the protein surfaces other than the real ligand-binding sites. The ligands bound most strongly to the real ligand-binding sites. The binding and unbinding rate constants obtained from the CGMD simulation of the levansucrase-sucrose system were approximately 10 times greater than the experimental values; this is mainly due to faster diffusion of the CG ligand in the CG water model. We could obtain dissociation constants close to the experimental values for both systems. Analysis of the ligand fluxes demonstrated that the CG ligand molecules entered the ligand-binding pockets through specific pathways. The ligands tended to move through grooves on the protein surface. Thus, the CGMD simulations produced reasonable results for the two different systems overall and are useful for studying the protein-ligand binding processes.
Bounded Satisfiability for PCTL
Bertrand, Nathalie; Schewe, Sven
2012-01-01
While model checking PCTL for Markov chains is decidable in polynomial-time, the decidability of PCTL satisfiability, as well as its finite model property, are long standing open problems. While general satisfiability is an intriguing challenge from a purely theoretical point of view, we argue that general solutions would not be of interest to practitioners: such solutions could be too big to be implementable or even infinite. Inspired by bounded synthesis techniques, we turn to the more applied problem of seeking models of a bounded size: we restrict our search to implementable -- and therefore reasonably simple -- models. We propose a procedure to decide whether or not a given PCTL formula has an implementable model by reducing it to an SMT problem. We have implemented our techniques and found that they can be applied to the practical problem of sanity checking -- a procedure that allows a system designer to check whether their formula has an unexpectedly small model.
Reaching Fleming's dicrimination bound
Gruebl, Gebhard
2012-01-01
Any rule for identifying a quantum system's state within a set of two non-orthogonal pure states by a single measurement is flawed. It has a non-zero probability of either yielding the wrong result or leaving the query undecided. This also holds if the measurement of an observable $A$ is repeated on a finite sample of $n$ state copies. We formulate a state identification rule for such a sample. This rule's probability of giving the wrong result turns out to be bounded from above by $1/n\\delta_{A}^{2}$ with $\\delta_{A}=|_{1}-_{2}|/(\\Delta_{1}A+\\Delta_{2}A).$ A larger $\\delta_{A}$ results in a smaller upper bound. Yet, according to Fleming, $\\delta_{A}$ cannot exceed $\\tan\\theta$ with $\\theta\\in(0,\\pi/2) $ being the angle between the pure states under consideration. We demonstrate that there exist observables $A$ which reach the bound $\\tan\\theta$ and we determine all of them.
Avenant, Chanel; Ronacher, Katharina; Stubsrud, Elisabeth; Louw, Ann; Hapgood, Janet P
2010-10-07
A central question in glucocorticoid mechanism of action via the glucocorticoid receptor (GR) is what determines ligand-selective transcriptional responses. Using a panel of 12 GR ligands, we show that the extent of GR phosphorylation at S226 and S211, GR half-life and transcriptional response, occur in a ligand-selective manner. While GR phosphorylation at S226 was shown to inhibit maximal transcription efficacy, phosphorylation at S211 is required for maximal transactivation, but not for transrepression efficacy. Both ligand-selective GR phosphorylation and half-life correlated with efficacy for transactivation and transrepression. For both expressed and endogenous GR, in two different cell lines, agonists resulted in the greatest extent of phosphorylation and the greatest extent of GR downregulation, suggesting a link between these functions. However, using phosphorylation-deficient GR mutants we established that phosphorylation of the GR at S226 or S211 does not determine the rank order of ligand-selective GR transactivation. These results are consistent with a model whereby ligand-selective GR phosphorylation and half-life are a consequence of upstream events, such as ligand-specific GR conformations, which are maintained in the phosphorylation mutants.
Riboswitch Structure: an Internal Residue Mimicking the Purine Ligand
Delfosse, V.; Bouchard, P; Bonneau, E; Dagenais, P; Lemay, J; Lafontaine, D; Legault, P
2009-01-01
The adenine and guanine riboswitches regulate gene expression in response to their purine ligand. X-ray structures of the aptamer moiety of these riboswitches are characterized by a compact fold in which the ligand forms a Watson-Crick base pair with residue 65. Phylogenetic analyses revealed a strict restriction at position 39 of the aptamer that prevents the G39-C65 and A39-U65 combinations, and mutational studies indicate that aptamers with these sequence combinations are impaired for ligand binding. In order to investigate the rationale for sequence conservation at residue 39, structural characterization of the U65C mutant from Bacillus subtilis pbuE adenine riboswitch aptamer was undertaken. NMR spectroscopy and X-ray crystallography studies demonstrate that the U65C mutant adopts a compact ligand-free structure, in which G39 occupies the ligand-binding site of purine riboswitch aptamers. These studies present a remarkable example of a mutant RNA aptamer that adopts a native-like fold by means of ligand mimicking and explain why this mutant is impaired for ligand binding. Furthermore, this work provides a specific insight into how the natural sequence has evolved through selection of nucleotide identities that contribute to formation of the ligand-bound state, but ensures that the ligand-free state remains in an active conformation.
BOUNDING PYRAMIDS AND BOUNDING CONES FOR TRIANGULAR BEZIER SURFACES
Jian-song Deng; Fa-lai Chen; Li-li Wang
2000-01-01
This paper describes practical approaches on how to construct bounding pyramids and bounding cones for triangular Bézier surfaces. Examples are provided to illustrate the process of construction and comparison is made between various surface bounding volumes. Furthermore, as a starting point for the construction,we provide a way to compute hodographs of triangular Bézier surfaces and improve the algorithm for computing the bounding cone of a set of vectors.
Ligand-specific conformational changes in the alpha1 glycine receptor ligand-binding domain
Pless, Stephan Alexander; Lynch, Joseph W
2009-01-01
indicate that channel opening is accompanied by conformational rearrangements in both beta-sheets. In an attempt to resolve ligand-dependent movements in the ligand-binding domain, we employed voltage-clamp fluorometry on alpha1 glycine receptors to compare changes mediated by the agonist, glycine......, and by the antagonist, strychnine. Voltage-clamp fluorometry involves labeling introduced cysteines with environmentally sensitive fluorophores and inferring structural rearrangements from ligand-induced fluorescence changes. In the inner beta-sheet, we labeled residues in loop 2 and in binding domain loops D and E....... At each position, strychnine and glycine induced distinct maximal fluorescence responses. The pre-M1 domain responded similarly; at each of four labeled positions glycine produced a strong fluorescence signal, whereas strychnine did not. This suggests that glycine induces conformational changes...
Davidowski, Stephen K; Lisowski, Carmen E; Yarger, Jeffery L
2016-03-01
The ligand capping of phosphonic acid functionalized CdSe/ZnS core-shell quantum dots (QDs) was investigated with a combination of solution and solid-state (31) P nuclear magnetic resonance (NMR) spectroscopy. Two phosphonic acid ligands were used in the synthesis of the QDs, tetradecylphosphonic acid and ethylphosphonic acid. Both alkyl phosphonic acids showed broad liquid and solid-state (31) P NMR resonances for the bound ligands, indicative of heterogeneous binding to the QD surface. In order to quantify the two ligand populations on the surface, ligand exchange facilitated by phenylphosphonic acid resulted in the displacement of the ethylphosphonic acid and tetradecylphosphonic acid and allowed for quantification of the free ligands using (31) P liquid-state NMR. After washing away the free ligand, two broad resonances were observed in the liquids' (31) P NMR corresponding to the alkyl and aromatic phosphonic acids. The washed samples were analyzed via solid-state (31) P NMR, which confirmed the ligand populations on the surface following the ligand exchange process. Copyright © 2015 John Wiley & Sons, Ltd.
Asymptotics of robust utility maximization
Knispel, Thomas
2012-01-01
For a stochastic factor model we maximize the long-term growth rate of robust expected power utility with parameter $\\lambda\\in(0,1)$. Using duality methods the problem is reformulated as an infinite time horizon, risk-sensitive control problem. Our results characterize the optimal growth rate, an optimal long-term trading strategy and an asymptotic worst-case model in terms of an ergodic Bellman equation. With these results we propose a duality approach to a "robust large deviations" criterion for optimal long-term investment.
Multivariate residues and maximal unitarity
Søgaard, Mads; Zhang, Yang
2013-12-01
We extend the maximal unitarity method to amplitude contributions whose cuts define multidimensional algebraic varieties. The technique is valid to all orders and is explicitly demonstrated at three loops in gauge theories with any number of fermions and scalars in the adjoint representation. Deca-cuts realized by replacement of real slice integration contours by higher-dimensional tori encircling the global poles are used to factorize the planar triple box onto a product of trees. We apply computational algebraic geometry and multivariate complex analysis to derive unique projectors for all master integral coefficients and obtain compact analytic formulae in terms of tree-level data.
Maximal Congruences on Some Semigroups
Jintana Sanwong; R.P. Sullivan
2007-01-01
In 1976 Howie proved that a finite congruence-free semigroup is a simple group if it has at least three elements but no zero elementInfinite congruence-free semigroups are far more complicated to describe, but some have been constructed using semigroups of transformations (for example, by Howie in 1981 and by Marques in 1983)Here, forcertain semigroups S of numbers and of transformations, we determine all congruences p on S such that S/p is congruence-free, that is, we describe all maximal congruences on such semigroups S.
Notch Ligand Endocytosis Generates Mechanical Pulling Force Dependent on Dynamin, Epsins and Actin
Meloty-Kapella, Laurence; Shergill, Bhupinder; Kuon, Jane; Botvinick, Elliot; Weinmaster, Gerry
2012-01-01
SUMMARY Notch signaling induced by cell surface ligands is critical to development and maintenance of many eukaryotic organisms. Notch and its ligands are integral membrane proteins that facilitate direct cell-cell interactions to activate Notch proteolysis and release the intracellular domain that directs Notch-specific cellular responses. Genetic studies suggest Notch ligands require endocytosis, ubiquitylation and epsin endocytic adaptors to activate signaling, yet the exact role ligand endocytosis serves remains unresolved. Here we characterize a molecularly distinct mode of clathrin-mediated endocytosis requiring ligand ubiquitylation, epsins and actin for ligand cells to activate signaling in Notch cells. Using a cell-bead optical tweezers system, we obtained evidence for cell-mediated mechanical force dependent on this distinct mode of ligand endocytosis. We propose mechanical pulling force produced by endocytosis of Notch-bound ligand drives conformational changes in Notch that permit activating proteolysis. PMID:22658936
Maximal-acceleration phase space relativity from Clifford algebras
Castro, C
2002-01-01
We present a new physical model that links the maximum speed of light with the minimal Planck scale into a maximal-acceleration Relativity principle in the spacetime tangent bundle and in phase spaces (cotangent bundle). Crucial in order to establish this link is the use of Clifford algebras in phase spaces. The maximal proper-acceleration bound is a = c^2/ \\Lambda in full agreement with the old predictions of Caianiello, the Finslerian geometry point of view of Brandt and more recent results in the literature. We present the reasons why an Extended Scale Relativity based on Clifford spaces is physically more appealing than those based on kappa-deformed Poincare algebras and the inhomogeneous quantum groups operating in quantum Minkowski spacetimes. The main reason being that the Planck scale should not be taken as a deformation parameter to construct quantum algebras but should exist already as the minimum scale in Clifford spaces.
Critical SQG in bounded domains
Constantin, Peter; Ignatova, Mihaela
2016-01-01
We consider the critical dissipative SQG equation in bounded domains, with the square root of the Dirichlet Laplacian dissipation. We prove global a priori interior $C^{\\alpha}$ and Lipschitz bounds for large data.
Maldacena, Juan [School of Natural Sciences, Institute for Advanced Study,1 Einstein Drive, Princeton, NJ (United States); Shenker, Stephen H. [Stanford Institute for Theoretical Physics and Department of Physics, Stanford University,382 Via Pueblo Mall, Stanford, CA (United States); Stanford, Douglas [School of Natural Sciences, Institute for Advanced Study,1 Einstein Drive, Princeton, NJ (United States)
2016-08-17
We conjecture a sharp bound on the rate of growth of chaos in thermal quantum systems with a large number of degrees of freedom. Chaos can be diagnosed using an out-of-time-order correlation function closely related to the commutator of operators separated in time. We conjecture that the influence of chaos on this correlator can develop no faster than exponentially, with Lyapunov exponent λ{sub L}≤2πk{sub B}T/ℏ. We give a precise mathematical argument, based on plausible physical assumptions, establishing this conjecture.
Faupin, Jeremy; Møller, Jacob Schach; Skibsted, Erik
2011-01-01
We study regularity of bound states pertaining to embedded eigenvalues of a self-adjoint operator H, with respect to an auxiliary operator A that is conjugate to H in the sense of Mourre. We work within the framework of singular Mourre theory which enables us to deal with confined massless Pauli–......–Fierz models, our primary example, and many-body AC-Stark Hamiltonians. In the simpler context of regular Mourre theory, our results boil down to an improvement of results obtained recently in [8, 9]....
Maldacena, Juan; Stanford, Douglas
2015-01-01
We conjecture a sharp bound on the rate of growth of chaos in thermal quantum systems with a large number of degrees of freedom. Chaos can be diagnosed using an out-of-time-order correlation function closely related to the commutator of operators separated in time. We conjecture that the influence of chaos on this correlator can develop no faster than exponentially, with Lyapunov exponent $\\lambda_L \\le 2 \\pi k_B T/\\hbar$. We give a precise mathematical argument, based on plausible physical assumptions, establishing this conjecture.
Maximizing Information on the Environment by Dynamically Controlled Qubit Probes
Zwick, Analia; Álvarez, Gonzalo A.; Kurizki, Gershon
2016-01-01
We explore the ability of a qubit probe to characterize unknown parameters of its environment. By resorting to the quantum estimation theory, we analytically find the ultimate bound on the precision of estimating key parameters of a broad class of ubiquitous environmental noises ("baths") which the qubit may probe. These include the probe-bath coupling strength, the correlation time of generic types of bath spectra, and the power laws governing these spectra, as well as their dephasing times T2. Our central result is that by optimizing the dynamical control on the probe under realistic constraints one may attain the maximal accuracy bound on the estimation of these parameters by the least number of measurements possible. Applications of this protocol that combines dynamical control and estimation theory tools to quantum sensing are illustrated for a nitrogen-vacancy center in diamond used as a probe.
Maximizing information on the environment by dynamically controlled qubit probes
Zwick, Analia; Kurizki, Gershon
2015-01-01
We explore the ability of a qubit probe to characterize unknown parameters of its environment. By resorting to quantum estimation theory, we analytically find the ultimate bound on the precision of estimating key parameters of a broad class of ubiquitous environmental noises ("baths") which the qubit may probe. These include the probe-bath coupling strength, the correlation time of generic bath spectra, the power laws governing these spectra, as well as their dephasing times T2. Our central result is that by optimizing the dynamical control on the probe under realistic constraints one may attain the maximal accuracy bound on the estimation of these parameters by the least number of measurements possible. Applications of this protocol that combines dynamical control and estimation theory tools to quantum sensing are illustrated for a nitrogen-vacancy center in diamond used as a probe.
On the Exponential Probability Bounds for the Bernoulli Random Variables
Nikulin, Vladimir
2010-01-01
We consider upper exponential bounds for the probability of the event that an absolute deviation of sample mean from mathematical expectation p is bigger comparing with some ordered level epsilon. These bounds include 2 coefficients {alpha, beta}. In order to optimize the bound we are interested to minimize linear coefficient alpha and to maximize exponential coefficient beta. Generally, the value of linear coefficient alpha may not be smaller than one. The following 2 settings were proved: 1) {1, 2} in the case of classical discreet problem as it was formulated by Bernoulli in the 17th century, and 2) {1, 2/(1+epsilon^2)} in the general discreet case with arbitrary rational p and epsilon. The second setting represents a new structure of the exponential bound which may be extended to continuous case.
Knowledge discovery by accuracy maximization.
Cacciatore, Stefano; Luchinat, Claudio; Tenori, Leonardo
2014-04-01
Here we describe KODAMA (knowledge discovery by accuracy maximization), an unsupervised and semisupervised learning algorithm that performs feature extraction from noisy and high-dimensional data. Unlike other data mining methods, the peculiarity of KODAMA is that it is driven by an integrated procedure of cross-validation of the results. The discovery of a local manifold's topology is led by a classifier through a Monte Carlo procedure of maximization of cross-validated predictive accuracy. Briefly, our approach differs from previous methods in that it has an integrated procedure of validation of the results. In this way, the method ensures the highest robustness of the obtained solution. This robustness is demonstrated on experimental datasets of gene expression and metabolomics, where KODAMA compares favorably with other existing feature extraction methods. KODAMA is then applied to an astronomical dataset, revealing unexpected features. Interesting and not easily predictable features are also found in the analysis of the State of the Union speeches by American presidents: KODAMA reveals an abrupt linguistic transition sharply separating all post-Reagan from all pre-Reagan speeches. The transition occurs during Reagan's presidency and not from its beginning.
Inapproximability of maximal strip recovery
Jiang, Minghui
2009-01-01
In comparative genomic, the first step of sequence analysis is usually to decompose two or more genomes into syntenic blocks that are segments of homologous chromosomes. For the reliable recovery of syntenic blocks, noise and ambiguities in the genomic maps need to be removed first. Maximal Strip Recovery (MSR) is an optimization problem proposed by Zheng, Zhu, and Sankoff for reliably recovering syntenic blocks from genomic maps in the midst of noise and ambiguities. Given $d$ genomic maps as sequences of gene markers, the objective of \\msr{d} is to find $d$ subsequences, one subsequence of each genomic map, such that the total length of syntenic blocks in these subsequences is maximized. For any constant $d \\ge 2$, a polynomial-time 2d-approximation for \\msr{d} was previously known. In this paper, we show that for any $d \\ge 2$, \\msr{d} is APX-hard, even for the most basic version of the problem in which all gene markers are distinct and appear in positive orientation in each genomic map. Moreover, we provi...
Maximal right smooth extension chains
Huang, Yun Bao
2010-01-01
If $w=u\\alpha$ for $\\alpha\\in \\Sigma=\\{1,2\\}$ and $u\\in \\Sigma^*$, then $w$ is said to be a \\textit{simple right extension}of $u$ and denoted by $u\\prec w$. Let $k$ be a positive integer and $P^k(\\epsilon)$ denote the set of all $C^\\infty$-words of height $k$. Set $u_{1},\\,u_{2},..., u_{m}\\in P^{k}(\\epsilon)$, if $u_{1}\\prec u_{2}\\prec ...\\prec u_{m}$ and there is no element $v$ of $P^{k}(\\epsilon)$ such that $v\\prec u_{1}\\text{or} u_{m}\\prec v$, then $u_{1}\\prec u_{2}\\prec...\\prec u_{m}$ is said to be a \\textit{maximal right smooth extension (MRSE) chains}of height $k$. In this paper, we show that \\textit{MRSE} chains of height $k$ constitutes a partition of smooth words of height $k$ and give the formula of the number of \\textit{MRSE} chains of height $k$ for each positive integer $k$. Moreover, since there exist the minimal height $h_1$ and maximal height $h_2$ of smooth words of length $n$ for each positive integer $n$, we find that \\textit{MRSE} chains of heights $h_1-1$ and $h_2+1$ are good candidates t...
Delay Bounds for Multiclass FIFO
Jiang, Yuming; Misra, Vishal
2016-01-01
FIFO is perhaps the simplest scheduling discipline. For single-class FIFO, its delay guarantee performance has been extensively studied: The well-known results include a stochastic delay bound for $GI/GI/1$ by Kingman and a deterministic delay bound for $D/D/1$ by Cruz. However, for multiclass FIFO, few such results are available. To fill the gap, we prove delay bounds for multiclass FIFO in this work, considering both deterministic and stochastic cases. Specifically, delay bounds are present...
Sulfur ligand mediated electrochemistry of gold surfaces and nanoparticles: what, how, and why
Chi, Qijin; Ford, Michael J.; Halder, Arnab;
2017-01-01
Gold surfaces are widely used in electrochemistry whilst gold nanoparticles have very many uses, with both the surfaces and the particles often being protected by sulfur-bound organic ligands. The ligands not only provide chemical stability but also directly participate in many desired processes....
Nielson, Hanne Riis; Nielson, Flemming
1992-01-01
they obtain a quadratic bound. These bounds are shown to be tight. Specializing the case of strict and additive functions to functionals of a form that would correspond to iterative programs they show that a linear bound is tight. This is related to several analyses studied in the literature (including...
Error bounds for set inclusions
ZHENG; Xiyin(郑喜印)
2003-01-01
A variant of Robinson-Ursescu Theorem is given in normed spaces. Several error bound theorems for convex inclusions are proved and in particular a positive answer to Li and Singer's conjecture is given under weaker assumption than the assumption required in their conjecture. Perturbation error bounds are also studied. As applications, we study error bounds for convex inequality systems.
Outer measures and weak type estimates of Hardy-Littlewood maximal operators
Terasawa Yutaka
2006-01-01
Full Text Available We will introduce the times modified centered and uncentered Hardy-Littlewood maximal operators on nonhomogeneous spaces for . We will prove that the times modified centered Hardy-Littlewood maximal operator is weak type bounded with constant when if the Radon measure of the space has "continuity" in some sense. In the proof, we will use the outer measure associated with the Radon measure. We will also prove other results of Hardy-Littlewood maximal operators on homogeneous spaces and on the real line by using outer measures.
Solid-Phase Parallel Synthesis of Phosphite Ligands
Swennenhuis, Bert H.G.; Chen, Ruifang; Leeuwen, Piet W.N.M. van; Vries, Johannes G. de; Kamer, Paul C.J.
2008-01-01
Various routes for the synthesis of polymer-bound phosphites and phosphoramidites have been investigated. In the presence of a suitable activator the supported phosphoramidites react cleanly with alcohols to give the corresponding monodentate phosphite ligands in solution. We have applied this novel
Automated docking of flexible ligands: applications of AutoDock.
Goodsell, D S; Morris, G M; Olson, A J
1996-01-01
AutoDock is a suite of C programs used to predict the bound conformations of a small, flexible ligand to a macromolecular target of known structure. The technique combines simulated annealing for conformation searching with a rapid grid-based method of energy evaluation. This paper reviews recent applications of the technique and describes the enhancements included in the current release.
Multifunctions of bounded variation
Vinter, R. B.
2016-02-01
Consider control systems described by a differential equation with a control term or, more generally, by a differential inclusion with velocity set F (t , x). Certain properties of state trajectories can be derived when it is assumed that F (t , x) is merely measurable w.r.t. the time variable t. But sometimes a refined analysis requires the imposition of stronger hypotheses regarding the time dependence. Stronger forms of necessary conditions for minimizing state trajectories can be derived, for example, when F (t , x) is Lipschitz continuous w.r.t. time. It has recently become apparent that significant addition properties of state trajectories can still be derived, when the Lipschitz continuity hypothesis is replaced by the weaker requirement that F (t , x) has bounded variation w.r.t. time. This paper introduces a new concept of multifunctions F (t , x) that have bounded variation w.r.t. time near a given state trajectory, of special relevance to control. We provide an application to sensitivity analysis.
Hay, B.P. [Pacific Northwest National Lab., Richland, WA (United States)
1997-10-01
The purpose of this work is to develop and implement a molecular design basis for selecting organic ligands that would be used in the cost-effective removal of specific radionuclides from nuclear waste streams. Organic ligands with metal ion specificity are critical components in the development of solvent extraction and ion exchange processes that are highly selective for targeted radionuclides. The traditional approach to the development of such ligands involves lengthy programs of organic synthesis and testing, which in the absence of reliable methods for screening compounds before synthesis, results in wasted research effort. The author`s approach breaks down and simplifies this costly process with the aid of computer-based molecular modeling techniques. Commercial software for organic molecular modeling is being configured to examine the interactions between organic ligands and metal ions, yielding an inexpensive, commercially or readily available computational tool that can be used to predict the structures and energies of ligand-metal complexes. Users will be able to correlate the large body of existing experimental data on structure, solution binding affinity, and metal ion selectivity to develop structural design criteria. These criteria will provide a basis for selecting ligands that can be implemented in separations technologies through collaboration with other DOE national laboratories and private industry. The initial focus will be to select ether-based ligands that can be applied to the recovery and concentration of the alkali and alkaline earth metal ions including cesium, strontium, and radium.
The maximal D = 4 supergravities
Wit, Bernard de [Institute for Theoretical Physics and Spinoza Institute, Utrecht University, Postbus 80.195, NL-3508 TD Utrecht (Netherlands); Samtleben, Henning [Laboratoire de Physique, ENS Lyon, 46 allee d' Italie, F-69364 Lyon CEDEX 07 (France); Trigiante, Mario [Dept. of Physics, Politecnico di Torino, Corso Duca degli Abruzzi 24, I-10129 Turin (Italy)
2007-06-15
All maximal supergravities in four space-time dimensions are presented. The ungauged Lagrangians can be encoded in an E{sub 7(7)}-Sp(56; R)/GL(28) matrix associated with the freedom of performing electric/magnetic duality transformations. The gauging is defined in terms of an embedding tensor {theta} which encodes the subgroup of E{sub 7(7)} that is realized as a local invariance. This embedding tensor may imply the presence of magnetic charges which require corresponding dual gauge fields. The latter can be incorporated by using a recently proposed formulation that involves tensor gauge fields in the adjoint representation of E{sub 7(7)}. In this formulation the results take a universal form irrespective of the electric/magnetic duality basis. We present the general class of supersymmetric and gauge invariant Lagrangians and discuss a number of applications.
Maximizing profit using recommender systems
Das, Aparna; Ricketts, Daniel
2009-01-01
Traditional recommendation systems make recommendations based solely on the customer's past purchases, product ratings and demographic data without considering the profitability the items being recommended. In this work we study the question of how a vendor can directly incorporate the profitability of items into its recommender so as to maximize its expected profit while still providing accurate recommendations. Our approach uses the output of any traditional recommender system and adjust them according to item profitabilities. Our approach is parameterized so the vendor can control how much the recommendation incorporating profits can deviate from the traditional recommendation. We study our approach under two settings and show that it achieves approximately 22% more profit than traditional recommendations.
The maximal D=5 supergravities
de Wit, Bernard; Trigiante, M; Wit, Bernard de; Samtleben, Henning; Trigiante, Mario
2007-01-01
The general Lagrangian for maximal supergravity in five spacetime dimensions is presented with vector potentials in the \\bar{27} and tensor fields in the 27 representation of E_6. This novel tensor-vector system is subject to an intricate set of gauge transformations, describing 3(27-t) massless helicity degrees of freedom for the vector fields and 3t massive spin degrees of freedom for the tensor fields, where the (even) value of t depends on the gauging. The kinetic term of the tensor fields is accompanied by a unique Chern-Simons coupling which involves both vector and tensor fields. The Lagrangians are completely encoded in terms of the embedding tensor which defines the E_6 subgroup that is gauged by the vectors. The embedding tensor is subject to two constraints which ensure the consistency of the combined vector-tensor gauge transformations and the supersymmetry of the full Lagrangian. This new formulation encompasses all possible gaugings.
Constraint Propagation as Information Maximization
Abdallah, A Nait
2012-01-01
Dana Scott used the partial order among partial functions for his mathematical model of recursively defined functions. He interpreted the partial order as one of information content. In this paper we elaborate on Scott's suggestion of regarding computation as a process of information maximization by applying it to the solution of constraint satisfaction problems. Here the method of constraint propagation can be interpreted as decreasing uncertainty about the solution -- that is, as gain in information about the solution. As illustrative example we choose numerical constraint satisfaction problems to be solved by interval constraints. To facilitate this approach to constraint solving we formulate constraint satisfaction problems as formulas in predicate logic. This necessitates extending the usual semantics for predicate logic so that meaning is assigned not only to sentences but also to formulas with free variables.
Riboswitch structure in the ligand-free state.
Liberman, Joseph A; Wedekind, Joseph E
2012-01-01
Molecular investigations of riboswitches bound to small-molecule effectors have produced a wealth of information on how these molecules achieve high affinity and specificity for a target ligand. X-ray crystal structures have been determined for the ligand-free state for representatives of the preQ₁-I, S-adenosylmethionine I, lysine, and glycine aptamer classes. These structures in conjunction with complimentary techniques, such as in-line probing, NMR spectroscopy, Förster resonance energy transfer, small-angle scattering, and computational simulations, have demonstrated that riboswitches adopt multiple conformations in the absence of ligand. Despite a number of investigations that support ligand-dependent folding, mounting evidence suggests that free-state riboswitches interact with their effectors in the sub-populations of largely prefolded states as embodied by the principle of conformational selection, which has been documented extensively for protein-mediated ligand interactions. Fundamental riboswitch investigations of the bound and free states have advanced our understanding of RNA folding, ligand recognition, and how these factors culminate in communication between an aptamer and its expression platform. An understanding of these topics is essential to comprehend riboswitch gene regulation at the molecular level, which has already provided a basis to understand the mechanism of action of natural antimicrobials.
Hay, B. [Pacific Northwest Lab., Richland, WA (United States)
1996-10-01
The purpose of this work is to develop and implement a molecular design basis for selecting organic ligands that would be used tin applications for the cost-effective removal of specific radionuclides from nuclear waste streams.
Nowak, K.; Kästner, M.; Miltner, A.
2009-04-01
During degradation of organic pollutants in soil, metabolites, microbial biomass, CO2and "bound" residues ("non-extractable" residues in soil organic matter) are formed. Enhanced transformation of these contaminants into "bound" residues has been proposed as an alternative remediation method for polluted soils. However, this kind of residues may pose a potential risk for the environment due to their chemical structure and possible remobilization under different conditions. Therefore particular attention is given actually to "bound" residues. Part of these non-extractable residues may be "biogenic," because microorganisms use the carbon from the pollutant to form their biomass components (fatty acids, amino acids, amino sugars), which subsequently may be incorporated into soil organic matter. Furthermore, the CO2 originating from mineralization of xenobiotics, can be re-assimilated by microorganisms and also incorporated into "biogenic residue". The hazard posed by "bound" residues may be overestimated because they are "biogenic" (contain microbial fatty acids and amino acids). The knowledge about the pathways of "biogenic residue" formation is necessary for a proper assessment of the fate of tested pollutants and their turnover in the soil environment. Moreover, these data are needed to establish the realistic degradation rates of the contaminants in soil. The main objectives of this study are: to quantify the extent of "biogenic residue" (fatty acids, amino acids, amino sugars) formation during the degradation of a model pollutant (2,4-dichlorophenoxyacetic acid = 2,4-D) and during CO2 assimilation by microorganisms and to evaluate which components are mainly incorporated into "bound" residues. To investigate the extent of "biogenic residue" formation in soil during the degradation of 2,4-D, experiments with either 14C-U-ring and 13C6-2,4-D or carboxyl-14C 2,4-D were performed. The incubation experiments were performed according to OECD test guideline 307, in the
Maximized Gust Loads of a Closed-Loop, Nonlinear Aeroelastic System Using Nonlinear Systems Theory
Silva, Walter A.
1999-01-01
The problem of computing the maximized gust load for a nonlinear, closed-loop aeroelastic aircraft is discusses. The Volterra theory of nonlinear systems is applied in order to define a linearized system that provides a bounds on the response of the nonlinear system of interest. The method is applied to a simplified model of an Airbus A310.
Average H2 performance and maximal parameter pertubation radius for uncertain systems
Zhao, K.-Y.; Grimble, M.J.; Stoustrup, Jakob
1999-01-01
In this paper methods are prsented for calculating the maximal parameter pertubation bounds under H2 performance constraints for a family of uncertain systems and for calculating the average H2 performance under such parameter variations. The uncertain systems are described by state space models ...
Maximal Parameter Perturbation Radius for Linear Uncertain Systems under H^2 Norm Constraints
Stoustrup, Jakob; Zhao, K.-Y.; Grimble, M.J.
1996-01-01
In this paper methods for calculating the maximal parameter-perturbation bounds are presented, under QTR H^2 performanceconstraints, for a family of systems. These are described by state-spacemodels with nonlinearly dependent on real uncertain parameters. Thestability and performance robustness a...
On Maximal Surfaces in Certain Non-Flat 3-Dimensional Robertson-Walker Spacetimes
Romero, Alfonso, E-mail: aromero@ugr.es [Universidad de Granada, Departamento de Geometria y Topologia (Spain); Rubio, Rafael M., E-mail: rmrubio@uco.es [Universidad de Cordoba, Departamento de Matematicas, Campus de Rabanales (Spain)
2012-09-15
An upper bound for the integral, on a geodesic disc, of the squared length of the gradient of a distinguished function on any maximal surface in certain non-flat 3-dimensional Robertson-Walker spacetimes is obtained. As an application, a new proof of a known Calabi-Bernstein's theorem is given.
