Adventures in Topological Field Theory

NASA Astrophysics Data System (ADS)

Horne, James H.

1990-01-01

This thesis consists of 5 parts. In part I, the topological Yang-Mills theory and the topological sigma model are presented in a superspace formulation. This greatly simplifies the field content of the theories, and makes the Q-invariance more obvious. The Feynman rules for the topological Yang -Mills theory are derived. We calculate the one-loop beta-functions of the topological sigma model in superspace. The lattice version of these theories is presented. The self-duality constraints of both models lead to spectrum doubling. In part II, we show that conformally invariant gravity in three dimensions is equivalent to the Yang-Mills gauge theory of the conformal group in three dimensions, with a Chern-Simons action. This means that conformal gravity is finite and exactly soluble. In part III, we derive the skein relations for the fundamental representations of SO(N), Sp(2n), Su(m| n), and OSp(m| 2n). These relations can be used recursively to calculate the expectation values of Wilson lines in three-dimensional Chern-Simons gauge theory with these gauge groups. A combination of braiding and tying of Wilson lines completely describes the skein relations. In part IV, we show that the k = 1 two dimensional gravity amplitudes at genus 3 agree precisely with the results from intersection theory on moduli space. Predictions for the genus 4 intersection numbers follow from the two dimensional gravity theory. In part V, we discuss the partition function in two dimensional gravity. For the one matrix model at genus 2, we use the partition function to derive a recursion relation. We show that the k = 1 amplitudes completely determine the partition function at arbitrary genus. We present a conjecture for the partition function for the arbitrary topological field theory coupled to topological gravity.

Localization of Gauge Theory on a Four-Sphere and Supersymmetric Wilson Loops

NASA Astrophysics Data System (ADS)

Pestun, Vasily

2012-07-01

We prove conjecture due to Erickson-Semenoff-Zarembo and Drukker-Gross which relates supersymmetric circular Wilson loop operators in the {N=4} supersymmetric Yang-Mills theory with a Gaussian matrix model. We also compute the partition function and give a new matrix model formula for the expectation value of a supersymmetric circular Wilson loop operator for the pure {N=2} and the {N=2^*} supersymmetric Yang-Mills theory on a four-sphere. A four-dimensional {N=2} superconformal gauge theory is treated similarly.

A string theory which isn't about strings

NASA Astrophysics Data System (ADS)

Lee, Kanghoon; Rey, Soo-Jong; Rosabal, J. A.

2017-11-01

Quantization of closed string proceeds with a suitable choice of worldsheet vacuum. A priori, the vacuum may be chosen independently for left-moving and right-moving sectors. We construct ab initio quantized bosonic string theory with left-right asymmetric worldsheet vacuum and explore its consequences and implications. We critically examine the validity of new vacuum and carry out first-quantization using standard operator formalism. Remarkably, the string spectrum consists only of a finite number of degrees of freedom: string gravity (massless spin-two, Kalb-Ramond and dilaton fields) and two massive spin-two Fierz-Pauli fields. The massive spin-two fields have negative norm, opposite mass-squared, and provides a Lee-Wick type extension of string gravity. We compute two physical observables: tree-level scattering amplitudes and one-loop cosmological constant. Scattering amplitude of four dilatons is shown to be a rational function of kinematic invariants, and in D = 26 factorizes into contributions of massless spin-two and a pair of massive spin-two fields. The string one loop partition function is shown to perfectly agree with one loop Feynman diagram of string gravity and two massive spin-two fields. In particular, it does not exhibit modular invariance. We critically compare our construction with recent studies and contrast differences.

Determination of air-loop volume and radon partition coefficient for measuring radon in water sample.

PubMed

Lee, Kil Yong; Burnett, William C

A simple method for the direct determination of the air-loop volume in a RAD7 system as well as the radon partition coefficient was developed allowing for an accurate measurement of the radon activity in any type of water. The air-loop volume may be measured directly using an external radon source and an empty bottle with a precisely measured volume. The partition coefficient and activity of radon in the water sample may then be determined via the RAD7 using the determined air-loop volume. Activity ratios instead of absolute activities were used to measure the air-loop volume and the radon partition coefficient. In order to verify this approach, we measured the radon partition coefficient in deionized water in the temperature range of 10-30 °C and compared the values to those calculated from the well-known Weigel equation. The results were within 5 % variance throughout the temperature range. We also applied the approach for measurement of the radon partition coefficient in synthetic saline water (0-75 ppt salinity) as well as tap water. The radon activity of the tap water sample was determined by this method as well as the standard RAD-H 2 O and BigBottle RAD-H 2 O. The results have shown good agreement between this method and the standard methods.

Quantum Dilogarithms and Partition q-Series

NASA Astrophysics Data System (ADS)

Kato, Akishi; Terashima, Yuji

2015-08-01

In our previous work (Kato and Terashima, Commun Math Phys. arXiv:1403.6569, 2014), we introduced the partition q-series for mutation loop γ—a loop in exchange quiver. In this paper, we show that for a certain class of mutation sequences, called reddening sequences, the graded version of partition q-series essentially coincides with the ordered product of quantum dilogarithm associated with each mutation; the partition q-series provides a state-sum description of combinatorial Donaldson-Thomas invariants introduced by Keller.

A Method to Predict the Structure and Stability of RNA/RNA Complexes.

PubMed

Xu, Xiaojun; Chen, Shi-Jie

2016-01-01

RNA/RNA interactions are essential for genomic RNA dimerization and regulation of gene expression. Intermolecular loop-loop base pairing is a widespread and functionally important tertiary structure motif in RNA machinery. However, computational prediction of intermolecular loop-loop base pairing is challenged by the entropy and free energy calculation due to the conformational constraint and the intermolecular interactions. In this chapter, we describe a recently developed statistical mechanics-based method for the prediction of RNA/RNA complex structures and stabilities. The method is based on the virtual bond RNA folding model (Vfold). The main emphasis in the method is placed on the evaluation of the entropy and free energy for the loops, especially tertiary kissing loops. The method also uses recursive partition function calculations and two-step screening algorithm for large, complicated structures of RNA/RNA complexes. As case studies, we use the HIV-1 Mal dimer and the siRNA/HIV-1 mutant (T4) to illustrate the method.

On distributed wavefront reconstruction for large-scale adaptive optics systems.

PubMed

de Visser, Cornelis C; Brunner, Elisabeth; Verhaegen, Michel

2016-05-01

The distributed-spline-based aberration reconstruction (D-SABRE) method is proposed for distributed wavefront reconstruction with applications to large-scale adaptive optics systems. D-SABRE decomposes the wavefront sensor domain into any number of partitions and solves a local wavefront reconstruction problem on each partition using multivariate splines. D-SABRE accuracy is within 1% of a global approach with a speedup that scales quadratically with the number of partitions. The D-SABRE is compared to the distributed cumulative reconstruction (CuRe-D) method in open-loop and closed-loop simulations using the YAO adaptive optics simulation tool. D-SABRE accuracy exceeds CuRe-D for low levels of decomposition, and D-SABRE proved to be more robust to variations in the loop gain.

