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https://www.readbyqxmd.com/read/29786460/counterexample-driven-genetic-programming-heuristic-program-synthesis-from-formal-specifications
#1
Iwo Błądek, Krzysztof Krawiec, Jerry Swan
Conventional genetic programming (GP) can only guarantee that synthesized programs pass tests given by the provided input-output examples. The alternative to such test-based approach is synthesizing programs by formal specification, typically realized with exact, non-heuristic algorithms. In this paper, we build on our earlier study on Counterexample-Based Genetic Programming (CDGP), an evolutionary heuristic that synthesizes programs from formal specifications. The candidate programs in CDGP undergo formal verification with a Satisfiability Modulo Theory (SMT) solver, which results in counterexamples that are subsequently turned into tests and used to calculate fitness...
May 22, 2018: Evolutionary Computation
https://www.readbyqxmd.com/read/29777317/using-smiles-strings-for-the-description-of-chemical-connectivity-in-the-crystallography-open-database
#2
Miguel Quirós, Saulius Gražulis, Saulė Girdzijauskaitė, Andrius Merkys, Antanas Vaitkus
Computer descriptions of chemical molecular connectivity are necessary for searching chemical databases and for predicting chemical properties from molecular structure. In this article, the ongoing work to describe the chemical connectivity of entries contained in the Crystallography Open Database (COD) in SMILES format is reported. This collection of SMILES is publicly available for chemical (substructure) search or for any other purpose on an open-access basis, as is the COD itself. The conventions that have been followed for the representation of compounds that do not fit into the valence bond theory are outlined for the most frequently found cases...
May 18, 2018: Journal of Cheminformatics
https://www.readbyqxmd.com/read/29758657/one-dimensional-reduction-of-viscous-jets-i-theory
#3
Cyril Pitrou
We build a general formalism to describe thin viscous jets as one-dimensional objects with an internal structure. We present in full generality the steps needed to describe the viscous jets around their central line, and we argue that the Taylor expansion of all fields around that line is conveniently expressed in terms of symmetric trace-free tensors living in the two dimensions of the fiber sections. We recover the standard results of axisymmetric jets and we report the first and second corrections to the lowest order description, also allowing for a rotational component around the axis of symmetry...
April 2018: Physical Review. E
https://www.readbyqxmd.com/read/29758629/physics-of-automated-driving-in-framework-of-three-phase-traffic-theory
#4
Boris S Kerner
We have revealed physical features of automated driving in the framework of the three-phase traffic theory for which there is no fixed time headway to the preceding vehicle. A comparison with the classical model approach to automated driving for which an automated driving vehicle tries to reach a fixed (desired or "optimal") time headway to the preceding vehicle has been made. It turns out that automated driving in the framework of the three-phase traffic theory can exhibit the following advantages in comparison with the classical model of automated driving: (i) The absence of string instability...
April 2018: Physical Review. E
https://www.readbyqxmd.com/read/29713952/tisk-1-0-an-easy-to-use-python-implementation-of-the-time-invariant-string-kernel-model-of-spoken-word-recognition
#5
Heejo You, James S Magnuson
This article describes a new Python distribution of TISK, the time-invariant string kernel model of spoken word recognition (Hannagan et al. in Frontiers in Psychology, 4, 563, 2013). TISK is an interactive-activation model similar to the TRACE model (McClelland & Elman in Cognitive Psychology, 18, 1-86, 1986), but TISK replaces most of TRACE's reduplicated, time-specific nodes with theoretically motivated time-invariant, open-diphone nodes. We discuss the utility of computational models as theory development tools, the relative merits of TISK as compared to other models, and the ways in which researchers might use this implementation to guide their own research and theory development...