THE MAXIMAL OPERATOR ON Hp(T×T)
无
2000-01-01
The two-dimensional classical Hardy space H,(T ×T) on the bidisc are introduced, and it is shoum that the maximal operator of the (C,a,ββ) means of a divtribation is bounded from the space Hp(T×T) to Lp(T2)(1/(a+ 1), 1/(ββ+1)＜p≤∞), and is of weak type (H#1 (T×T) ,L1 (T2)), where the Hardy space H#1 (T×T) is defined by the hybrid maximal function. As a consequence we obtain that the ( C,a,β) means of a function f ∈ H#1 (T×T) LlogL(T2) convergs a.e. to the function in question. Moreover, we prove that the (C,a,β)means are uniformly bounded on the spaces Hp(T×T) whenver 1/(a+ 1),1/(β+ 1)＜p＜∞. Thus, in case f∈Hp(T×T), the (C,a,β) means convergs to f ia Hp(T×T) norm whenever (1/ (a+1) , 1/ (β+1)＜ p＜∞). The same results are proved for the conjugate (C,a,β) means, too.
Maximal switchability of centralized networks
Vakulenko, Sergei; Morozov, Ivan; Radulescu, Ovidiu
2016-08-01
We consider continuous time Hopfield-like recurrent networks as dynamical models for gene regulation and neural networks. We are interested in networks that contain n high-degree nodes preferably connected to a large number of N s weakly connected satellites, a property that we call n/N s -centrality. If the hub dynamics is slow, we obtain that the large time network dynamics is completely defined by the hub dynamics. Moreover, such networks are maximally flexible and switchable, in the sense that they can switch from a globally attractive rest state to any structurally stable dynamics when the response time of a special controller hub is changed. In particular, we show that a decrease of the controller hub response time can lead to a sharp variation in the network attractor structure: we can obtain a set of new local attractors, whose number can increase exponentially with N, the total number of nodes of the nework. These new attractors can be periodic or even chaotic. We provide an algorithm, which allows us to design networks with the desired switching properties, or to learn them from time series, by adjusting the interactions between hubs and satellites. Such switchable networks could be used as models for context dependent adaptation in functional genetics or as models for cognitive functions in neuroscience.
A Maximally Supersymmetric Kondo Model
Harrison, Sarah; Kachru, Shamit; Torroba, Gonzalo; /Stanford U., Phys. Dept. /SLAC
2012-02-17
We study the maximally supersymmetric Kondo model obtained by adding a fermionic impurity to N = 4 supersymmetric Yang-Mills theory. While the original Kondo problem describes a defect interacting with a free Fermi liquid of itinerant electrons, here the ambient theory is an interacting CFT, and this introduces qualitatively new features into the system. The model arises in string theory by considering the intersection of a stack of M D5-branes with a stack of N D3-branes, at a point in the D3 worldvolume. We analyze the theory holographically, and propose a dictionary between the Kondo problem and antisymmetric Wilson loops in N = 4 SYM. We perform an explicit calculation of the D5 fluctuations in the D3 geometry and determine the spectrum of defect operators. This establishes the stability of the Kondo fixed point together with its basic thermodynamic properties. Known supergravity solutions for Wilson loops allow us to go beyond the probe approximation: the D5s disappear and are replaced by three-form flux piercing a new topologically non-trivial S3 in the corrected geometry. This describes the Kondo model in terms of a geometric transition. A dual matrix model reflects the basic properties of the corrected gravity solution in its eigenvalue distribution.
Lower bounds for eigenvalues of the Dirac-Witten operator
无
2009-01-01
We get optimal lower bounds for the eigenvalues of the Dirac-Witten operator of compact(with or without boundary) spacelike hypersurfaces of Lorentian manifold satisfying certain conditions,just in terms of the mean curvature and the scalar curvature and the spinor energy-momentum tensor. In the limiting case,the spacelike hypersurface is either maximal and Einstein manifold with positive scalar curvature or Ricci-flat manifold with nonzero constant mean curvature.
Lower bounds for eigenvalues of the Dirac-Witten operator
CHEN YongFa
2009-01-01
We get optimal lower bounds for the eigenvalues of the Dirac-Witten operator of compact (with or without boundary) spacelike hypersuffaces of Lorentian manifold satisfying certain conditions, just in terms of the mean curvature and the scalar curvature and the spinor energy-momentum tensor. In the limiting case, the spacelike hypersurface is either maximal and Einstein manifold with positive scalar curvature or Ricci-flat manifold with nonzero constant mean curvature.
Bounding approaches to system identification
Norton, John; Piet-Lahanier, Hélène; Walter, Éric
1996-01-01
In response to the growing interest in bounding error approaches, the editors of this volume offer the first collection of papers to describe advances in techniques and applications of bounding of the parameters, or state variables, of uncertain dynamical systems. Contributors explore the application of the bounding approach as an alternative to the probabilistic analysis of such systems, relating its importance to robust control-system design.
On functions of bounded variation
Aistleitner, Christoph; Pausinger, Florian; Svane, Anne Marie; Tichy, Robert F.
2015-01-01
The recently introduced concept of $\\mathcal{D}$-variation unifies previous concepts of variation of multivariate functions. In this paper, we give an affirmative answer to the open question from Pausinger \\& Svane (J. Complexity, 2014) whether every function of bounded Hardy--Krause variation is Borel measurable and has bounded $\\mathcal{D}$-variation. Moreover, we show that the space of functions of bounded $\\mathcal{D}$-variation can be turned into a commutative Banach algebra.
Bukh, Boris
2011-01-01
In 2008, Bukh, Matousek, and Nivasch conjectured that for every n-point set S in R^d and every k, 0 <= k <= d-1, there exists a k-flat f in R^d (a "centerflat") that lies at "depth" (k+1) n / (k+d+1) - O(1) in S, in the sense that every halfspace that contains f contains at least that many points of S. This claim is true and tight for k=0 (this is Rado's centerpoint theorem), as well as for k = d-1 (trivial). Bukh et al. showed the existence of a (d-2)-flat at depth (d-1) n / (2d-1) - O(1) (the case k = d-2). In this paper we concentrate on the case k=1 (the case of "centerlines"), in which the conjectured value for the leading constant is 2/(d+2). We prove that 2/(d+2) is an *upper bound* for the leading constant. Specifically, we show that for every fixed d and every n there exists an n-point set in R^d for which no line in R^d lies at depth larger than 2n/(d+2) + o(n). This point set is the "stretched grid"---a set which has been previously used by Bukh et al. for other related purposes.
Maximal hypersurfaces and foliations of constant mean curvature in general relativity
Marsden, Jerrold E.; Tipler, Frank J.
1980-12-01
We prove theorems on existence, uniqueness and smoothness of maximal and constant mean curvature compact spacelike hypersurfaces in globally hyperbolic spacetimes. The uniqueness theorem for maximal hypersurfaces of Brill and Flaherty, which assumed matter everywhere, is extended to spacetimes that are vacuum and non-flat or that satisfy a generic-type condition. In this connection we show that under general hypotheses, a spatially closed universe with a maximal hypersurface must be Wheeler universe; i.e. be closed in time as well. The existence of Lipschitz achronal maximal volume hypersurfaces under the hypothesis that candidate hypersurfaces are bounded away from the singularity is proved. This hypothesis is shown to be valid in two cases of interest: when the singularities are of strong curvature type, and when the singularity is a single ideal point. Some properties of these maximal volume hypersurfaces and difficulties with Avez' original arguments are discussed. The difficulties involve the possibility that the maximal volume hypersurface can be null on certain portions; we present an incomplete argument which suggests that these hypersurfaces are always smooth, but prove that an a priori bound on the second fundamental form does imply smoothness. An extension of the perturbation theorem of Choquet-Bruhat, Fischer and Marsden is given and conditions under which local foliations by constant mean curvature hypersurfaces can be extended to global ones is obtained.
Mutation in Fas Ligand Impairs Maturation of Thymocytes Bearing Moderate Affinity T Cell Receptors
2003-01-01
Fas ligand, best known as a death-inducer, is also a costimulatory molecule required for maximal proliferation of mature antigen-specific CD4+ and CD8+ T cells. We now extend the role of Fas ligand by showing that it can also influence thymocyte development. T cell maturation in some, but not all, strains of TCR transgenic mice is severely impaired in thymocytes expressing mutant Fas ligand incapable of interacting with Fas. Mutant Fas ligand inhibits neither negative selection nor death by n...
Coordinate unsaturation with fluorinated ligands
Rack, J.L.; Hurlburt, P.K.; Anderson, O.P.; Strauss, S.H. [Colorado State Univ., Ft. Collins, CO (United States)
1993-12-31
The preparation and characterization of Zn(OTeF{sub 5}){sub 2} has resulted in a model compound with which to explore the concept of coordinative unsaturation. The coordination of solvents of varying donicity and dielectric constant to the Zn(II) ions in Zn(OTeF{sub 5}){sub 2} was studied by vapor phase monometry, NMR and IR spectroscopy, conductimetry, and X-Ray crystallography. The structures of [Zn(C{sub 6}H{sub 5}NO{sub 2}){sub 2}(OTeF{sub 5})2]2 and Zn(C{sub 6}H{sub 5}NO{sub 2}){sub 3}(OTEF{sub 5}){sub 2} demonstrate the electronic flexibility of some weakly coordinating solvents in that nitrobenzene can function as either an {eta}{sup 1}O or {eta}{sup 2}O,O`-ligand. The dependence of the number of bound solvent molecules and the degree of OTeF{sub 5}{minus} dissociation on solvent donor number and dielectric constant will be presented.
Maximal inequalities for demimartingales and their applications
WANG XueJun; HU ShuHe
2009-01-01
In this paper,we establish some maximal inequalities for demimartingales which generalize and improve the results of Christofides.The maximal inequalities for demimartingales are used as key inequalities to establish other results including Doob's type maximal inequality for demimartingales,strong laws of large numbers and growth rate for demimartingales and associated random variables.At last,we give an equivalent condition of uniform integrability for demisubmartingales.
Maximal inequalities for demimartingales and their applications
无
2009-01-01
In this paper, we establish some maximal inequalities for demimartingales which generalize and improve the results of Christofides. The maximal inequalities for demimartingales are used as key inequalities to establish other results including Doob’s type maximal inequality for demimartingales, strong laws of large numbers and growth rate for demimartingales and associated random variables. At last, we give an equivalent condition of uniform integrability for demisubmartingales.
Hung, Chih-Chang; Yabushita, Atsushi; Kobayashi, Takayoshi; Chen, Pei-Feng; Liang, Keng S
2016-01-01
Ultrafast transient absorption spectroscopy of endothelial NOS oxygenase domain (eNOS-oxy) was performed to study dynamics of ligand or substrate interaction under Soret band excitation. Photo-excitation dissociates imidazole ligand in 4ps. The eNOS-oxy without additive is partially bound with water molecule, thus its photoexcited dynamics also shows ligand dissociation in <800fs. Then it followed by vibrational cooling coupled with charge transfer in 4.8ps, and recombination of ligand to distal side of heme in 12ps.
Task-oriented maximally entangled states
Agrawal, Pankaj; Pradhan, B, E-mail: agrawal@iopb.res.i, E-mail: bpradhan@iopb.res.i [Institute of Physics, Sachivalaya Marg, Bhubaneswar, Orissa 751 005 (India)
2010-06-11
We introduce the notion of a task-oriented maximally entangled state (TMES). This notion depends on the task for which a quantum state is used as the resource. TMESs are the states that can be used to carry out the task maximally. This concept may be more useful than that of a general maximally entangled state in the case of a multipartite system. We illustrate this idea by giving an operational definition of maximally entangled states on the basis of communication tasks of teleportation and superdense coding. We also give examples and a procedure to obtain such TMESs for n-qubit systems.
LIU Li-Guo; TIAN Cheng-Lin; CHEN Ping-Xing; YUAN Nai-Chang
2009-01-01
We derive an analytical lower bound on the concurrence for bipartite quantum systems with an improved computable cross norm or realignment criterion and an improved positive partial transpose criterion respectively.Furthermore we demonstrate that our bound is better than that obtained from the local uncertainty relations criterion with optimal local orthogonal observables which is known as one of the best estimations of concurrence.
Bounds for Asian basket options
Deelstra, Griselda; Diallo, Ibrahima; Vanmaele, Michèle
2008-09-01
In this paper we propose pricing bounds for European-style discrete arithmetic Asian basket options in a Black and Scholes framework. We start from methods used for basket options and Asian options. First, we use the general approach for deriving upper and lower bounds for stop-loss premia of sums of non-independent random variables as in Kaas et al. [Upper and lower bounds for sums of random variables, Insurance Math. Econom. 27 (2000) 151-168] or Dhaene et al. [The concept of comonotonicity in actuarial science and finance: theory, Insurance Math. Econom. 31(1) (2002) 3-33]. We generalize the methods in Deelstra et al. [Pricing of arithmetic basket options by conditioning, Insurance Math. Econom. 34 (2004) 55-57] and Vanmaele et al. [Bounds for the price of discrete sampled arithmetic Asian options, J. Comput. Appl. Math. 185(1) (2006) 51-90]. Afterwards we show how to derive an analytical closed-form expression for a lower bound in the non-comonotonic case. Finally, we derive upper bounds for Asian basket options by applying techniques as in Thompson [Fast narrow bounds on the value of Asian options, Working Paper, University of Cambridge, 1999] and Lord [Partially exact and bounded approximations for arithmetic Asian options, J. Comput. Finance 10 (2) (2006) 1-52]. Numerical results are included and on the basis of our numerical tests, we explain which method we recommend depending on moneyness and time-to-maturity.
Anaphoric Pronouns and Bound Variables
Wasow, Thomas
1975-01-01
Deals with certain problems inherent in deriving anaphoric pronouns from bound variables. Syntactic rules applied to determine anaphora relations cannot be applied if anaphoric pronouns and their antecedents have identical underlying forms. An approach to anaphora which preserves some advantages of the bound-variable theory without the problems is…
Inflation in maximal gauged supergravities
Kodama, Hideo [Theory Center, KEK,Tsukuba 305-0801 (Japan); Department of Particles and Nuclear Physics,The Graduate University for Advanced Studies,Tsukuba 305-0801 (Japan); Nozawa, Masato [Dipartimento di Fisica, Università di Milano, and INFN, Sezione di Milano,Via Celoria 16, 20133 Milano (Italy)
2015-05-18
We discuss the dynamics of multiple scalar fields and the possibility of realistic inflation in the maximal gauged supergravity. In this paper, we address this problem in the framework of recently discovered 1-parameter deformation of SO(4,4) and SO(5,3) dyonic gaugings, for which the base point of the scalar manifold corresponds to an unstable de Sitter critical point. In the gauge-field frame where the embedding tensor takes the value in the sum of the 36 and 36’ representations of SL(8), we present a scheme that allows us to derive an analytic expression for the scalar potential. With the help of this formalism, we derive the full potential and gauge coupling functions in analytic forms for the SO(3)×SO(3)-invariant subsectors of SO(4,4) and SO(5,3) gaugings, and argue that there exist no new critical points in addition to those discovered so far. For the SO(4,4) gauging, we also study the behavior of 6-dimensional scalar fields in this sector near the Dall’Agata-Inverso de Sitter critical point at which the negative eigenvalue of the scalar mass square with the largest modulus goes to zero as the deformation parameter s approaches a critical value s{sub c}. We find that when the deformation parameter s is taken sufficiently close to the critical value, inflation lasts more than 60 e-folds even if the initial point of the inflaton allows an O(0.1) deviation in Planck units from the Dall’Agata-Inverso critical point. It turns out that the spectral index n{sub s} of the curvature perturbation at the time of the 60 e-folding number is always about 0.96 and within the 1σ range n{sub s}=0.9639±0.0047 obtained by Planck, irrespective of the value of the η parameter at the critical saddle point. The tensor-scalar ratio predicted by this model is around 10{sup −3} and is close to the value in the Starobinsky model.
Market Access through Bound Tariffs
Sala, Davide; Schröder, Philipp J.H.; Yalcin, Erdal
on the risk that exporters face in destination markets. The present paper formalizes the underlying interaction of risk, fixed export costs and firms' market entry decisions based on techniques known from the real options literature; doing so we highlight the important role of bound tariffs at the extensive......WTO negotiations deal predominantly with bound - besides applied - tariff rates. But, how can reductions in tariffs ceilings, i.e. tariff rates that no exporter may ever actually be confronted with, generate market access? The answer to this question relates to the effects of tariff bindings...... margin of trade. We find that bound tariffs are more effective with higher risk destination markets, that a large binding overhang may still command substantial market access, and that reductions in bound tariffs generate effective market access even when bound rates are above current and long...
Market access through bound tariffs
Sala, Davide; Schröder, Philipp J.H.; Yalcin, Erdal
2010-01-01
on the risk that exporters face in destination markets. The present paper formalizes the underlying interaction of risk, fixed export costs and firms' market entry decisions based on techniques known from the real options literature; doing so we highlight the important role of bound tariffs at the extensive......WTO negotiations deal predominantly with bound - besides applied - tariff rates. But, how can reductions in tariffs ceilings, i.e. tariff rates that no exporter may ever actually be confronted with, generate market access? The answer to this question relates to the effects of tariff bindings...... margin of trade. We find that bound tariffs are more effective with higher risk destination markets, that a large binding overhang may still command substantial market access, and that reductions in bound tariffs generate effective market access even when bound rates are above current and longterm...
Asynchronous Bounded Expected Delay Networks
Bakhshi, Rena; Fokkink, Wan; Pang, Jun
2010-01-01
The commonly used asynchronous bounded delay (ABD) network models assume a fixed bound on message delay. We propose a probabilistic network model, called asynchronous bounded expected delay (ABE) model. Instead of a strict bound, the ABE model requires only a bound on the expected message delay. While the conditions of ABD networks restrict the set of possible executions, in ABE networks all asynchronous executions are possible, but executions with extremely long delays are less probable. In contrast to ABD networks, ABE networks cannot be synchronised efficiently. At the example of an election algorithm, we show that the minimal assumptions of ABE networks are sufficient for the development of efficient algorithms. For anonymous, unidirectional ABE rings of known size N we devise a probabilistic leader election algorithm having average message and time complexity O(N).
Computing an upper bound on contact stress with surrogate duality
Xuan, Zhaocheng; Papadopoulos, Panayiotis
2016-07-01
We present a method for computing an upper bound on the contact stress of elastic bodies. The continuum model of elastic bodies with contact is first modeled as a constrained optimization problem by using finite elements. An explicit formulation of the total contact force, a fraction function with the numerator as a linear function and the denominator as a quadratic convex function, is derived with only the normalized nodal contact forces as the constrained variables in a standard simplex. Then two bounds are obtained for the sum of the nodal contact forces. The first is an explicit formulation of matrices of the finite element model, derived by maximizing the fraction function under the constraint that the sum of the normalized nodal contact forces is one. The second bound is solved by first maximizing the fraction function subject to the standard simplex and then using Dinkelbach's algorithm for fractional programming to find the maximum—since the fraction function is pseudo concave in a neighborhood of the solution. These two bounds are solved with the problem dimensions being only the number of contact nodes or node pairs, which are much smaller than the dimension for the original problem, namely, the number of degrees of freedom. Next, a scheme for constructing an upper bound on the contact stress is proposed that uses the bounds on the sum of the nodal contact forces obtained on a fine finite element mesh and the nodal contact forces obtained on a coarse finite element mesh, which are problems that can be solved at a lower computational cost. Finally, the proposed method is verified through some examples concerning both frictionless and frictional contact to demonstrate the method's feasibility, efficiency, and robustness.
Computing Maximally Supersymmetric Scattering Amplitudes
Stankowicz, James Michael, Jr.
This dissertation reviews work in computing N = 4 super-Yang--Mills (sYM) and N = 8 maximally supersymmetric gravity (mSUGRA) scattering amplitudes in D = 4 spacetime dimensions in novel ways. After a brief introduction and overview in Ch. 1, the various techniques used to construct amplitudes in the remainder of the dissertation are discussed in Ch. 2. This includes several new concepts such as d log and pure integrand bases, as well as how to construct the amplitude using exactly one kinematic point where it vanishes. Also included in this chapter is an outline of the Mathematica package on shell diagrams and numerics.m (osdn) that was developed for the computations herein. The rest of the dissertation is devoted to explicit examples. In Ch. 3, the starting point is tree-level sYM amplitudes that have integral representations with residues that obey amplitude relations. These residues are shown to have corresponding residue numerators that allow a double copy prescription that results in mSUGRA residues. In Ch. 4, the two-loop four-point sYM amplitude is constructed in several ways, showcasing many of the techniques of Ch. 2; this includes an example of how to use osdn. The two-loop five-point amplitude is also presented in a pure integrand representation with comments on how it was constructed from one homogeneous cut of the amplitude. On-going work on the two-loop n-point amplitude is presented at the end of Ch. 4. In Ch. 5, the three-loop four-point amplitude is presented in the d log representation and in the pure integrand representation. In Ch. 6, there are several examples of four- through seven-loop planar diagrams that illustrate how considerations of the singularity structure of the amplitude underpin dual-conformal invariance. Taken with the previous examples, this is additional evidence that the structure known to exist in the planar sector extends to the full theory. At the end of this chapter is a proof that all mSUGRA amplitudes have a pole at
2017-01-01
Crystal structures of protein–ligand complexes are often used to infer biology and inform structure-based drug discovery. Hence, it is important to build accurate, reliable models of ligands that give confidence in the interpretation of the respective protein–ligand complex. This paper discusses key stages in the ligand-fitting process, including ligand binding-site identification, ligand description and conformer generation, ligand fitting, refinement and subsequent validation. The CCP4 suite contains a number of software tools that facilitate this task: AceDRG for the creation of ligand descriptions and conformers, Lidia and JLigand for two-dimensional and three-dimensional ligand editing and visual analysis, Coot for density interpretation, ligand fitting, analysis and validation, and REFMAC5 for macromolecular refinement. In addition to recent advancements in automatic carbohydrate building in Coot (LO/Carb) and ligand-validation tools (FLEV), the release of the CCP4i2 GUI provides an integrated solution that streamlines the ligand-fitting workflow, seamlessly passing results from one program to the next. The ligand-fitting process is illustrated using instructive practical examples, including problematic cases such as post-translational modifications, highlighting the need for careful analysis and rigorous validation. PMID:28177312
Are all maximally entangled states pure?
Cavalcanti, D; Terra-Cunha, M O
2005-01-01
In this Letter we study if all maximally entangled states are pure through several entanglement monotones. Our conclusions allow us to generalize the idea of monogamy of entanglement. Then we propose a polygamy of entanglement, which express that if a general multipartite state is maximally entangled it is necessarily factorized by any other system.
An ethical justification of profit maximization
Koch, Carsten Allan
2010-01-01
In much of the literature on business ethics and corporate social responsibility, it is more or less taken for granted that attempts to maximize profits are inherently unethical. The purpose of this paper is to investigate whether an ethical argument can be given in support of profit maximizing b...
Alternative trailer configurations for maximizing payloads
Jason D. Thompson; Dana Mitchell; John Klepac
2017-01-01
In order for harvesting contractors to stay ahead of increasing costs, it is imperative that they employ all options to maximize productivity and efficiency. Transportation can account for half the cost to deliver wood to a mill. Contractors seek to maximize truck payload to increase productivity. The Forest Operations Research Unit, Southern Research Station, USDA...
Cohomology of Weakly Reducible Maximal Triangular Algebras
董浙; 鲁世杰
2000-01-01
In this paper, we introduce the concept of weakly reducible maximal triangular algebras φwhich form a large class of maximal triangular algebras. Let B be a weakly closed algebra containing 5φ, we prove that the cohomology spaces Hn(φ, B) (n≥1) are trivial.
SuperLigands – a database of ligand structures derived from the Protein Data Bank
Preissner Robert
2005-05-01
Full Text Available Abstract Background Currently, the PDB contains approximately 29,000 protein structures comprising over 70,000 experimentally determined three-dimensional structures of over 5,000 different low molecular weight compounds. Information about these PDB ligands can be very helpful in the field of molecular modelling and prediction, particularly for the prediction of protein binding sites and function. Description Here we present an Internet accessible database delivering PDB ligands in the MDL Mol file format which, in contrast to the PDB format, includes information about bond types. Structural similarity of the compounds can be detected by calculation of Tanimoto coefficients and by three-dimensional superposition. Topological similarity of PDB ligands to known drugs can be assessed via Tanimoto coefficients. Conclusion SuperLigands supplements the set of existing resources of information about small molecules bound to PDB structures. Allowing for three-dimensional comparison of the compounds as a novel feature, this database represents a valuable means of analysis and prediction in the field of biological and medical research.
SuperLigands – a database of ligand structures derived from the Protein Data Bank
Michalsky, Elke; Dunkel, Mathias; Goede, Andrean; Preissner, Robert
2005-01-01
Background Currently, the PDB contains approximately 29,000 protein structures comprising over 70,000 experimentally determined three-dimensional structures of over 5,000 different low molecular weight compounds. Information about these PDB ligands can be very helpful in the field of molecular modelling and prediction, particularly for the prediction of protein binding sites and function. Description Here we present an Internet accessible database delivering PDB ligands in the MDL Mol file format which, in contrast to the PDB format, includes information about bond types. Structural similarity of the compounds can be detected by calculation of Tanimoto coefficients and by three-dimensional superposition. Topological similarity of PDB ligands to known drugs can be assessed via Tanimoto coefficients. Conclusion SuperLigands supplements the set of existing resources of information about small molecules bound to PDB structures. Allowing for three-dimensional comparison of the compounds as a novel feature, this database represents a valuable means of analysis and prediction in the field of biological and medical research. PMID:15943884
Inclusive fitness maximization: An axiomatic approach.
Okasha, Samir; Weymark, John A; Bossert, Walter
2014-06-07
Kin selection theorists argue that evolution in social contexts will lead organisms to behave as if maximizing their inclusive, as opposed to personal, fitness. The inclusive fitness concept allows biologists to treat organisms as akin to rational agents seeking to maximize a utility function. Here we develop this idea and place it on a firm footing by employing a standard decision-theoretic methodology. We show how the principle of inclusive fitness maximization and a related principle of quasi-inclusive fitness maximization can be derived from axioms on an individual׳s 'as if preferences' (binary choices) for the case in which phenotypic effects are additive. Our results help integrate evolutionary theory and rational choice theory, help draw out the behavioural implications of inclusive fitness maximization, and point to a possible way in which evolution could lead organisms to implement it. Copyright © 2014 Elsevier Ltd. All rights reserved.
The Out-bound and In-bound Travelling Market
Emily Yu
2009-01-01
@@ As the Spring Festival of China with a long vocation of seven days nationally is approaching,more and more attention is paid to the out-bound and inn-bound trayeling market.Will people hold their pockets firmly in the"cold winter"of world-wide financial crisis,or will they grab the great discount of traveling and take a good relax?
Combining Alphas via Bounded Regression
Zura Kakushadze
2015-11-01
Full Text Available We give an explicit algorithm and source code for combining alpha streams via bounded regression. In practical applications, typically, there is insufficient history to compute a sample covariance matrix (SCM for a large number of alphas. To compute alpha allocation weights, one then resorts to (weighted regression over SCM principal components. Regression often produces alpha weights with insufficient diversification and/or skewed distribution against, e.g., turnover. This can be rectified by imposing bounds on alpha weights within the regression procedure. Bounded regression can also be applied to stock and other asset portfolio construction. We discuss illustrative examples.
Bounds for Certain Character Sums
杨锦; 郑志勇
2003-01-01
This paper shows a connection between exponential sums and character sums. In particular, we introduce a character sum that is an analog of the classical Kloosterman sums and establish the analogous Weil-Estermann's upper bound for it. The paper also analyzes a generalized Hardy-Littlewood example for character sums, which shows that the upper bounds given here are the best possible. The analysis makes use of local bounds for the exponential sums and character sums. The basic theorems have been previously established.
Zhi-Hong Tao; Cong-Hua Zhou; Zhong Chen; Li-Fu Wang
2007-01-01
Bounded Model Checking has been recently introduced as an efficient verification method for reactive systems.This technique reduces model checking of linear temporal logic to propositional satisfiability.In this paper we first present how quantified Boolean decision procedures can replace BDDs.We introduce a bounded model checking procedure for temporal logic CTL* which reduces model checking to the satisfiability of quantified Boolean formulas.Our new technique avoids the space blow up of BDDs, and extends the concept of bounded model checking.
Cyclic ferrocenylnaphthalene diimide derivative as a new class of G-quadruplex DNA binding ligand.
Islam, Md Monirul; Sato, Shinobu; Shinozaki, Shingo; Takenaka, Shigeori
2017-01-15
To identify an effective ligand that binds to a G-quadruplex structure but not a double-stranded DNA (dsDNA), a set of biophysical and biochemical experiments were carried out using newly synthesized cyclic ferrocenylnaphthalene diimide (cFNDI, 1) or the non-cyclic derivative (2) with various structures of G-quadruplex DNAs and dsDNA. Compound 1 bound strongly to G-quadruplexes DNAs (10(6)M(-1) order) with diminished binding to dsDNA (10(4)M(-1) order) in 100mM AcOH-AcOK buffer (pH 5.5) containing 100mM KCl. Interestingly, 1 showed an approximately 50-fold higher selectivity to mixed hybrid-type telomeric G-quadruplex DNA (K=3.4×10(6)M(-1) and a 2:1 stoichiometry) than dsDNA (K=7.5×10(4)M(-1)) did. Furthermore, 1 showed higher thermal stability to G-quadruplex DNAs than it did to dsDNA with a preference for c-kit and c-myc G-quadruplex DNAs over telomeric and thrombin binding aptamers. Additionally, 1 exhibited telomerase inhibitory activity with a half-maximal inhibitory concentration (IC50) of 0.4μM. Compound 2 showed a preference for G-quadruplex; however, the binding affinity magnitude and preference were improved in 1 because the former had a cyclic structure.
Monti, Chiara; Gennari, Cesare; Piarulli, Umberto; Vries, Johannes G. de; Vries, André H.M. de; Lefort, Laurent
2005-01-01
A library of 19 chiral tropos phosphorus ligands, based on a flexible (tropos) biphenol unit and a chiral P-bound alcohol (11 phosphites) or secondary amine (8 phosphoramidites), was synthesized. These ligands were screened, individually and as a combination of two, in the rhodium-catalyzed
HUANG, Z; JANSSEN, MJ; PAULUSSEN, RJA; DEZEEUW, RA; FRANKE, JP; ENSING, FK
1995-01-01
In ligand binding assays, the separation of bound and free fraction of the labeled ligand is very important. Dialysis is generally overlooked as separation technique since it requires large volumes and long analysis times. The availability of the ASTED-system (Automated Sequential Trace Enrichment o
Choi, Joshua J.
2011-03-09
The assembly of colloidal nanocrystals (NCs) into superstructures with long-range translational and orientational order is sensitive to the molecular interactions between ligands bound to the NC surface. We illustrate how ligand coverage on colloidal PbS NCs can be exploited as a tunable parameter to direct the self-assembly of superlattices with predefined symmetry. We show that PbS NCs with dense ligand coverage assemble into face-centered cubic (fcc) superlattices whereas NCs with sparse ligand coverage assemble into body-centered cubic (bcc) superlattices which also exhibit orientational ordering of NCs in their lattice sites. Surface chemistry characterization combined with density functional theory calculations suggest that the loss of ligands occurs preferentially on {100} than on reconstructed {111} NC facets. The resulting anisotropic ligand distribution amplifies the role of NC shape in the assembly and leads to the formation of superlattices with translational and orientational order. © 2011 American Chemical Society.
Computing Constrained Cramer Rao Bounds
Tune, Paul
2012-01-01
We revisit the problem of computing submatrices of the Cram\\'er-Rao bound (CRB), which lower bounds the variance of any unbiased estimator of a vector parameter $\\vth$. We explore iterative methods that avoid direct inversion of the Fisher information matrix, which can be computationally expensive when the dimension of $\\vth$ is large. The computation of the bound is related to the quadratic matrix program, where there are highly efficient methods for solving it. We present several methods, and show that algorithms in prior work are special instances of existing optimization algorithms. Some of these methods converge to the bound monotonically, but in particular, algorithms converging non-monotonically are much faster. We then extend the work to encompass the computation of the CRB when the Fisher information matrix is singular and when the parameter $\\vth$ is subject to constraints. As an application, we consider the design of a data streaming algorithm for network measurement.
An Inequality for Bounded Functions
Kouba, Omran
2012-01-01
In this note we prove optimal inequalities for bounded functions in terms of their deviation from their mean. These results extend and generalize some known inequalities due to Thong (2011) and Perfetti (2011)
Schulz, Marc Daniel; Dusuel, Sébastien; Vidal, Julien
2016-11-01
We discuss the emergence of bound states in the low-energy spectrum of the string-net Hamiltonian in the presence of a string tension. In the ladder geometry, we show that a single bound state arises either for a finite tension or in the zero-tension limit depending on the theory considered. In the latter case, we perturbatively compute the binding energy as a function of the total quantum dimension. We also address this issue in the honeycomb lattice where the number of bound states in the topological phase depends on the total quantum dimension. Finally, the internal structure of these bound states is analyzed in the zero-tension limit.
Schulz, M D; Vidal, J
2016-01-01
We discuss the emergence of bound states in the low-energy spectrum of the string-net Hamiltonian in the presence of a string tension. In the ladder geometry, we show that a single bound state arises either for a finite tension or in the zero-tension limit depending on the theory considered. In the latter case, we perturbatively compute the binding energy as a function of the total quantum dimension. We also address this issue in the honeycomb lattice where the number of bound states in the topological phase depends on the total quantum dimension. Finally, the internal structure of these bound states is analyzed in the zero-tension limit.