Simulation of magnetoelastic response of iron nanowire loop

NASA Astrophysics Data System (ADS)

Huang, Junping; Peng, Xianghe; Wang, Zhongchang; Hu, Xianzhi

2018-03-01

We analyzed the magnetoelastic responses of one-dimensional iron nanowire loop systems with quantum statistical mechanics, treating the particles in the systems as identical bosons with an arbitrary integer spin. Under the assumptions adopted, we demonstrated that the Hamiltonian of the system can be separated into two parts, corresponding to two Ising subsystems, describing the particle spin and the particle displacement, respectively. Because the energy of the particle motion at atomic scale is quantized, there should be more the strict constraint on the particle displacement Ising subsystem. Making use of the existing results for Ising system, the partition function of the system was derived into two parts, corresponding respectively to the two Ising subsystems. Then the Gibbs distribution was obtained by statistical mechanics, and the description for the magnetoelastic response was derived. The magnetoelastic responses were predicted with the developed approach, and the comparison with the results calculated with VASP demonstrates the validity of the developed approach.

Gauging Variational Inference

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chertkov, Michael; Ahn, Sungsoo; Shin, Jinwoo

Computing partition function is the most important statistical inference task arising in applications of Graphical Models (GM). Since it is computationally intractable, approximate methods have been used to resolve the issue in practice, where meanfield (MF) and belief propagation (BP) are arguably the most popular and successful approaches of a variational type. In this paper, we propose two new variational schemes, coined Gauged-MF (G-MF) and Gauged-BP (G-BP), improving MF and BP, respectively. Both provide lower bounds for the partition function by utilizing the so-called gauge transformation which modifies factors of GM while keeping the partition function invariant. Moreover, we provemore » that both G-MF and G-BP are exact for GMs with a single loop of a special structure, even though the bare MF and BP perform badly in this case. Our extensive experiments, on complete GMs of relatively small size and on large GM (up-to 300 variables) confirm that the newly proposed algorithms outperform and generalize MF and BP.« less

The Response of Ω-Loop D Dynamics to Truncation of Trimethyllysine 72 of Yeast Iso-1-cytochrome c Depends on the Nature of Loop Deformation

PubMed Central

McClelland, Levi J.; Seagraves, Sean M.; Khan, Khurshid Alam; Cherney, Melisa M.; Bandi, Swati; Culbertson, Justin E.; Bowler, Bruce E.

2015-01-01

Trimethyllysine 72 (tmK72) has been suggested to play a role in sterically constraining the heme crevice dynamics of yeast iso-1-cytochrome c mediated by the Ω-loop D cooperative substructure (residues 70 to 85). A tmK72A mutation causes a gain in peroxidase activity, a function of cytochrome c that is important early in apoptosis. More than one higher energy state is accessible for the Ω-loop D substructure via tier 0 dynamics. Two of these are alkaline conformers mediated by Lys73 and Lys79. In the current work, the effect of the tmK72A mutation on the thermodynamic and kinetic properties of wild type iso-1-cytochrome c (yWT versus WT*) and on variants carrying a K73H mutation (yWT/K73H versus WT*/K73H) is studied. Whereas the tmK72A mutation confers increased peroxidase activity in wild type yeast iso-1-cytochrome c and increased dynamics for formation of a previously studied His79-heme alkaline conformer, the tmK72A mutation speeds return of the His73-heme alkaline conformer to the native state through destabilization of the His73-heme alkaline conformer relative to the native conformer. These opposing behaviors demonstrate that the response of the dynamics of a protein substructure to mutation depends on the nature of the perturbation to the substructure. For a protein substructure which mediates more than one function of a protein through multiple non-native structures, a mutation could change the partitioning between these functions. The current results suggest that the tier 0 dynamics of Ω-loop D that mediates peroxidase activity has similarities to the tier 0 dynamics required to form the His79-heme alkaline conformer. PMID:25948392

Wilson loops and chiral correlators on squashed spheres

NASA Astrophysics Data System (ADS)

Fucito, F.; Morales, J. F.; Poghossian, R.

2015-11-01

We study chiral deformations of N=2 and N=4 supersymmetric gauge theories obtained by turning on τ J tr Φ J interactions with Φ the N=2 superfield. Using localization, we compute the deformed gauge theory partition function Z(overrightarrow{τ}|q) and the expectation value of circular Wilson loops W on a squashed four-sphere. In the case of the deformed {N}=4 theory, exact formulas for Z and W are derived in terms of an underlying U( N) interacting matrix model replacing the free Gaussian model describing the {N}=4 theory. Using the AGT correspondence, the τ J -deformations are related to the insertions of commuting integrals of motion in the four-point CFT correlator and chiral correlators are expressed as τ-derivatives of the gauge theory partition function on a finite Ω-background. In the so called Nekrasov-Shatashvili limit, the entire ring of chiral relations is extracted from the ɛ-deformed Seiberg-Witten curve. As a byproduct of our analysis we show that SU(2) gauge theories on rational Ω-backgrounds are dual to CFT minimal models.

Run-time scheduling and execution of loops on message passing machines

NASA Technical Reports Server (NTRS)

Crowley, Kay; Saltz, Joel; Mirchandaney, Ravi; Berryman, Harry

1989-01-01

Sparse system solvers and general purpose codes for solving partial differential equations are examples of the many types of problems whose irregularity can result in poor performance on distributed memory machines. Often, the data structures used in these problems are very flexible. Crucial details concerning loop dependences are encoded in these structures rather than being explicitly represented in the program. Good methods for parallelizing and partitioning these types of problems require assignment of computations in rather arbitrary ways. Naive implementations of programs on distributed memory machines requiring general loop partitions can be extremely inefficient. Instead, the scheduling mechanism needs to capture the data reference patterns of the loops in order to partition the problem. First, the indices assigned to each processor must be locally numbered. Next, it is necessary to precompute what information is needed by each processor at various points in the computation. The precomputed information is then used to generate an execution template designed to carry out the computation, communication, and partitioning of data, in an optimized manner. The design is presented for a general preprocessor and schedule executer, the structures of which do not vary, even though the details of the computation and of the type of information are problem dependent.

Run-time scheduling and execution of loops on message passing machines

NASA Technical Reports Server (NTRS)

Saltz, Joel; Crowley, Kathleen; Mirchandaney, Ravi; Berryman, Harry

1990-01-01

Sparse system solvers and general purpose codes for solving partial differential equations are examples of the many types of problems whose irregularity can result in poor performance on distributed memory machines. Often, the data structures used in these problems are very flexible. Crucial details concerning loop dependences are encoded in these structures rather than being explicitly represented in the program. Good methods for parallelizing and partitioning these types of problems require assignment of computations in rather arbitrary ways. Naive implementations of programs on distributed memory machines requiring general loop partitions can be extremely inefficient. Instead, the scheduling mechanism needs to capture the data reference patterns of the loops in order to partition the problem. First, the indices assigned to each processor must be locally numbered. Next, it is necessary to precompute what information is needed by each processor at various points in the computation. The precomputed information is then used to generate an execution template designed to carry out the computation, communication, and partitioning of data, in an optimized manner. The design is presented for a general preprocessor and schedule executer, the structures of which do not vary, even though the details of the computation and of the type of information are problem dependent.

Experiences with Cray multi-tasking

NASA Technical Reports Server (NTRS)

Miya, E. N.

1985-01-01

The issues involved in modifying an existing code for multitasking is explored. They include Cray extensions to FORTRAN, an examination of the application code under study, designing workable modifications, specific code modifications to the VAX and Cray versions, performance, and efficiency results. The finished product is a faster, fully synchronous, parallel version of the original program. A production program is partitioned by hand to run on two CPUs. Loop splitting multitasks three key subroutines. Simply dividing subroutine data and control structure down the middle of a subroutine is not safe. Simple division produces results that are inconsistent with uniprocessor runs. The safest way to partition the code is to transfer one block of loops at a time and check the results of each on a test case. Other issues include debugging and performance. Task startup and maintenance (e.g., synchronization) are potentially expensive.