April 30, 2018: Behavior Research Methods
https://www.readbyqxmd.com/read/29675633/vapor-nucleation-paths-in-lyophobic-nanopores
#6
Antonio Tinti, Alberto Giacomello, Carlo Massimo Casciola
In recent years, technologies revolving around the use of lyophobic nanopores gained considerable attention in both fundamental and applied research. Owing to the enormous internal surface area, heterogeneous lyophobic systems (HLS), constituted by a nanoporous lyophobic material and a non-wetting liquid, are promising candidates for the efficient storage or dissipation of mechanical energy. These diverse applications both rely on the forced intrusion and extrusion of the non-wetting liquid inside the pores; the behavior of HLS for storage or dissipation depends on the hysteresis between these two processes, which, in turn, are determined by the microscopic details of the system...
April 19, 2018: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29668273/filling-the-gap-in-extended-metal-atom-chains-ferromagnetic-interactions-in-a-tetrairon-ii-string-supported-by-oligo-%C3%AE-pyridylamido-ligands
#7
Alessio Nicolini, Rita Galavotti, Anne-Laure Barra, Marco Borsari, Matteo Caleffi, Guangpu Luo, Ghenadie Novitchi, Kyungwha Park, Antonio Ranieri, Luca Rigamonti, Fabrizio Roncaglia, Cyrille Train, Andrea Cornia
The stringlike complex [Fe4 (tpda)3 Cl2 ] (2; H2 tpda = N2 , N6 -bis(pyridin-2-yl)pyridine-2,6-diamine) was obtained as the first homometallic extended metal atom chain based on iron(II) and oligo-α-pyridylamido ligands. The synthesis was performed under strictly anaerobic and anhydrous conditions using dimesityliron, [Fe2 (Mes)4 ] (1; HMes = mesitylene), as both an iron source and a deprotonating agent for H2 tpda. The four lined-up iron(II) ions in the structure of 2 (Fe···Fe = 2.94-2.99 Å, Fe···Fe···Fe = 171...
April 18, 2018: Inorganic Chemistry
https://www.readbyqxmd.com/read/29628212/chromatin-higher-order-folding-a-perspective-with-linker-dna-angles
#8
REVIEW
Sergei A Grigoryev
The mechanism by which the "beads-on-a-string" nucleosome chain folds into various higher-order chromatin structures in eukaryotic cell nuclei is still poorly understood. The various models depicting higher-order chromatin as regular helical fibers and the very opposite "polymer melt" theory imply that interactions between nucleosome "beads" make the main contribution to the chromatin compaction. Other models in which the geometry of linker DNA "strings" entering and exiting the nucleosome define the three-dimensional structure predict that small changes in the linker DNA configuration may strongly affect nucleosome chain folding and chromatin higher-order structure...
April 5, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/29548103/universality-in-chaos-lyapunov-spectrum-and-random-matrix-theory
#9
Masanori Hanada, Hidehiko Shimada, Masaki Tezuka
We propose the existence of a new universality in classical chaotic systems when the number of degrees of freedom is large: the statistical property of the Lyapunov spectrum is described by random matrix theory. We demonstrate it by studying the finite-time Lyapunov exponents of the matrix model of a stringy black hole and the mass-deformed models. The massless limit, which has a dual string theory interpretation, is special in that the universal behavior can be seen already at t=0, while in other cases it sets in at late time...
February 2018: Physical Review. E
https://www.readbyqxmd.com/read/29420471/experimental-observation-of-bethe-strings
#10
Zhe Wang, Jianda Wu, Wang Yang, Anup Kumar Bera, Dmytro Kamenskyi, A T M Nazmul Islam, Shenglong Xu, Joseph Matthew Law, Bella Lake, Congjun Wu, Alois Loidl
Almost a century ago, string states-complex bound states of magnetic excitations-were predicted to exist in one-dimensional quantum magnets. However, despite many theoretical studies, the experimental realization and identification of string states in a condensed-matter system have yet to be achieved. Here we use high-resolution terahertz spectroscopy to resolve string states in the antiferromagnetic Heisenberg-Ising chain SrCo2 V2 O8 in strong longitudinal magnetic fields. In the field-induced quantum-critical regime, we identify strings and fractional magnetic excitations that are accurately described by the Bethe ansatz...