Some bounds for quantum copying
Rastegin, A E
2001-01-01
We derive lower bounds on the absolute error and the relative error of an abstract copying of two-state set. We do not specify a copying transformation and a dimension of state space. Only the unitarity of quantum mechanical transformations is used. Our approach is based on the notion of angle between two states. We first prove several useful statements, simply expressed in terms of angles. We then examine a lower bound on the absolute error, that was first considered by Hillery and Buzek. Our reasonings supplement and reinforce the results, obtained by them. So, we derive more strong bounds on the absolute error, and we also consider a tradeoff between size of error and corresponding probability distributions. After that we examine a lower bound on the relative error.
Algorithms for k-Colouring and Finding Maximal Independent Sets
Byskov, Jesper Makholm
2003-01-01
In this extended abstract, we construct algorithms that decide for a graph with n vertices whether there exists a 4-, 5- or 6-colouring of the vertices running in time O(1.7504n), O(2.1592 n) and O(2.3289n), respectively, using polynomial space. For 6- or 7-colouring we construct algorithms running...... in time (9(2.2680 n) and O(2.4023n), respectively, using exponential space. To do this, we prove that the number of maximal independent sets of size at most k (k-MIS's) in a graph is at most (d -1)dk - n am-(d -1)k for any d > 4. Eppstein shows the same bound for d = 4....
LigandRNA: computational predictor of RNA-ligand interactions.
Philips, Anna; Milanowska, Kaja; Lach, Grzegorz; Bujnicki, Janusz M
2013-12-01
RNA molecules have recently become attractive as potential drug targets due to the increased awareness of their importance in key biological processes. The increase of the number of experimentally determined RNA 3D structures enabled structure-based searches for small molecules that can specifically bind to defined sites in RNA molecules, thereby blocking or otherwise modulating their function. However, as of yet, computational methods for structure-based docking of small molecule ligands to RNA molecules are not as well established as analogous methods for protein-ligand docking. This motivated us to create LigandRNA, a scoring function for the prediction of RNA-small molecule interactions. Our method employs a grid-based algorithm and a knowledge-based potential derived from ligand-binding sites in the experimentally solved RNA-ligand complexes. As an input, LigandRNA takes an RNA receptor file and a file with ligand poses. As an output, it returns a ranking of the poses according to their score. The predictive power of LigandRNA favorably compares to five other publicly available methods. We found that the combination of LigandRNA and Dock6 into a "meta-predictor" leads to further improvement in the identification of near-native ligand poses. The LigandRNA program is available free of charge as a web server at http://ligandrna.genesilico.pl.
Analysis of macromolecules, ligands and macromolecule-ligand complexes
Von Dreele, Robert B [Los Alamos, NM
2008-12-23
A method for determining atomic level structures of macromolecule-ligand complexes through high-resolution powder diffraction analysis and a method for providing suitable microcrystalline powder for diffraction analysis are provided. In one embodiment, powder diffraction data is collected from samples of polycrystalline macromolecule and macromolecule-ligand complex and the refined structure of the macromolecule is used as an approximate model for a combined Rietveld and stereochemical restraint refinement of the macromolecule-ligand complex. A difference Fourier map is calculated and the ligand position and points of interaction between the atoms of the macromolecule and the atoms of the ligand can be deduced and visualized. A suitable polycrystalline sample of macromolecule-ligand complex can be produced by physically agitating a mixture of lyophilized macromolecule, ligand and a solvent.
Bongrand, Pierre
2008-01-01
The formation and dissociation of specific noncovalent interactions between a variety of macromolecules play a crucial role in the function of biological systems. During the last few years, three main lines of research led to a dramatic improvement of our understanding of these important phenomena. First, combination of genetic engineering and X ray cristallography made available a simultaneous knowledg of the precise structure and affinity of series or related ligand-receptor systems differing by a few well-defined atoms. Second, improvement of computer power and simulation techniques allowed extended exploration of the interaction of realistic macromolecules. Third, simultaneous development of a variety of techniques based on atomic force microscopy, hydrodynamic flow, biomembrane probes, optical tweezers, magnetic fields or flexible transducers yielded direct experimental information of the behavior of single ligand receptor bonds. At the same time, investigation of well defined cellular models raised the ...
Therapeutic androgen receptor ligands
Allan, George F.; Sui, Zhihua
2003-01-01
In the past several years, the concept of tissue-selective nuclear receptor ligands has emerged. This concept has come to fruition with estrogens, with the successful marketing of drugs such as raloxifene. The discovery of raloxifene and other selective estrogen receptor modulators (SERMs) has raised the possibility of generating selective compounds for other pathways, including androgens (that is, selective androgen receptor modulators, or SARMs).
Are all maximally entangled states pure?
Cavalcanti, D.; Brandão, F. G. S. L.; Terra Cunha, M. O.
2005-10-01
We study if all maximally entangled states are pure through several entanglement monotones. In the bipartite case, we find that the same conditions which lead to the uniqueness of the entropy of entanglement as a measure of entanglement exclude the existence of maximally mixed entangled states. In the multipartite scenario, our conclusions allow us to generalize the idea of the monogamy of entanglement: we establish the polygamy of entanglement, expressing that if a general state is maximally entangled with respect to some kind of multipartite entanglement, then it is necessarily factorized of any other system.
An ethical justification of profit maximization
Koch, Carsten Allan
2010-01-01
In much of the literature on business ethics and corporate social responsibility, it is more or less taken for granted that attempts to maximize profits are inherently unethical. The purpose of this paper is to investigate whether an ethical argument can be given in support of profit maximizing...... behaviour. It is argued that some form of consequential ethics must be applied, and that both profit seeking and profit maximization can be defended from a rule-consequential point of view. It is noted, however, that the result does not apply unconditionally, but requires that certain form of profit (and...
Robust utility maximization in a discontinuous filtration
Jeanblanc, Monique; Ngoupeyou, Armand
2012-01-01
We study a problem of utility maximization under model uncertainty with information including jumps. We prove first that the value process of the robust stochastic control problem is described by the solution of a quadratic-exponential backward stochastic differential equation with jumps. Then, we establish a dynamic maximum principle for the optimal control of the maximization problem. The characterization of the optimal model and the optimal control (consumption-investment) is given via a forward-backward system which generalizes the result of Duffie and Skiadas (1994) and El Karoui, Peng and Quenez (2001) in the case of maximization of recursive utilities including model with jumps.
Agbaba Danica
2012-01-01
Full Text Available Extensive biochemical and pharmacological studies have determined three different subtypes of imidazoline receptors: I1-imidazoline receptors (I1-IR involved in central inhibition of sympathicus that produce hypotensive effect; I2-imidazoline receptors (I2-IR modulate monoamine oxidase B activity (MAO-B; I3-imidazoline receptors (I3-IR regulate insulin secretion from pancreatic β-cells. Therefore, the I1/I2/I3 imidazoline receptors are selected as new, interesting targets for drug design and discovery. Novel selective I1/I2/I3 agonists and antagonists have been recently developed. In the present review, we provide a brief update to the field of imidazoline research, highlighting some of the chemical diversity and progress made in the 2D-QSAR, 3D-QSAR and quantitative pharmacophore development studies of I1-IR and I2-IR imidazoline receptor ligands. Theoretical studies of I3-IR ligands are not yet performed because of insufficient number of synthesized I3-IR ligands.
Influence Maximization in Social Networks: Towards an Optimal Algorithmic Solution
Borgs, Christian; Chayes, Jennifer; Lucier, Brendan
2012-01-01
Diffusion is a fundamental graph process, underpinning such phenomena as epidemic disease contagion and the spread of innovation by word-of-mouth. We address the algorithmic problem of finding a set of k initial seed nodes in a network so that the expected size of the resulting cascade is maximized, under the standard independent cascade model of network diffusion. Our main result is an algorithm for the influence maximization problem that obtains the near-optimal approximation factor of (1 - 1/e - epsilon), for any epsilon > 0, in time O((m+n)log(n) / epsilon^3) where n and m are the number of vertices and edges in the network. Our algorithm is nearly runtime-optimal (up to a logarithmic factor) as we establish a lower bound of Omega(m+n) on the runtime required to obtain a constant approximation. Our method also allows a provable tradeoff between solution quality and runtime: we obtain an O(1/beta)-approximation in time O(n log^3(n) * a(G) / beta) for any beta > 1, where a(G) denotes the arboricity of the d...
Activation of Neuropeptide FF Receptors by Kisspeptin Receptor Ligands.
Oishi, Shinya; Misu, Ryosuke; Tomita, Kenji; Setsuda, Shohei; Masuda, Ryo; Ohno, Hiroaki; Naniwa, Yousuke; Ieda, Nahoko; Inoue, Naoko; Ohkura, Satoshi; Uenoyama, Yoshihisa; Tsukamura, Hiroko; Maeda, Kei-Ichiro; Hirasawa, Akira; Tsujimoto, Gozoh; Fujii, Nobutaka
2011-01-13
Kisspeptin is a member of the RFamide neuropeptide family that is implicated in gonadotropin secretion. Because kisspeptin-GPR54 signaling is implicated in the neuroendocrine regulation of reproduction, GPR54 ligands represent promising therapeutic agents against endocrine secretion disorders. In the present study, the selectivity profiles of GPR54 agonist peptides were investigated for several GPCRs, including RFamide receptors. Kisspeptin-10 exhibited potent binding and activation of neuropeptide FF receptors (NPFFR1 and NPFFR2). In contrast, short peptide agonists bound with much lower affinity to NPFFRs while showing relatively high selectivity toward GPR54. The possible localization of secondary kisspeptin targets was also demonstrated by variation in the levels of GnRH release from the median eminence and the type of GPR54 agonists used. Negligible affinity of the reported NPFFR ligands to GPR54 was observed and indicates the unidirectional cross-reactivity between both ligands.
HEALTH INSURANCE: CONTRIBUTIONS AND REIMBURSEMENT MAXIMAL
HR Division
2000-01-01
Affected by both the salary adjustment index on 1.1.2000 and the evolution of the staff members and fellows population, the average reference salary, which is used as an index for fixed contributions and reimbursement maximal, has changed significantly. An adjustment of the amounts of the reimbursement maximal and the fixed contributions is therefore necessary, as from 1 January 2000.Reimbursement maximalThe revised reimbursement maximal will appear on the leaflet summarising the benefits for the year 2000, which will soon be available from the divisional secretariats and from the AUSTRIA office at CERN.Fixed contributionsThe fixed contributions, applicable to some categories of voluntarily insured persons, are set as follows (amounts in CHF for monthly contributions):voluntarily insured member of the personnel, with complete coverage:815,- (was 803,- in 1999)voluntarily insured member of the personnel, with reduced coverage:407,- (was 402,- in 1999)voluntarily insured no longer dependent child:326,- (was 321...
Maximizing throughput by evaluating critical utilization paths
Weeda, P.J.
1991-01-01
Recently the relationship between batch structure, bottleneck machine and maximum throughput has been explored for serial, convergent and divergent process configurations consisting of two machines and three processes. In three of the seven possible configurations a multiple batch structure maximize
Relationship between maximal exercise parameters and individual ...
Relationship between maximal exercise parameters and individual time trial ... It is widely accepted that the ventilatory threshold (VT) is an important ... This study investigated whether the physiological responses during a 20km time trial (TT) ...
Simple technique for maximal thoracic muscle harvest.
Marshall, M Blair; Kaiser, Larry R; Kucharczuk, John C
2004-04-01
We present a modification of technique for standard muscle flap harvest, the placement of cutaneous traction sutures. This technique allows for maximal dissection of the thoracic muscles even through minimal incisions. Through improved exposure and traction, complete dissection of the muscle bed can be performed and the tissue obtained maximized. Because more muscle bulk is obtained with this technique, the need for a second muscle may be prevented.
MAXIMAL POINTS OF A REGULAR TRUTH FUNCTION
Every canonical linearly separable truth function is a regular function, but not every regular truth function is linearly separable. The most...promising method of determining which of the regular truth functions are linearly separable r quires finding their maximal and minimal points. In this...report is developed a quick, systematic method of finding the maximal points of any regular truth function in terms of its arithmetic invariants. (Author)
Maximal Subgroups of Skew Linear Groups
M. Mahdavi-Hezavehi
2002-01-01
Let D be an infinite division algebra of finite dimension over its centre Z(D) = F, and n a positive integer. The structure of maximal subgroups of skew linear groups are investigated. In particular, assume N is a normal subgroup of GLn(D) and M is a maximal subgroup of N containing Z(N). It is shown that if M/Z(N) is finite, then N is central.
Additive Approximation Algorithms for Modularity Maximization
Kawase, Yasushi; Matsui, Tomomi; Miyauchi, Atsushi
2016-01-01
The modularity is a quality function in community detection, which was introduced by Newman and Girvan (2004). Community detection in graphs is now often conducted through modularity maximization: given an undirected graph $G=(V,E)$, we are asked to find a partition $\\mathcal{C}$ of $V$ that maximizes the modularity. Although numerous algorithms have been developed to date, most of them have no theoretical approximation guarantee. Recently, to overcome this issue, the design of modularity max...
Fluorescent ligands for studying neuropeptide receptors by confocal microscopy
Beaudet A.
1998-01-01
Full Text Available This paper reviews the use of confocal microscopy as it pertains to the identification of G-protein coupled receptors and the study of their dynamic properties in cell cultures and in mammalian brain following their tagging with specific fluorescent ligands. Principles that should guide the choice of suitable ligands and fluorophores are discussed. Examples are provided from the work carried out in the authors' laboratory using custom synthetized fluoresceinylated or BODIPY-tagged bioactive peptides. The results show that confocal microscopic detection of specifically bound fluorescent ligands permits high resolution appraisal of neuropeptide receptor distribution both in cell culture and in brain sections. Within the framework of time course experiments, it also allows for a dynamic assessment of the internalization and subsequent intracellular trafficking of bound fluorescent molecules. Thus, it was found that neurotensin, somatostatin and mu- and delta-selective opioid peptides are internalized in a receptor-dependent fashion and according to receptor-specific patterns into their target cells. In the case of neurotensin, this internalization process was found to be clathrin-mediated, to proceed through classical endosomal pathways and, in neurons, to result in a mobilization of newly formed endosomes from neural processes to nerve cell bodies and from the periphery of cell bodies towards the perinuclear zone. These mechanisms are likely to play an important role for ligand inactivation, receptor regulation and perhaps also transmembrane signaling.
Schneider, Pascal; Willen, Laure; Smulski, Cristian R
2014-01-01
Ligands and receptors of the TNF superfamily are therapeutically relevant targets in a wide range of human diseases. This chapter describes assays based on ELISA, immunoprecipitation, FACS, and reporter cell lines to monitor interactions of tagged receptors and ligands in both soluble and membrane-bound forms using unified detection techniques. A reporter cell assay that is sensitive to ligand oligomerization can identify ligands with high probability of being active on endogenous receptors. Several assays are also suitable to measure the activity of agonist or antagonist antibodies, or to detect interactions with proteoglycans. Finally, self-interaction of membrane-bound receptors can be evidenced using a FRET-based assay. This panel of methods provides a large degree of flexibility to address questions related to the specificity, activation, or inhibition of TNF-TNF receptor interactions in independent assay systems, but does not substitute for further tests in physiologically relevant conditions.
Expectation-Maximization Method for EEG-Based Continuous Cursor Control
Yixiao Wang
2007-01-01
Full Text Available To develop effective learning algorithms for continuous prediction of cursor movement using EEG signals is a challenging research issue in brain-computer interface (BCI. In this paper, we propose a novel statistical approach based on expectation-maximization (EM method to learn the parameters of a classifier for EEG-based cursor control. To train a classifier for continuous prediction, trials in training data-set are first divided into segments. The difficulty is that the actual intention (label at each time interval (segment is unknown. To handle the uncertainty of the segment label, we treat the unknown labels as the hidden variables in the lower bound on the log posterior and maximize this lower bound via an EM-like algorithm. Experimental results have shown that the averaged accuracy of the proposed method is among the best.
Maximal Frequent Itemset Generation Using Segmentation Apporach
M.Rajalakshmi
2011-09-01
Full Text Available Finding frequent itemsets in a data source is a fundamental operation behind Association Rule Mining.Generally, many algorithms use either the bottom-up or top-down approaches for finding these frequentitemsets. When the length of frequent itemsets to be found is large, the traditional algorithms find all thefrequent itemsets from 1-length to n-length, which is a difficult process. This problem can be solved bymining only the Maximal Frequent Itemsets (MFS. Maximal Frequent Itemsets are frequent itemsets whichhave no proper frequent superset. Thus, the generation of only maximal frequent itemsets reduces thenumber of itemsets and also time needed for the generation of all frequent itemsets as each maximal itemsetof length m implies the presence of 2m-2 frequent itemsets. Furthermore, mining only maximal frequentitemset is sufficient in many data mining applications like minimal key discovery and theory extraction. Inthis paper, we suggest a novel method for finding the maximal frequent itemset from huge data sourcesusing the concept of segmentation of data source and prioritization of segments. Empirical evaluationshows that this method outperforms various other known methods.
Natural selection and the maximization of fitness.
Birch, Jonathan
2016-08-01
The notion that natural selection is a process of fitness maximization gets a bad press in population genetics, yet in other areas of biology the view that organisms behave as if attempting to maximize their fitness remains widespread. Here I critically appraise the prospects for reconciliation. I first distinguish four varieties of fitness maximization. I then examine two recent developments that may appear to vindicate at least one of these varieties. The first is the 'new' interpretation of Fisher's fundamental theorem of natural selection, on which the theorem is exactly true for any evolving population that satisfies some minimal assumptions. The second is the Formal Darwinism project, which forges links between gene frequency change and optimal strategy choice. In both cases, I argue that the results fail to establish a biologically significant maximization principle. I conclude that it may be a mistake to look for universal maximization principles justified by theory alone. A more promising approach may be to find maximization principles that apply conditionally and to show that the conditions were satisfied in the evolution of particular traits.
Mutual information challenges entropy bounds
Casini, H
2006-01-01
We consider some formulations of the entropy bounds at the semiclassical level. The entropy S(V) localized in a region V is divergent in quantum field theory (QFT). Instead of it we focus on the mutual information I(V,W)=S(V)+S(W)-S(V U W) between two different non-intersecting sets V and W. This is a low energy quantity, independent of the regularization scheme. In addition, the mutual information is bounded above by twice the entropy corresponding to the sets involved. Calculations of I(V,W) in QFT show that the entropy in empty space cannot be renormalized to zero, and must be actually very large. We find that this entropy due to the vacuum fluctuations violates the FMW bound in Minkowski space. The mutual information also gives a precise, cutoff independent meaning to the statement that the number of degrees of freedom increases with the volume in QFT. If the holographic bound holds, this points to the essential non locality of the physical cutoff. Violations of the Bousso bound would require conformal th...
Preparation and Catalytic Properties of Polymer-Bound Schiff Base Ternary Complexes
HAO Cheng-jun; WANG Rong-min; HE Yu-feng; WANG Yun-pu; XIA Chun-gu
2004-01-01
The polymer-bound Schiff base ternary manganese complexes [PS-SalPhe-Mn-L (L = Phen, Bipy and 8HQ)-] have been prepared from the polymer-bound Schiff base ligand, a manganese salt and the second ligand, such as 1,10-phenanthroline(phen), 2,2′-bipyridyl(bipy) and 8-quinolinol(8HQ). The polymer-bound Schiff base ternary manganese complexes were characterized by means of infrared spectrometry and ICPAES. The catalytic activities of the complexes have been studied in the aerobic epoxidation of long-chain linear a[iphatic olefins. It is shown that 1-octene or 1-decene can be directly oxidized by molecular oxygen when catalyzed by PS-SalPhe-Mn-L(L=Phen, Bipy and 8HQ), and 1,2-epoxy alkane can be afforded in these reactions.
On Characterizing the Local Pooling Factor of Greedy Maximal Scheduling in Random Graphs
Wildman, Jeffrey; Weber, Steven
2014-01-01
The study of the optimality of low-complexity greedy scheduling techniques in wireless communications networks is a very complex problem. The Local Pooling (LoP) factor provides a single-parameter means of expressing the achievable capacity region (and optimality) of one such scheme, greedy maximal scheduling (GMS). The exact LoP factor for an arbitrary network graph is generally difficult to obtain, but may be evaluated or bounded based on the network graph's particular structure. In this pa...
Maximal stochastic transport in the Lorenz equations
Agarwal, Sahil, E-mail: sahil.agarwal@yale.edu [Program in Applied Mathematics, Yale University, New Haven (United States); Wettlaufer, J.S., E-mail: john.wettlaufer@yale.edu [Program in Applied Mathematics, Yale University, New Haven (United States); Departments of Geology & Geophysics, Mathematics and Physics, Yale University, New Haven (United States); Mathematical Institute, University of Oxford, Oxford (United Kingdom); Nordita, Royal Institute of Technology and Stockholm University, Stockholm (Sweden)
2016-01-08
We calculate the stochastic upper bounds for the Lorenz equations using an extension of the background method. In analogy with Rayleigh–Bénard convection the upper bounds are for heat transport versus Rayleigh number. As might be expected, the stochastic upper bounds are larger than the deterministic counterpart of Souza and Doering [1], but their variation with noise amplitude exhibits interesting behavior. Below the transition to chaotic dynamics the upper bounds increase monotonically with noise amplitude. However, in the chaotic regime this monotonicity depends on the number of realizations in the ensemble; at a particular Rayleigh number the bound may increase or decrease with noise amplitude. The origin of this behavior is the coupling between the noise and unstable periodic orbits, the degree of which depends on the degree to which the ensemble represents the ergodic set. This is confirmed by examining the close returns plots of the full solutions to the stochastic equations and the numerical convergence of the noise correlations. The numerical convergence of both the ensemble and time averages of the noise correlations is sufficiently slow that it is the limiting aspect of the realization of these bounds. Finally, we note that the full solutions of the stochastic equations demonstrate that the effect of noise is equivalent to the effect of chaos.
Bexarotene ligand pharmaceuticals.
Hurst, R E
2000-12-01
Bexarotene (LGD-1069), from Ligand, was the first retinoid X receptor (RXR)-selective, antitumor retinoid to enter clinical trials. The company launched the drug for the treatment of cutaneous T-cell lymphoma (CTCL), as Targretin capsules, in the US in January 2000 [359023]. The company filed an NDA for Targretin capsules in June 1999, and for topical gel in December 1999 [329011], [349982] specifically for once-daily oral administration for the treatment of patients with early-stage CTCL who have not tolerated other therapies, patients with refractory or persistent early stage CTCL and patients with refractory advanced stage CTCL. The FDA approved Targretin capsules at the end of December 1999 for once-daily oral treatment of all stages of CTCL in patients refractory to at least one prior systemic therapy, at an initial dose of 300 mg/m2/day. After an NDA was submitted in December 1999 for Targretin gel, the drug received Priority Review status for use as a treatment of cutaneous lesions in patients with stage IA, IB or IIA CTCL [354836]. The FDA issued an approvable letter in June 2000, and granted marketing clearance for CTCL in the same month [370687], [372768], [372769], [373279]. Ligand had received Orphan Drug designation for this indication [329011]. At the request of the FDA, Ligand agreed to carry out certain post-approval phase IV and pharmacokinetic studies [351604]. The company filed an MAA with the EMEA for Targretin Capsules to treat lymphoma in November 1999 [348944]. The NDA for Targretin gel is based on a multicenter phase III trial that was conducted in the US, Canada, Europe and Australia involving 50 patients and a multicenter phase I/II clinical program involving 67 patients. Targretin gel was evaluated for the treatment of patients with early stage CTCL (IA-IIA) who were refractory to, intolerant to, or reached a response plateau for at least 6 months on at least two prior therapies. Efficacy results exceeded the protocol-defined response
Eta nuclear bound states revisited
Friedman, E; Mareš, J
2013-01-01
The strong energy dependence of the s-wave eta-N scattering amplitude at and below threshold, as evident in coupled-channels K-matrix fits and chiral models that incorporate the S11 N*(1535) resonance, is included self consistently in eta-nuclear bound state calculations. This approach, applied recently in calculations of kaonic atoms and Kbar-nuclear bound states, is found to impose stronger constraints than ever on the onset of eta-nuclear binding, with a minimum value of Re a_{eta N} approximately 0.9 fm required to accommodate an eta-4He bound state. Binding energies and widths of eta-nuclear states are calculated within several underlying eta-N models for nuclei across the periodic table, including eta-25Mg for which some evidence was proposed in a recent COSY experiment.
Improved Range Searching Lower Bounds
Larsen, Kasper Green; Nguyen, Huy L.
2012-01-01
Table of Contents -------------------------------------------------------------------------------- In this paper we present a number of improved lower bounds for range searching in the pointer machine and the group model. In the pointer machine, we prove lower bounds for the approximate simplex...... range reporting problem. In approximate simplex range reporting, points that lie within a distance of ε ⋅ Diam(s) from the border of a query simplex s, are free to be included or excluded from the output, where ε ≥ 0 is an input parameter to the range searching problem. We prove our lower bounds...... by constructing a hard input set and query set, and then invoking Chazelle and Rosenberg's [CGTA'96] general theorem on the complexity of navigation in the pointer machine. For the group model, we show that input sets and query sets that are hard for range reporting in the pointer machine (i.e. by Chazelle...
Experimental activation of bound entanglement.
Kaneda, Fumihiro; Shimizu, Ryosuke; Ishizaka, Satoshi; Mitsumori, Yasuyoshi; Kosaka, Hideo; Edamatsu, Keiichi
2012-07-27
Entanglement is one of the essential resources in quantum information and communication technology (QICT). The entanglement thus far explored and applied to QICT has been pure and distillable entanglement. Yet, there is another type of entanglement, called "bound entanglement," which is not distillable by local operations and classical communication. We demonstrate the experimental "activation" of the bound entanglement held in the four-qubit Smolin state, unleashing its immanent entanglement in distillable form, with the help of auxiliary two-qubit entanglement and local operations and classical communication. We anticipate that it opens the way to a new class of QICT applications that utilize more general classes of entanglement than ever, including bound entanglement.
The “Fallacy” of Maximizing the Geometric Mean in Long Sequences of Investing or Gambling
Samuelson, Paul A.
1971-01-01
Because the outcomes of repeated investments or gambles involve products of variables, authorities have repeatedly been tempted to the belief that, in a long sequence, maximization of the expected value of terminal utility can be achieved or well-approximated by a strategy of maximizing at each stage the geometric mean of outcome (or its equivalent, the expected value of the logarithm of principal plus return). The law of large numbers or of the central limit theorem as applied to the logs can validate the conclusion that a maximum-geometric-mean strategy does indeed make it “virtually certain” that, in a “long” sequence, one will end with a higher terminal wealth and utility. However, this does not imply the false corollary that the geometric-mean strategy is optimal for any finite number of periods, however long, or that it becomes asymptotically a good approximation. As a trivial counter-example, it is shown that for utility proportional to xγ/γ, whenever γ ≠ 0, the geometric strategy is suboptimal for all T and never a good approximation. For utility bounded above, as when γ < 0, the same conclusion holds. If utility is bounded above and finite at zero wealth, no uniform strategy can be optimal, even though it can be that the best uniform strategy will be that of the maximum geometric mean. However, asymptotically the same level of utility can be reached by an infinity of nearby uniform strategies. The true optimum in the bounded case involves nonuniform strategies, usually being more risky than the geometric-mean maximizer's strategy at low wealths and less risky at high wealths. The novel criterion of maximizing the expected average compound return, which asymptotically leads to maximizing of geometric mean, is shown to be arbitrary. PMID:16591949
Directed evolution of estrogen receptor proteins with altered ligand-binding specificities.
Islam, Kazi Mohammed Didarul; Dilcher, Meik; Thurow, Corinna; Vock, Carsten; Krimmelbein, Ilga Kristine; Tietze, Lutz Friedjan; Gonzalez, Victor; Zhao, Huimin; Gatz, Christiane
2009-01-01
Transcriptional activators that respond to ligands with no cellular targets are powerful tools that can confer regulated expression of a transgene in almost all biological systems. In this study, we altered the ligand-binding specificity of the human estrogen receptor alpha (hER alpha) so that it would recognize a non-steroidal synthetic compound with structural similarities to the phytoestrogen resveratrol. For this purpose, we performed iterative rounds of site-specific saturation mutagenesis of a fixed set of ligand-contacting residues and subsequent random mutagenesis of the entire ligand-binding domain. Selection of the receptor mutants and quantification of the interaction were carried out by exploiting a yeast two-hybrid system that reports the ligand-dependent interaction between hER alpha and steroid receptor coactivator-1 (SRC-1). The screen was performed with a synthetic ligand (CV3320) that promoted growth of the reporter yeast strain to half maximal levels at a concentration of 3.7 microM. The optimized receptor mutant (L384F/L387M/Y537S) showed a 67-fold increased activity to the synthetic ligand CV3320 (half maximal yeast growth at 0.055 microM) and a 10-fold decreased activity to 17beta-estradiol (E2; half maximal yeast growth at 4 nM). The novel receptor-ligand pair partially fulfills the requirements for a specific 'gene switch' as it responds to concentrations of the synthetic ligand which do not activate the wildtype receptor. Due to its residual responsiveness to E2 at concentrations (4 nM) that might occur in vivo, further improvements have to be performed to render the system applicable in organisms with endogenous E2 synthesis.
Modeling agreement on bounded scales.
Vanbelle, Sophie; Lesaffre, Emmanuel
2017-01-01
Agreement is an important concept in medical and behavioral sciences, in particular in clinical decision making where disagreements possibly imply a different patient management. The concordance correlation coefficient is an appropriate measure to quantify agreement between two scorers on a quantitative scale. However, this measure is based on the first two moments, which could poorly summarize the shape of the score distribution on bounded scales. Bounded outcome scores are common in medical and behavioral sciences. Typical examples are scores obtained on visual analog scales and scores derived as the number of positive items on a questionnaire. These kinds of scores often show a non-standard distribution, like a J- or U-shape, questioning the usefulness of the concordance correlation coefficient as agreement measure. The logit-normal distribution has shown to be successful in modeling bounded outcome scores of two types: (1) when the bounded score is a coarsened version of a latent score with a logit-normal distribution on the [0,1] interval and (2) when the bounded score is a proportion with the true probability having a logit-normal distribution. In the present work, a model-based approach, based on a bivariate generalization of the logit-normal distribution, is developed in a Bayesian framework to assess the agreement on bounded scales. This method permits to directly study the impact of predictors on the concordance correlation coefficient and can be simply implemented in standard Bayesian softwares, like JAGS and WinBUGS. The performances of the new method are compared to the classical approach using simulations. Finally, the methodology is used in two different medical domains: cardiology and rheumatology.
Lower Bounds for Sparse Recovery
Ba, Khanh Do; Price, Eric; Woodruff, David P
2011-01-01
We consider the following k-sparse recovery problem: design an m x n matrix A, such that for any signal x, given Ax we can efficiently recover x' satisfying ||x-x'||_1 <= C min_{k-sparse} x"} ||x-x"||_1. It is known that there exist matrices A with this property that have only O(k log (n/k)) rows. In this paper we show that this bound is tight. Our bound holds even for the more general /randomized/ version of the problem, where A is a random variable and the recovery algorithm is required to work for any fixed x with constant probability (over A).
Variables Bounding Based Retiming Algorithm
宫宗伟; 林争辉; 陈后鹏
2002-01-01
Retiming is a technique for optimizing sequential circuits. In this paper, wediscuss this problem and propose an improved retiming algorithm based on variables bounding.Through the computation of the lower and upper bounds on variables, the algorithm can signi-ficantly reduce the number of constraints and speed up the execution of retiming. Furthermore,the elements of matrixes D and W are computed in a demand-driven way, which can reducethe capacity of memory. It is shown through the experimental results on ISCAS89 benchmarksthat our algorithm is very effective for large-scale sequential circuits.
Bounds for Completely Decomposable Jacobians
Duursma, Iwan
2010-01-01
A curve over the field of two elements with completely decomposable Jacobian is shown to have at most six rational points and genus at most 26. The bounds are sharp. The previous upper bound for the genus was 145. We also show that a curve over the field of $q$ elements with more than $q^{m/2}+1$ rational points has at least one Frobenius angle in the open interval $(\\pi/m,3\\pi/m)$. The proofs make use of the explicit formula method.
Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop.