The Application of Hardware in the Loop Testing for Distributed Engine Control

NASA Technical Reports Server (NTRS)

Thomas, George L.; Culley, Dennis E.; Brand, Alex

2016-01-01

The essence of a distributed control system is the modular partitioning of control function across a hardware implementation. This type of control architecture requires embedding electronics in a multitude of control element nodes for the execution of those functions, and their integration as a unified system. As the field of distributed aeropropulsion control moves toward reality, questions about building and validating these systems remain. This paper focuses on the development of hardware-in-the-loop (HIL) test techniques for distributed aero engine control, and the application of HIL testing as it pertains to potential advanced engine control applications that may now be possible due to the intelligent capability embedded in the nodes.

Laparoscopic stomach-partitioning gastrojejunostomy with reduced-port techniques for unresectable distal gastric cancer.

PubMed

Hirahara, Noriyuki; Matsubara, Takeshi; Hyakudomi, Ryoji; Hari, Yoko; Fujii, Yusuke; Tajima, Yoshitsugu

2014-03-01

The improvement of quality of life is of great importance in managing patients with far-advanced gastric cancer. We report a new cure and less invasive method of creating a stomach-partitioning gastrojejunostomy in reduced-port laparoscopic surgery for unresectable gastric cancers with gastric outlet obstruction. A 2.5-cm vertical intraumbilical incision was made, and EZ Access (Hakko Co., Ltd., Tokyo, Japan) was placed. After pneumoperitoneum was created, an additional 5-mm trocar was inserted in the right upper abdomen. A gastrojejunostomy was performed in the form of an antiperistaltic side-to-side anastomosis, in which the jejunal loop was elevated in the antecolic route and anastomosed to the greater curvature of the stomach using an endoscopic linear stapler. The jejunal loop together with the stomach was dissected with additional linear staplers just proximal to the common entry hole so that a functional end-to-end gastrojejunostomy was completed. At the same time, the stomach was partitioned using a linear stapler to leave a 2-cm-wide lumen in the lesser curvature. Subsequently, jejunojejunostomy was performed 30 cm distal to the gastrojejunostomy, and the stomach-partitioning gastrojejunostomy resembling Roux-en Y anastomosis was completed. All patients resumed oral intake on the day of operation. Neither anastomotic leakage nor anastomotic stricture was observed. Our less invasive palliative operation offers the utmost priority to improve quality of life for patients with unresectable gastric cancer.

Application of controller partitioning optimization procedure to integrated flight/propulsion control design for a STOVL aircraft

NASA Technical Reports Server (NTRS)

Garg, Sanjay; Schmidt, Phillip H.

1993-01-01

A parameter optimization framework has earlier been developed to solve the problem of partitioning a centralized controller into a decentralized, hierarchical structure suitable for integrated flight/propulsion control implementation. This paper presents results from the application of the controller partitioning optimization procedure to IFPC design for a Short Take-Off and Vertical Landing (STOVL) aircraft in transition flight. The controller partitioning problem and the parameter optimization algorithm are briefly described. Insight is provided into choosing various 'user' selected parameters in the optimization cost function such that the resulting optimized subcontrollers will meet the characteristics of the centralized controller that are crucial to achieving the desired closed-loop performance and robustness, while maintaining the desired subcontroller structure constraints that are crucial for IFPC implementation. The optimization procedure is shown to improve upon the initial partitioned subcontrollers and lead to performance comparable to that achieved with the centralized controller. This application also provides insight into the issues that should be addressed at the centralized control design level in order to obtain implementable partitioned subcontrollers.

Wilson loops in supersymmetric gauge theories

NASA Astrophysics Data System (ADS)

Pestun, Vasily

This thesis is devoted to several exact computations in four-dimensional supersymmetric gauge field theories. In the first part of the thesis we prove conjecture due to Erickson-Semenoff-Zarembo and Drukker-Gross which relates supersymmetric circular Wilson loop operators in the N = 4 supersymmetric Yang-Mills theory with a Gaussian matrix model. We also compute the partition function and give a new matrix model formula for the expectation value of a supersymmetric circular Wilson loop operator for the pure N = 2 and the N* = 2 supersymmetric Yang-Mills theory on a four-sphere. Circular supersymmetric Wilson loops in four-dimensional N = 2 superconformal gauge theory are treated similarly. In the second part we consider supersymmetric Wilson loops of arbitrary shape restricted to a two-dimensional sphere in the four-dimensional N = 4 supersymmetric Yang-Mills theory. We show that expectation value for these Wilson loops can be exactly computed using a two-dimensional theory closely related to the topological two-dimensional Higgs-Yang-Mills theory, or two-dimensional Yang-Mills theory for the complexified gauge group.

Tensor Spectral Clustering for Partitioning Higher-order Network Structures.

PubMed

Benson, Austin R; Gleich, David F; Leskovec, Jure

2015-01-01

Spectral graph theory-based methods represent an important class of tools for studying the structure of networks. Spectral methods are based on a first-order Markov chain derived from a random walk on the graph and thus they cannot take advantage of important higher-order network substructures such as triangles, cycles, and feed-forward loops. Here we propose a Tensor Spectral Clustering (TSC) algorithm that allows for modeling higher-order network structures in a graph partitioning framework. Our TSC algorithm allows the user to specify which higher-order network structures (cycles, feed-forward loops, etc.) should be preserved by the network clustering. Higher-order network structures of interest are represented using a tensor, which we then partition by developing a multilinear spectral method. Our framework can be applied to discovering layered flows in networks as well as graph anomaly detection, which we illustrate on synthetic networks. In directed networks, a higher-order structure of particular interest is the directed 3-cycle, which captures feedback loops in networks. We demonstrate that our TSC algorithm produces large partitions that cut fewer directed 3-cycles than standard spectral clustering algorithms.

Tensor Spectral Clustering for Partitioning Higher-order Network Structures

PubMed Central

Benson, Austin R.; Gleich, David F.; Leskovec, Jure

2016-01-01

Spectral graph theory-based methods represent an important class of tools for studying the structure of networks. Spectral methods are based on a first-order Markov chain derived from a random walk on the graph and thus they cannot take advantage of important higher-order network substructures such as triangles, cycles, and feed-forward loops. Here we propose a Tensor Spectral Clustering (TSC) algorithm that allows for modeling higher-order network structures in a graph partitioning framework. Our TSC algorithm allows the user to specify which higher-order network structures (cycles, feed-forward loops, etc.) should be preserved by the network clustering. Higher-order network structures of interest are represented using a tensor, which we then partition by developing a multilinear spectral method. Our framework can be applied to discovering layered flows in networks as well as graph anomaly detection, which we illustrate on synthetic networks. In directed networks, a higher-order structure of particular interest is the directed 3-cycle, which captures feedback loops in networks. We demonstrate that our TSC algorithm produces large partitions that cut fewer directed 3-cycles than standard spectral clustering algorithms. PMID:27812399

A Solution Space for a System of Null-State Partial Differential Equations: Part 1

NASA Astrophysics Data System (ADS)