February 7, 2018: Nature
https://www.readbyqxmd.com/read/29400526/surface-induced-near-field-scaling-in-the-knudsen-layer-of-a-rarefied-gas
#11
R R Gazizulin, O Maillet, X Zhou, A Maldonado Cid, O Bourgeois, E Collin
We report on experiments performed within the Knudsen boundary layer of a low-pressure gas. The noninvasive probe we use is a suspended nanoelectromechanical string, which interacts with ^{4}He gas at cryogenic temperatures. When the pressure P is decreased, a reduction of the damping force below molecular friction ∝P had been first reported in Phys. Rev. Lett. 113, 136101 (2014)PRLTAO0031-900710.1103/PhysRevLett.113.136101 and never reproduced since. We demonstrate that this effect is independent of geometry, but dependent on temperature...
January 19, 2018: Physical Review Letters
https://www.readbyqxmd.com/read/29360359/quadratic-string-method-for-locating-instantons-in-tunneling-splitting-calculations
#12
Marko T Cvitaš
The ring-polymer instanton (RPI) method is an efficient technique for calculating approximate tunneling splittings in high-dimensional molecular systems. In the RPI method, tunneling splitting is evaluated from the properties of the minimum action path (MAP) connecting the symmetric wells, whereby the extensive sampling of the full potential energy surface of the exact quantum-dynamics methods is avoided. Nevertheless, the search for the MAP is usually the most time-consuming step in the standard numerical procedures...
March 13, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29347384/bifurcation-analysis-and-phase-diagram-of-a-spin-string-model-with-buckled-states
#13
M Ruiz-Garcia, L L Bonilla, A Prados
We analyze a one-dimensional spin-string model, in which string oscillators are linearly coupled to their two nearest neighbors and to Ising spins representing internal degrees of freedom. String-spin coupling induces a long-range ferromagnetic interaction among spins that competes with a spin-spin antiferromagnetic coupling. As a consequence, the complex phase diagram of the system exhibits different flat rippled and buckled states, with first or second order transition lines between states. This complexity translates to the two-dimensional version of the model, whose numerical solution has been recently used to explain qualitatively the rippled to buckled transition observed in scanning tunneling microscopy experiments with suspended graphene sheets...
December 2017: Physical Review. E
https://www.readbyqxmd.com/read/29347269/length-of-excitable-knots
#14
Fabian Maucher, Paul Sutcliffe
In this paper, we present extensive numerical simulations of an excitable medium to study the long-term dynamics of knotted vortex strings for all torus knots up to crossing number 11. We demonstrate that FitzHugh-Nagumo evolution preserves the knot topology for all the examples presented, thereby providing a field theory approach to the study of knots. Furthermore, the evolution yields a well-defined minimal length for each knot that is comparable to the ropelength of ideal knots. We highlight the role of the medium boundary in stabilizing the length of the knot and discuss the implications beyond torus knots...
July 2017: Physical Review. E
https://www.readbyqxmd.com/read/29345709/chain-conformation-of-poly-acrylic-acid-graft-poly-ethylene-oxide-graft-dodecyl-in-solution-an-anomalous-counter-ions-condensation
#15
Xinlu Zhou, Kongshuang Zhao
A dielectric spectroscopy study on a polyelectrolyte in aqueous solutions, which contains hydrophobic groups in part of the side chains poly(acrylic acid)-graft-poly(ethylene oxide)-graft-dodecyl (PAA-g-PEO-g-dodecyl) is reported. A refined double layer polarization model was proposed to analyze the double dielectric relaxations in the dielectric spectra. Various electrical and structural parameters of the copolymers were obtained. Besides the crossover concentration, another turning point around 4 mg mL-1 was identified through the analysis of all the dielectrical parameters including dielectric increment, relaxation time and correlation length...