Adams, Paul D; Aertgeerts, Kathleen; Bauer, Cary; Bell, Jeffrey A; Berman, Helen M; Bhat, Talapady N; Blaney, Jeff M; Bolton, Evan; Bricogne, Gerard; Brown, David; Burley, Stephen K; Case, David A; Clark, Kirk L; Darden, Tom; Emsley, Paul; Feher, Victoria A; Feng, Zukang; Groom, Colin R; Harris, Seth F; Hendle, Jorg; Holder, Thomas; Joachimiak, Andrzej; Kleywegt, Gerard J; Krojer, Tobias; Marcotrigiano, Joseph; Mark, Alan E; Markley, John L; Miller, Matthew; Minor, Wladek; Montelione, Gaetano T; Murshudov, Garib; Nakagawa, Atsushi; Nakamura, Haruki; Nicholls, Anthony; Nicklaus, Marc; Nolte, Robert T; Padyana, Anil K; Peishoff, Catherine E; Pieniazek, Susan; Read, Randy J; Shao, Chenghua; Sheriff, Steven; Smart, Oliver; Soisson, Stephen; Spurlino, John; Stouch, Terry; Svobodova, Radka; Tempel, Wolfram; Terwilliger, Thomas C; Tronrud, Dale; Velankar, Sameer; Ward, Suzanna C; Warren, Gregory L; Westbrook, John D; Williams, Pamela; Yang, Huanwang; Young, Jasmine
2016-04-05
Crystallographic studies of ligands bound to biological macromolecules (proteins and nucleic acids) represent an important source of information concerning drug-target interactions, providing atomic level insights into the physical chemistry of complex formation between macromolecules and ligands. Of the more than 115,000 entries extant in the Protein Data Bank (PDB) archive, ∼75% include at least one non-polymeric ligand. Ligand geometrical and stereochemical quality, the suitability of ligand models for in silico drug discovery and design, and the goodness-of-fit of ligand models to electron-density maps vary widely across the archive. We describe the proceedings and conclusions from the first Worldwide PDB/Cambridge Crystallographic Data Center/Drug Design Data Resource (wwPDB/CCDC/D3R) Ligand Validation Workshop held at the Research Collaboratory for Structural Bioinformatics at Rutgers University on July 30-31, 2015. Experts in protein crystallography from academe and industry came together with non-profit and for-profit software providers for crystallography and with experts in computational chemistry and data archiving to discuss and make recommendations on best practices, as framed by a series of questions central to structural studies of macromolecule-ligand complexes. What data concerning bound ligands should be archived in the PDB? How should the ligands be best represented? How should structural models of macromolecule-ligand complexes be validated? What supplementary information should accompany publications of structural studies of biological macromolecules? Consensus recommendations on best practices developed in response to each of these questions are provided, together with some details regarding implementation. Important issues addressed but not resolved at the workshop are also enumerated. Copyright © 2016 Elsevier Ltd. All rights reserved.
Heidi Koldsø
Full Text Available The competitive inhibitor cocaine and the non-competitive inhibitor ibogaine induce different conformational states of the human serotonin transporter. It has been shown from accessibility experiments that cocaine mainly induces an outward-facing conformation, while the non-competitive inhibitor ibogaine, and its active metabolite noribogaine, have been proposed to induce an inward-facing conformation of the human serotonin transporter similar to what has been observed for the endogenous substrate, serotonin. The ligand induced conformational changes within the human serotonin transporter caused by these three different types of ligands, substrate, non-competitive and competitive inhibitors, are studied from multiple atomistic molecular dynamics simulations initiated from a homology model of the human serotonin transporter. The results reveal that diverse conformations of the human serotonin transporter are captured from the molecular dynamics simulations depending on the type of the ligand bound. The inward-facing conformation of the human serotonin transporter is reached with noribogaine bound, and this state resembles a previously identified inward-facing conformation of the human serotonin transporter obtained from molecular dynamics simulation with bound substrate, but also a recently published inward-facing conformation of a bacterial homolog, the leucine transporter from Aquifex Aoelicus. The differences observed in ligand induced behavior are found to originate from different interaction patterns between the ligands and the protein. Such atomic-level understanding of how an inhibitor can dictate the conformational response of a transporter by ligand binding may be of great importance for future drug design.
Koldsø, Heidi; Autzen, Henriette Elisabeth; Grouleff, Julie; Schiøtt, Birgit
2013-01-01
The competitive inhibitor cocaine and the non-competitive inhibitor ibogaine induce different conformational states of the human serotonin transporter. It has been shown from accessibility experiments that cocaine mainly induces an outward-facing conformation, while the non-competitive inhibitor ibogaine, and its active metabolite noribogaine, have been proposed to induce an inward-facing conformation of the human serotonin transporter similar to what has been observed for the endogenous substrate, serotonin. The ligand induced conformational changes within the human serotonin transporter caused by these three different types of ligands, substrate, non-competitive and competitive inhibitors, are studied from multiple atomistic molecular dynamics simulations initiated from a homology model of the human serotonin transporter. The results reveal that diverse conformations of the human serotonin transporter are captured from the molecular dynamics simulations depending on the type of the ligand bound. The inward-facing conformation of the human serotonin transporter is reached with noribogaine bound, and this state resembles a previously identified inward-facing conformation of the human serotonin transporter obtained from molecular dynamics simulation with bound substrate, but also a recently published inward-facing conformation of a bacterial homolog, the leucine transporter from Aquifex Aoelicus. The differences observed in ligand induced behavior are found to originate from different interaction patterns between the ligands and the protein. Such atomic-level understanding of how an inhibitor can dictate the conformational response of a transporter by ligand binding may be of great importance for future drug design.
Bounding Radionuclide Inventory and Accident Consequence Calculation for the 1L Target
Kelsey, Charles T. IV [Los Alamos National Laboratory
2011-01-01
A bounding radionuclide inventory for the tungsten of the Los Alamos Neutron Science Center (LANSCE) IL Target is calculated. Based on the bounding inventory, the dose resulting from the maximum credible incident (MCI) is calculated for the maximally exposed offsite individual (MEOl). The design basis accident involves tungsten target oxidation following a loss of cooling accident. Also calculated for the bounding radionuclide inventory is the ratio to the LANSCE inventory threshold for purposes of inventory control as described in the target inventory control policy. A bounding radionuclide inventory calculation for the lL Target was completed using the MCNPX and CINDER'90 codes. Continuous beam delivery at 200 {micro}A to 2500 mA{center_dot}h was assumed. The total calculated activity following this irradiation period is 205,000 Ci. The dose to the MEOI from the MCI is 213 mrem for the bounding inventory. The LANSCE inventory control threshold ratio is 132.
Welfare-maximizing and revenue-maximizing tariffs with a few domestic firms
Bruno Larue; Jean-Philippe Gervais
2002-01-01
In this paper we compare the orthodox optimal tariff formula with the appropriate welfare-maximizing tariff when there are a few producing or importing firms. The welfare-maximizing tariff can be very low, voire negative in some cases, while in others it can even exceed the maximum-revenue tariff. The relationship between the welfare-maximizing tariff and the number of firms need not be monotonically increasing, because the tariff is not strictly used to internalize terms of trade externality...
On the existence of maximizing measures for irreducible countable Markov shifts: a dynamical proof
Bissacot, Rodrigo
2011-01-01
We prove that if $\\Sigma_{\\mathbf A}(\\mathbb N)$ is an irreducible Markov shift space over $\\mathbb N$ and $f:\\Sigma_{\\mathbf A}(\\mathbb N) \\rightarrow \\mathbb R$ is coercive with bounded variation then there exists a maxi-mizing probability measure for $f$, whose support lies on a Markov subshift over a finite alphabet. Furthermore, the support of any maximizing measure is contained in this same compact subshift. To the best of our knowledge, this is the first proof of the existence of maximizing measures beyond the finitely primitive case on the non-compact setting. It's also noteworthy that our technique works in the case of the full shift over positive real sequences.
Carathéodory系统的最大解%Maximal Solutions of Carathéodory Systems
马学敏
2012-01-01
By using the Henstock-Kurzweil integral,the maximal solutions and its properties of continuous and bounded variation solutions for Carathéodory systems are discussed.%利用Henstock-kurzweil积分,讨论了Carathéodory系统的连续有界变差解的最大解及其性质.
Bounded Nonlinear Control of a Rotating Pendulum System
Luyckx, L.; Loccufier, M.; Noldus, E.
2004-08-01
We are interested in the output feedback control of mechanical systems governed by the Euler-Lagrange formalism. The systems are collocated actuator-sensor controlled and underactuated. We present a design method by means of a specific example : the set point control of a rotating pendulum. We use constrained output feedback, whereby the control inputs satisfy a priori imposed upper bounds. The closed loop stability analysis relies on the direct method of Liapunov. This results in a frequency criterion on the controller's linear dynamic component and some restrictions on its nonlinearities. The control parameters are tuned for maximizing closed loop damping.
Maximizing Complementary Quantities by Projective Measurements
M. Souza, Leonardo A.; Bernardes, Nadja K.; Rossi, Romeu
2017-04-01
In this work, we study the so-called quantitative complementarity quantities. We focus in the following physical situation: two qubits ( q A and q B ) are initially in a maximally entangled state. One of them ( q B ) interacts with a N-qubit system ( R). After the interaction, projective measurements are performed on each of the qubits of R, in a basis that is chosen after independent optimization procedures: maximization of the visibility, the concurrence, and the predictability. For a specific maximization procedure, we study in detail how each of the complementary quantities behave, conditioned on the intensity of the coupling between q B and the N qubits. We show that, if the coupling is sufficiently "strong," independent of the maximization procedure, the concurrence tends to decay quickly. Interestingly enough, the behavior of the concurrence in this model is similar to the entanglement dynamics of a two qubit system subjected to a thermal reservoir, despite that we consider finite N. However, the visibility shows a different behavior: its maximization is more efficient for stronger coupling constants. Moreover, we investigate how the distinguishability, or the information stored in different parts of the system, is distributed for different couplings.
Real weights, bound states and duality orbits
Marrani, Alessio; Romano, Luca
2015-01-01
We show that the duality orbits of extremal black holes in supergravity theories with symmetric scalar manifolds can be derived by studying the stabilizing subalgebras of suitable representatives, realized as bound states of specific weight vectors of the corresponding representation of the duality symmetry group. The weight vectors always correspond to weights that are real, where the reality properties are derived from the Tits-Satake diagram that identifies the real form of the Lie algebra of the duality symmetry group. Both N=2 magic Maxwell-Einstein supergravities and the semisimple infinite sequences of N=2 and N=4 theories in D=4 and 5 are considered, and various results, obtained over the years in the literature using different methods, are retrieved. In particular, we show that the stratification of the orbits of these theories occurs because of very specific properties of the representations: in the case of the theory based on the real numbers, whose symmetry group is maximally non-compact and there...
More bounds on the diameters of convex polytopes
Bremner, David; Hua, William; Schewe, Lars
2009-01-01
Finding a good bound on the maximal edge diameter $\\Delta(d,n)$ of a polytope in terms of its dimension $d$ and the number of its facets $n$ is one of the basic open questions in polytope theory \\cite{BG}. Although some bounds are known, the behaviour of the function $\\Delta(d,n)$ is largely unknown. The Hirsch conjecture, formulated in 1957 and reported in \\cite{GD}, states that $\\Delta(d,n)$ is linear in $n$ and $d$: $\\Delta(d,n) \\leq n-d$. The conjecture is known to hold in small dimensions, i.e., for $d \\leq 3$ \\cite{VK}, along with other specific pairs of $d$ and $n$ (Table \\ref{before}). However, the asymptotic behaviour of $\\Delta(d,n)$ is not well understood: the best upper bound -- due to Kalai and Kleitman -- is quasi-polynomial \\cite{GKDK}. In this article we will show that $\\Delta(4,12)=7$ and present strong evidence for $\\Delta(5,12)=\\Delta(6,13)=7$. The first of these new values is of particular interest since it indicates that the Hirsch bound is not sharp in dimension 4.
Higgs Mass Triviality Bounds on F(4) Lattices
Klomfass, Markus
In order to accurately describe the cutoff dependence of the Higgs mass triviality bound, the varphi ^4 theory is formulated on an F_4 lattice which preserves Lorentz invariance to a higher degree than the commonly used hypercubic lattice. We solve this model non-perturbatively by evaluating the linked cluster expansion through 12th order following the approach of Luscher and Weisz. The results are continued across the transition line into the broken phase by integrating the perturbative renormalization group equations. In the Goldstone phase, the renormalized coupling never exceeds 2/3 of the tree level unitarity bound when Lambda /m_{R}>= 2. Our results confirm recent Monte Carlo data and we obtain as an upper bound for the Higgs mass m_{R }/f_pi=2.45(7) at Lambda/m_{R }=2. Attempting to produce a heavier Higgs on the lattice, additional four-derivative terms are introduced in the naive action which serve to parameterize the leading order cutoff effects. Using a cluster reflection algorithm of the Swendsen-Wang-Wolff type, we simulate this action on an F_4 lattice in a region where the region where the effects of the new terms are expected to be maximal. As an upper bound we now obtain M _sigma/f_pi~ 2.8, an increase of about 20% compared to the simplest non-linear action. Despite triviality, the scalar sector may thus not be weakly interacting.
Market access through bound tariffs
Sala, Davide; Schröder, Philipp J.H.; Yalcin, Erdal
2010-01-01
WTO negotiations deal predominantly with bound - besides applied - tariff rates. But, how can reductions in tariffs ceilings, i.e. tariff rates that no exporter may ever actually be confronted with, generate market access? The answer to this question relates to the effects of tariff bindings on t...
Market Access through Bound Tariffs
Sala, Davide; Schröder, Philipp J.H.; Yalcin, Erdal
WTO negotiations deal predominantly with bound - besides applied - tariff rates. But, how can reductions in tariffs ceilings, i.e. tariff rates that no exporter may ever actually be confronted with, generate market access? The answer to this question relates to the effects of tariff bindings on t...
Bounded Densities and Their Derivatives
Kozine, Igor; Krymsky, V.
2009-01-01
This paper describes how one can compute interval-valued statistical measures given limited information about the underlying distribution. The particular focus is on a bounded derivative of a probability density function and its combination with other available statistical evidence for computing ...
Wronskian Method for Bound States
Fernandez, Francisco M.
2011-01-01
We propose a simple and straightforward method based on Wronskians for the calculation of bound-state energies and wavefunctions of one-dimensional quantum-mechanical problems. We explicitly discuss the asymptotic behaviour of the wavefunction and show that the allowed energies make the divergent part vanish. As illustrative examples we consider…
Variational Bounds for Creeping Composites
Procházka, Petr
2010-05-01
In the paper time dependent variational bounds are derived based on Extended Hashin-Shtrikman variational principles. Direct calculation leads to explicit formulas to be presented in the text. For various mechanical properties easy coding in Excel, say, can be used and verification of accuracy for numerical procedures is available using the derived formulas.
Pieter Paul Rubens, "Prometheus Bound."
Shoemaker, Marla K.
1986-01-01
Provides a full-color reproduction of Pieter Paul Rubens' painting, "Prometheus Bound," and a lesson plan for using it with students in grades 10 through 12. The goal of the lesson is to introduce students to the techniques of design and execution used by Rubens. (JDH)
Carvalho, Catarina; MarkoviÄ, Petar; Maróti, Miklós
2007-01-01
We prove that the constraint languages invariant under a short sequence of J\\'onsson terms (containing at most three non-trivial ternary terms) are tractable by showing that they have bounded width. This improves the previous result by Kiss and Valeriote and presents some evidence that the Larose-Zadori conjecture holds in the congruence-distributive case.
Pieter Paul Rubens, "Prometheus Bound."
Shoemaker, Marla K.
1986-01-01
Provides a full-color reproduction of Pieter Paul Rubens' painting, "Prometheus Bound," and a lesson plan for using it with students in grades 10 through 12. The goal of the lesson is to introduce students to the techniques of design and execution used by Rubens. (JDH)
Conformational dynamics of a ligand-free adenylate kinase.
Hyun Deok Song
Full Text Available Adenylate kinase (AdK is a phosphoryl-transfer enzyme with important physiological functions. Based on a ligand-free open structure and a ligand-bound closed structure solved by crystallography, here we use molecular dynamics simulations to examine the stability and dynamics of AdK conformations in the absence of ligands. We first perform multiple simulations starting from the open or the closed structure, and observe their free evolutions during a simulation time of 100 or 200 nanoseconds. In all seven simulations starting from the open structure, AdK remained stable near the initial conformation. The eight simulations initiated from the closed structure, in contrast, exhibited large variation in the subsequent evolutions, with most (seven undergoing large-scale spontaneous conformational changes and approaching or reaching the open state. To characterize the thermodynamics of the transition, we propose and apply a new sampling method that employs a series of restrained simulations to calculate a one-dimensional free energy along a curved pathway in the high-dimensional conformational space. Our calculated free energy profile features a single minimum at the open conformation, and indicates that the closed state, with a high (∼13 kcal/mol free energy, is not metastable, consistent with the observed behaviors of the unrestrained simulations. Collectively, our simulations suggest that it is energetically unfavorable for the ligand-free AdK to access the closed conformation, and imply that ligand binding may precede the closure of the enzyme.
A Functional Calculus for Quotient Bounded Operators
Sorin Mirel Stoian
2006-12-01
Full Text Available If (X, P is a sequentially locally convex space, then a quotient bounded operator T beloging to QP is regular (in the sense of Waelbroeck if and only if it is a bounded element (in the sense of Allan of algebra QP. The classic functional calculus for bounded operators on Banach space is generalized for bounded elements of algebra QP.
Polyploidy Induction of Pteroceltis tatarinowii Maxim
Lin ZHANG; Feng WANG; Zhongkui SUN; Cuicui ZHU; Rongwei CHEN
2015-01-01
3%Objective] This study was conducted to obtain tetraploid Pteroceltis tatari-nowi Maxim. with excel ent ornamental traits. [Method] The stem apex growing points of Pteroceltis tatarinowi Maxim. were treated with different concentrations of colchicine solution for different hours to figure out a proper method and obtain poly-ploids. [Result] The most effective induction was obtained by treatment with 0.6%-0.8% colchicine for 72 h with 34.2% mutation rate. Flow cytometry and chromosome observation of the stem apex growing point of P. tatarinowi Maxim. proved that the tetraploid plants were successful y obtained with chromosome number 2n=4x=36. [Conclusion] The result not only fil s the blank of polyploid breeding of P. tatarinowi , but also provides an effective way to broaden the methods of cultivation of fast-growing, high-quality, disease-resilience, new varieties of Pteroceltis.
Quantum theory allows for absolute maximal contextuality
Amaral, Barbara; Cunha, Marcelo Terra; Cabello, Adán
2015-12-01
Contextuality is a fundamental feature of quantum theory and a necessary resource for quantum computation and communication. It is therefore important to investigate how large contextuality can be in quantum theory. Linear contextuality witnesses can be expressed as a sum S of n probabilities, and the independence number α and the Tsirelson-like number ϑ of the corresponding exclusivity graph are, respectively, the maximum of S for noncontextual theories and for the theory under consideration. A theory allows for absolute maximal contextuality if it has scenarios in which ϑ /α approaches n . Here we show that quantum theory allows for absolute maximal contextuality despite what is suggested by the examination of the quantum violations of Bell and noncontextuality inequalities considered in the past. Our proof is not constructive and does not single out explicit scenarios. Nevertheless, we identify scenarios in which quantum theory allows for almost-absolute-maximal contextuality.
The maximal process of nonlinear shot noise
Eliazar, Iddo; Klafter, Joseph
2009-05-01
In the nonlinear shot noise system-model shots’ statistics are governed by general Poisson processes, and shots’ decay-dynamics are governed by general nonlinear differential equations. In this research we consider a nonlinear shot noise system and explore the process tracking, along time, the system’s maximal shot magnitude. This ‘maximal process’ is a stationary Markov process following a decay-surge evolution; it is highly robust, and it is capable of displaying both a wide spectrum of statistical behaviors and a rich variety of random decay-surge sample-path trajectories. A comprehensive analysis of the maximal process is conducted, including its Markovian structure, its decay-surge structure, and its correlation structure. All results are obtained analytically and in closed-form.
Energy Band Calculations for Maximally Even Superlattices
Krantz, Richard; Byrd, Jason
2007-03-01
Superlattices are multiple-well, semiconductor heterostructures that can be described by one-dimensional potential wells separated by potential barriers. We refer to a distribution of wells and barriers based on the theory of maximally even sets as a maximally even superlattice. The prototypical example of a maximally even set is the distribution of white and black keys on a piano keyboard. Black keys may represent wells and the white keys represent barriers. As the number of wells and barriers increase, efficient and stable methods of calculation are necessary to study these structures. We have implemented a finite-element method using the discrete variable representation (FE-DVR) to calculate E versus k for these superlattices. Use of the FE-DVR method greatly reduces the amount of calculation necessary for the eigenvalue problem.
Singular Value Decomposition and Ligand Binding Analysis
André Luiz Galo
2013-01-01
Full Text Available Singular values decomposition (SVD is one of the most important computations in linear algebra because of its vast application for data analysis. It is particularly useful for resolving problems involving least-squares minimization, the determination of matrix rank, and the solution of certain problems involving Euclidean norms. Such problems arise in the spectral analysis of ligand binding to macromolecule. Here, we present a spectral data analysis method using SVD (SVD analysis and nonlinear fitting to determine the binding characteristics of intercalating drugs to DNA. This methodology reduces noise and identifies distinct spectral species similar to traditional principal component analysis as well as fitting nonlinear binding parameters. We applied SVD analysis to investigate the interaction of actinomycin D and daunomycin with native DNA. This methodology does not require prior knowledge of ligand molar extinction coefficients (free and bound, which potentially limits binding analysis. Data are acquired simply by reconstructing the experimental data and by adjusting the product of deconvoluted matrices and the matrix of model coefficients determined by the Scatchard and McGee and von Hippel equation.
Absence of parasympathetic reactivation after maximal exercise.
de Oliveira, Tiago Peçanha; de Alvarenga Mattos, Raphael; da Silva, Rhenan Bartels Ferreira; Rezende, Rafael Andrade; de Lima, Jorge Roberto Perrout
2013-03-01
The ability of the human organism to recover its autonomic balance soon after physical exercise cessation has an important impact on the individual's health status. Although the dynamics of heart rate recovery after maximal exercise has been studied, little is known about heart rate variability after this type of exercise. The aim of this study is to analyse the dynamics of heart rate and heart rate variability recovery after maximal exercise in healthy young men. Fifteen healthy male subjects (21·7 ± 3·4 years; 24·0 ± 2·1 kg m(-2) ) participated in the study. The experimental protocol consisted of an incremental maximal exercise test on a cycle ergometer, until maximal voluntary exhaustion. After the test, recovery R-R intervals were recorded for 5 min. From the absolute differences between peak heart rate values and the heart rate values at 1 and 5 min of the recovery, the heart rate recovery was calculated. Postexercise heart rate variability was analysed from calculations of the SDNN and RMSSD indexes, in 30-s windows (SDNN(30s) and RMSSD(30s) ) throughout recovery. One and 5 min after maximal exercise cessation, the heart rate recovered 34·7 (±6·6) and 75·5 (±6·1) bpm, respectively. With regard to HRV recovery, while the SDNN(30s) index had a slight increase, RMSSD(30s) index remained totally suppressed throughout the recovery, suggesting an absence of vagal modulation reactivation and, possibly, a discrete sympathetic withdrawal. Therefore, it is possible that the main mechanism associated with the fall of HR after maximal exercise is sympathetic withdrawal or a vagal tone restoration without vagal modulation recovery. © 2012 The Authors Clinical Physiology and Functional Imaging © 2012 Scandinavian Society of Clinical Physiology and Nuclear Medicine.
Maximizing band gaps in plate structures
Halkjær, Søren; Sigmund, Ole; Jensen, Jakob Søndergaard
2006-01-01
Band gaps, i.e., frequency ranges in which waves cannot propagate, can be found in elastic structures for which there is a certain periodic modulation of the material properties or structure. In this paper, we maximize the band gap size for bending waves in a Mindlin plate. We analyze an infinite...... periodic plate using Bloch theory, which conveniently reduces the maximization problem to that of a single base cell. Secondly, we construct a finite periodic plate using a number of the optimized base cells in a postprocessed version. The dynamic properties of the finite plate are investigated...
Maximal and Minimal Congruences on Some Semigroups
Jintana SANWONG; Boorapa SINGHA; R.P.SULLIVAN
2009-01-01
In 2006,Sanwong and Sullivan described the maximal congruences on the semigroup N consisting of all non-negative integers under standard multiplication,and on the semigroup T(X) consisting of all total transformations of an infinite set X under composition. Here,we determine all maximal congruences on the semigroup Zn under multiplication modulo n. And,when Y X,we do the same for the semigroup T(X,Y) consisting of all elements of T(X) whose range is contained in Y. We also characterise the minimal congruences on T(X,Y).
Maximizing oil yields may not optimize economics
1987-03-01
The Los Alamos National Laboratory has used the ASPEN computer code to calculate the economics of different hydroretorting conditions. When the oil yield was maximized and a oil shale plant designed around this process, the costs turned out much higher than expected. However, calculations based on runs of less than maximum yields showed lower cost estimates. It is recommended that future efforts should be concentrated on minimizing production costs rather than maximizing yields. An oil shale plant has been designed around minimum production cost, but has not been able to be tested experimentally.
Maximal Inequalities for Dependent Random Variables
Hoffmann-Jorgensen, Jorgen
2016-01-01
Maximal inequalities play a crucial role in many probabilistic limit theorem; for instance, the law of large numbers, the law of the iterated logarithm, the martingale limit theorem and the central limit theorem. Let X-1, X-2,... be random variables with partial sums S-k = X-1 + ... + X-k. Then a......Maximal inequalities play a crucial role in many probabilistic limit theorem; for instance, the law of large numbers, the law of the iterated logarithm, the martingale limit theorem and the central limit theorem. Let X-1, X-2,... be random variables with partial sums S-k = X-1 + ... + X...
Singularity Structure of Maximally Supersymmetric Scattering Amplitudes
Arkani-Hamed, Nima; Bourjaily, Jacob L.; Cachazo, Freddy
2014-01-01
We present evidence that loop amplitudes in maximally supersymmetric (N=4) Yang-Mills theory (SYM) beyond the planar limit share some of the remarkable structures of the planar theory. In particular, we show that through two loops, the four-particle amplitude in full N=4 SYM has only logarithmic ...... singularities and is free of any poles at infinity—properties closely related to uniform transcendentality and the UV finiteness of the theory. We also briefly comment on implications for maximal (N=8) supergravity theory (SUGRA)....
Selenolate complexes of CYP101 and the heme-bound hHO-1/H25A proximal cavity mutant.
Jiang, Yongying; Ortiz de Montellano, Paul R
2008-05-05
Thiolate and selenolate complexes of CYP101 (P450cam) and the H25A proximal cavity mutant of heme-bound human heme oxygenase-1 (hHO-1) have been examined by UV-vis spectroscopy. Both thiolate and selenolate ligands bound to the heme distal side in CYP101 and gave rise to characteristic hyperporphyrin spectra. Thiolate ligands also bound to the proximal side of the heme in the cavity created by the H25A mutation in hHO-1, giving a Soret absorption similar to that of the H25C hHO-1 mutant. Selenolate ligands also bound to this cavity mutant under anaerobic conditions but reduced the heme iron to the ferrous state, as shown by the formation of a ferrous CO complex. Under aerobic conditions, the selenolate ligand but not the thiolate ligand was rapidly oxidized. These results indicate that selenocysteine-coordinated heme proteins will not be stable species in the absence of a redox potential stabilizing effect.
Hadar, Ido; Abir, Tsafrir; Halivni, Shira; Faust, Adam; Banin, Uri
2015-10-12
Colloidal semiconductor nanocrystals (NC) have reached a high level of synthetic control allowing the tuning of their properties, and their use in various applications. However, the surface of NCs and in particular their size-dependent capping organic ligand behavior, which play an important role in the NC synthesis, dispersibility, and optoelectronic properties, is still not well understood. We study the size-dependent properties of the ligand shell on the surface of NCs, by embedding surface bound dyes as a probe within the ligand shell. The reorientation times for these dyes show a linear dependence on the NC surface curvature indicating size-dependent change in viscosity, which is related to a change in the density of the ligand layer because of the geometry of the surface, a unique feature of NCs. Understanding the properties of the ligand shell will allow rational design of the surface to achieve the desired properties, providing an additional important knob for tuning their functionality.
Ligand Binding and Conformational Changes in the Purine-Binding Riboswitch Aptamer Domains
Noeske, Jonas; Buck, Janina; Wöhnert, Jens; Schwalbe, Harald
Riboswitches are highly structured mRNA elements that regulate gene expression upon specific binding of small metabolite molecules. The purine-binding riboswitches bind different purine ligands by forming both canonical Watson—Crick and non-canonical intermolecular base pairs, involving a variety of hydrogen bonds between the riboswitch aptamer domain and the purine ligand. Here, we summarize work on the ligand binding modes of both purine-binding aptamer domains, their con-formational characteristics in the free and ligand-bound forms, and their ligand-induced folding. The adenine- and guanine-binding riboswitch aptamer domains display different conformations in their free forms, despite nearly identical nucleotide loop sequences that form a loop—loop interaction in the ligand-bound forms. Interestingly, the stability of helix II is crucial for the formation of the loop—loop interaction in the free form. A more stable helix II in the guanine riboswitch leads to a preformed loop—loop interaction in its free form. In contrast, a less stable helix II in the adenine riboswitch results in a lack of this loop—loop interaction in the absence of ligand and divalent cations.
Melatonin: functions and ligands.
Singh, Mahaveer; Jadhav, Hemant R
2014-09-01
Melatonin is a chronobiotic substance that acts as synchronizer by stabilizing bodily rhythms. Its synthesis occurs in various locations throughout the body, including the pineal gland, skin, lymphocytes and gastrointestinal tract (GIT). Its synthesis and secretion is controlled by light and dark conditions, whereby light decreases and darkness increases its production. Thus, melatonin is also known as the 'hormone of darkness'. Melatonin and analogs that bind to the melatonin receptors are important because of their role in the management of depression, insomnia, epilepsy, Alzheimer's disease (AD), diabetes, obesity, alopecia, migraine, cancer, and immune and cardiac disorders. In this review, we discuss the mechanism of action of melatonin in these disorders, which could aid in the design of novel melatonin receptor ligands.
Maximal entanglement achievable by controlled dynamics
Serafini, Alessio
2009-01-01
We consider the feedback control of quantum systems comprised of any number of bosonic degrees of freedom. We derive a general upper bound for the logarithmic negativity achievable, at steady state, with continuous Gaussian measurements on the environment and linear driving on the system. Our results apply to rotating wave system-bath couplings and to any quadratic system's Hamiltonian. Furthermore, we apply this upper bound to parametric processes, show it to be tight, and compare it to feedback strategies limited to local measurements.
Macrocyclic G-quadruplex ligands
Nielsen, M C; Ulven, Trond
2010-01-01
G-quadruplex stabilizing compounds have recently received increased interest due to their potential application as anticancer therapeutics. A significant number of structurally diverse G-quadruplex ligands have been developed. Some of the most potent and selective ligands currently known are macr...
Gradient dynamics and entropy production maximization
Janečka, Adam
2016-01-01
Gradient dynamics describes irreversible evolution by means of a dissipation potential, which leads to several advantageous features like Maxwell--Onsager relations, distinguishing between thermodynamic forces and fluxes or geometrical interpretation of the dynamics. Entropy production maximization is a powerful tool for predicting constitutive relations in engineering. In this paper, both approaches are compared and their shortcomings and advantages are discussed.
Robust Utility Maximization Under Convex Portfolio Constraints
Matoussi, Anis, E-mail: anis.matoussi@univ-lemans.fr [Université du Maine, Risk and Insurance institut of Le Mans Laboratoire Manceau de Mathématiques (France); Mezghani, Hanen, E-mail: hanen.mezghani@lamsin.rnu.tn; Mnif, Mohamed, E-mail: mohamed.mnif@enit.rnu.tn [University of Tunis El Manar, Laboratoire de Modélisation Mathématique et Numérique dans les Sciences de l’Ingénieur, ENIT (Tunisia)
2015-04-15
We study a robust maximization problem from terminal wealth and consumption under a convex constraints on the portfolio. We state the existence and the uniqueness of the consumption–investment strategy by studying the associated quadratic backward stochastic differential equation. We characterize the optimal control by using the duality method and deriving a dynamic maximum principle.
Maximizing the Motivated Mind for Emergent Giftedness.
Rea, Dan
2001-01-01
This article explains how the theory of the motivated mind conceptualizes the productive interaction of intelligence, creativity, and achievement motivation and how this theory can help educators to maximize students' emergent potential for giftedness. It discusses the integration of cold-order thinking and hot-chaotic thinking into fluid-adaptive…
The Winning Edge: Maximizing Success in College.
Schmitt, David E.
This book offers college students ideas on how to maximize their success in college by examining the personal management techniques a student needs to succeed. Chapters are as follows: "Getting and Staying Motivated"; "Setting Goals and Tapping Your Resources"; "Conquering Time"; "Think Yourself to College Success"; "Understanding and Remembering…
MAXIMAL ELEMENTS AND EQUILIBRIUM OF ABSTRACT ECONOMY
刘心歌; 蔡海涛
2001-01-01
An existence theorem of maximal elements for a new type of preference correspondences which are Qθ-majorized is given. Then some existence theorems of equilibrium for abstract economy and qualitative game in which the constraint or preference correspondences are Qθ-majorized are obtained in locally convex topological vector spaces.
DNA solution of the maximal clique problem.
Ouyang, Q; Kaplan, P D; Liu, S; Libchaber, A
1997-10-17
The maximal clique problem has been solved by means of molecular biology techniques. A pool of DNA molecules corresponding to the total ensemble of six-vertex cliques was built, followed by a series of selection processes. The algorithm is highly parallel and has satisfactory fidelity. This work represents further evidence for the ability of DNA computing to solve NP-complete search problems.