Flores, Steven M.; Kleban, Peter

2015-01-01

This article is the first of four that completely and rigorously characterize a solution space for a homogeneous system of 2 N + 3 linear partial differential equations (PDEs) in 2 N variables that arises in conformal field theory (CFT) and multiple Schramm-Löwner evolution (SLE). In CFT, these are null-state equations and conformal Ward identities. They govern partition functions for the continuum limit of a statistical cluster or loop-gas model, such as percolation, or more generally the Potts models and O( n) models, at the statistical mechanical critical point. (SLE partition functions also satisfy these equations.) For such a lattice model in a polygon with its 2 N sides exhibiting a free/fixed side-alternating boundary condition , this partition function is proportional to the CFT correlation function where the w i are the vertices of and where is a one-leg corner operator. (Partition functions for "crossing events" in which clusters join the fixed sides of in some specified connectivity are linear combinations of such correlation functions.) When conformally mapped onto the upper half-plane, methods of CFT show that this correlation function satisfies the system of PDEs that we consider. In this first article, we use methods of analysis to prove that the dimension of this solution space is no more than C N , the Nth Catalan number. While our motivations are based in CFT, our proofs are completely rigorous. This proof is contained entirely within this article, except for the proof of Lemma 14, which constitutes the second article (Flores and Kleban, in Commun Math Phys, arXiv:1404.0035, 2014). In the third article (Flores and Kleban, in Commun Math Phys, arXiv:1303.7182, 2013), we use the results of this article to prove that the solution space of this system of PDEs has dimension C N and is spanned by solutions constructed with the CFT Coulomb gas (contour integral) formalism. In the fourth article (Flores and Kleban, in Commun Math Phys, arXiv:1405.2747, 2014), we prove further CFT-related properties about these solutions, some useful for calculating cluster-crossing probabilities of critical lattice models in polygons.

Deformations of super Riemann surfaces

NASA Astrophysics Data System (ADS)

Ninnemann, Holger

1992-11-01

Two different approaches to (Kostant-Leites-) super Riemann surfaces are investigated. In the local approach, i.e. glueing open superdomains by superconformal transition functions, deformations of the superconformal structure are discussed. On the other hand, the representation of compact super Riemann surfaces of genus greater than one as a fundamental domain in the Poincaré upper half-plane provides a simple description of super Laplace operators acting on automorphic p-forms. Considering purely odd deformations of super Riemann surfaces, the number of linear independent holomorphic sections of arbitrary holomorphic line bundles will be shown to be independent of the odd moduli, leading to a simple proof of the Riemann-Roch theorem for compact super Riemann surfaces. As a further consequence, the explicit connections between determinants of super Laplacians and Selberg's super zeta functions can be determined, allowing to calculate at least the 2-loop contribution to the fermionic string partition function.

Approximate inference on planar graphs using loop calculus and belief progagation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chertkov, Michael; Gomez, Vicenc; Kappen, Hilbert

We introduce novel results for approximate inference on planar graphical models using the loop calculus framework. The loop calculus (Chertkov and Chernyak, 2006b) allows to express the exact partition function Z of a graphical model as a finite sum of terms that can be evaluated once the belief propagation (BP) solution is known. In general, full summation over all correction terms is intractable. We develop an algorithm for the approach presented in Chertkov et al. (2008) which represents an efficient truncation scheme on planar graphs and a new representation of the series in terms of Pfaffians of matrices. We analyzemore » in detail both the loop series and the Pfaffian series for models with binary variables and pairwise interactions, and show that the first term of the Pfaffian series can provide very accurate approximations. The algorithm outperforms previous truncation schemes of the loop series and is competitive with other state-of-the-art methods for approximate inference.« less

The strainrange conversion principle for treating cumulative fatigue damage in the creep range

NASA Technical Reports Server (NTRS)

Manson, S. S.

1983-01-01

A formula is derived for combining effects of successive hysteresis loops in the creep range of materials when one loop has excess tensile creep, while the other contains excess compressive creep. The resultant effect resembles single loops involving balanced tensile and compressive creep. The attempt to use the Interaction Damage Rule as a tool in combining loops of non-equal size and complex strainrange content has led to important new concepts useful in future studies of creep-fatigue. It turns out that the Interaction Damage Rule is basically an expression of how a set of hysteresis loops involving only single generic strains can combine to produce the same micromechanistic damage as the loop containing the combined strainranges which it analyzes. Making use of the underlying concept of Strainrange Partitioning that only the strainrange content of a hysteresis loop governs fatigue life, not order of introducing strainranges, a rational derivation of the Interaction Damage Rule is provided, showing also how it can effectively be used to synthesize independent loops and determine both damaging and healing effects.

Dual simulation of the massless lattice Schwinger model with topological term and non-zero chemical potential

NASA Astrophysics Data System (ADS)

Göschl, Daniel

2018-03-01

We discuss simulation strategies for the massless lattice Schwinger model with a topological term and finite chemical potential. The simulation is done in a dual representation where the complex action problem is solved and the partition function is a sum over fermion loops, fermion dimers and plaquette-occupation numbers. We explore strategies to update the fermion loops coupled to the gauge degrees of freedom and check our results with conventional simulations (without topological term and at zero chemical potential), as well as with exact summation on small volumes. Some physical implications of the results are discussed.

Exact partition functions for gauge theories on Rλ3

NASA Astrophysics Data System (ADS)

Wallet, Jean-Christophe

2016-11-01

The noncommutative space Rλ3, a deformation of R3, supports a 3-parameter family of gauge theory models with gauge-invariant harmonic term, stable vacuum and which are perturbatively finite to all orders. Properties of this family are discussed. The partition function factorizes as an infinite product of reduced partition functions, each one corresponding to the reduced gauge theory on one of the fuzzy spheres entering the decomposition of Rλ3. For a particular sub-family of gauge theories, each reduced partition function is exactly expressible as a ratio of determinants. A relation with integrable 2-D Toda lattice hierarchy is indicated.

Phylogenetically conserved resource partitioning in the coastal microbial loop

DOE PAGES

Bryson, Samuel; Li, Zhou; Chavez, Francisco; ...

2017-08-11

Resource availability influences marine microbial community structure, suggesting that population-specific resource partitioning defines discrete niches. Identifying how resources are partitioned among populations, thereby characterizing functional guilds within the communities, remains a challenge for microbial ecologists. We used proteomic stable isotope probing (SIP) and NanoSIMS analysis of phylogenetic microarrays (Chip-SIP) along with 16S rRNA gene amplicon and metagenomic sequencing to characterize the assimilation of six 13C-labeled common metabolic substrates and changes in the microbial community structure within surface water collected from Monterey Bay, CA. Both sequencing approaches indicated distinct substrate-specific community shifts. However, observed changes in relative abundance for individual populationsmore » did not correlate well with directly measured substrate assimilation. The complementary SIP techniques identified assimilation of all six substrates by diverse taxa, but also revealed differential assimilation of substrates into protein and ribonucleotide biomass between taxa. Substrate assimilation trends indicated significantly conserved resource partitioning among populations within the Flavobacteriia, Alphaproteobacteria and Gammaproteobacteria classes, suggesting that functional guilds within marine microbial communities are phylogenetically cohesive. However, populations within these classes exhibited heterogeneity in biosynthetic activity, which distinguished high-activity copiotrophs from low-activity oligotrophs. These results indicate distinct growth responses between populations that is not apparent by genome sequencing alone.« less

Phylogenetically conserved resource partitioning in the coastal microbial loop

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bryson, Samuel; Li, Zhou; Chavez, Francisco