January 18, 2018: Soft Matter
https://www.readbyqxmd.com/read/29328703/asymptotic-one-point-functions-in-gauge-string-duality-with-defects
#16
Isak Buhl-Mortensen, Marius de Leeuw, Asger C Ipsen, Charlotte Kristjansen, Matthias Wilhelm
We take the first step in extending the integrability approach to one-point functions in AdS/dCFT to higher loop orders. More precisely, we argue that the formula encoding all tree-level one-point functions of SU(2) operators in the defect version of N=4 supersymmetric Yang-Mills theory, dual to the D5-D3 probe-brane system with flux, has a natural asymptotic generalization to higher loop orders. The asymptotic formula correctly encodes the information about the one-loop correction to the one-point functions of nonprotected operators once dressed by a simple flux-dependent factor, as we demonstrate by an explicit computation involving a novel object denoted as an amputated matrix product state...
December 29, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/29307192/enrofloxacin-permeation-pathways-across-the-porin-ompc
#17
Jigneshkumar Dahyabhai Prajapati, Carlos José Fernández Solano, Mathias Winterhalter, Ulrich Kleinekathöfer
In Gram-negative bacteria, the lack or quenching of antibiotic translocation across the outer membrane is one of the main factors for acquiring antibiotic resistance. An atomic-level comprehension of the key features governing the transport of drugs by outer-membrane protein channels would be very helpful in developing the next generation of antibiotics. In a previous study [ J. D. Prajapati et al. J. Chem. Theory Comput. 2017 , 13 , 4553 ], we characterized the diffusion pathway of a ciprofloxacin molecule through the outer membrane porin OmpC of Escherichia coli by combining metadynamics and a zero-temperature string method...
February 1, 2018: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29286820/recognizing-axionic-dark-matter-by-compton-and-de-broglie-scale-modulation-of-pulsar-timing
#18
Ivan De Martino, Tom Broadhurst, S-H Henry Tye, Tzihong Chiueh, Hsi-Yu Schive, Ruth Lazkoz
Light axionic dark matter, motivated by string theory, is increasingly favored for the "no weakly interacting massive particle era". Galaxy formation is suppressed below a Jeans scale of ≃10^{8}  M_{⊙} by setting the axion mass to m_{B}∼10^{-22}  eV, and the large dark cores of dwarf galaxies are explained as solitons on the de Broglie scale. This is persuasive, but detection of the inherent scalar field oscillation at the Compton frequency ω_{B}=(2.5  months)^{-1}(m_{B}/10^{-22}  eV) would be definitive...
December 1, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/29216433/aging-jamming-and-the-limits-of-stability-of-amorphous-solids
#19
Vassiliy Lubchenko, Peter G Wolynes
Apart from not having crystallized, supercooled liquids can be considered as being properly equilibrated and thus can be described by a few thermodynamic control variables. In contrast, glasses and other amorphous solids can be arbitrarily far away from equilibrium and require a description of the history of the conditions under which they formed. In this paper we describe how the locality of interactions intrinsic to finite-dimensional systems affects the stability of amorphous solids far off equilibrium. Our analysis encompasses both structural glasses formed by cooling and colloidal assemblies formed by compression...
January 9, 2018: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29197663/prediction-of-potential-drivers-connecting-different-dysfunctional-levels-in-lung-adenocarcinoma-via-a-protein-protein-interaction-network
#20
Fei Yuan, WenCong Lu
Lung cancer is a serious disease that threatens an affected individual's life. Its pathogenesis has not yet to be fully described, thereby impeding the development of effective treatments and preventive measures. "Cancer driver" theory considers that tumor initiation can be associated with a number of specific mutations in genes called cancer driver genes. Four omics levels, namely, (1) methylation, (2) microRNA, (3) mutation, and (4) mRNA levels, are utilized to cluster cancer driver genes. In this study, the known dysfunctional genes of these four levels were used to identify novel driver genes of lung adenocarcinoma, a subtype of lung cancer...
December 2, 2017: Biochimica et Biophysica Acta
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