Maximal workload capacity on moving platforms
Heus, R.; Wertheim, A.H.
1996-01-01
Physical tasks on a moving platform required more energy than the same tasks on a non-moving platform. In this study the maximum aerobic performance (defined as V_O2max) of people working on a moving floor was established compared to the maximal aerobic performance on a non-moving floor. The main
Maximal workload capacity on moving platforms
Heus, R.; Wertheim, A.H.
1996-01-01
Physical tasks on a moving platform required more energy than the same tasks on a non-moving platform. In this study the maximum aerobic performance (defined as V_O2max) of people working on a moving floor was established compared to the maximal aerobic performance on a non-moving floor. The main qu
Maximizing Resource Utilization in Video Streaming Systems
Alsmirat, Mohammad Abdullah
2013-01-01
Video streaming has recently grown dramatically in popularity over the Internet, Cable TV, and wire-less networks. Because of the resource demanding nature of video streaming applications, maximizing resource utilization in any video streaming system is a key factor to increase the scalability and decrease the cost of the system. Resources to…
Maximizing throughput in an automated test system
朱君
2007-01-01
@@ Overview This guide is collection of whitepapers designed to help you develop test systems that lower your cost, increase your test throughput, and can scale with future requirements. This whitepaper provides strategies for maximizing system throughput. To download the complete developers guide (120 pages), visit ni. com/automatedtest.
The gaugings of maximal D=6 supergravity
Bergshoeff, E.; Samtleben, H.; Sezgin, E.
2008-01-01
We construct the most general gaugings of the maximal D = 6 supergravity. The theory is ( 2, 2) supersymmetric, and possesses an on-shell SO( 5, 5) duality symmetry which plays a key role in determining its couplings. The field content includes 16 vector fields that carry a chiral spinor representat
WEIGHTED BOUNDEDNESS OF A ROUGH MAXIMAL OPERATOR
无
2000-01-01
In this note the authors give the weighted Lp-boundedness fora class of maximal singular integral operators with rough kernel.The result in this note is an improvement and extension ofthe result obtained by Chen and Lin in 1990.
Maximizing the Range of a Projectile.
Brown, Ronald A.
1992-01-01
Discusses solutions to the problem of maximizing the range of a projectile. Presents three references that solve the problem with and without the use of calculus. Offers a fourth solution suitable for introductory physics courses that relies more on trigonometry and the geometry of the problem. (MDH)
Ehrenfest's Lottery--Time and Entropy Maximization
Ashbaugh, Henry S.
2010-01-01
Successful teaching of the Second Law of Thermodynamics suffers from limited simple examples linking equilibrium to entropy maximization. I describe a thought experiment connecting entropy to a lottery that mixes marbles amongst a collection of urns. This mixing obeys diffusion-like dynamics. Equilibrium is achieved when the marble distribution is…
Testing maximality in muon neutrino flavor mixing
Choubey, S; Choubey, Sandhya; Roy, Probir
2003-01-01
The small difference between the survival probabilities of muon neutrino and antineutrino beams, traveling through earth matter in a long baseline experiment such as MINOS, is shown to be an important measure of any possible deviation from maximality in the flavor mixing of those states.
Average utility maximization: A preference foundation
A.V. Kothiyal (Amit); V. Spinu (Vitalie); P.P. Wakker (Peter)
2014-01-01
textabstractThis paper provides necessary and sufficient preference conditions for average utility maximization over sequences of variable length. We obtain full generality by using a new algebraic technique that exploits the richness structure naturally provided by the variable length of the sequen
On the Hardy-Littlewood maximal theorem
Shinji Yamashita
1982-01-01
Full Text Available The Hardy-Littlewood maximal theorem is extended to functions of class PL in the sense of E. F. Beckenbach and T. Radó, with a more precise expression of the absolute constant in the inequality. As applications we deduce some results on hyperbolic Hardy classes in terms of the non-Euclidean hyperbolic distance in the unit disk.
Maximal Cartel Pricing and Leniency Programs
Houba, H.E.D.; Motchenkova, E.; Wen, Q.
2008-01-01
For a general class of oligopoly models with price competition, we analyze the impact of ex-ante leniency programs in antitrust regulation on the endogenous maximal-sustainable cartel price. This impact depends upon industry characteristics including its cartel culture. Our analysis disentangles the
How to Generate Good Profit Maximization Problems
Davis, Lewis
2014-01-01
In this article, the author considers the merits of two classes of profit maximization problems: those involving perfectly competitive firms with quadratic and cubic cost functions. While relatively easy to develop and solve, problems based on quadratic cost functions are too simple to address a number of important issues, such as the use of…
Ehrenfest's Lottery--Time and Entropy Maximization
Ashbaugh, Henry S.
2010-01-01
Successful teaching of the Second Law of Thermodynamics suffers from limited simple examples linking equilibrium to entropy maximization. I describe a thought experiment connecting entropy to a lottery that mixes marbles amongst a collection of urns. This mixing obeys diffusion-like dynamics. Equilibrium is achieved when the marble distribution is…
Maximally entangled mixed states made easy
Aiello, A; Voigt, D; Woerdman, J P
2006-01-01
We show that, contrarily to a recent claim [M. Ziman and V. Bu\\v{z}ek, Phys. Rev. A. \\textbf{72}, 052325 (2005)], it is possible to achieve maximally entangled mixed states of two qubits from the singlet state via the action of local nonunital quantum channels. Moreover, we present a simple, feasible linear optical implementation of one of such channels.
Maximizing Resource Utilization in Video Streaming Systems
Alsmirat, Mohammad Abdullah
2013-01-01
Video streaming has recently grown dramatically in popularity over the Internet, Cable TV, and wire-less networks. Because of the resource demanding nature of video streaming applications, maximizing resource utilization in any video streaming system is a key factor to increase the scalability and decrease the cost of the system. Resources to…
Maximizing scientific knowledge from randomized clinical trials
Gustafsson, Finn; Atar, Dan; Pitt, Bertram
2010-01-01
Trialists have an ethical and financial responsibility to plan and conduct clinical trials in a manner that will maximize the scientific knowledge gained from the trial. However, the amount of scientific information generated by randomized clinical trials in cardiovascular medicine is highly...
Maximal Heat Generation in Nanoscale Systems
ZHOU Li-Ling; LI Shu-Shen; ZENG Zhao-Yang
2009-01-01
We investigate the heat generation in a nanoscale system coupled to normal leads and find that it is maximal when the average occupation of the electrons in the nanoscale system is 0.5,no matter what mechanism induces the heat generation.
Understanding violations of Gricean maxims in preschoolers and adults.
Okanda, Mako; Asada, Kosuke; Moriguchi, Yusuke; Itakura, Shoji
2015-01-01
This study used a revised Conversational Violations Test to examine Gricean maxim violations in 4- to 6-year-old Japanese children and adults. Participants' understanding of the following maxims was assessed: be informative (first maxim of quantity), avoid redundancy (second maxim of quantity), be truthful (maxim of quality), be relevant (maxim of relation), avoid ambiguity (second maxim of manner), and be polite (maxim of politeness). Sensitivity to violations of Gricean maxims increased with age: 4-year-olds' understanding of maxims was near chance, 5-year-olds understood some maxims (first maxim of quantity and maxims of quality, relation, and manner), and 6-year-olds and adults understood all maxims. Preschoolers acquired the maxim of relation first and had the greatest difficulty understanding the second maxim of quantity. Children and adults differed in their comprehension of the maxim of politeness. The development of the pragmatic understanding of Gricean maxims and implications for the construction of developmental tasks from early childhood to adulthood are discussed.
Understanding Violations of Gricean Maxims in Preschoolers and Adults
Mako eOkanda
2015-07-01
Full Text Available This study used a revised Conversational Violations Test to examine Gricean maxim violations in 4- to 6-year-old Japanese children and adults. Participants’ understanding of the following maxims was assessed: be informative (first maxim of quantity, avoid redundancy (second maxim of quantity, be truthful (maxim of quality, be relevant (maxim of relation, avoid ambiguity (second maxim of manner, and be polite (maxim of politeness. Sensitivity to violations of Gricean maxims increased with age: 4-year-olds’ understanding of maxims was near chance, 5-year-olds understood some maxims (first maxim of quantity and maxims of quality, relation, and manner, and 6-year-olds and adults understood all maxims. Preschoolers acquired the maxim of relation first and had the greatest difficulty understanding the second maxim of quantity. Children and adults differed in their comprehension of the maxim of politeness. The development of the pragmatic understanding of Gricean maxims and implications for the construction of developmental tasks from early childhood to adulthood are discussed.
Physics with loosely bound nuclei
Chhanda Samanta
2001-08-01
The essential aspect of contemporary physics is to understand properties of nucleonic matter that constitutes the world around us. Over the years research in nuclear physics has provided strong guidance in understanding the basic principles of nuclear interactions. But, the scenario of nuclear physics changed drastically as the new generation of accelerators started providing more and more rare isotopes, which are away from the line of stability. These weakly bound nuclei are found to exhibit new forms of nuclear matter and unprecedented exotic behaviour. The low breakup thresholds of these rare nuclei are posing new challenges to both theory and experiments. Fortunately, nature has provided a few loosely bound stable nuclei that have been studied thoroughly for decades. Attempts are being made to ﬁnd a consistent picture for the unstable nuclei starting from their stable counterparts. Some signiﬁcant differences in the structure and reaction mechanisms are found.
Space-bounded communication complexity
Brody, Joshua Eric; Chen, Shiteng; Papakonstantinou, Periklis A.
2013-01-01
In the past thirty years, Communication Complexity has emerged as a foundational tool to proving lower bounds in many areas of computer science. Its power comes from its generality, but this generality comes at a price---no superlinear communication lower bound is possible, since a player may...... communicate his entire input. However, what if the players are limited in their ability to recall parts of their interaction? We introduce memory models for 2-party communication complexity. Our general model is as follows: two computationally unrestricted players, Alice and Bob, each have s(n) bits of memory....... When a player receives a bit of communication, he "compresses" his state. This compression may be an arbitrary function of his current memory contents, his input, and the bit of communication just received; the only restriction is that the compression must return at most s(n) bits. We obtain memory...
Lower Bounds on Paraclique Density.
Hagan, Ronald D; Langston, Michael A; Wang, Kai
2016-05-11
The scientific literature teems with clique-centric clustering strategies. In this paper we analyze one such method, the paraclique algorithm. Paraclique has found practical utility in a variety of application domains, and has been successfully employed to reduce the effects of noise. Nevertheless, its formal analysis and worst-case guarantees have remained elusive. We address this issue by deriving a series of lower bounds on paraclique densities.
Wronskian method for bound states
Fernandez, Francisco M, E-mail: fernande@quimica.unlp.edu.ar [INIFTA (UNLP, CONICET), Division Quimica Teorica, Boulevard 113 S/N, Sucursal 4, Casilla de Correo 16, 1900 La Plata (Argentina)
2011-05-15
We propose a simple and straightforward method based on Wronskians for the calculation of bound-state energies and wavefunctions of one-dimensional quantum-mechanical problems. We explicitly discuss the asymptotic behaviour of the wavefunction and show that the allowed energies make the divergent part vanish. As illustrative examples we consider an exactly solvable model, the Gaussian potential well, and a two-well potential proposed earlier for the interpretation of the infrared spectrum of ammonia.
Bound Modes in Dielectric Microcavities
Visser, P M; Lenstra, D
2002-01-01
We demonstrate how exactly bound cavity modes can be realized in dielectric structures other than 3d photonic crystals. For a microcavity consisting of crossed anisotropic layers, we derive the cavity resonance frequencies, and spontaneous emission rates. For a dielectric structure with dissipative loss and central layer with gain, the beta factor of direct spontaneous emission into a cavity mode and the laser threshold is calculated.
Entropy Bounds in Spherical Space
Brevik, I; Odintsov, S D; Brevik, Iver; Milton, Kimball A.; Odintsov, Sergei D.
2002-01-01
Exact calculations are given for the Casimir energy for various fields in $R\\times S^3$ geometry. The Green's function method naturally gives a result in a form convenient in the high-temperature limit, while the statistical mechanical approach gives a form appropriate for low temperatures. The equivalence of these two representations is demonstrated. Some discrepancies with previous work are noted. In no case, even for ${\\cal N}=4$ SUSY, is the ratio of entropy to energy found to be bounded.
2013-03-26
... Agency Information Collection Activities; Comment Request; Upward Bound and Upward Bound Math Science... Upward Bound Math Science Annual Performance Report. OMB Control Number: 1840-NEW. Type of Review: New... under the regular Upward Bound (UB) and Upward Bound Math and Science (UBMS) Programs. The Department is...
Kim, Hyo-Sil
2011-01-01
We study the motion-planning problem for a car-like robot whose turning radius is bounded from below by one and which is allowed to move in the forward direction only (Dubins car). For two robot configurations $\\sigma, \\sigma'$, let $\\ell(\\sigma, \\sigma')$ be the shortest bounded-curvature path from $\\sigma$ to $\\sigma'$. For $d \\geq 0$, let $\\ell(d)$ be the supremum of $\\ell(\\sigma, \\sigma')$, over all pairs $(\\sigma, \\sigma')$ that are at Euclidean distance $d$. We study the function $\\dub(d) = \\ell(d) - d$, which expresses the difference between the bounded-curvature path length and the Euclidean distance of its endpoints. We show that $\\dub(d)$ decreases monotonically from $\\dub(0) = 7\\pi/3$ to $\\dub(\\ds) = 2\\pi$, and is constant for $d \\geq \\ds$. Here $\\ds \\approx 1.5874$. We describe pairs of configurations that exhibit the worst-case of $\\dub(d)$ for every distance $d$.
Daly, Ruth A
2009-01-01
Beam powers and black hole masses of 48 extended radio sources are combined to obtain lower bounds on the spins and magnetic field strengths of supermassive black holes. This is done in the context of the models of Blandford & Znajek (1977) (the 'BZ' model) and Meier (1999); a parameterization for bounds in the context of other models is suggested. The bounds obtained for very powerful classical double radio sources in the BZ model are consistent with black hole spins of order unity for sources at high redshift. The black hole spins are largest for the highest redshift sources and decrease for sources at lower redshift; the sources studied have redshifts between zero and two. Lower power radio sources associated with central dominant galaxies may have black hole spins that are significantly less than one. Combining this analysis with other results suggests that the maximum values of black hole spin associated with powerful radio galaxies decline from values of order unity at a redshift of 2 to values of o...
Bounds on Generalized Huffman Codes
Baer, Michael B
2007-01-01
New lower and upper bounds are obtained for the compression of optimal binary prefix codes according to various nonlinear codeword length objectives. Like the coding bounds for Huffman coding - which concern the traditional linear code objective of minimizing average codeword length -- these are in terms of a form of entropy and the probability of the most probable input symbol. As in Huffman coding, some upper bounds can be found using sufficient conditions for the codeword corresponding to the most probable symbol being one bit long. Whereas having probability no less than 0.4 is a tight sufficient condition for this to be the case in Huffman coding, other penalties differ, some having a tighter condition, some a looser condition, and others having no such sufficient condition. The objectives explored here are ones for which optimal codes can be found using a generalized form of Huffman coding. These objectives include one related to queueing (an increasing exponential average), one related to single-shot c...
A solvated ligand rotamer approach and its application in computational protein design.
Huang, Xiaoqiang; Yang, Ji; Zhu, Yushan
2013-03-01
The structure-based design of protein-ligand interfaces with respect to different small molecules is of great significance in the discovery of functional proteins. By statistical analysis of a set of protein-ligand complex structures, it was determined that water-mediated hydrogen bonding at the protein-ligand interface plays a crucial role in governing the binding between the protein and the ligand. Based on the novel statistic results, a solvated ligand rotamer approach was developed to explicitly describe the key water molecules at the protein-ligand interface and a water-mediated hydrogen bonding model was applied in the computational protein design context to complement the continuum solvent model. The solvated ligand rotamer approach produces only one additional solvated rotamer for each rotamer in the ligand rotamer library and does not change the number of side-chain rotamers at each protein design site. This has greatly reduced the total combinatorial number in sequence selection for protein design, and the accuracy of the model was confirmed by two tests. For the water placement test, 61% of the crystal water molecules were predicted correctly in five protein-ligand complex structures. For the sequence recapitulation test, 44.7% of the amino acid identities were recovered using the solvated ligand rotamer approach and the water-mediated hydrogen bonding model, while only 30.4% were recovered when the explicitly bound waters were removed. These results indicated that the developed solvated ligand rotamer approach is promising for functional protein design targeting novel protein-ligand interactions.
On interpretations of bounded arithmetic and bounded set theory
Pettigrew, Richard
2008-01-01
In a recent paper, Kaye and Wong proved the following result, which they considered to belong to the folklore of mathematical logic. THEOREM: The first-order theories of Peano arithmetic and ZF with the axiom of infinity negated are mutually interpretable with interpretations that are inverse to each other. In this note, I describe a theory of sets that stands in the same relation to the bounded arithmetic IDelta0 + exp. Because of the weakness of this theory of sets, I cannot straightforwardly adapt Kaye and Wong's interpretation of the arithmetic in the set theory. Instead, I am forced to produce a different interpretation.
Das, Pradip Kumar; Dey, Abhishek
2014-07-21
Resonance Raman (rR), electron paramagnetic resonance (EPR), and density functional theory (DFT) calculations of a phenolate-bound iron porphyrin complex are reported. The complex is found to exist in a five-coordinate high-spin state in a noncoordinating solvent and in a six-coordinate low-spin state in a coordinating solvent. The vibrations originating from the iron phenolate-bound chromophores reproduced those reported for heme tyrosine active sites in nature. The EPR parameters and iron-pyrrole (Fe-Npyr) vibrations of phenolate, thiolate, and imidazole ligated iron porphyrin complexes indicate that the phenolate axial ligand acts as a π anisotropic ligand, which is more covalent than a neutral imidazole ligand but less covalent than a thiolate axial ligand. While the Fe(III/II) potential of the phenolate compound in a noncoordinating solvent is 500 mV more negative than that of the imidazole-bound complex, it is also 110 mV more negative than that of the thiolate-bound complex. DFT calculations reproduce the geometry and vibrational frequencies and show that while both phenolate and thiolate axial ligands bear π and σ interaction with the ferric center, the former is significantly less covalent than the thiolate. The higher covalency of the thiolate ligand is responsible for the lower Fe-Npyr vibration and higher V/λ (from EPR) of the thiolate-bound complexes relative to those of the phenolate-bound complex, whereas the greater electrostatic stabilization of the Fe(III)-OPh bond is responsible for lowering the Fe(III/II) E° of the phenolate-bound complex relative to that of the thiolate-bound complex in a medium having a reasonable dielectric constant.
Upper Bounds on Numerical Approximation Errors
Raahauge, Peter
2004-01-01
This paper suggests a method for determining rigorous upper bounds on approximationerrors of numerical solutions to infinite horizon dynamic programming models.Bounds are provided for approximations of the value function and the policyfunction as well as the derivatives of the value function....... The bounds apply to moregeneral problems than existing bounding methods do. For instance, since strict concavityis not required, linear models and piecewise linear approximations can bedealt with. Despite the generality, the bounds perform well in comparison with existingmethods even when applied...... to approximations of a standard (strictly concave)growth model.KEYWORDS: Numerical approximation errors, Bellman contractions, Error bounds...
Structure of the [delta]-opioid receptor bound to naltrindole
Granier, Sébastien; Manglik, Aashish; Kruse, Andrew C.; Kobilka, Tong Sun; Thian, Foon Sun; Weis, William I.; Kobilka, Brian K. (Stanford-MED)
2012-07-11
The opioid receptor family comprises three members, the {mu}-, {delta}- and {kappa}-opioid receptors, which respond to classical opioid alkaloids such as morphine and heroin as well as to endogenous peptide ligands like endorphins. They belong to the G-protein-coupled receptor (GPCR) superfamily, and are excellent therapeutic targets for pain control. The {delta}-opioid receptor ({delta}-OR) has a role in analgesia, as well as in other neurological functions that remain poorly understood. The structures of the {mu}-OR and {kappa}-OR have recently been solved. Here we report the crystal structure of the mouse {delta}-OR, bound to the subtype-selective antagonist naltrindole. Together with the structures of the {mu}-OR and {kappa}-OR, the {delta}-OR structure provides insights into conserved elements of opioid ligand recognition while also revealing structural features associated with ligand-subtype selectivity. The binding pocket of opioid receptors can be divided into two distinct regions. Whereas the lower part of this pocket is highly conserved among opioid receptors, the upper part contains divergent residues that confer subtype selectivity. This provides a structural explanation and validation for the 'message-address' model of opioid receptor pharmacology, in which distinct 'message' (efficacy) and 'address' (selectivity) determinants are contained within a single ligand. Comparison of the address region of the {delta}-OR with other GPCRs reveals that this structural organization may be a more general phenomenon, extending to other GPCR families as well.
Rosati, Fiora; Boersma, Arnold J.; Klijn, Jaap E.; Meetsma, Auke; Feringa, Ben L.; Roelfes, Gerard
2009-01-01
The recently developed concept of DNA-based asymmetric catalysis involves the transfer of chirality from the DNA double helix in reactions using a noncovalently bound catalyst. To date, two generations of DNA-based catalysts have been reported that differ in the design of the ligand for the metal. H
MengLingzhi; QiLiangwei; 等
1998-01-01
Acrylate terpolymer-bound Se,N bidentate ligand was synthesized from the side chain chlorine of copolymer and β-dimethylamino-β′-hydroxyl-diethyl selenoether.The polymer-supported platinum complex exhibited high catalytic activity in the hydrosilylation of olefins with triethoxysilane.
Guldbrandt, Mette; Johansen, Tommy N; Frydenvang, Karla Andrea;
2002-01-01
Homologation and substitution on the carbon backbone of (S)-glutamic acid [(S)-Glu, 1], as well as absolute stereochemistry, are structural parameters of key importance for the pharmacological profile of (S)-Glu receptor ligands. We describe a series of methyl-substituted 2-aminoadipic acid (AA......-ray crystallographic analyses, chemical correlation, and CD spectral analyses. The effects of the individual stereoisomers at ionotropic and metabotropic (S)-Glu receptors (iGluRs and mGluRs) were characterized. Compounds with S-configuration at the alpha-carbon generally showed mGluR2 agonist activity of similar...... limited effect on pharmacology. Structure-activity relationships at iGluRs in the rat cortical wedge preparation showed a complex pattern, some compounds being NMDA receptor agonists [e.g., EC(50) =110 microM for (2S,5RS)-5-methyl-AA (6a,b)] and some compounds showing NMDA receptor antagonist effects [e...
Maximal temperature in a simple thermodynamical system
Dai, De-Chang
2016-01-01
Temperature in a simple thermodynamical system is not limited from above. It is also widely believed that it does not make sense talking about temperatures higher than the Planck temperature in the absence of the full theory of quantum gravity. Here, we demonstrate that there exist a maximal achievable temperature in a system where particles obey the laws of quantum mechanics and classical gravity before we reach the realm of quantum gravity. Namely, if two particles with a given center of mass energy come at the distance shorter than the Schwarzschild diameter apart, according to classical gravity they will form a black hole. It is possible to calculate that a simple thermodynamical system will be dominated by black holes at a critical temperature which is about three times lower than the Planck temperature. That represents the maximal achievable temperature in a simple thermodynamical system.
Hamiltonian formalism and path entropy maximization
Davis, Sergio; González, Diego
2015-10-01
Maximization of the path information entropy is a clear prescription for constructing models in non-equilibrium statistical mechanics. Here it is shown that, following this prescription under the assumption of arbitrary instantaneous constraints on position and velocity, a Lagrangian emerges which determines the most probable trajectory. Deviations from the probability maximum can be consistently described as slices in time by a Hamiltonian, according to a nonlinear Langevin equation and its associated Fokker-Planck equation. The connections unveiled between the maximization of path entropy and the Langevin/Fokker-Planck equations imply that missing information about the phase space coordinate never decreases in time, a purely information-theoretical version of the second law of thermodynamics. All of these results are independent of any physical assumptions, and thus valid for any generalized coordinate as a function of time, or any other parameter. This reinforces the view that the second law is a fundamental property of plausible inference.
Predicting Contextual Sequences via Submodular Function Maximization
Dey, Debadeepta; Hebert, Martial; Bagnell, J Andrew
2012-01-01
Sequence optimization, where the items in a list are ordered to maximize some reward has many applications such as web advertisement placement, search, and control libraries in robotics. Previous work in sequence optimization produces a static ordering that does not take any features of the item or context of the problem into account. In this work, we propose a general approach to order the items within the sequence based on the context (e.g., perceptual information, environment description, and goals). We take a simple, efficient, reduction-based approach where the choice and order of the items is established by repeatedly learning simple classifiers or regressors for each "slot" in the sequence. Our approach leverages recent work on submodular function maximization to provide a formal regret reduction from submodular sequence optimization to simple cost-sensitive prediction. We apply our contextual sequence prediction algorithm to optimize control libraries and demonstrate results on two robotics problems: ...
Nonlinear trading models through Sharpe Ratio maximization.
Choey, M; Weigend, A S
1997-08-01
While many trading strategies are based on price prediction, traders in financial markets are typically interested in optimizing risk-adjusted performance such as the Sharpe Ratio, rather than the price predictions themselves. This paper introduces an approach which generates a nonlinear strategy that explicitly maximizes the Sharpe Ratio. It is expressed as a neural network model whose output is the position size between a risky and a risk-free asset. The iterative parameter update rules are derived and compared to alternative approaches. The resulting trading strategy is evaluated and analyzed on both computer-generated data and real world data (DAX, the daily German equity index). Trading based on Sharpe Ratio maximization compares favorably to both profit optimization and probability matching (through cross-entropy optimization). The results show that the goal of optimizing out-of-sample risk-adjusted profit can indeed be achieved with this nonlinear approach.
Maximally Symmetric Spacetimes emerging from thermodynamic fluctuations
Bravetti, A; Quevedo, H
2015-01-01
In this work we prove that the maximally symmetric vacuum solutions of General Relativity emerge from the geometric structure of statistical mechanics and thermodynamic fluctuation theory. To present our argument, we begin by showing that the pseudo-Riemannian structure of the Thermodynamic Phase Space is a solution to the vacuum Einstein-Gauss-Bonnet theory of gravity with a cosmological constant. Then, we use the geometry of equilibrium thermodynamics to demonstrate that the maximally symmetric vacuum solutions of Einstein's Field Equations -- Minkowski, de-Sitter and Anti-de-Sitter spacetimes -- correspond to thermodynamic fluctuations. Moreover, we argue that these might be the only possible solutions that can be derived in this manner. Thus, the results presented here are the first concrete examples of spacetimes effectively emerging from the thermodynamic limit over an unspecified microscopic theory without any further assumptions.
Consistent 4-form fluxes for maximal supergravity
Godazgar, Hadi; Krueger, Olaf; Nicolai, Hermann
2015-01-01
We derive new ansaetze for the 4-form field strength of D=11 supergravity corresponding to uplifts of four-dimensional maximal gauged supergravity. In particular, the ansaetze directly yield the components of the 4-form field strength in terms of the scalars and vectors of the four-dimensional maximal gauged supergravity---in this way they provide an explicit uplift of all four-dimensional consistent truncations of D=11 supergravity. The new ansaetze provide a substantially simpler method for uplifting d=4 flows compared to the previously available method using the 3-form and 6-form potential ansaetze. The ansatz for the Freund-Rubin term allows us to conjecture a `master formula' for the latter in terms of the scalar potential of d=4 gauged supergravity and its first derivative. We also resolve a long-standing puzzle concerning the antisymmetry of the flux obtained from uplift ansaetze.
Modularity maximization using completely positive programming
Yazdanparast, Sakineh; Havens, Timothy C.
2017-04-01
Community detection is one of the most prominent problems of social network analysis. In this paper, a novel method for Modularity Maximization (MM) for community detection is presented which exploits the Alternating Direction Augmented Lagrangian (ADAL) method for maximizing a generalized form of Newman's modularity function. We first transform Newman's modularity function into a quadratic program and then use Completely Positive Programming (CPP) to map the quadratic program to a linear program, which provides the globally optimal maximum modularity partition. In order to solve the proposed CPP problem, a closed form solution using the ADAL merged with a rank minimization approach is proposed. The performance of the proposed method is evaluated on several real-world data sets used for benchmarks community detection. Simulation results shows the proposed technique provides outstanding results in terms of modularity value for crisp partitions.
Moving multiple sinks through wireless sensor networks for lifetime maximization.
Petrioli, Chiara (Universita di Roma); Carosi, Alessio (Universita di Roma); Basagni, Stefano (Northeastern University); Phillips, Cynthia Ann
2008-01-01
Unattended sensor networks typically watch for some phenomena such as volcanic events, forest fires, pollution, or movements in animal populations. Sensors report to a collection point periodically or when they observe reportable events. When sensors are too far from the collection point to communicate directly, other sensors relay messages for them. If the collection point location is static, sensor nodes that are closer to the collection point relay far more messages than those on the periphery. Assuming all sensor nodes have roughly the same capabilities, those with high relay burden experience battery failure much faster than the rest of the network. However, since their death disconnects the live nodes from the collection point, the whole network is then dead. We consider the problem of moving a set of collectors (sinks) through a wireless sensor network to balance the energy used for relaying messages, maximizing the lifetime of the network. We show how to compute an upper bound on the lifetime for any instance using linear and integer programming. We present a centralized heuristic that produces sink movement schedules that produce network lifetimes within 1.4% of the upper bound for realistic settings. We also present a distributed heuristic that produces lifetimes at most 25:3% below the upper bound. More specifically, we formulate a linear program (LP) that is a relaxation of the scheduling problem. The variables are naturally continuous, but the LP relaxes some constraints. The LP has an exponential number of constraints, but we can satisfy them all by enforcing only a polynomial number using a separation algorithm. This separation algorithm is a p-median facility location problem, which we can solve efficiently in practice for huge instances using integer programming technology. This LP selects a set of good sensor configurations. Given the solution to the LP, we can find a feasible schedule by selecting a subset of these configurations, ordering them
Utility maximization in incomplete markets with default
Lim, Thomas
2008-01-01
We adress the maximization problem of expected utility from terminal wealth. The special feature of this paper is that we consider a financial market where the price process of risky assets can have a default time. Using dynamic programming, we characterize the value function with a backward stochastic differential equation and the optimal portfolio policies. We separately treat the cases of exponential, power and logarithmic utility.
Operational Modal Analysis using Expectation Maximization Algorithm
Cara Cañas, Francisco Javier; Carpio Huertas, Jaime; Juan Ruiz, Jesús; Alarcón Álvarez, Enrique
2011-01-01
This paper presents a time-domain stochastic system identification method based on Maximum Likelihood Estimation and the Expectation Maximization algorithm. The effectiveness of this structural identification method is evaluated through numerical simulation in the context of the ASCE benchmark problem on structural health monitoring. Modal parameters (eigenfrequencies, damping ratios and mode shapes) of the benchmark structure have been estimated applying the proposed identification method...
Revenue Maximizing Head Starts in Contests
Franke, Jörg; Leininger, Wolfgang; Wasser, Cédric
2014-01-01
We characterize revenue maximizing head starts for all-pay auctions and lottery contests with many heterogeneous players. We show that under optimal head starts all-pay auctions revenue-dominate lottery contests for any degree of heterogeneity among players. Moreover, all-pay auctions with optimal head starts induce higher revenue than any multiplicatively biased all-pay auction or lottery contest. While head starts are more effective than multiplicative biases in all-pay auctions, they are l...
Approximate Revenue Maximization in Interdependent Value Settings
Chawla, Shuchi; Fu, Hu; Karlin, Anna
2014-01-01
We study revenue maximization in settings where agents' values are interdependent: each agent receives a signal drawn from a correlated distribution and agents' values are functions of all of the signals. We introduce a variant of the generalized VCG auction with reserve prices and random admission, and show that this auction gives a constant approximation to the optimal expected revenue in matroid environments. Our results do not require any assumptions on the signal distributions, however, ...
The crystal structure of tryptophan hydroxylase with bound amino acid substrate
Windahl, Michael Skovbo; Petersen, Charlotte Rode; Christensen, Hans Erik Mølager
2008-01-01
acid hydroxylase with bound natural amino acid substrate. The iron coordination can be described as distorted trigonal bipyramidal coordination with His273, His278, and Glu318 (partially bidentate) and one imidazole as ligands. The tryptophan stacks against Pro269 with a distance of 3.9 Å between...... of the neurotransmitter and hormone serotonin (5-hydroxytryptamine). We have determined the 1.9 Å resolution crystal structure of the catalytic domain (Δ1−100/Δ415−445) of chicken TPH isoform 1 (TPH1) in complex with the tryptophan substrate and an iron-bound imidazole. This is the first structure of any aromatic amino...