Resource availability influences marine microbial community structure, suggesting that population-specific resource partitioning defines discrete niches. Identifying how resources are partitioned among populations, thereby characterizing functional guilds within the communities, remains a challenge for microbial ecologists. We used proteomic stable isotope probing (SIP) and NanoSIMS analysis of phylogenetic microarrays (Chip-SIP) along with 16S rRNA gene amplicon and metagenomic sequencing to characterize the assimilation of six 13C-labeled common metabolic substrates and changes in the microbial community structure within surface water collected from Monterey Bay, CA. Both sequencing approaches indicated distinct substrate-specific community shifts. However, observed changes in relative abundance for individual populationsmore » did not correlate well with directly measured substrate assimilation. The complementary SIP techniques identified assimilation of all six substrates by diverse taxa, but also revealed differential assimilation of substrates into protein and ribonucleotide biomass between taxa. Substrate assimilation trends indicated significantly conserved resource partitioning among populations within the Flavobacteriia, Alphaproteobacteria and Gammaproteobacteria classes, suggesting that functional guilds within marine microbial communities are phylogenetically cohesive. However, populations within these classes exhibited heterogeneity in biosynthetic activity, which distinguished high-activity copiotrophs from low-activity oligotrophs. These results indicate distinct growth responses between populations that is not apparent by genome sequencing alone.« less

Phylogenetically conserved resource partitioning in the coastal microbial loop

PubMed Central

Bryson, Samuel; Li, Zhou; Chavez, Francisco; Weber, Peter K; Pett-Ridge, Jennifer; Hettich, Robert L; Pan, Chongle; Mayali, Xavier; Mueller, Ryan S

2017-01-01

Resource availability influences marine microbial community structure, suggesting that population-specific resource partitioning defines discrete niches. Identifying how resources are partitioned among populations, thereby characterizing functional guilds within the communities, remains a challenge for microbial ecologists. We used proteomic stable isotope probing (SIP) and NanoSIMS analysis of phylogenetic microarrays (Chip-SIP) along with 16S rRNA gene amplicon and metagenomic sequencing to characterize the assimilation of six 13C-labeled common metabolic substrates and changes in the microbial community structure within surface water collected from Monterey Bay, CA. Both sequencing approaches indicated distinct substrate-specific community shifts. However, observed changes in relative abundance for individual populations did not correlate well with directly measured substrate assimilation. The complementary SIP techniques identified assimilation of all six substrates by diverse taxa, but also revealed differential assimilation of substrates into protein and ribonucleotide biomass between taxa. Substrate assimilation trends indicated significantly conserved resource partitioning among populations within the Flavobacteriia, Alphaproteobacteria and Gammaproteobacteria classes, suggesting that functional guilds within marine microbial communities are phylogenetically cohesive. However, populations within these classes exhibited heterogeneity in biosynthetic activity, which distinguished high-activity copiotrophs from low-activity oligotrophs. These results indicate distinct growth responses between populations that is not apparent by genome sequencing alone. PMID:28800138

Discrete geometric analysis of message passing algorithm on graphs

NASA Astrophysics Data System (ADS)

Watanabe, Yusuke

2010-04-01

We often encounter probability distributions given as unnormalized products of non-negative functions. The factorization structures are represented by hypergraphs called factor graphs. Such distributions appear in various fields, including statistics, artificial intelligence, statistical physics, error correcting codes, etc. Given such a distribution, computations of marginal distributions and the normalization constant are often required. However, they are computationally intractable because of their computational costs. One successful approximation method is Loopy Belief Propagation (LBP) algorithm. The focus of this thesis is an analysis of the LBP algorithm. If the factor graph is a tree, i.e. having no cycle, the algorithm gives the exact quantities. If the factor graph has cycles, however, the LBP algorithm does not give exact results and possibly exhibits oscillatory and non-convergent behaviors. The thematic question of this thesis is "How the behaviors of the LBP algorithm are affected by the discrete geometry of the factor graph?" The primary contribution of this thesis is the discovery of a formula that establishes the relation between the LBP, the Bethe free energy and the graph zeta function. This formula provides new techniques for analysis of the LBP algorithm, connecting properties of the graph and of the LBP and the Bethe free energy. We demonstrate applications of the techniques to several problems including (non) convexity of the Bethe free energy, the uniqueness and stability of the LBP fixed point. We also discuss the loop series initiated by Chertkov and Chernyak. The loop series is a subgraph expansion of the normalization constant, or partition function, and reflects the graph geometry. We investigate theoretical natures of the series. Moreover, we show a partial connection between the loop series and the graph zeta function.

Recurrence relations in one-dimensional Ising models.

PubMed

da Conceição, C M Silva; Maia, R N P

2017-09-01

The exact finite-size partition function for the nonhomogeneous one-dimensional (1D) Ising model is found through an approach using algebra operators. Specifically, in this paper we show that the partition function can be computed through a trace from a linear second-order recurrence relation with nonconstant coefficients in matrix form. A relation between the finite-size partition function and the generalized Lucas polynomials is found for the simple homogeneous model, thus establishing a recursive formula for the partition function. This is an important property and it might indicate the possible existence of recurrence relations in higher-dimensional Ising models. Moreover, assuming quenched disorder for the interactions within the model, the quenched averaged magnetic susceptibility displays a nontrivial behavior due to changes in the ferromagnetic concentration probability.

Complexities of high temperature metal fatigue: Some steps toward understanding

NASA Technical Reports Server (NTRS)

Manson, S. S.; Halford, G. R.

1983-01-01

After pointing out many of the complexities that attend high temperature metal fatigue beyond those already studied in the sub-creep range, a description of the micromechanisms of deformation and fracture is presented for several classes of materials that were studied over the past dozen years. Strainrange Partitioning (SRP) is used as a framework for interpreting the results. Several generic types of behavior were observed with regard both to deformation and fracture and each is discussed in the context of the micromechanisms involved. Treatment of cumulative fatigue damage and the possibility of ""healing'' of damage in successive loading loops, has led to a new interpretation of the Interaction Damage Rule of SRP. Using the concept of ""equivalent micromechanistic damage'' -- that the same damage on a microscopic scale is induced if the same hysteresis loops are generated, element for element -- it turns out the Interaction Damage Rule essentially compounds a number of variants of hysteresis loops, all of which have the same damage according to SRP concepts, into a set of loops each containing only one of the generic SRP strainranges. Thus the damage associcated with complex loops comprising several types of strainrange is analyzed by considering a combination of loops each containing only one type of strainrange. This concept is expanded to show how several independent loops can combine to ""heal'' creep damage in a complex loading history.

Compile-time estimation of communication costs in multicomputers

NASA Technical Reports Server (NTRS)

Gupta, Manish; Banerjee, Prithviraj

1991-01-01

An important problem facing numerous research projects on parallelizing compilers for distributed memory machines is that of automatically determining a suitable data partitioning scheme for a program. Any strategy for automatic data partitioning needs a mechanism for estimating the performance of a program under a given partitioning scheme, the most crucial part of which involves determining the communication costs incurred by the program. A methodology is described for estimating the communication costs at compile-time as functions of the numbers of processors over which various arrays are distributed. A strategy is described along with its theoretical basis, for making program transformations that expose opportunities for combining of messages, leading to considerable savings in the communication costs. For certain loops with regular dependences, the compiler can detect the possibility of pipelining, and thus estimate communication costs more accurately than it could otherwise. These results are of great significance to any parallelization system supporting numeric applications on multicomputers. In particular, they lay down a framework for effective synthesis of communication on multicomputers from sequential program references.

Network clustering and community detection using modulus of families of loops.

PubMed

Shakeri, Heman; Poggi-Corradini, Pietro; Albin, Nathan; Scoglio, Caterina

2017-01-01

We study the structure of loops in networks using the notion of modulus of loop families. We introduce an alternate measure of network clustering by quantifying the richness of families of (simple) loops. Modulus tries to minimize the expected overlap among loops by spreading the expected link usage optimally. We propose weighting networks using these expected link usages to improve classical community detection algorithms. We show that the proposed method enhances the performance of certain algorithms, such as spectral partitioning and modularity maximization heuristics, on standard benchmarks.