Maximal supersymmetry and B-mode targets
Kallosh, Renata; Linde, Andrei; Wrase, Timm; Yamada, Yusuke
2017-04-01
Extending the work of Ferrara and one of the authors [1], we present dynamical cosmological models of α-attractors with plateau potentials for 3 α = 1, 2, 3, 4, 5, 6, 7. These models are motivated by geometric properties of maximally supersymmetric theories: M-theory, superstring theory, and maximal N = 8 supergravity. After a consistent truncation of maximal to minimal supersymmetry in a seven-disk geometry, we perform a two-step procedure: 1) we introduce a superpotential, which stabilizes the moduli of the seven-disk geometry in a supersymmetric minimum, 2) we add a cosmological sector with a nilpotent stabilizer, which breaks supersymmetry spontaneously and leads to a desirable class of cosmological attractor models. These models with n s consistent with observational data, and with tensor-to-scalar ratio r ≈ 10-2 - 10-3, provide natural targets for future B-mode searches. We relate the issue of stability of inflationary trajectories in these models to tessellations of a hyperbolic geometry.
Maximal respiratory pressures among adolescent swimmers.
Rocha Crispino Santos, M A; Pinto, M L; Couto Sant'Anna, C; Bernhoeft, M
2011-01-01
Maximal inspiratory pressures (MIP) and maximal expiratory pressures (MEP) are useful indices of respiratory muscle strength in athletes. The aims of this study were: to describe the strength of the respiratory muscles of Olympic junior swim team, at baseline and after a standard physical training; and to determine if there is a differential inspiratory and expiratory pressure response to the physical training. A cross-sectional study evaluated 28 international-level swimmers with ages ranging from 15 to 17 years, 19 (61 %) being males. At baseline, MIP was found to be lower in females (P = .001). The mean values reached by males and females were: MIP(cmH2O) = M: 100.4 (± 26.5)/F: 67.8 (± 23.2); MEP (cmH2O) = M: 87.4 (± 20.7)/F: 73.9 (± 17.3). After the physical training they reached: MIP (cmH2O) = M: 95.3 (± 30.3)/F: 71.8 (± 35.6); MEP (cmH2O) = M: 82.8 (± 26.2)/F: 70.4 (± 8.3). No differential pressure responses were observed in either males or females. These results suggest that swimmers can sustain the magnitude of the initial maximal pressures. Other studies should be developed to clarify if MIP and MEP could be used as a marker of an athlete's performance.
Bound Polaron Pair Formation in Poly (phenylenevinylenes)
Rothberg, Lewis
The following sections are included: * INTRODUCTION * PHOTOGENERATED YIELD OF SINGLET EXCITONS * AGGREGRATION EFFECTS ON EXCITED STATE PHOTO-GENERATION * ASSIGNMENT TO BOUND POLARON PAIRS AND DISCUSSION * PROBLEMS WITH THE BOUND POLARON PAIR PICTURE AND CONCLUSION * REFERENCES
An Exponential Bound for Cox Regression☆
Kosorok, M. R.
2012-01-01
We present an asymptotic exponential bound for the deviation of the survival function estimator of the Cox model. We show that the bound holds even when the proportional hazards assumption does not hold. PMID:23565013
An Exponential Bound for Cox Regression.
Goldberg, Y; Kosorok, M R
2012-07-01
We present an asymptotic exponential bound for the deviation of the survival function estimator of the Cox model. We show that the bound holds even when the proportional hazards assumption does not hold.
Maximal function characterizations of Hardy spaces on RD-spaces and their applications
Loukas; GRAFAKOS
2008-01-01
Let X be an RD-space, i.e., a space of homogeneous type in the sense of Coifman and Weiss, which has the reverse doubling property. Assume that X has a "dimension" n. For α∈ (0, ∞) denote by Hαp(X ), Hdp(X ), and H?,p(X ) the corresponding Hardy spaces on X defined by the nontangential maximal function, the dyadic maximal function and the grand maximal function, respectively. Using a new inhomogeneous Calder′on reproducing formula, it is shown that all these Hardy spaces coincide with Lp(X ) when p ∈ (1, ∞] and with each other when p ∈ (n/(n + 1), 1]. An atomic characterization for H*,p(X ) with p ∈ (n/(n + 1), 1] is also established; moreover, in the range p ∈ (n/(n + 1), 1], it is proved that the space H?,p(X ), the Hardy space Hp(X ) defined via the Littlewood-Paley function, and the atomic Hardy space of Coifman and Weiss coincide. Furthermore, it is proved that a sublinear operator T uniquely extends to a bounded sublinear operator from Hp(X ) to some quasi-Banach space B if and only if T maps all (p, q)-atoms when q ∈ (p, ∞)∩[1, ∞) or continuous (p, ∞)-atoms into uniformly bounded elements of B.
Syed, Aleem; Zhu, Qiaochu; Smith, Emily A
2016-12-01
The effect of ligand on the lateral diffusion of receptor for advanced glycation endproducts (RAGE), a receptor involved in numerous pathological conditions, remains unknown. Single particle tracking experiments that use quantum dots specifically bound to hemagglutinin (HA)-tagged RAGE (HA-RAGE) are reported to elucidate the effect of ligand binding on HA-RAGE diffusion in GM07373 cell membranes. The ligand used in these studies is methylglyoxal modified-bovine serum albumin (MGO-BSA) containing advanced glycation end products modifications. The binding affinity between soluble RAGE and MGO-BSA increases by 1.8 to 9.7-fold as the percent primary amine modification increases from 24 to 74% and with increasing negative charge on the MGO-BSA. Ligand incubation affects the HA-RAGE diffusion coefficient, the radius of confinement, and duration of confinement. There is, however, no correlation between MGO-BSA ligand binding affinity with soluble RAGE and the extent of the changes in HA-RAGE lateral diffusion. The ligand induced changes to HA-RAGE lateral diffusion do not occur when cholesterol is depleted from the cell membrane, indicating the mechanism for ligand-induced changes to HA-RAGE diffusion is cholesterol dependent. The results presented here serve as a first step in unraveling how ligand influences RAGE lateral diffusion. Copyright © 2016. Published by Elsevier B.V.
On revenue maximization for selling multiple independently distributed items.
Li, Xinye; Yao, Andrew Chi-Chih
2013-07-09
Consider the revenue-maximizing problem in which a single seller wants to sell k different items to a single buyer, who has independently distributed values for the items with additive valuation. The k = 1 case was completely resolved by Myerson's classical work in 1981, whereas for larger k the problem has been the subject of much research efforts ever since. Recently, Hart and Nisan analyzed two simple mechanisms: selling the items separately, or selling them as a single bundle. They showed that selling separately guarantees at least a c/log2 k fraction of the optimal revenue; and for identically distributed items, bundling yields at least a c/log k fraction of the optimal revenue. In this paper, we prove that selling separately guarantees at least c/log k fraction of the optimal revenue, whereas for identically distributed items, bundling yields at least a constant fraction of the optimal revenue. These bounds are tight (up to a constant factor), settling the open questions raised by Hart and Nisan. The results are valid for arbitrary probability distributions without restrictions. Our results also have implications on other interesting issues, such as monotonicity and randomization of selling mechanisms.
Excap: maximization of haplotypic diversity of linked markers.
André Kahles
Full Text Available Genetic markers, defined as variable regions of DNA, can be utilized for distinguishing individuals or populations. As long as markers are independent, it is easy to combine the information they provide. For nonrecombinant sequences like mtDNA, choosing the right set of markers for forensic applications can be difficult and requires careful consideration. In particular, one wants to maximize the utility of the markers. Until now, this has mainly been done by hand. We propose an algorithm that finds the most informative subset of a set of markers. The algorithm uses a depth first search combined with a branch-and-bound approach. Since the worst case complexity is exponential, we also propose some data-reduction techniques and a heuristic. We implemented the algorithm and applied it to two forensic caseworks using mitochondrial DNA, which resulted in marker sets with significantly improved haplotypic diversity compared to previous suggestions. Additionally, we evaluated the quality of the estimation with an artificial dataset of mtDNA. The heuristic is shown to provide extensive speedup at little cost in accuracy.
Size Bounds for Conjunctive Queries with General Functional Dependencies
Valiant, Gregory
2009-01-01
This paper resolves the main open question left by Gottlob, Lee, and Valiant (PODS 2009)[GLV09], establishing tight worst-case bounds for the size of the result Q(D) of a conjunctive query Q to a database D given an arbitrary set of functional dependencies. We show that the lower bound presented in [GLV09] in which the variables of the query are "colored" so as to yield a coloring number C(Q) for each query Q is, in fact, also an upper bound. To show this, we formalize the original intuition that each color used represents some possible entropy of that variable, and express the maximum possible size increase as a linear program that seeks to maximize how much more entropy is in the result of the query than the input. Although this linear program has exponentially many variables, we also show that we can decide in polynomial time whether the result can be any larger than the input database.
New bounds for multi-dimensional packing
Seiden, S.; Stee, van, Rob
2001-01-01
New upper and lower bounds are presented for a multi-dimensional generalization of bin packing called box packing. Several variants of this problem, including bounded space box packing, square packing, variable sized box packing and resource augmented box packing are also studied. The main results, stated for d=2, are as follows: A new upper bound of 2.66013 for online box packing, a new $14/9 + varepsilon$ polynomial time offline approximation algorithm for square packing, a new upper bound ...
Cardiorespiratory Coordination in Repeated Maximal Exercise
Sergi Garcia-Retortillo
2017-06-01
Full Text Available Increases in cardiorespiratory coordination (CRC after training with no differences in performance and physiological variables have recently been reported using a principal component analysis approach. However, no research has yet evaluated the short-term effects of exercise on CRC. The aim of this study was to delineate the behavior of CRC under different physiological initial conditions produced by repeated maximal exercises. Fifteen participants performed 2 consecutive graded and maximal cycling tests. Test 1 was performed without any previous exercise, and Test 2 6 min after Test 1. Both tests started at 0 W and the workload was increased by 25 W/min in males and 20 W/min in females, until they were not able to maintain the prescribed cycling frequency of 70 rpm for more than 5 consecutive seconds. A principal component (PC analysis of selected cardiovascular and cardiorespiratory variables (expired fraction of O2, expired fraction of CO2, ventilation, systolic blood pressure, diastolic blood pressure, and heart rate was performed to evaluate the CRC defined by the number of PCs in both tests. In order to quantify the degree of coordination, the information entropy was calculated and the eigenvalues of the first PC (PC1 were compared between tests. Although no significant differences were found between the tests with respect to the performed maximal workload (Wmax, maximal oxygen consumption (VO2 max, or ventilatory threshold (VT, an increase in the number of PCs and/or a decrease of eigenvalues of PC1 (t = 2.95; p = 0.01; d = 1.08 was found in Test 2 compared to Test 1. Moreover, entropy was significantly higher (Z = 2.33; p = 0.02; d = 1.43 in the last test. In conclusion, despite the fact that no significant differences were observed in the conventionally explored maximal performance and physiological variables (Wmax, VO2 max, and VT between tests, a reduction of CRC was observed in Test 2. These results emphasize the interest of CRC
Cardiorespiratory Coordination in Repeated Maximal Exercise.
Garcia-Retortillo, Sergi; Javierre, Casimiro; Hristovski, Robert; Ventura, Josep L; Balagué, Natàlia
2017-01-01
Increases in cardiorespiratory coordination (CRC) after training with no differences in performance and physiological variables have recently been reported using a principal component analysis approach. However, no research has yet evaluated the short-term effects of exercise on CRC. The aim of this study was to delineate the behavior of CRC under different physiological initial conditions produced by repeated maximal exercises. Fifteen participants performed 2 consecutive graded and maximal cycling tests. Test 1 was performed without any previous exercise, and Test 2 6 min after Test 1. Both tests started at 0 W and the workload was increased by 25 W/min in males and 20 W/min in females, until they were not able to maintain the prescribed cycling frequency of 70 rpm for more than 5 consecutive seconds. A principal component (PC) analysis of selected cardiovascular and cardiorespiratory variables (expired fraction of O2, expired fraction of CO2, ventilation, systolic blood pressure, diastolic blood pressure, and heart rate) was performed to evaluate the CRC defined by the number of PCs in both tests. In order to quantify the degree of coordination, the information entropy was calculated and the eigenvalues of the first PC (PC1) were compared between tests. Although no significant differences were found between the tests with respect to the performed maximal workload (Wmax), maximal oxygen consumption (VO2 max), or ventilatory threshold (VT), an increase in the number of PCs and/or a decrease of eigenvalues of PC1 (t = 2.95; p = 0.01; d = 1.08) was found in Test 2 compared to Test 1. Moreover, entropy was significantly higher (Z = 2.33; p = 0.02; d = 1.43) in the last test. In conclusion, despite the fact that no significant differences were observed in the conventionally explored maximal performance and physiological variables (Wmax, VO2 max, and VT) between tests, a reduction of CRC was observed in Test 2. These results emphasize the interest of CRC evaluation in
Identification of ligands that target the HCV-E2 binding site on CD81
Olaby, Reem Al; Azzazy, Hassan M.; Harris, Rodney; Chromy, Brett; Vielmetter, Jost; Balhorn, Rod
2013-04-01
Hepatitis C is a global health problem. While many drug companies have active R&D efforts to develop new drugs for treating Hepatitis C virus (HCV), most target the viral enzymes. The HCV glycoprotein E2 has been shown to play an essential role in hepatocyte invasion by binding to CD81 and other cell surface receptors. This paper describes the use of AutoDock to identify ligand binding sites on the large extracellular loop of the open conformation of CD81 and to perform virtual screening runs to identify sets of small molecule ligands predicted to bind to two of these sites. The best sites selected by AutoLigand were located in regions identified by mutational studies to be the site of E2 binding. Thirty-six ligands predicted by AutoDock to bind to these sites were subsequently tested experimentally to determine if they bound to CD81-LEL. Binding assays conducted using surface Plasmon resonance revealed that 26 out of 36 (72 %) of the ligands bound in vitro to the recombinant CD81-LEL protein. Competition experiments performed using dual polarization interferometry showed that one of the ligands predicted to bind to the large cleft between the C and D helices was also effective in blocking E2 binding to CD81-LEL.
Identification of ligands that target the HCV-E2 binding site on CD81.
Olaby, Reem Al; Azzazy, Hassan M; Harris, Rodney; Chromy, Brett; Vielmetter, Jost; Balhorn, Rod
2013-04-01
Hepatitis C is a global health problem. While many drug companies have active R&D efforts to develop new drugs for treating Hepatitis C virus (HCV), most target the viral enzymes. The HCV glycoprotein E2 has been shown to play an essential role in hepatocyte invasion by binding to CD81 and other cell surface receptors. This paper describes the use of AutoDock to identify ligand binding sites on the large extracellular loop of the open conformation of CD81 and to perform virtual screening runs to identify sets of small molecule ligands predicted to bind to two of these sites. The best sites selected by AutoLigand were located in regions identified by mutational studies to be the site of E2 binding. Thirty-six ligands predicted by AutoDock to bind to these sites were subsequently tested experimentally to determine if they bound to CD81-LEL. Binding assays conducted using surface Plasmon resonance revealed that 26 out of 36 (72 %) of the ligands bound in vitro to the recombinant CD81-LEL protein. Competition experiments performed using dual polarization interferometry showed that one of the ligands predicted to bind to the large cleft between the C and D helices was also effective in blocking E2 binding to CD81-LEL.
Ligand-induced changes in estrogen receptor conformation as measured by site-directed spin labeling.
Hurth, Kyle M; Nilges, Mark J; Carlson, Kathryn E; Tamrazi, Anobel; Belford, R Linn; Katzenellenbogen, John A
2004-02-24
Site-directed spin labeling (SDSL), the site-specific incorporation of nitroxide spin-labels into a protein, has allowed us to investigate ligand-induced conformational changes in the ligand-binding domain of human estrogen receptor alpha (hERalpha-LBD). EPR (electron paramagnetic resonance) spectroscopy of the nitroxide probe attached to ER produces different spectra depending upon the identity of the bound ligand; these differences are indicative of changes in the type and degree of motional character of the spin-label induced by different ligand-induced conformations of labeled ER. Visual inspection of EPR spectra, construction of B versus C cross-correlation plots, and cross-comparison of spectral pairs using a relative squared difference (RSD) calculation allowed receptor-ligand complexes to be profiled according to their conformational character. Plotting B and C parameters allowed us to evaluate the liganded receptor according to the motional characteristics of the attached spin-label, and they were particularly illustrative for the receptor labeled at position 530, which had motion between the fast and intermediate regimes. RSD analysis allowed us to directly compare the similarity or difference between two different spectra, and these comparisons produced groupings that paralleled those seen in B versus C cross-correlation plots, again relating meaningfully with the pharmacological nature of the bound ligand. RSD analysis was also particularly useful for qualifying differences seen with the receptor labeled at position 417, which had motion between the intermediate and slow motional regimes. This work demonstrates that B and C formulas from EPR line shape theory are useful for qualitative analysis of spectra with differences subtler than those that are often analyzed by EPR spectroscopists. This work also provides evidence that the ER can exist in a range of conformations, with specific conformations resulting from preferential stabilization of ER by the
The Acquisition of Bound and Free Anaphora.
Koster, Jan; Koster, Charlotte
Most linguists assume that bound anaphors such as "himself" are connected with their antecedents in a different way from free anaphors such as "him." Bound anaphora resolution is deterministic, based on Principle A of Chomsky's binding theory. Free anaphors, pronominals, cannot be bound in the domain of reflexives (principle…
Bounded rationality and heterogeneous expectations in macroeconomics
D. Massaro
2012-01-01
This thesis studies the effect of individual bounded rationality on aggregate macroeconomic dynamics. Boundedly rational agents are specified as using simple heuristics in their decision making. An important aspect of the type of bounded rationality described in this thesis is that the population of
Bound entangled states invariant under Ux
Wang Zhen; Wang Zhi-Xi
2008-01-01
This paper obtains an entangled condition for isotropic-like states by using an atomic map. It constructs a class of bound entangled states from the entangled condition and shows that the partial transposition of the state from the constructed bound entangled class is an edge bound entangled state by using range criterion.
Tight adversary bounds for composite functions
Hoyer, P.; Spalek, R.
2005-01-01
The quantum adversary method is a very versatile method for proving lower bounds on quantum algorithms. It has many equivalent formulations, yields tight bounds for many computational problems, and has natural connections to classical lower bounds. One of its formulations is in terms of the spectral
Determining Normal-Distribution Tolerance Bounds Graphically
Mezzacappa, M. A.
1983-01-01
Graphical method requires calculations and table lookup. Distribution established from only three points: mean upper and lower confidence bounds and lower confidence bound of standard deviation. Method requires only few calculations with simple equations. Graphical procedure establishes best-fit line for measured data and bounds for selected confidence level and any distribution percentile.
Computing the bounds on the loss rates
Fourneau J.-M.; Mokdad L.; Pekergin N.
2002-01-01
We consider an example network where we compute the bounds on cell loss rates. The stochastic bounds for these loss rates using simple arguments lead to models easier to solve. We proved, using stochastic orders, that the loss rates of these easier models are really the bounds of our original model. For ill-balanced configurations these models give good estimates of loss rates.
Labeling schemes for bounded degree graphs
Adjiashvili, David; Rotbart, Noy Galil
2014-01-01
graphs. Our results complement a similar bound recently obtained for bounded depth trees [Fraigniaud and Korman, SODA 2010], and may provide new insights for closing the long standing gap for adjacency in trees [Alstrup and Rauhe, FOCS 2002]. We also provide improved labeling schemes for bounded degree...
Counting Young Tableaux of Bounded Height
Bergeron, Francois; Gascon, Francis
2000-03-01
We show that formulas of Gessel, for the generating functions for Young standard tableaux of height bounded by k (see [2]), satisfy linear differential equations, with polynomial coefficients, equivalent to P-recurrences conjectured by Favreau, Krob and the first author (see [1]) for the number of bounded height tableaux and pairs of bounded height tableaux.
HAO Chengjun; ZhAO Ganqing
2007-01-01
Polymer-bound Schiff-base ligand (PS-Sal-Cys) was prepared from the polystyrene-bound salicylaldehyde and L-cysteine, its complex (PS-Sal-Cys-Mn) was also synthesized. The polymer ligand and its complex were characterized by infrared spectra (IR), small area X-ray photoelectron spectroscopy (XPS), and inductively coupled plasma-atomic emission spectro (ICP-AES). In the presence of complex, cyclohexane can be effectively oxidized by molecular oxygen without a reductant. The major products of the reaction are 2-cyclohexen-1-ol, 2-cyclohexen-1-one, and 2-cyclohexen-1-hydroperoxide, which is different from the typical oxidation of cyclohexene. The mechanism of cyclohexene oxidation is also discussed.
Boosting equal time bound states
Dietrich, Dennis D; Jarvinen, Matti
2012-01-01
We present an explicit and exact boost of a relativistic bound state defined at equal time of the constituents in the Born approximation (lowest order in hbar). To this end, we construct the Poincar\\'e generators of QED and QCD in D=1+1 dimensions, using Gauss' law to express A^0 in terms of the fermion fields in A^1=0 gauge. We determine the fermion-antifermion bound states in the Born approximation as eigenstates of the time and space translation generators P^0 and P^1. The boost operator is combined with a gauge transformation so as to maintain the gauge condition A^1=0 in the new frame. We verify that the boosted state remains an eigenstate of P^0 and P^1 with appropriately transformed eigenvalues and determine the transformation law of the equal-time, relativistic wave function. The shape of the wave function is independent of the CM momentum when expressed in terms of a variable, which is quadratically related to the distance x between the fermions. As a consequence, the Lorentz contraction of the wave ...
Asymmetric dark matter bound state
Bi, Xiao-Jun; Kang, Zhaofeng; Ko, P.; Li, Jinmian; Li, Tianjun
2017-02-01
We propose an interesting framework for asymmetric scalar dark matter (ADM), which has novel collider phenomenology in terms of an unstable ADM bound state (ADMonium) produced via Higgs portals. ADMonium is a natural consequence of the basic features of ADM: the (complex scalar) ADM is charged under a dark local U (1 )d symmetry which is broken at a low scale and provides a light gauge boson X . The dark gauge coupling is strong and then ADM can annihilate away into X -pair effectively. Therefore, the ADM can form a bound state due to its large self-interaction via X mediation. To explore the collider signature of ADMonium, we propose that ADM has a two-Higgs doublet portal. The ADMonium can have a sizable mixing with the heavier Higgs boson, which admits a large cross section of ADMonium production associated with b b ¯. The resulting signature at the LHC depends on the decays of X . In this paper we consider a case of particular interest: p p →b b ¯ +ADMonium followed by ADMonium→2 X →2 e+e- where the electrons are identified as (un)converted photons. It may provide a competitive explanation to heavy di-photon resonance searches at the LHC.
Qin, Shanshan; Ren, Yiran; Fu, Xu; Shen, Jie; Chen, Xin; Wang, Quan; Bi, Xin; Liu, Wenjing; Li, Lixin; Liang, Guangxin; Yang, Cheng; Shui, Wenqing
2015-07-30
Binding affinity of a small molecule drug candidate to a therapeutically relevant biomolecular target is regarded the first determinant of the candidate's efficacy. Although the ultrafiltration-LC/MS (UF-LC/MS) assay enables efficient ligand discovery for a specific target from a mixed pool of compounds, most previous analysis allowed for relative affinity ranking of different ligands. Moreover, the reliability of affinity measurement for multiple ligands with UF-LC/MS has hardly been strictly evaluated. In this study, we examined the accuracy of K(d) determination through UF-LC/MS by comparison with classical ITC measurement. A single-point K(d) calculation method was found to be suitable for affinity measurement of multiple ligands bound to the same target when binding competition is minimized. A second workflow based on analysis of the unbound fraction of compounds was then developed, which simplified sample preparation as well as warranted reliable ligand discovery. The new workflow implemented in a fragment mixture screen afforded rapid and sensitive detection of low-affinity ligands selectively bound to the RNA polymerase NS5B of hepatitis C virus. More importantly, ligand identification and affinity measurement for mixture-based fragment screens by UF-LC/MS were in good accordance with single ligand evaluation by conventional SPR analysis. This new approach is expected to become a valuable addition to the arsenal of high-throughput screening techniques for fragment-based drug discovery.
Ísberg, Vignir; Balle, Thomas; Sander, Tommy
2011-01-01
A 5-HT(2A) receptor model was constructed by homology modeling based on the ß(2)-adrenergic receptor and the G protein-bound opsin crystal structures. The 5-HT(2A) receptor model was transferred into an active conformation by an agonist ligand and a G(aq) peptide in four subsequent steered...
Application of chiral thiazolidine ligands to asymmetric hydrosilation
李弘; 姚金水; 何炳林
1997-01-01
Seven chiral thiazolidines bound rhodium complexes were synthesized and their catalytic asymmetric hydrosilation properties were investigated It was found through investigation that the configuration of newly formed chiral centre C2 of substituted chiral thiazolidines prepared from L-cysteine or its esters has no effect on the final results of catalytic asymmetric hydrosilation.The direct reason for causing this phenomenon is reported by the present quantitative results for the first time:the rapid racemation of chiral center C2 of chiral thiazolidine ligands takes place under the catalysis of rhodium(Ⅰ) complex [Rh(COD)CI]2
Decoherence in time evolution of bound entanglement
Sun, Z; Sun, C P; Wang, X; Sun, Zhe; Wang, Xiaoguang
2007-01-01
We study a dynamic process of disentanglement by considering the time evolution of bound entanglement for a quantum open system, two qutrits coupling to a common environment. Here, the initial quantum correlations of the two qutrits are characterized by the bound entanglement. In order to show the universality of the role of environment on bound entanglement, both bosonic and spin environments are considered. We found that the bound entanglement displays collapses and revivals, and it can be stable against small temperature and time change. The thermal fluctuation effects on bound entanglement are also considered.
Postactivation Potentiation Biases Maximal Isometric Strength Assessment
Leonardo Coelho Rabello Lima
2014-01-01
Full Text Available Postactivation potentiation (PAP is known to enhance force production. Maximal isometric strength assessment protocols usually consist of two or more maximal voluntary isometric contractions (MVCs. The objective of this study was to determine if PAP would influence isometric strength assessment. Healthy male volunteers (n=23 performed two five-second MVCs separated by a 180-seconds interval. Changes in isometric peak torque (IPT, time to achieve it (tPTI, contractile impulse (CI, root mean square of the electromyographic signal during PTI (RMS, and rate of torque development (RTD, in different intervals, were measured. Significant increases in IPT (240.6 ± 55.7 N·m versus 248.9 ± 55.1 N·m, RTD (746 ± 152 N·m·s−1versus 727 ± 158 N·m·s−1, and RMS (59.1 ± 12.2% RMSMAX versus 54.8 ± 9.4% RMSMAX were found on the second MVC. tPTI decreased significantly on the second MVC (2373 ± 1200 ms versus 2784 ± 1226 ms. We conclude that a first MVC leads to PAP that elicits significant enhancements in strength-related variables of a second MVC performed 180 seconds later. If disconsidered, this phenomenon might bias maximal isometric strength assessment, overestimating some of these variables.
Maj, Michał; Kwak, Kyungwon; Cho, Minhaeng
2015-11-16
Structural dynamics within the distal cavity of myoglobin protein is investigated using 2D-IR and IR pump-probe spectroscopy of the N≡C stretch modes of heme-bound thiocyanate and selenocyanate ions. Although myoglobin-bound thiocyanate group shows a doublet in its IR absorption spectrum, no cross peaks originating from chemical exchange between the two components are observed in the time-resolved 2D IR spectra within the experimental time window. Frequency-frequency correlation functions of the two studied anionic ligands are obtained by means of a few different analysis approaches; these functions were then used to elucidate the differences in structural fluctuation around ligand, ligand-protein interactions, and the degree of structural heterogeneity within the hydrophobic pocket of these myoglobin complexes.
Maximizing versus satisficing: happiness is a matter of choice.
Schwartz, Barry; Ward, Andrew; Monterosso, John; Lyubomirsky, Sonja; White, Katherine; Lehman, Darrin R
2002-11-01
Can people feel worse off as the options they face increase? The present studies suggest that some people--maximizers--can. Study 1 reported a Maximization Scale, which measures individual differences in desire to maximize. Seven samples revealed negative correlations between maximization and happiness, optimism, self-esteem, and life satisfaction, and positive correlations between maximization and depression, perfectionism, and regret. Study 2 found maximizers less satisfied than nonmaximizers (satisficers) with consumer decisions, and more likely to engage in social comparison. Study 3 found maximizers more adversely affected by upward social comparison. Study 4 found maximizers more sensitive to regret and less satisfied in an ultimatum bargaining game. The interaction between maximizing and choice is discussed in terms of regret, adaptation, and self-blame.
ON THE SPACES OF THE MAXIMAL POINTS
梁基华; 刘应明
2003-01-01
For a continuous domain D, some characterization that the convex powerdomain CD is adomain hull of Max(CD) is given in terms of compact subsets of D. And in this case, it isproved that the set of the maximal points Max(CD) of CD with the relative Scott topology ishomeomorphic to the set of all Scott compact subsets of Max(D) with the topology induced bythe Hausdorff metric derived from a metric on Max(D) when Max(D) is metrizable.
Understanding of English Contracts though Relation Maxims
XU Chi-ying; JIANG Li-hui
2013-01-01
Contract is the legal evidence of the concerning parties of business. And this lead to its unique characteristics:technical terms, archaism, borrowed words, juxtaposition, and abbreviation. The understanding of contracts is of vital importance for each party, because it concerns the share of interests. In order to avoid ambiguity that some words or sentence in English contracts may lead to, and achieve“best relevance and least effort”of communication, this paper, by applying relation maxim, deeply analyze how to understand English contracts though selection of words, modification, the complexity and simplicity of sentence.
Maximizing results in reconstruction of cheek defects.
Mureau, Marc A M; Hofer, Stefan O P
2009-07-01
The face is exceedingly important, as it is the medium through which individuals interact with the rest of society. Reconstruction of cheek defects after trauma or surgery is a continuing challenge for surgeons who wish to reliably restore facial function and appearance. Important in aesthetic facial reconstruction are the aesthetic unit principles, by which the face can be divided in central facial units (nose, lips, eyelids) and peripheral facial units (cheeks, forehead, chin). This article summarizes established options for reconstruction of cheek defects and provides an overview of several modifications as well as tips and tricks to avoid complications and maximize aesthetic results.
Maximizing policy learning in international committees
Nedergaard, Peter
2007-01-01
, this article demonstrates that valuable lessons can be learned about policy learning, in practice and theoretically, by analysing the cooperation in the OMC committees. Using the Advocacy Coalition Framework as the starting point of analysis, 15 hypotheses on policy learning are tested. Among other things......, it is concluded that in order to maximize policy learning in international committees, empirical data should be made available to committees and provided by sources close to the participants (i.e. the Commission). In addition, the work in the committees should be made prestigious in order to attract well...
Capacity Bounds for Parallel Optical Wireless Channels
Chaaban, Anas
2016-01-01
A system consisting of parallel optical wireless channels with a total average intensity constraint is studied. Capacity upper and lower bounds for this system are derived. Under perfect channel-state information at the transmitter (CSIT), the bounds have to be optimized with respect to the power allocation over the parallel channels. The optimization of the lower bound is non-convex, however, the KKT conditions can be used to find a list of possible solutions one of which is optimal. The optimal solution can then be found by an exhaustive search algorithm, which is computationally expensive. To overcome this, we propose low-complexity power allocation algorithms which are nearly optimal. The optimized capacity lower bound nearly coincides with the capacity at high SNR. Without CSIT, our capacity bounds lead to upper and lower bounds on the outage probability. The outage probability bounds meet at high SNR. The system with average and peak intensity constraints is also discussed.
Exact entanglement bases and general bound entanglement
Zhong, Z Z
2004-01-01
In this paper, we give the more general bound entangled states associated with the unextendible product bases (UPB), i.e. by using of the exact entanglement bases (EEB) and the complete basis with unextendible product bases (CBUPB), we prove that the arbitrary convex sums of the uniform mixtures (bound entangled states) associated with UPBs are still bound entangled states. Further, we discuss the equivalent transformation group and classification of the CBUPBs, and by using this classification, we prove that in the meaning of indistinguishability, the set of the above all possible bound entangled states can be reduced to the set of all possible mixtures of some fixed basic bound entangled states. At last, we prove that every operating of the partial transposition (PT) map acting upon a density matrix under any bipartite partitioning induces a mapping from the above reduced set of bound entangled states to oneself, which corresponds to a non-identical permutation of the basic bound entangled states.
Thermodynamic law from the entanglement entropy bound
Park, Chanyong
2015-01-01
From black hole thermodynamics, the Bekenstein bound has been proposed as a universal thermal entropy bound. It has been further generalized to an entanglement entropy bound which is valid even in a quantum system. In a quantumly entangled system, the non-negativity of the relative entropy leads to the entanglement entropy bound. When the entanglement entropy bound is saturated, a quantum system satisfies the thermodynamics-like law with an appropriately defined entanglement temperature. We show that the saturation of the entanglement entropy bound accounts for a universal feature of the entanglement temperature proportional to the inverse of the system size. In addition, we also find that a global quench unlike the excitation does not preserve the entanglement entropy bound.