Soft functions for generic jet algorithms and observables at hadron colliders

DOE PAGES

Bertolini, Daniele; Kolodrubetz, Daniel; Neill, Duff Austin; ...

2017-07-20

Here, we introduce a method to compute one-loop soft functions for exclusive N - jet processes at hadron colliders, allowing for different definitions of the algorithm that determines the jet regions and of the measurements in those regions. In particular, we generalize the N -jettiness hemisphere decomposition of ref. [1] in a manner that separates the dependence on the jet boundary from the observables measured inside the jet and beam regions. Results are given for several factorizable jet definitions, including anti- kT , XCone, and other geometric partitionings. We calculate explicitly the soft functions for angularity measurements, including jet massmore » and jet broadening, in pp → L + 1 jet and explore the differences for various jet vetoes and algorithms. This includes a consistent treatment of rapidity divergences when applicable. We also compute analytic results for these soft functions in an expansion for a small jet radius R. We find that the small- R results, including corrections up to O(R 2), accurately capture the full behavior over a large range of R.« less

Soft functions for generic jet algorithms and observables at hadron colliders

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bertolini, Daniele; Kolodrubetz, Daniel; Neill, Duff Austin

Here, we introduce a method to compute one-loop soft functions for exclusive N - jet processes at hadron colliders, allowing for different definitions of the algorithm that determines the jet regions and of the measurements in those regions. In particular, we generalize the N -jettiness hemisphere decomposition of ref. [1] in a manner that separates the dependence on the jet boundary from the observables measured inside the jet and beam regions. Results are given for several factorizable jet definitions, including anti- kT , XCone, and other geometric partitionings. We calculate explicitly the soft functions for angularity measurements, including jet massmore » and jet broadening, in pp → L + 1 jet and explore the differences for various jet vetoes and algorithms. This includes a consistent treatment of rapidity divergences when applicable. We also compute analytic results for these soft functions in an expansion for a small jet radius R. We find that the small- R results, including corrections up to O(R 2), accurately capture the full behavior over a large range of R.« less

The Homotopic Probability Distribution and the Partition Function for the Entangled System Around a Ribbon Segment Chain

NASA Astrophysics Data System (ADS)

Qian, Shang-Wu; Gu, Zhi-Yu

2001-12-01

Using the Feynman's path integral with topological constraints arising from the presence of one singular line, we find the homotopic probability distribution P_L^n for the winding number n and the partition function P_L of the entangled system around a ribbon segment chain. We find that when the width of the ribbon segment chain 2a increases,the partition function exponentially decreases, whereas the free energy increases an amount, which is proportional to the square of the width. When the width tends to zero we obtain the same results as those of a single chain with one singular point.

Controller partitioning for integrated flight/propulsion control implementation

NASA Technical Reports Server (NTRS)

Garg, Sanjay

1993-01-01

The notion of partitioning a centralized controller into a decentralized, hierarchical structure suitable for integrated flight/propulsion control (IFPC) implementation is discussed. A systematic procedure is developed for determining partitioned airframe and engine subsystem controllers (subcontrollers), with the desired interconnection structure, that approximate the closed-loop performance and robustness characteristics of a given centralized controller. The procedure is demonstrated by application to IFPC design for a Short Take-Off and Vertical Landing (STOVL) aircraft in the landing approach to hover transition flight phase.

Partitioning of centralized integrated flight/propulsion control design for decentralized implementation

NASA Technical Reports Server (NTRS)

Garg, Sanjay

1993-01-01

The notion of partitioning a centralized controller into a decentralized, hierarchical structure suitable for integrated flight/propulsion control (IFPC) implementation is discussed. A systematic procedure is developed for determining partitioned airframe and engine subsystem controllers (subcontrollers), with the desired interconnection structure, that approximate the closed-loop performance and robustness characteristics of a given centralized controller. The procedure is demonstrated by application to IFPC design for a short take-off and vertical landing (STOVL) aircraft in the landing-approach-to-hover-transition flight phase.

Treatment of low strains and long hold times in high temperature metal fatigue by strainrange partitioning

NASA Technical Reports Server (NTRS)

Manson, S. S.; Zab, R.

1977-01-01

A procedure for treating creep-fatigue for low strainranges and long hold times is outlined. A semi-experimental approach, wherein several cycles of the imposed loading is actually applied to a specimen in order to determine the stable hysteresis loop, can be very useful in the analysis. Because such tests require only a small fraction of the total failure time, they are not inherently prohibitive if experimental equipment is available. The need for accurate constitutive equations is bypassed because the material itself acts to translate the imposed loading into the responsive hysteresis loops. When strainrange partitioning has been applied in such cases very good results have been obtained.

Dominant partition method. [based on a wave function formalism

NASA Technical Reports Server (NTRS)

Dixon, R. M.; Redish, E. F.

1979-01-01

By use of the L'Huillier, Redish, and Tandy (LRT) wave function formalism, a partially connected method, the dominant partition method (DPM) is developed for obtaining few body reductions of the many body problem in the LRT and Bencze, Redish, and Sloan (BRS) formalisms. The DPM maps the many body problem to a fewer body one by using the criterion that the truncated formalism must be such that consistency with the full Schroedinger equation is preserved. The DPM is based on a class of new forms for the irreducible cluster potential, which is introduced in the LRT formalism. Connectivity is maintained with respect to all partitions containing a given partition, which is referred to as the dominant partition. Degrees of freedom corresponding to the breakup of one or more of the clusters of the dominant partition are treated in a disconnected manner. This approach for simplifying the complicated BRS equations is appropriate for physical problems where a few body reaction mechanism prevails.

Analytic Result for the Two-loop Six-point NMHV Amplitude in N = 4 Super Yang-Mills Theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dixon, Lance J.; /SLAC; Drummond, James M.

2012-02-15

We provide a simple analytic formula for the two-loop six-point ratio function of planar N = 4 super Yang-Mills theory. This result extends the analytic knowledge of multi-loop six-point amplitudes beyond those with maximal helicity violation. We make a natural ansatz for the symbols of the relevant functions appearing in the two-loop amplitude, and impose various consistency conditions, including symmetry, the absence of spurious poles, the correct collinear behavior, and agreement with the operator product expansion for light-like (super) Wilson loops. This information reduces the ansatz to a small number of relatively simple functions. In order to fix these parametersmore » uniquely, we utilize an explicit representation of the amplitude in terms of loop integrals that can be evaluated analytically in various kinematic limits. The final compact analytic result is expressed in terms of classical polylogarithms, whose arguments are rational functions of the dual conformal cross-ratios, plus precisely two functions that are not of this type. One of the functions, the loop integral {Omega}{sup (2)}, also plays a key role in a new representation of the remainder function R{sub 6}{sup (2)} in the maximally helicity violating sector. Another interesting feature at two loops is the appearance of a new (parity odd) x (parity odd) sector of the amplitude, which is absent at one loop, and which is uniquely determined in a natural way in terms of the more familiar (parity even) x (parity even) part. The second non-polylogarithmic function, the loop integral {tilde {Omega}}{sup (2)}, characterizes this sector. Both {Omega}{sup (2)} and {tilde {Omega}}{sup (2)} can be expressed as one-dimensional integrals over classical polylogarithms with rational arguments.« less

Functional determinants, index theorems, and exact quantum black hole entropy

NASA Astrophysics Data System (ADS)

Murthy, Sameer; Reys, Valentin

2015-12-01

The exact quantum entropy of BPS black holes can be evaluated using localization in supergravity. An important ingredient in this program, that has been lacking so far, is the one-loop effect arising from the quadratic fluctuations of the exact deformation (the QV operator). We compute the fluctuation determinant for vector multiplets and hyper multiplets around Q-invariant off-shell configurations in four-dimensional N=2 supergravity with AdS 2 × S 2 boundary conditions, using the Atiyah-Bott fixed-point index theorem and a subsequent zeta function regularization. Our results extend the large-charge on-shell entropy computations in the literature to a regime of finite charges. Based on our results, we present an exact formula for the quantum entropy of BPS black holes in N=2 supergravity. We explain cancellations concerning 1/8 -BPS black holes in N=8 supergravity that were observed in arXiv:1111.1161. We also make comments about the interpretation of a logarithmic term in the topological string partition function in the low energy supergravity theory.

The Duration of Energy Deposition on Unresolved Flaring Loops in the Solar Corona

NASA Astrophysics Data System (ADS)

Reep, Jeffrey W.; Polito, Vanessa; Warren, Harry P.; Crump, Nicholas A.

2018-04-01

Solar flares form and release energy across a large number of magnetic loops. The global parameters of flares, such as the total energy released, duration, physical size, etc., are routinely measured, and the hydrodynamics of a coronal loop subjected to intense heating have been extensively studied. It is not clear, however, how many loops comprise a flare, nor how the total energy is partitioned between them. In this work, we employ a hydrodynamic model to better understand the energy partition by synthesizing Si IV and Fe XXI line emission and comparing to observations of these lines with the Interface Region Imaging Spectrograph (IRIS). We find that the observed temporal evolution of the Doppler shifts holds important information on the heating duration. To demonstrate this, we first examine a single loop model, and find that the properties of chromospheric evaporation seen in Fe XXI can be reproduced by loops heated for long durations, while persistent redshifts seen in Si IV cannot be reproduced by any single loop model. We then examine a multithreaded model, assuming both a fixed heating duration on all loops and a distribution of heating durations. For a fixed heating duration, we find that durations of 100–200 s do a fair job of reproducing both the red- and blueshifts, while a distribution of durations, with a median of about 50–100 s, does a better job. Finally, we compare our simulations directly to observations of an M-class flare seen by IRIS, and find good agreement between the modeled and observed values given these constraints.

Field theoretic approach to roughness corrections

NASA Astrophysics Data System (ADS)

Wu, Hua Yao; Schaden, Martin

2012-02-01

We develop a systematic field theoretic description of roughness corrections to the Casimir free energy of a massless scalar field in the presence of parallel plates with mean separation a. Roughness is modeled by specifying a generating functional for correlation functions of the height profile. The two-point correlation function being characterized by its variance, σ2, and correlation length, ℓ. We obtain the partition function of a massless scalar quantum field interacting with the height profile of the surface via a δ-function potential. The partition function is given by a holographic reduction of this model to three coupled scalar fields on a two-dimensional plane. The original three-dimensional space with a flat parallel plate at a distance a from the rough plate is encoded in the nonlocal propagators of the surface fields on its boundary. Feynman rules for this equivalent 2+1-dimensional model are derived and its counterterms constructed. The two-loop contribution to the free energy of this model gives the leading roughness correction. The effective separation, aeff, to a rough plate is measured to a plane that is displaced a distance ρ∝σ2/ℓ from the mean of its profile. This definition of the separation eliminates corrections to the free energy of order 1/a4 and results in unitary scattering matrices. We obtain an effective low-energy model in the limit ℓ≪a. It determines the scattering matrix and equivalent planar scattering surface of a very rough plate in terms of the single length scale ρ. The Casimir force on a rough plate is found to always weaken with decreasing correlation length ℓ. The two-loop approximation to the free energy interpolates between the free energy of the effective low-energy model and that of the proximity force approximation - the force on a very rough plate with σ≳0.5ℓ being weaker than on a planar Dirichlet surface at any separation.

Thermodynamics of single polyethylene and polybutylene glycols with hydrogen-bonding ends: A transition from looped to open conformations

NASA Astrophysics Data System (ADS)

Lee, Eunsang; Paul, Wolfgang

2018-02-01

A variety of linear polymer precursors with hydrogen bonding motifs at both ends enable us to design supramolecular polymer systems with tailored macroscopic properties including self-healing. In this study, we investigate thermodynamic properties of single polyethylene and polybutylene glycols with hydrogen bonding motifs. In this context, we first build a coarse-grained model of building blocks of the supramolecular polymer system based on all-atom molecular structures. The density of states of the single precursor is obtained using the stochastic approximation Monte Carlo method. Constructing canonical partition functions from the density of states, we find the transition from looped to open conformations at transition temperatures which are non-monotonously changing with an increasing degree of polymerization due to the competition between chain stiffness and loop-forming entropy penalty. In the complete range of chain length under investigation, a coexistence of the looped and open morphologies at the transition temperature is shown regardless of whether the transition is first-order-like or continuous. Polyethylene and polybutylene glycols show similar behavior in all the thermodynamic properties but the transition temperature of the more flexible polybutylene glycol is shown to change more gradually.

Note: A dual temperature closed loop batch reactor for determining the partitioning of trace gases within CO2-water systems.

PubMed

Warr, Oliver; Rochelle, Christopher A; Masters, Andrew J; Ballentine, Christopher J

2016-01-01

An experimental approach is presented which can be used to determine partitioning of trace gases within CO2-water systems. The key advantages of this system are (1) The system can be isolated with no external exchange, making it ideal for experiments with conservative tracers. (2) Both phases can be sampled concurrently to give an accurate composition at each phase at any given time. (3) Use of a lower temperature flow loop outside of the reactor removes contamination and facilitates sampling. (4) Rapid equilibration at given pressure/temperature conditions is significantly aided by stirring and circulating the water phase using a magnetic stirrer and high-pressure liquid chromatography pump, respectively.

Entanglement entropy of ABJM theory and entropy of topological black hole

NASA Astrophysics Data System (ADS)

Nian, Jun; Zhang, Xinyu

2017-07-01

In this paper we discuss the supersymmetric localization of the 4D N = 2 offshell gauged supergravity on the background of the AdS4 neutral topological black hole, which is the gravity dual of the ABJM theory defined on the boundary {S}^1× H^2 . We compute the large- N expansion of the supergravity partition function. The result gives the black hole entropy with the logarithmic correction, which matches the previous result of the entanglement entropy of the ABJM theory up to some stringy effects. Our result is consistent with the previous on-shell one-loop computation of the logarithmic correction to black hole entropy. It provides an explicit example of the identification of the entanglement entropy of the boundary conformal field theory with the bulk black hole entropy beyond the leading order given by the classical Bekenstein-Hawking formula, which consequently tests the AdS/CFT correspondence at the subleading order.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rivasseau, Vincent, E-mail: vincent.rivasseau@th.u-psud.fr, E-mail: adrian.tanasa@ens-lyon.org; Tanasa, Adrian, E-mail: vincent.rivasseau@th.u-psud.fr, E-mail: adrian.tanasa@ens-lyon.org

The Loop Vertex Expansion (LVE) is a quantum field theory (QFT) method which explicitly computes the Borel sum of Feynman perturbation series. This LVE relies in a crucial way on symmetric tree weights which define a measure on the set of spanning trees of any connected graph. In this paper we generalize this method by defining new tree weights. They depend on the choice of a partition of a set of vertices of the graph, and when the partition is non-trivial, they are no longer symmetric under permutation of vertices. Nevertheless we prove they have the required positivity property tomore » lead to a convergent LVE; in fact we formulate this positivity property precisely for the first time. Our generalized tree weights are inspired by the Brydges-Battle-Federbush work on cluster expansions and could be particularly suited to the computation of connected functions in QFT. Several concrete examples are explicitly given.« less

A closed expression for the UV-divergent parts of one-loop tensor integrals in dimensional regularization

NASA Astrophysics Data System (ADS)

Sulyok, G.