Universal localizing bounds for compact invariant sets of natural polynomial Hamiltonian systems
Starkov, Konstantin E. [CITEDI-IPN, Av. del Parque 1310, Mesa de Otay, Tijuana, BC (Mexico)], E-mail: konst@citedi.mx
2008-10-06
In this Letter we study the localization problem of compact invariant sets of natural Hamiltonian systems with a polynomial Hamiltonian. Our results are based on applying the first order extremum conditions. We compute universal localizing bounds for some domain containing all compact invariant sets of a Hamiltonian system by using one quadratic function of a simple form. These bounds depend on the value of the total energy of the system, degree and some coefficients of a potential and, in addition, some positive number got as a result of a solution of one maximization problem. Besides, under some quasihomogeneity condition(s) we generalize our construction of the localization set.
Tight Bounds on the Average Length, Entropy, and Redundancy of Anti-Uniform Huffman Codes
Mohajer, Soheil
2007-01-01
In this paper we consider the class of anti-uniform Huffman codes and derive tight lower and upper bounds on the average length, entropy, and redundancy of such codes in terms of the alphabet size of the source. The Fibonacci distributions are introduced which play a fundamental role in AUH codes. It is shown that such distributions maximize the average length and the entropy of the code for a given alphabet size. Another previously known bound on the entropy for given average length follows immediately from our results.
Spectral computations for bounded operators
Ahues, Mario; Limaye, Balmohan
2001-01-01
Exact eigenvalues, eigenvectors, and principal vectors of operators with infinite dimensional ranges can rarely be found. Therefore, one must approximate such operators by finite rank operators, then solve the original eigenvalue problem approximately. Serving as both an outstanding text for graduate students and as a source of current results for research scientists, Spectral Computations for Bounded Operators addresses the issue of solving eigenvalue problems for operators on infinite dimensional spaces. From a review of classical spectral theory through concrete approximation techniques to finite dimensional situations that can be implemented on a computer, this volume illustrates the marriage of pure and applied mathematics. It contains a variety of recent developments, including a new type of approximation that encompasses a variety of approximation methods but is simple to verify in practice. It also suggests a new stopping criterion for the QR Method and outlines advances in both the iterative refineme...
Hsu, Chia Wei; Zhen, Bo; Stone, A. Douglas; Joannopoulos, John D.; Soljačić, Marin
2016-09-01
Bound states in the continuum (BICs) are waves that remain localized even though they coexist with a continuous spectrum of radiating waves that can carry energy away. Their very existence defies conventional wisdom. Although BICs were first proposed in quantum mechanics, they are a general wave phenomenon and have since been identified in electromagnetic waves, acoustic waves in air, water waves and elastic waves in solids. These states have been studied in a wide range of material systems, such as piezoelectric materials, dielectric photonic crystals, optical waveguides and fibres, quantum dots, graphene and topological insulators. In this Review, we describe recent developments in this field with an emphasis on the physical mechanisms that lead to BICs across seemingly very different materials and types of waves. We also discuss experimental realizations, existing applications and directions for future work.
Towards Bounded Infeasible Code Detection
Christ, Jürgen; Schäf, Martin
2012-01-01
A first step towards more reliable software is to execute each statement and each control-flow path in a method once. In this paper, we present a formal method to automatically compute test cases for this purpose based on the idea of a bounded infeasible code detection. The method first unwinds all loops in a program finitely often and then encodes all feasible executions of the loop-free programs in a logical formula. Helper variables are introduced such that a theorem prover can reconstruct the control-flow path of a feasible execution from a satisfying valuation of this formula. Based on this formula, we present one algorithm that computes a feasible path cover and one algorithm that computes a feasible statement cover. We show that the algorithms are complete for loop-free programs and that they can be implemented efficiently. We further provide a sound algorithm to compute procedure summaries which makes the method scalable to larger programs.
Reactivity of Metal Ions Bound to Water-Soluble Polymers
Sauer, N.N.; Watkins, J.G.; Lin, M.; Birnbaum, E.R.; Robison, T.W.; Smith, B.F.; Gohdes, J.W.; McDonald, J.G.
1999-06-29
The intent of this work is to determine the effectiveness of catalysts covalently bound to polymers and to understand the consequences of supporting the catalysts on catalyst efficiency and selectivity. Rhodium phosphine complexes with functional groups for coupling to polymers were prepared. These catalyst precursors were characterized using standard techniques including IR, NMR, and elemental analysis. Studies on the modified catalysts showed that they were still active hydrogenation catalysts. However, tethering of the catalysts to polyamines gave systems with low hydrogenation activity. Analogous biphasic systems were also explored. Phosphine ligands with a surfactant-like structure have been synthesized and used to prepare catalytically active complexes of palladium. The palladium complexes were utilized in Heck-type coupling reactions (e.g. coupling of iodobenzene and ethyl acrylate to produce ethyl cinnamate) under vigorously stirred biphasic reaction conditions, and were found to offer superior performance over a standard water-soluble palladium catalyst under analogous conditions.
Colloidal metal oxide nanocrystal catalysis by sustained chemically driven ligand displacement
de Roo, Jonathan; van Driessche, Isabel; Martins, José C.; Hens, Zeger
2016-05-01
Surface chemistry is a key enabler for colloidal nanocrystal applications. In this respect, metal oxide nanocrystals (NCs) stand out from other NCs as carboxylic acid ligands adsorb on their surface by dissociation to carboxylates and protons, the latter proving essential in electron transfer reactions. Here, we show that this binding motif sets the stage for chemically driven ligand displacement where the binding of amines or alcohols to HfO2 NCs is promoted by the conversion of a bound carboxylic acid into a non-coordinating amide or ester. Furthermore, the sustained ligand displacement, following the addition of excess carboxylic acid, provides a catalytic pathway for ester formation, whereas the addition of esters leads to NC-catalysed transesterification. Because sustained, chemically driven ligand displacement leaves the NCs--including their surface composition--unchanged and preserves colloidal stability, metal oxide nanocrystals are thus turned into effective nanocatalysts that bypass the tradeoff between colloidal stability and catalytic activity.
Structure of the human M2 muscarinic acetylcholine receptor bound to an antagonist
Haga, Kazuko; Kruse, Andrew C.; Asada, Hidetsugu; Yurugi-Kobayashi, Takami; Shiroishi, Mitsunori; Zhang, Cheng; Weis, William I.; Okada, Tetsuji; Kobilka, Brian K.; Haga, Tatsuya; Kobayashi, Takuya (Stanford-MED); (Kyoto); (Gakushuin); (Kyushu)
2012-03-15
The parasympathetic branch of the autonomic nervous system regulates the activity of multiple organ systems. Muscarinic receptors are G-protein-coupled receptors that mediate the response to acetylcholine released from parasympathetic nerves. Their role in the unconscious regulation of organ and central nervous system function makes them potential therapeutic targets for a broad spectrum of diseases. The M2 muscarinic acetylcholine receptor (M2 receptor) is essential for the physiological control of cardiovascular function through activation of G-protein-coupled inwardly rectifying potassium channels, and is of particular interest because of its extensive pharmacological characterization with both orthosteric and allosteric ligands. Here we report the structure of the antagonist-bound human M2 receptor, the first human acetylcholine receptor to be characterized structurally, to our knowledge. The antagonist 3-quinuclidinyl-benzilate binds in the middle of a long aqueous channel extending approximately two-thirds through the membrane. The orthosteric binding pocket is formed by amino acids that are identical in all five muscarinic receptor subtypes, and shares structural homology with other functionally unrelated acetylcholine binding proteins from different species. A layer of tyrosine residues forms an aromatic cap restricting dissociation of the bound ligand. A binding site for allosteric ligands has been mapped to residues at the entrance to the binding pocket near this aromatic cap. The structure of the M2 receptor provides insights into the challenges of developing subtype-selective ligands for muscarinic receptors and their propensity for allosteric regulation.
UV-Visible Spectroscopy-Based Quantification of Unlabeled DNA Bound to Gold Nanoparticles.
Baldock, Brandi L; Hutchison, James E
2016-12-20
DNA-functionalized gold nanoparticles have been increasingly applied as sensitive and selective analytical probes and biosensors. The DNA ligands bound to a nanoparticle dictate its reactivity, making it essential to know the type and number of DNA strands bound to the nanoparticle surface. Existing methods used to determine the number of DNA strands per gold nanoparticle (AuNP) require that the sequences be fluorophore-labeled, which may affect the DNA surface coverage and reactivity of the nanoparticle and/or require specialized equipment and other fluorophore-containing reagents. We report a UV-visible-based method to conveniently and inexpensively determine the number of DNA strands attached to AuNPs of different core sizes. When this method is used in tandem with a fluorescence dye assay, it is possible to determine the ratio of two unlabeled sequences of different lengths bound to AuNPs. Two sizes of citrate-stabilized AuNPs (5 and 12 nm) were functionalized with mixtures of short (5 base) and long (32 base) disulfide-terminated DNA sequences, and the ratios of sequences bound to the AuNPs were determined using the new method. The long DNA sequence was present as a lower proportion of the ligand shell than in the ligand exchange mixture, suggesting it had a lower propensity to bind the AuNPs than the short DNA sequence. The ratio of DNA sequences bound to the AuNPs was not the same for the large and small AuNPs, which suggests that the radius of curvature had a significant influence on the assembly of DNA strands onto the AuNPs.
A Low-Dimensional Model for the Maximal Amplification Factor of Bichromatic Wave Groups
W. N. Tan
2003-11-01
Full Text Available We consider a low-dimensional model derived from the nonlinear-Schrödinger equation that describes the evolution of a special class of surface gravity wave groups, namely bichromatic waves. The model takes only two modes into account, namely the primary mode and the third order mode which is known to be most relevant for bichromatic waves with small frequency difference. Given an initial condition, an analytical expression for the maximal amplitude of the evolution of this initial wave group according to the model can be readily obtained. The aim of this investigation is to predict the amplification factor defined as the quotient between the maximal amplitude over all time & space and the initial maximal amplitude. Although this is a problem of general interest, as a case study, initial conditions in the form of a bichromatic wave group are taken. Using the low dimensional model it is found that the least upper bound of the maximal amplification factor for this bichromatic wave group is √2. To validate the analytical results of this model, a numerical simulation on the full model is also performed. As can be expected, good agreement is observed between analytical and numerical solutions for a certain range of parameters; when the initial amplitude is not too large, or when the difference of frequency is not too small. The results are relevant and motivated for the generation of waves in hydrodynamic laboratories.
Maximal subbundles, quot schemes, and curve counting
Gillam, W D
2011-01-01
Let $E$ be a rank 2, degree $d$ vector bundle over a genus $g$ curve $C$. The loci of stable pairs on $E$ in class $2[C]$ fixed by the scaling action are expressed as products of $\\Quot$ schemes. Using virtual localization, the stable pairs invariants of $E$ are related to the virtual intersection theory of $\\Quot E$. The latter theory is extensively discussed for an $E$ of arbitrary rank; the tautological ring of $\\Quot E$ is defined and is computed on the locus parameterizing rank one subsheaves. In case $E$ has rank 2, $d$ and $g$ have opposite parity, and $E$ is sufficiently generic, it is known that $E$ has exactly $2^g$ line subbundles of maximal degree. Doubling the zero section along such a subbundle gives a curve in the total space of $E$ in class $2[C]$. We relate this count of maximal subbundles with stable pairs/Donaldson-Thomas theory on the total space of $E$. This endows the residue invariants of $E$ with enumerative significance: they actually \\emph{count} curves in $E$.
Maximal coherence in a generic basis
Yao, Yao; Dong, G. H.; Ge, Li; Li, Mo; Sun, C. P.
2016-12-01
Since quantum coherence is an undoubted characteristic trait of quantum physics, the quantification and application of quantum coherence has been one of the long-standing central topics in quantum information science. Within the framework of a resource theory of quantum coherence proposed recently, a fiducial basis should be preselected for characterizing the quantum coherence in specific circumstances, namely, the quantum coherence is a basis-dependent quantity. Therefore, a natural question is raised: what are the maximum and minimum coherences contained in a certain quantum state with respect to a generic basis? While the minimum case is trivial, it is not so intuitive to verify in which basis the quantum coherence is maximal. Based on the coherence measure of relative entropy, we indicate the particular basis in which the quantum coherence is maximal for a given state, where the Fourier matrix (or more generally, complex Hadamard matrices) plays a critical role in determining the basis. Intriguingly, though we can prove that the basis associated with the Fourier matrix is a stationary point for optimizing the l1 norm of coherence, numerical simulation shows that it is not a global optimal choice.
Symmetry and approximability of submodular maximization problems
Vondrak, Jan
2011-01-01
A number of recent results on optimization problems involving submodular functions have made use of the multilinear relaxation of the problem. These results hold typically in the value oracle model, where the objective function is accessible via a black box returning f(S) for a given S. We present a general approach to deriving inapproximability results in the value oracle model, based on the notion of symmetry gap. Our main result is that for any fixed instance that exhibits a certain symmetry gap in its multilinear relaxation, there is a naturally related class of instances for which a better approximation factor than the symmetry gap would require exponentially many oracle queries. This unifies several known hardness results for submodular maximization, and implies several new ones. In particular, we prove that there is no constant-factor approximation for the problem of maximizing a non-negative submodular function over the bases of a matroid. We also provide a closely matching approximation algorithm for...
Visualization of Metal-to-Ligand and Ligand-to-Ligand Charge Transfer in Metal-Ligand Complexes
Yong Ding; Jian-xiu Guo; Xiang-si Wang; Sha-sha Liu; Feng-cai Ma
2009-01-01
Three methods including the atomic resolved density of state, charge difference density, and the transition density matrix are used to visualize metal to ligand charge transfer (MLCT) in ruthenium(Ⅱ) ammine complex. The atomic resolved density of state shows that there is density of Ru on the HOMOs. All the density is localized on the ammine, which reveals that the excited electrons in the Ru complex are delocalized over the ammine ligand. The charge difference density shows that all the holes are localized on the Ru and the electrons on the ammine. The localization explains the MLCT on excitation. The transition density matrix shows that there is electron-hole coherence between Ru and ammine. These methods are also used to examine the MLCT in Os(bpy)(p0p)Cl ("Osp0p"; bpy=2,2'-bipyridyl; p0p=4,4'-bipyridyl) and the ligand-to-ligand charge transfer (LLCT) in Alq3. The calculated results show that these methods are powerful to examine MLCT and LLCT in the metal-ligand system.
Using tolerance bounds in scientific investigations
Wendelberger, J.R.
1996-07-01
Assessment of the variability in population values plays an important role in the analysis of scientific data. Analysis of scientific data often involves developing a bound on a proportion of a population. Sometimes simple probability bounds are obtained using formulas involving known mean and variance parameters and replacing the parameters by sample estimates. The resulting bounds are only approximate and fail to account for the variability in the estimated parameters. Tolerance bounds provide bounds on population proportions which account for the variation resulting from the estimated mean and variance parameters. A beta content, gamma confidence tolerance interval is constructed so that a proportion beta of the population lies within the region bounded by the interval with confidence gamma. An application involving corrosion measurements is used to illustrate the use of tolerance bounds for different situations. Extensions of standard tolerance intervals are applied to generate regression tolerance bounds, tolerance bounds for more general models of measurements collected over time, and tolerance intervals for varying precision data. Tolerance bounds also provide useful information for designing the collection of future data.
A Fluid Membrane-Based Soluble Ligand Display System for Live CellAssays
Nam, Jwa-Min; Nair, Pradeep N.; Neve, Richard M.; Gray, Joe W.; Groves, Jay T.
2005-10-14
Cell communication modulates numerous biological processes including proliferation, apoptosis, motility, invasion and differentiation. Correspondingly, there has been significant interest in the development of surface display strategies for the presentation of signaling molecules to living cells. This effort has primarily focused on naturally surface-bound ligands, such as extracellular matrix components and cell membranes. Soluble ligands (e.g. growth factors and cytokines) play an important role in intercellular communications, and their display in a surface-bound format would be of great utility in the design of array-based live cell assays. Recently, several cell microarray systems that display cDNA, RNAi, or small molecules in a surface array format were proven to be useful in accelerating high-throughput functional genetic studies and screening therapeutic agents. These surface display methods provide a flexible platform for the systematic, combinatorial investigation of genes and small molecules affecting cellular processes and phenotypes of interest. In an analogous sense, it would be an important advance if one could display soluble signaling ligands in a surface assay format that allows for systematic, patterned presentation of soluble ligands to live cells. Such a technique would make it possible to examine cellular phenotypes of interest in a parallel format with soluble signaling ligands as one of the display parameters. Herein we report a ligand-modified fluid supported lipid bilayer (SLB) assay system that can be used to functionally display soluble ligands to cells in situ (Figure 1A). By displaying soluble ligands on a SLB surface, both solution behavior (the ability to become locally enriched by reaction-diffusion processes) and solid behavior (the ability to control the spatial location of the ligands in an open system) could be combined. The method reported herein benefits from the naturally fluid state of the supported membrane, which allows
High-Throughput Identification of Combinatorial Ligands for DNA Delivery in Cell Culture
Svahn, Mathias G.; Rabe, Kersten S.; Barger, Geoffrey; EL-Andaloussi, Samir; Simonson, Oscar E.; Didier, Boturyn; Olivier, Renaudet; Dumy, Pascal; Brandén, Lars J.; Niemeyer, Christof M.; Smith, C. I. Edvard
2008-10-01
Finding the optimal combinations of ligands for tissue-specific delivery is tedious even if only a few well-established compounds are tested. The cargo affects the receptor-ligand interaction, especially when it is charged like DNA. The ligand should therefore be evaluated together with its cargo. Several viruses have been shown to interact with more than one receptor, for efficient internalization. We here present a DNA oligonucleotide-based method for inexpensive and rapid screening of biotin labeled ligands for combinatorial effects on cellular binding and uptake. The oligonucleotide complex was designed as a 44 bp double-stranded DNA oligonucleotide with one central streptavidin molecule and a second streptavidin at the terminus. The use of a highly advanced robotic platform ensured stringent processing and execution of the experiments. The oligonucleotides were fluorescently labeled and used for detection and analysis of cell-bound, internalized and intra-cellular compartmentalized constructs by an automated line-scanning confocal microscope, IN Cell Analyzer 3000. All possible combinations of 22 ligands were explored in sets of 2 and tested on 6 different human cell lines in triplicates. In total, 10 000 transfections were performed on the automation platform. Cell-specific combinations of ligands were identified and their relative position on the scaffold oligonucleotide was found to be of importance. The ligands were found to be cargo dependent, carbohydrates were more potent for DNA delivery whereas cell penetrating peptides were more potent for delivery of less charged particles.
VS-APPLE: A Virtual Screening Algorithm Using Promiscuous Protein-Ligand Complexes.
Okuno, Tatsuya; Kato, Koya; Terada, Tomoki P; Sasai, Masaki; Chikenji, George
2015-06-22
As the number of structurally resolved protein-ligand complexes increases, the ligand-binding pockets of many proteins have been found to accommodate multiple different compounds. Effective use of these structural data is important for developing virtual screening (VS) methods that identify bioactive compounds. Here, we introduce a VS method, VS-APPLE (Virtual Screening Algorithm using Promiscuous Protein-Ligand complExes), based on promiscuous protein-ligand binding structures. In VS-APPLE, multiple ligands bound to a pocket are combined into a query template for screening. Both the structural match between a test compound and the multiple-ligand template and the possible collisions between the test compound and the target protein are evaluated by an efficient geometric hashing method. The performance of VS-APPLE was examined on a filtered, clustered version of the Directory of Useful Decoys data set. In Area Under the Curve analyses of this data set, VS-APPLE outperformed several popular screening programs. Judging from the performance of VS-APPLE, the structural data of promiscuous protein-ligand bindings could be further analyzed and exploited for developing VS methods.
PANP is a novel O-glycosylated PILR{alpha} ligand expressed in neural tissues
Kogure, Amane [Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871 (Japan); Laboratory of Immunochemistry, WPI Immunology Frontier Research Center, Osaka University, Osaka 565-0871 (Japan); Shiratori, Ikuo [Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871 (Japan); Wang, Jing [Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871 (Japan); Laboratory of Immunochemistry, WPI Immunology Frontier Research Center, Osaka University, Osaka 565-0871 (Japan); Lanier, Lewis L. [Department of Microbiology and Immunology and the Cancer Research Institute, University of California San Francisco, San Francisco, CA 94143 (United States); Arase, Hisashi, E-mail: arase@biken.osaka-u.ac.jp [Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871 (Japan); Laboratory of Immunochemistry, WPI Immunology Frontier Research Center, Osaka University, Osaka 565-0871 (Japan); JST CREST, Saitama 332-0012 (Japan)
2011-02-18
Research highlights: {yields} A Novel molecule, PANP, was identified to be a PILR{alpha} ligand. {yields} Sialylated O-glycan structures on PANP were required for PILR{alpha} recognition. {yields} Transcription of PANP was mainly observed in neural tissues. {yields} PANP seems to be involved in immune regulation as a ligand for PILR{alpha}. -- Abstract: PILR{alpha} is an immune inhibitory receptor possessing an immunoreceptor tyrosine-based inhibitory motif (ITIM) in its cytoplasmic domain enabling it to deliver inhibitory signals. Binding of PILR{alpha} to its ligand CD99 is involved in immune regulation; however, whether there are other PILR{alpha} ligands in addition to CD99 is not known. Here, we report that a novel molecule, PILR-associating neural protein (PANP), acts as an additional ligand for PILR{alpha}. Transcription of PANP was mainly observed in neural tissues. PILR{alpha}-Ig fusion protein bound cells transfected with PANP and the transfectants stimulated PILR{alpha} reporter cells. Specific O-glycan structures on PANP were found to be required for PILR recognition of this ligand. These results suggest that PANP is involved in immune regulation as a ligand of the PILR{alpha}.
Determinants governing ligand specificity of the Vibrio harveyi LuxN quorum-sensing receptor.
Ke, Xiaobo; Miller, Laura C; Bassler, Bonnie L
2015-01-01
Quorum sensing is a process of bacterial cell-cell communication that relies on the production, release and receptor-driven detection of extracellular signal molecules called autoinducers. The quorum-sensing bacterium Vibrio harveyi exclusively detects the autoinducer N-((R)-3-hydroxybutanoyl)-L-homoserine lactone (3OH-C4 HSL) via the two-component receptor LuxN. To discover the principles underlying the exquisite selectivity LuxN has for its ligand, we identified LuxN mutants with altered specificity. LuxN uses three mechanisms to verify that the bound molecule is the correct ligand: in the context of the overall ligand-binding site, His210 validates the C3 modification, Leu166 surveys the chain-length and a strong steady-state kinase bias imposes an energetic hurdle for inappropriate ligands to elicit signal transduction. Affinities for the LuxN kinase on and kinase off states underpin whether a ligand will act as an antagonist or an agonist. Mutations that bias LuxN to the agonized, kinase off, state are clustered in a region adjacent to the ligand-binding site, suggesting that this region acts as the switch that triggers signal transduction. Together, our analyses illuminate how a histidine sensor kinase differentiates between ligands and exploits those differences to regulate its signaling activity.
Bound anionic states of adenine
Haranczyk, Maciej; Gutowski, Maciej S; Li, Xiang; Bowen, Kit H
2007-03-20
Anionic states of nucleic acid bases are involved in DNA damage by low-energy electrons and in charge transfer through DNA. Previous gas phase studies of free, unsolvated nucleic acid base parent anions probed only dipole-bound states, which are not present in condensed phase environments, but did not observe valence anionic states, which for purine bases, are thought to be adiabatically unbound. Contrary to this expectation, we have demonstrated that some thus far ignored tautomers of adenine, which result from enamine-imine transformations, support valence anionic states with electron vertical detachment energies as large as 2.2 eV, and at least one of these anionic tautomers is adiabatically bound. Moreover, we predict that the new anionic tautomers should also dominate in solutions and should be characterized by larger values of electron vertical detachment energy than the canonical valence anion. All of the new-found anionic tautomers might be formed in the course of dissociative electron attachment followed by a hydrogen atom attachment to a carbon atom, and they might affect the structure and properties of DNA and RNA exposed to low-energy electrons. The discovery of these valence anionic states of adenine was facilitated by the development of: (i) a new experimental method for preparing parent anions of nucleic acid bases for photoelectron experiments, and (ii) a new combinatorial/ quantum chemical approach for identification of the most stable tautomers of organic molecules. The computational portion of this work was supported by the: (i) Polish State Committee for Scientific Research (KBN) Grants: DS/8000-4-0140-7 (M.G.) and N204 127 31/2963 (M.H.), (ii) European Social Funds (EFS) ZPORR/2.22/II/2.6/ARP/U/2/05 (M.H.), and (iii) US DOE Office of Biological and Environmental Research, Low Dose Radiation Research Program (M.G.). M.H. holds the Foundation for Polish Science (FNP) award for young scientists. The calculations were performed at the Academic
Molecular Recognition and Ligand Association
Baron, Riccardo; McCammon, J. Andrew
2013-04-01
We review recent developments in our understanding of molecular recognition and ligand association, focusing on two major viewpoints: (a) studies that highlight new physical insight into the molecular recognition process and the driving forces determining thermodynamic signatures of binding and (b) recent methodological advances in applications to protein-ligand binding. In particular, we highlight the challenges posed by compensating enthalpic and entropic terms, competing solute and solvent contributions, and the relevance of complex configurational ensembles comprising multiple protein, ligand, and solvent intermediate states. As more complete physics is taken into account, computational approaches increase their ability to complement experimental measurements, by providing a microscopic, dynamic view of ensemble-averaged experimental observables. Physics-based approaches are increasingly expanding their power in pharmacology applications.
Why mercury prefers soft ligands
Riccardi, Demian M [ORNL; Guo, Hao-Bo [ORNL; Gu, Baohua [ORNL; Parks, Jerry M [ORNL; Summers, Anne [University of Georgia, Athens, GA; Miller, S [University of California, San Francisco; Liang, Liyuan [ORNL; Smith, Jeremy C [ORNL
2013-01-01
Mercury (Hg) is a major global pollutant arising from both natural and anthropogenic sources. Defining the factors that determine the relative affinities of different ligands for the mercuric ion, Hg2+, is critical to understanding its speciation, transformation, and bioaccumulation in the environment. Here, we use quantum chemistry to dissect the relative binding free energies for a series of inorganic anion complexes of Hg2+. Comparison of Hg2+ ligand interactions in the gaseous and aqueous phases shows that differences in interactions with a few, local water molecules led to a clear periodic trend within the chalcogenide and halide groups and resulted in the well-known experimentally observed preference of Hg2+ for soft ligands such as thiols. Our approach establishes a basis for understanding Hg speciation in the biosphere.
Qian, Hai-Long; Yang, Cheng-Xiong; Yan, Xiu-Ping
2016-07-12
Covalent organic frameworks (COFs) are a novel class of porous materials, and offer great potential for various applications. However, the applications of COFs in chiral separation and chiral catalysis are largely underexplored due to the very limited chiral COFs available and their challenging synthesis. Here we show a bottom-up strategy to construct chiral COFs and an in situ growth approach to fabricate chiral COF-bound capillary columns for chiral gas chromatography. We incorporate the chiral centres into one of the organic ligands for the synthesis of the chiral COFs. We subsequently in situ prepare the COF-bound capillary columns. The prepared chiral COFs and their bound capillary columns give high resolution for the separation of enantiomers with excellent repeatability and reproducibility. The proposed strategy provides a promising platform for the synthesis of chiral COFs and their chiral separation application.
Qian, Hai-Long; Yang, Cheng-Xiong; Yan, Xiu-Ping
2016-07-01
Covalent organic frameworks (COFs) are a novel class of porous materials, and offer great potential for various applications. However, the applications of COFs in chiral separation and chiral catalysis are largely underexplored due to the very limited chiral COFs available and their challenging synthesis. Here we show a bottom-up strategy to construct chiral COFs and an in situ growth approach to fabricate chiral COF-bound capillary columns for chiral gas chromatography. We incorporate the chiral centres into one of the organic ligands for the synthesis of the chiral COFs. We subsequently in situ prepare the COF-bound capillary columns. The prepared chiral COFs and their bound capillary columns give high resolution for the separation of enantiomers with excellent repeatability and reproducibility. The proposed strategy provides a promising platform for the synthesis of chiral COFs and their chiral separation application.
Nonadditivity of Rains' bound for distillable entanglement
Wang, Xin; Duan, Runyao
2017-06-01
Rains' bound is arguably the best known upper bound of the distillable entanglement by operations completely preserving positivity of partial transpose (PPT) and was conjectured to be additive and coincide with the asymptotic relative entropy of entanglement. We disprove both conjectures by explicitly constructing a special class of mixed two-qubit states. We then introduce an additive semidefinite programming lower bound (EM) for the asymptotic Rains' bound, and it immediately becomes a computable lower bound for entanglement cost of bipartite states. Furthermore, EM is also proved to be the best known upper bound of the PPT-assisted deterministic distillable entanglement and gives the asymptotic rates for all pure states and some class of genuinely mixed states.
Process expression of bounded Petri nets
吴哲辉
1996-01-01
The concept of process expression of bounded Petri nets is presented.Moreover,an algorithm to find the process expression for a bounded Petri net is given.A process expression of a bounded Petri net is a regular expression whose every alphabet symbol represents a basic subprocess of the net.The regular set expressed by the regular expression is the set of all surjective processes of a bounded Petri net.A surjective process of a bounded Petri net is a process of this net in which every s-cut corresponds to a reachable marking of the net.Therefore,all surjective processes of a bounded Petri net can be obtained as long as its process expression and the basic subprocess represented by the alphabet symbols of the process expression are given.
Thermodynamic law from the entanglement entropy bound
Park, Chanyong
2016-04-01
From black hole thermodynamics, the Bekenstein bound has been proposed as a universal thermal entropy bound. It has been further generalized to an entanglement entropy bound which is valid even in a quantum system. In a quantumly entangled system, the non-negativity of the relative entropy leads to the entanglement entropy bound. When the entanglement entropy bound is saturated, a quantum system satisfies the thermodynamicslike law with an appropriately defined entanglement temperature. We show that the saturation of the entanglement entropy bound accounts for a universal feature of the entanglement temperature proportional to the inverse of the system size. In addition, we show that the deformed modular Hamiltonian under a global quench also satisfies the generalized entanglement entropy boundary after introducing a new quantity called the entanglement chemical potential.
Bounds on double-diffusive convection
Balmforth, Neil J.; Ghadge, Shilpa A.; Kettapun, Atichart; Mandre, Shreyas D.
2006-12-01
We consider double-diffusive convection between two parallel plates and compute bounds on the flux of the unstably stratified species using the background method. The bound on the heat flux for Rayleigh Bénard convection also serves as a bound on the double-diffusive problem (with the thermal Rayleigh number equal to that of the unstably stratified component). In order to incorporate a dependence of the bound on the stably stratified component, an additional constraint must be included, like that used by Joseph (Stability of Fluid Motion, 1976, Springer) to improve the energy stability analysis of this system. Our bound extends Joseph's result beyond his energy stability boundary. At large Rayleigh number, the bound is found to behave like R_T(1/2) for fixed ratio R_S/R_T, where R_T and R_S are the Rayleigh numbers of the unstably and stably stratified components, respectively.
Instanton bound states in ABJM theory
Hatsuda, Yasuyuki [DESY Hamburg (Germany). Theory Group; Tokyo Institute of Technology (Japan). Dept. of Physics; Moriyama, Sanefumi [Nagoya Univ. (Japan). Kobayashi Maskawa Inst. and Graduate School of Mathematics; Okuyama, Kazumi [Shinshu Univ., Matsumoto, Nagano (Japan). Dept. of Physics
2013-06-15
The partition function of the ABJM theory receives non-perturbative corrections due to instanton effects. We study these non-perturbative corrections, including bound states of worldsheet instantons and membrane instantons, in the Fermi-gas approach. We require that the total non-perturbative correction should be always finite for arbitrary Chern-Simons level. This finiteness is realized quite non-trivially because each bound state contribution naively diverges at some levels. The poles of each contribution should be canceled out in total. We use this pole cancellation mechanism to find unknown bound state corrections from known ones. We conjecture a general expression of the bound state contribution. Summing up all the bound state contributions, we find that the effect of bound states is simply incorporated into the worldsheet instanton correction by a redefinition of the chemical potential in the Fermi-gas system. Analytic expressions of the 3- and 4-membrane instanton corrections are also proposed.
Sharp Bounds on the Ranks of Negativity of Certain Sums
Torben Maack Bisgaard
2008-08-01
If is a complex vector space and $\\langle\\cdot p,\\cdot p\\rangle$ a Hermitian sesquilinear form on with a finite rank of negativity (i.e., is the maximal dimension of any linear subspace of satisfying $\\langle x,x\\rangle < 0$ for each nonzero in ), if is a positive integer, and if $a_1,\\ldots,a_n$ are endomorphisms of , then it is easy to see that the Hermitian sesquilinear form \\begin{equation*}(x, y)\\mapsto\\sum\\limits_{v=1}^n\\langle a_v x, a_v y\\rangle\\end{equation*} on has rank of negativity at most . It is also fairly easy to see that the bound cannot be improved in general. Less trivial is the fact that it cannot be improved by making the following assumption: (a) the space is the *-algebra $A:=C[[_1,_2
Experimental violation of Tsirelson's bound by Maxwell fields
Sandeau, N.; Akhouayri, H.; Matzkin, A.; Durt, T.
2016-05-01
In analogy with quantum optics it is possible to impose nonseparability between different degrees of freedom of an optical beam. The resulting correlations between these degrees of freedom can be investigated with correlations functions traditionally employed in quantum mechanics, such as the well-known Clauser-Horne-Shimony-Holt (CHSH) correlation function. In this paper we present results achieving a maximal violation of Tsirelson's bound on CHSH correlations between spatial and polarization degrees of freedom of classical (Maxwell) fields. We describe the theoretical method, based on the realization of a nonunitary gate, and then proceed to its experimental implementation carried out with classical optical techniques. Our approach relies on the realization at the level of classical Maxwell fields of a so-called POVM (positive operator valued measure) which is traditionally discussed in the realm of quantum physics.
Maximal lattice free bodies, test sets and the Frobenius problem
Jensen, Anders Nedergaard; Lauritzen, Niels; Roune, Bjarke Hammersholt
Maximal lattice free bodies are maximal polytopes without interior integral points. Scarf initiated the study of maximal lattice free bodies relative to the facet normals in a fixed matrix. In this paper we give an efficient algorithm for computing the maximal lattice free bodies of an integral...... method is inspired by the novel algorithm by Einstein, Lichtblau, Strzebonski and Wagon and the Groebner basis approach by Roune....
Maximizing scientific knowledge from randomized clinical trials
Gustafsson, Finn; Atar, Dan; Pitt, Bertram;
2010-01-01
Trialists have an ethical and financial responsibility to plan and conduct clinical trials in a manner that will maximize the scientific knowledge gained from the trial. However, the amount of scientific information generated by randomized clinical trials in cardiovascular medicine is highly...... variable. Generation of trial databases and/or biobanks originating in large randomized clinical trials has successfully increased the knowledge obtained from those trials. At the 10th Cardiovascular Trialist Workshop, possibilities and pitfalls in designing and accessing clinical trial databases were......, in particular with respect to collaboration with the trial sponsor and to analytic pitfalls. The advantages of creating screening databases in conjunction with a given clinical trial are described; and finally, the potential for posttrial database studies to become a platform for training young scientists...
Characterizing maximally singular phase-space distributions
Sperling, J.
2016-07-01
Phase-space distributions are widely applied in quantum optics to access the nonclassical features of radiations fields. In particular, the inability to interpret the Glauber-Sudarshan distribution in terms of a classical probability density is the fundamental benchmark for quantum light. However, this phase-space distribution cannot be directly reconstructed for arbitrary states, because of its singular behavior. In this work, we perform a characterization of the Glauber-Sudarshan representation in terms of distribution theory. We address important features of such distributions: (i) the maximal degree of their singularities is studied, (ii) the ambiguity of representation is shown, and (iii) their dual space for nonclassicality tests is specified. In this view, we reconsider the methods for regularizing the Glauber-Sudarshan distribution for verifying its nonclassicality. This treatment is supported with comprehensive examples and counterexamples.
Maximization of eigenvalues using topology optimization
Pedersen, Niels Leergaard
2000-01-01
Topology optimization is used to optimize the eigenvalues of plates. The results are intended especially for MicroElectroMechanical Systems (MEMS) but call be seen as more general. The problem is not formulated as a case of reinforcement of an existing structure, so there is a problem related...... to localized modes in low density areas. The topology optimization problem is formulated using the SIMP method. Special attention is paid to a numerical method for removing localized eigenmodes in low density areas. The method is applied to numerical examples of maximizing the first eigenfrequency, One example...... is a practical MEMS application; a probe used in an Atomic Force Microscope (AFM). For the AFM probe the optimization is complicated by a constraint on the stiffness and constraints on higher order eigenvalues....
MAXIMIZING THE BENEFITS OF ERP SYSTEMS
Paulo André da Conceição Menezes
2010-04-01
Full Text Available The ERP (Enterprise Resource Planning systems have been consolidated in companies with different sizes and sectors, allowing their real benefits to be definitively evaluated. In this study, several interactions have been studied in different phases, such as the strategic priorities and strategic planning defined as ERP Strategy; business processes review and the ERP selection in the pre-implementation phase, the project management and ERP adaptation in the implementation phase, as well as the ERP revision and integration efforts in the post-implementation phase. Through rigorous use of case study methodology, this research led to developing and to testing a framework for maximizing the benefits of the ERP systems, and seeks to contribute for the generation of ERP initiatives to optimize their performance.
MAXIMIZING THE BENEFITS OF ERP SYSTEMS
Paulo André Da Conceiçao Menezes
2010-04-01
Full Text Available The ERP (Enterprise Resource Planning systems have been consolidated in companies with different sizes and sectors, allowing their real benefits to be definitively evaluated. In this study, several interactions have been studied in different phases, such as the strategic priorities and strategic planning defined as ERP Strategy; business processes review and the ERP selection in the pre-implementation phase, the project management and ERP adaptation in the implementation phase, as well as the ERP revision and integration efforts in the post-implementation phase. Through rigorous use of case study methodology, this research led to developing and to testing a framework for maximizing the benefits of the ERP systems, and seeks to contribute for the generation of ERP initiatives to optimize their performance.
Reflection Quasilattices and the Maximal Quasilattice
Boyle, Latham
2016-01-01
We introduce the concept of a {\\it reflection quasilattice}, the quasiperiodic generalization of a Bravais lattice with irreducible reflection symmetry. Among their applications, reflection quasilattices are the reciprocal (i.e. Bragg diffraction) lattices for quasicrystals and quasicrystal tilings, such as Penrose tilings, with irreducible reflection symmetry and discrete scale invariance. In a follow-up paper, we will show that reflection quasilattices can be used to generate tilings in real space with properties analogous to those in Penrose tilings, but with different symmetries and in various dimensions. Here we prove that reflection quasilattices only exist in dimensions two, three and four, and we prove that there is a unique reflection quasilattice in dimension four: the "maximal reflection quasilattice" in terms of dimensionality and symmetry. We further show that, unlike crystallographic Bravais lattices, all reflection quasilattices are invariant under rescaling by certain discrete scale factors. W...
Distributed Maximality based CTL Model Checking
Djamel Eddine Saidouni
2010-05-01
Full Text Available In this paper we investigate an approach to perform a distributed CTL Model checker algorithm on a network of workstations using Kleen three value logic, the state spaces is partitioned among the network nodes, We represent the incomplete state spaces as a Maximality labeled Transition System MLTS which are able to express true concurrency. we execute in parallel the same algorithm in each node, for a certain property on an incomplete MLTS , this last compute the set of states which satisfy or which if they fail are assigned the value .The third value mean unknown whether true or false because the partial state space lacks sufficient information needed for a precise answer concerning the complete state space .To solve this problem each node exchange the information needed to conclude the result about the complete state space. The experimental version of the algorithm is currently being implemented using the functional programming language Erlang.
Evolution of correlated multiplexity through stability maximization
Dwivedi, Sanjiv K
2016-01-01
Investigating relation between various structural patterns found in real-world networks and stability of underlying systems is crucial to understand importance and evolutionary origin of such patterns. We evolve multiplex networks, comprising of anti-symmetric couplings in one layer, depicting predator-prey relation, and symmetric couplings in the other, depicting mutualistic (or competitive) relation, based on stability maximization through the largest eigenvalue. We find that the correlated multiplexity emerges as evolution progresses. The evolved values of the correlated multiplexity exhibit a dependence on the inter-link coupling strength. Furthermore, the inter-layer coupling strength governs the evolution of disassortativity property in the individual layers. We provide analytical understanding to these findings by considering star like networks in both the layers. The model and tools used here are useful for understanding the principles governing the stability as well as importance of such patterns in ...
Witten spinors on maximal, conformally flat hypersurfaces
Frauendiener, Jörg; Szabados, László B
2011-01-01
The boundary conditions that exclude zeros of the solutions of the Witten equation (and hence guarantee the existence of a 3-frame satisfying the so-called special orthonormal frame gauge conditions) are investigated. We determine the general form of the conformally invariant boundary conditions for the Witten equation, and find the boundary conditions that characterize the constant and the conformally constant spinor fields among the solutions of the Witten equations on compact domains in extrinsically and intrinsically flat, and on maximal, intrinsically globally conformally flat spacelike hypersurfaces, respectively. We also provide a number of exact solutions of the Witten equation with various boundary conditions (both at infinity and on inner or outer boundaries) that single out nowhere vanishing spinor fields on the flat, non-extreme Reissner--Nordstr\\"om and Brill--Lindquist data sets. Our examples show that there is an interplay between the boundary conditions, the global topology of the hypersurface...
Dispatch Scheduling to Maximize Exoplanet Detection
Johnson, Samson; McCrady, Nate; MINERVA
2016-01-01
MINERVA is a dedicated exoplanet detection telescope array using radial velocity measurements of nearby stars to detect planets. MINERVA will be a completely robotic facility, with a goal of maximizing the number of exoplanets detected. MINERVA requires a unique application of queue scheduling due to its automated nature and the requirement of high cadence observations. A dispatch scheduling algorithm is employed to create a dynamic and flexible selector of targets to observe, in which stars are chosen by assigning values through a weighting function. I designed and have begun testing a simulation which implements the functions of a dispatch scheduler and records observations based on target selections through the same principles that will be used at the commissioned site. These results will be used in a larger simulation that incorporates weather, planet occurrence statistics, and stellar noise to test the planet detection capabilities of MINERVA. This will be used to heuristically determine an optimal observing strategy for the MINERVA project.
A New Biflavone from Selaginella pulvinata Maxim
XU Kang-Ping; XU Zhi; DENG Yin-Hua; LI Fu-Shuang; ZHOU Ying-Jun; HU Gao-Yun; TAN Gui-Shan
2003-01-01
@@ Selaginella pulvinata Maxim. distributes all over the country of China and is used for the treatment for haemor rhage. [1] We studied on the chemical constituents of S. pulvinata in order to find the active compounds. Dried stems and leaves of S. pulvinata (6.5 kg) were extracted with 70% ethanol twice. The extract was evaporated under vacuum and than suspended in water, extracted with petroleum and EtOAc sequentially. The EtOAc extract was chromatographed on silica gel, eluted with CHCl3-MeOH. As a result, a novel biflavone, named pulvinatabiflavone, was obtained from fractions 75 ～ 78. Its structure was determined on the basis of spectroscopic analysis as 5,5″, 4′″ trihydroxy-7,7″-dimethoxy-[4′-O-6″]-biflavone (compound 1).
Baek, Sung Hee; Ohgi, Kenneth A.; Nelson, Charles A.; Welsbie, Derek; Chen, Charlie; Sawyers, Charles L.; Rose, David W.; Rosenfeld, Michael G.
2006-01-01
The androgen receptor not only mediates prostate development but also serves as a key regulator of primary prostatic cancer growth. Although initially responsive to selective androgen receptor modulators (SARMs), which cause recruitment of the nuclear receptor–corepressor (N-CoR) complex, resistance invariably occurs, perhaps in response to inflammatory signals. Here we report that dismissal of nuclear receptor–corepressor complexes by specific signals or androgen receptor overexpression results in recruitment of many of the cohorts of coactivator complexes that permits SARMs and natural ligands to function as agonists. SARM-bound androgen receptors appear to exhibit failure to recruit specific components of the coactivators generally bound by liganded nuclear receptors, including cAMP response element-binding protein (CBP)/p300 or coactivator-associated arginine methyltransferase 1 (CARM1) to the SARM-bound androgen receptor, although still causing transcriptional activation of androgen receptor target genes. SARM-bound androgen receptors use distinct LXXLL (L, leucine; X, any amino acid) helices in the p160 nuclear receptor interaction domains that may impose selective allosteric effects, providing a component of the molecular basis of differential responses to different classes of ligands by androgen receptor. PMID:16492776
Conditionally bounding analytic ranks of elliptic curves
Bober, Jonathan W
2011-01-01
We describe a method for bounding the rank of an elliptic curve under the assumptions of the Birch and Swinnerton-Dyer conjecture and the generalized Riemann hypothesis. As an example, we compute, under these conjectures, exact upper bounds for curves which are known to have rank at least as large as 20, 21, 22, 23, and 24. For the known curve of rank at least 28, we get a bound of 30.
Computing the bounds on the loss rates
Fourneau J.-M.
2002-01-01
Full Text Available We consider an example network where we compute the bounds on cell loss rates. The stochastic bounds for these loss rates using simple arguments lead to models easier to solve. We proved, using stochastic orders, that the loss rates of these easier models are really the bounds of our original model. For ill-balanced configurations these models give good estimates of loss rates.
Scalable Capacity Bounding Models for Wireless Networks
Du, Jinfeng; Medard, Muriel; Xiao, Ming; Skoglund, Mikael
2014-01-01
The framework of network equivalence theory developed by Koetter et al. introduces a notion of channel emulation to construct noiseless networks as upper (resp. lower) bounding models, which can be used to calculate the outer (resp. inner) bounds for the capacity region of the original noisy network. Based on the network equivalence framework, this paper presents scalable upper and lower bounding models for wireless networks with potentially many nodes. A channel decoupling method is proposed...
Wyse, Adam E.; Babcock, Ben
2016-01-01
A common suggestion made in the psychometric literature for fixed-length classification tests is that one should design tests so that they have maximum information at the cut score. Designing tests in this way is believed to maximize the classification accuracy and consistency of the assessment. This article uses simulated examples to illustrate…
From entropy-maximization to equality-maximization: Gauss, Laplace, Pareto, and Subbotin
Eliazar, Iddo
2014-12-01
The entropy-maximization paradigm of statistical physics is well known to generate the omnipresent Gauss law. In this paper we establish an analogous socioeconomic model which maximizes social equality, rather than physical disorder, in the context of the distributions of income and wealth in human societies. We show that-on a logarithmic scale-the Laplace law is the socioeconomic equality-maximizing counterpart of the physical entropy-maximizing Gauss law, and that this law manifests an optimized balance between two opposing forces: (i) the rich and powerful, striving to amass ever more wealth, and thus to increase social inequality; and (ii) the masses, struggling to form more egalitarian societies, and thus to increase social equality. Our results lead from log-Gauss statistics to log-Laplace statistics, yield Paretian power-law tails of income and wealth distributions, and show how the emergence of a middle-class depends on the underlying levels of socioeconomic inequality and variability. Also, in the context of asset-prices with Laplace-distributed returns, our results imply that financial markets generate an optimized balance between risk and predictability.
THE EFFECTS MAXIMAL AND SUB MAXIMAL AEROBIC EXERCISE ON THE BRONCHOSPASM INDICES IN NON ATHLETIC
Amir GANJİ
2012-08-01
Full Text Available Background: Exercise-induced bronchospasm (EIB is a transient airway obstruction that occurs during and after the exercise. Exercise-induced bronchospasm is observed in healthy individuals as well as the asthmatic and allergic rhinitis patients. Research question: The study compared the effects of one session of submaximal aerobic exercise and a maximal one on the prevalence of exercise-induced bronchospasm in non-athletic students. Type of study: An experimental study, using human subjects, was designed. Methods: 20 non-athletic male students participated in two sessions of aerobic exercise. The prevalence of EIB was investigated among them. The criteria for assessing exercise-induced bronchospasm were ≥10% fall in FEV1, ≥15% fall in FEF25-75%, or ≥25% fall in PEFR. Results: The results revealed that the maximal exercise did not affect FEF25-75% and PEF, but it led to a meaningful reduction in FEV1. Contrarily, the submaximal exercise affected none of these indices. That is, in both protocols the same result was obtained for PEF and FEF25-75. Moreover, the prevalence of EIB was 15% in the submaximal exercise and 20% in the maximal one. Actually, this difference was significant. Conclusion: This study demonstrated that in contrast to the subjects who performed submaximal exercise, those who participated in the maximal protocol showed more changes in the pulmonary function indices and the prevalence of EIB was greater among them.
Influence of ligand structure on anticancer and antioxidant properties of rhenium cluster compounds
I. V. Leus
2009-11-01
Full Text Available Under the model growth of T8 Guerin’s carcinoma in rats we studied the anticancer activity of the system rhenium-platinum, which includes cis-dicarboxylates of rhenium (III with different alkyl ligands, erythrocytes number and its morphological structure, erythrocytic stability, blood haemoglobin concentration, catalase activity and concentration of TBA-active products in the rats blood plasma. The renium-platinum system had considerable antioxidat effect and prevented the growth of tumour, that was maximal for a compound with the pivalate ligand.
Maximal elements of non necessarily acyclic binary relations
Josep Enric Peris Ferrando; Begoña Subiza Martínez
1992-01-01
The existence of maximal elements for binary preference relations is analyzed without imposing transitivity or convexity conditions. From each preference relation a new acyclic relation is defined in such a way that some maximal elements of this new relation characterize maximal elements of the original one. The result covers the case whereby the relation is acyclic.
Maximal codeword lengths in Huffman codes
Abu-Mostafa, Y. S.; Mceliece, R. J.
1992-01-01
The following question about Huffman coding, which is an important technique for compressing data from a discrete source, is considered. If p is the smallest source probability, how long, in terms of p, can the longest Huffman codeword be? It is shown that if p is in the range 0 less than p less than or equal to 1/2, and if K is the unique index such that 1/F(sub K+3) less than p less than or equal to 1/F(sub K+2), where F(sub K) denotes the Kth Fibonacci number, then the longest Huffman codeword for a source whose least probability is p is at most K, and no better bound is possible. Asymptotically, this implies the surprising fact that for small values of p, a Huffman code's longest codeword can be as much as 44 percent larger than that of the corresponding Shannon code.
Risk Bounds for Infinitely Divisible Distribution
Zhang, Chao
2012-01-01
In this paper, we study the risk bounds for samples independently drawn from an infinitely divisible (ID) distribution. In particular, based on a martingale method, we develop two deviation inequalities for a sequence of random variables of an ID distribution with zero Gaussian component. By applying the deviation inequalities, we obtain the risk bounds based on the covering number for the ID distribution. Finally, we analyze the asymptotic convergence of the risk bound derived from one of the two deviation inequalities and show that the convergence rate of the bound is faster than the result for the generic i.i.d. empirical process (Mendelson, 2003).
Some Improved Nonperturbative Bounds for Fermionic Expansions
Lohmann, Martin, E-mail: marlohmann@gmail.com [Universita di Roma Tre, Dipartimento di Matematica (Italy)
2016-06-15
We reconsider the Gram-Hadamard bound as it is used in constructive quantum field theory and many body physics to prove convergence of Fermionic perturbative expansions. Our approach uses a recursion for the amplitudes of the expansion, discovered in a model problem by Djokic (2013). It explains the standard way to bound the expansion from a new point of view, and for some of the amplitudes provides new bounds, which avoid the use of Fourier transform, and are therefore superior to the standard bounds for models like the cold interacting Fermi gas.
Bounds in the location-allocation problem
Juel, Henrik
1981-01-01
Develops a family of stronger lower bounds on the objective function value of the location-allocation problem. Solution methods proposed to solve problems in location-allocation; Efforts to develop a more efficient bound solution procedure; Determination of the locations of the sources.......Develops a family of stronger lower bounds on the objective function value of the location-allocation problem. Solution methods proposed to solve problems in location-allocation; Efforts to develop a more efficient bound solution procedure; Determination of the locations of the sources....
Conductivity bounds in probe brane models
Ikeda, Tatsuhiko N; Nakai, Yuichiro
2016-01-01
We discuss upper and lower bounds on the electrical conductivity of finite temperature strongly coupled quantum field theories, holographically dual to probe brane models, within linear response. In a probe limit where disorder is introduced entirely through an inhomogeneous background charge density, we find simple lower and upper bounds on the electrical conductivity in arbitrary dimensions. In field theories in two spatial dimensions, we show that both bounds persist even when disorder is included in the bulk metric. We discuss the challenges with finding sharp lower bounds on conductivity in three or more spatial dimensions when the metric is inhomogeneous.
A violation of the covariant entropy bound?
Masoumi, Ali
2014-01-01
Several arguments suggest that the entropy density at high energy density $\\rho$ should be given by the expression $s=K\\sqrt{\\rho/G}$, where $K$ is a constant of order unity. On the other hand the covariant entropy bound requires that the entropy on a light sheet be bounded by $A/4G$, where $A$ is the area of the boundary of the sheet. We find that in a suitably chosen cosmological geometry, the above expression for $s$ violates the covariant entropy bound. We consider different possible explanations for this fact; in particular the possibility that entropy bounds should be defined in terms of volumes of regions rather than areas of surfaces.
Hydrophobic side chain dynamics of a glutamate receptor ligand binding domain.
Maltsev, Alexander S; Oswald, Robert E
2010-03-26
Ionotropic glutamate receptors are ligand-gated ion channels that mediate much of the fast excitatory neurotransmission in the central nervous system. The extracellular ligand binding core (S1S2) of the GluR2 subtype of ionotropic glutamate receptors can be produced as a soluble protein with properties essentially identical to the corresponding domain in the intact, membrane-bound protein. Using a variety of biophysical techniques, much has been learned about the structure and dynamics of S1S2 and the relationship between its ligand-induced conformational changes and the function of the receptor. It is clear that dynamic processes are essential to the function of ionotropic glutamate receptors. We have isotopically labeled side chain methyls of GluR2 S1S2 and used NMR spectroscopy to study their dynamics on the ps-ns and mus-ms time scales. Increased disorder is seen in regions that are part of the key dimer interface in the intact protein. When glutamate is bound, the degree of ps-ns motion is less than that observed with other ligands, suggesting that the physiological agonist binds to a preformed binding site. At the slower time scales, the degree of S1S2 flexibility induced by ligand binding is greatest for willardiine partial agonists, least for antagonists, and intermediate for full agonists. Notable differences among bound ligands are in the region of the protein that forms a hinge between two lobes that close upon agonist binding, and along the beta-sheet in Lobe 2. These motions provide clues as to the functional properties of partial agonists and to the conformational changes associated with lobe closure and channel activation.
A Stronger LP Bound for Formula Size Lower Bounds via Clique Constraints
Ueno, Kenya
2009-01-01
We introduce a new technique proving formula size lower bounds based on the linear programming bound originally introduced by Karchmer, Kushilevitz and Nisan [11] and the theory of stable set polytope. We apply it to majority functions and prove their formula size lower bounds improved from the classical result of Khrapchenko [13]. Moreover, we introduce a notion of unbalanced recursive ternary majority functions motivated by a decomposition theory of monotone self-dual functions and give integrally matching upper and lower bounds of their formula size. We also show monotone formula size lower bounds of balanced recursive ternary majority functions improved from the quantum adversary bound of Laplante, Lee and Szegedy [15].
Decoding the Role of Water Dynamics in Ligand-Protein Unbinding: CRF1R as a Test Case.
Bortolato, Andrea; Deflorian, Francesca; Weiss, Dahlia R; Mason, Jonathan S
2015-09-28
The residence time of a ligand-protein complex is a crucial aspect in determining biological effect in vivo. Despite its importance, the prediction of ligand koff still remains challenging for modern computational chemistry. We have developed aMetaD, a fast and generally applicable computational protocol to predict ligand-protein unbinding events using a molecular dynamics (MD) method based on adiabatic-bias MD and metadynamics. This physics-based, fully flexible, and pose-dependent ligand scoring function evaluates the maximum energy (RTscore) required to move the ligand from the bound-state energy basin to the next. Unbinding trajectories are automatically analyzed and translated into atomic solvation factor (SF) values representing the water dynamics during the unbinding event. This novel computational protocol was initially tested on two M3 muscarinic receptor and two adenosine A2A receptor antagonists and then evaluated on a test set of 12 CRF1R ligands. The resulting RTscores were used successfully to classify ligands with different residence times. Additionally, the SF analysis was used to detect key differences in the degree of accessibility to water molecules during the predicted ligand unbinding events. The protocol provides actionable working hypotheses that are applicable in a drug discovery program for the rational optimization of ligand binding kinetics.
An outer bound for 2-receiver discrete memoryless broadcast channels
Nair, Chandra
2008-01-01
An outer bound to the two-receiver discrete memoryless broadcast channel is presented. We compare it to the known outer bounds and show that the outer bound presented is at least as tight as the existing bounds.
Taskinen, Jukka P; van Aalten, Daan M; Knudsen, Jens;
2007-01-01
The acyl-CoA binding protein (ACBP) is essential for the fatty acid metabolism, membrane structure, membrane fusion, and ceramide synthesis. Here high resolution crystal structures of human cytosolic liver ACBP, unliganded and liganded with a physiological ligand, myristoyl-CoA are described....... The binding of the acyl-CoA molecule induces only few structural differences near the binding pocket. The crystal form of the liganded ACBP, which has two ACBP molecules in the asymmetric unit, shows that in human ACBP the same acyl-CoA binding pocket is present as previously described for the bovine...... and Plasmodium falciparum ACBP and the mode of binding of the 3'-phosphate-AMP moiety is conserved. Unexpectedly, in one of the acyl-CoA binding pockets the acyl moiety is bound in a reversed mode as compared with the bovine and P. falciparum structures. In this binding mode, the myristoyl-CoA molecule is fully...
Docking validation resources: protein family and ligand flexibility experiments.
Mukherjee, Sudipto; Balius, Trent E; Rizzo, Robert C
2010-11-22
A database consisting of 780 ligand-receptor complexes, termed SB2010, has been derived from the Protein Databank to evaluate the accuracy of docking protocols for regenerating bound ligand conformations. The goal is to provide easily accessible community resources for development of improved procedures to aid virtual screening for ligands with a wide range of flexibilities. Three core experiments using the program DOCK, which employ rigid (RGD), fixed anchor (FAD), and flexible (FLX) protocols, were used to gauge performance by several different metrics: (1) global results, (2) ligand flexibility, (3) protein family, and (4) cross-docking. Global spectrum plots of successes and failures vs rmsd reveal well-defined inflection regions, which suggest the commonly used 2 Å criteria is a reasonable choice for defining success. Across all 780 systems, success tracks with the relative difficulty of the calculations: RGD (82.3%) > FAD (78.1%) > FLX (63.8%). In general, failures due to scoring strongly outweigh those due to sampling. Subsets of SB2010 grouped by ligand flexibility (7-or-less, 8-to-15, and 15-plus rotatable bonds) reveal that success degrades linearly for FAD and FLX protocols, in contrast to RGD, which remains constant. Despite the challenges associated with FLX anchor orientation and on-the-fly flexible growth, success rates for the 7-or-less (74.5%) and, in particular, the 8-to-15 (55.2%) subset are encouraging. Poorer results for the very flexible 15-plus set (39.3%) indicate substantial room for improvement. Family-based success appears largely independent of ligand flexibility, suggesting a strong dependence on the binding site environment. For example, zinc-containing proteins are generally problematic, despite moderately flexible ligands. Finally, representative cross-docking examples, for carbonic anhydrase, thermolysin, and neuraminidase families, show the utility of family-based analysis for rapid identification of particularly good or bad
Calix[6]azacryptand Ligand with a Sterically Protected Tren-Based Coordination Site for Metal Ions.
Zahim, Sara; Wickramasinghe, Lasantha A; Evano, Gwilherm; Jabin, Ivan; Schrock, Richard R; Müller, Peter
2016-04-01
A new calix[6]azacryptand ligand has been prepared in six steps starting from 1,3,5-trismethoxycalix[6]arene. An X-ray study shows that this ligand has a sterically protected tren-based binding site at the bottom of a polyaromatic bowl and ether sites around its rim. It binds Zn(2+) to give a complex in which zinc is in a trigonal bipyramidal geometry with a water bound in one apical position and two additional hydrogen-bonded waters that fill the calixarene cavity.
P-selectin glycoprotein ligand-1 mediates rolling of human neutrophils on P-selectin
1995-01-01
Neutrophils roll on P-selectin expressed by activated platelets or endothelial cells under the shear stresses in the microcirculation. P- selectin glycoprotein ligand-1 (PSGL-1) is a high affinity ligand for P- selectin on myeloid cells. However, it has not been demonstrated that PSGL-1 contributes to the rolling of neutrophils on P-selectin. We developed two IgG mAbs, PL1 and PL2, that appear to recognize protein- dependent epitopes on human PSGL-1. The mAbs bound to PSGL-1 on all leukocytes...
Schleicher, Erwin D
2010-08-01
In experimental animals a causal involvement of the multiligand receptor for advanced glycation end products (RAGE) in the development of diabetic vascular complications has been demonstrated. However, the nature of RAGE ligands present in patients with diabetic nephropathy has not yet been defined; this leaves open the relevance of the RAGE system to the human disease.
UMR: A utility-maximizing routing algorithm for delay-sensitive service in LEO satellite networks
Lu Yong
2015-04-01
Full Text Available This paper develops a routing algorithm for delay-sensitive packet transmission in a low earth orbit multi-hop satellite network consists of micro-satellites. The micro-satellite low earth orbit (MS-LEO network endures unstable link connection and frequent link congestion due to the uneven user distribution and the link capacity variations. The proposed routing algorithm, referred to as the utility maximizing routing (UMR algorithm, improve the network utility of the MS-LEO network for carrying flows with strict end-to-end delay bound requirement. In UMR, first, a link state parameter is defined to capture the link reliability on continuing to keep the end-to-end delay into constraint; then, on the basis of this parameter, a routing metric is formulated and a routing scheme is designed for balancing the reliability in delay bound guarantee among paths and building a path maximizing the network utility expectation. While the UMR algorithm has many advantages, it may result in a higher blocking rate of new calls. This phenomenon is discussed and a weight factor is introduced into UMR to provide a flexible performance option for network operator. A set of simulations are conducted to verify the good performance of UMR, in terms of balancing the traffic distribution on inter-satellite links, reducing the flow interruption rate, and improving the network utility.
Maximization Paradox: Result of Believing in an Objective Best.
Luan, Mo; Li, Hong
2017-05-01
The results from four studies provide reliable evidence of how beliefs in an objective best influence the decision process and subjective feelings. A belief in an objective best serves as the fundamental mechanism connecting the concept of maximizing and the maximization paradox (i.e., expending great effort but feeling bad when making decisions, Study 1), and randomly chosen decision makers operate similar to maximizers once they are manipulated to believe that the best is objective (Studies 2A, 2B, and 3). In addition, the effect of a belief in an objective best on the maximization paradox is moderated by the presence of a dominant option (Study 3). The findings of this research contribute to the maximization literature by demonstrating that believing in an objective best leads to the maximization paradox. The maximization paradox is indeed the result of believing in an objective best.
MIMO-OFDM Precoding Technique for Minimizing BER Upper Bound of MLD
Pitakdumrongkija, Boonsarn; Fukawa, Kazuhiko; Suzuki, Hiroshi; Hagiwara, Takashi
This paper proposes a new MIMO-OFDM precoding technique that aims to minimize a bit error rate (BER) upper bound of the maximum likelihood detection (MLD) in mobile radio communications. Using a steepest descent algorithm, the proposed method estimates linear precoding matrices that can minimize the upper bound of BER under power constraints. Since the upper bound is derived from all the pairwise error probabilities, this method can effectively optimize overall Euclidean distances between signals received by multiple antennas and their replicas. Computer simulations evaluate the BER performance and channel capacity of the proposed scheme for 2×2 and 4×4 MIMO-OFDM systems with BPSK, QPSK, and 16QAM. It is demonstrated that the proposed precoding technique is superior in terms of average BER to conventional precoding methods including a precoder which maximizes only the minimum Euclidean distance as the worst case.
Bounding the Failure Probability Range of Polynomial Systems Subject to P-box Uncertainties
Crespo, Luis G.; Kenny, Sean P.; Giesy, Daniel P.
2012-01-01
This paper proposes a reliability analysis framework for systems subject to multiple design requirements that depend polynomially on the uncertainty. Uncertainty is prescribed by probability boxes, also known as p-boxes, whose distribution functions have free or fixed functional forms. An approach based on the Bernstein expansion of polynomials and optimization is proposed. In particular, we search for the elements of a multi-dimensional p-box that minimize (i.e., the best-case) and maximize (i.e., the worst-case) the probability of inner and outer bounding sets of the failure domain. This technique yields intervals that bound the range of failure probabilities. The offset between this bounding interval and the actual failure probability range can be made arbitrarily tight with additional computational effort.
No-arbitrage bounds for financial scenarios
Geyer, Alois; Hanke, Michael; Weissensteiner, Alex
2014-01-01
We derive no-arbitrage bounds for expected excess returns to generate scenarios used in financial applications. The bounds allow to distinguish three regions: one where arbitrage opportunities will never exist, a second where arbitrage may be present, and a third, where arbitrage opportunities...
Optimal online bounded space multidimensional packing
L. Epstein (Lea); R. van Stee (Rob)
2003-01-01
textabstractWe solve an open problem in the literature by providing an online algorithm for multidimensional bin packing that uses only bounded space. We show that it is optimal among bounded space algorithms for any dimension $d>1$. Its asymptotic performance ratio is $(Pi_{infty})^d$, where
New bounds for multi-dimensional packing
S. Seiden; R. van Stee (Rob)
2001-01-01
textabstractNew upper and lower bounds are presented for a multi-dimensional generalization of bin packing called box packing. Several variants of this problem, including bounded space box packing, square packing, variable sized box packing and resource augmented box packing are also studied. The