2017-07-01

Starting from the general definition of a one-loop tensor N-point function, we use its Feynman parametrization to calculate the ultraviolet (UV-)divergent part of an arbitrary tensor coefficient in the framework of dimensional regularization. In contrast to existing recursion schemes, we are able to present a general analytic result in closed form that enables direct determination of the UV-divergent part of any one-loop tensor N-point coefficient independent from UV-divergent parts of other one-loop tensor N-point coefficients. Simplified formulas and explicit expressions are presented for A-, B-, C-, D-, E-, and F-functions.

Improving RNA nearest neighbor parameters for helices by going beyond the two-state model.

PubMed

Spasic, Aleksandar; Berger, Kyle D; Chen, Jonathan L; Seetin, Matthew G; Turner, Douglas H; Mathews, David H

2018-06-01

RNA folding free energy change nearest neighbor parameters are widely used to predict folding stabilities of secondary structures. They were determined by linear regression to datasets of optical melting experiments on small model systems. Traditionally, the optical melting experiments are analyzed assuming a two-state model, i.e. a structure is either complete or denatured. Experimental evidence, however, shows that structures exist in an ensemble of conformations. Partition functions calculated with existing nearest neighbor parameters predict that secondary structures can be partially denatured, which also directly conflicts with the two-state model. Here, a new approach for determining RNA nearest neighbor parameters is presented. Available optical melting data for 34 Watson-Crick helices were fit directly to a partition function model that allows an ensemble of conformations. Fitting parameters were the enthalpy and entropy changes for helix initiation, terminal AU pairs, stacks of Watson-Crick pairs and disordered internal loops. The resulting set of nearest neighbor parameters shows a 38.5% improvement in the sum of residuals in fitting the experimental melting curves compared to the current literature set.

Reovirus FAST Proteins Drive Pore Formation and Syncytiogenesis Using a Novel Helix-Loop-Helix Fusion-Inducing Lipid Packing Sensor

PubMed Central

Sarker, Muzaddid; de Antueno, Roberto; Langelaan, David N.; Parmar, Hiren B.; Shin, Kyungsoo; Rainey, Jan K.; Duncan, Roy

2015-01-01

Pore formation is the most energy-demanding step during virus-induced membrane fusion, where high curvature of the fusion pore rim increases the spacing between lipid headgroups, exposing the hydrophobic interior of the membrane to water. How protein fusogens breach this thermodynamic barrier to pore formation is unclear. We identified a novel fusion-inducing lipid packing sensor (FLiPS) in the cytosolic endodomain of the baboon reovirus p15 fusion-associated small transmembrane (FAST) protein that is essential for pore formation during cell-cell fusion and syncytiogenesis. NMR spectroscopy and mutational studies indicate the dependence of this FLiPS on a hydrophobic helix-loop-helix structure. Biochemical and biophysical assays reveal the p15 FLiPS preferentially partitions into membranes with high positive curvature, and this partitioning is impeded by bis-ANS, a small molecule that inserts into hydrophobic defects in membranes. Most notably, the p15 FLiPS can be functionally replaced by heterologous amphipathic lipid packing sensors (ALPS) but not by other membrane-interactive amphipathic helices. Furthermore, a previously unrecognized amphipathic helix in the cytosolic domain of the reptilian reovirus p14 FAST protein can functionally replace the p15 FLiPS, and is itself replaceable by a heterologous ALPS motif. Anchored near the cytoplasmic leaflet by the FAST protein transmembrane domain, the FLiPS is perfectly positioned to insert into hydrophobic defects that begin to appear in the highly curved rim of nascent fusion pores, thereby lowering the energy barrier to stable pore formation. PMID:26061049

One-loop β-function for an infinite-parameter family of gauge theories

NASA Astrophysics Data System (ADS)

Krasnov, Kirill

2015-03-01

We continue to study an infinite-parametric family of gauge theories with an arbitrary function of the self-dual part of the field strength as the Lagrangian. The arising one-loop divergences are computed using the background field method. We show that they can all be absorbed by a local redefinition of the gauge field, as well as multiplicative renormalisations of the couplings. Thus, this family of theories is one-loop renormalisable. The infinite set of β-functions for the couplings is compactly stored in a renormalisation group flow for a single function of the curvature. The flow is obtained explicitly.

Cosmological perturbation theory using the FFTLog: formalism and connection to QFT loop integrals

NASA Astrophysics Data System (ADS)

Simonović, Marko; Baldauf, Tobias; Zaldarriaga, Matias; Carrasco, John Joseph; Kollmeier, Juna A.

2018-04-01

We present a new method for calculating loops in cosmological perturbation theory. This method is based on approximating a ΛCDM-like cosmology as a finite sum of complex power-law universes. The decomposition is naturally achieved using an FFTLog algorithm. For power-law cosmologies, all loop integrals are formally equivalent to loop integrals of massless quantum field theory. These integrals have analytic solutions in terms of generalized hypergeometric functions. We provide explicit formulae for the one-loop and the two-loop power spectrum and the one-loop bispectrum. A chief advantage of our approach is that the difficult part of the calculation is cosmology independent, need be done only once, and can be recycled for any relevant predictions. Evaluation of standard loop diagrams then boils down to a simple matrix multiplication. We demonstrate the promise of this method for applications to higher multiplicity/loop correlation functions.

Note: A dual temperature closed loop batch reactor for determining the partitioning of trace gases within CO{sub 2}-water systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Warr, Oliver, E-mail: oliver.warr@earth.ox.ac.uk; Ballentine, Christopher J.; Rochelle, Christopher A.

An experimental approach is presented which can be used to determine partitioning of trace gases within CO{sub 2}-water systems. The key advantages of this system are (1) The system can be isolated with no external exchange, making it ideal for experiments with conservative tracers. (2) Both phases can be sampled concurrently to give an accurate composition at each phase at any given time. (3) Use of a lower temperature flow loop outside of the reactor removes contamination and facilitates sampling. (4) Rapid equilibration at given pressure/temperature conditions is significantly aided by stirring and circulating the water phase using a magneticmore » stirrer and high-pressure liquid chromatography pump, respectively.« less

Late-time structure of the Bunch-Davies de Sitter wavefunction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Anninos, Dionysios; Anous, Tarek; Freedman, Daniel Z.

2015-11-30

We examine the late time behavior of the Bunch-Davies wavefunction for interacting light fields in a de Sitter background. We use perturbative techniques developed in the framework of AdS/CFT, and analytically continue to compute tree and loop level contributions to the Bunch-Davies wavefunction. We consider self-interacting scalars of general mass, but focus especially on the massless and conformally coupled cases. We show that certain contributions grow logarithmically in conformal time both at tree and loop level. We also consider gauge fields and gravitons. The four-dimensional Fefferman-Graham expansion of classical asymptotically de Sitter solutions is used to show that the wavefunctionmore » contains no logarithmic growth in the pure graviton sector at tree level. Finally, assuming a holographic relation between the wavefunction and the partition function of a conformal field theory, we interpret the logarithmic growths in the language of conformal field theory.« less

Does one need the O({epsilon})- and O({epsilon}{sup 2})-terms of one-loop amplitudes in a next-to-next-to-leading order calculation ?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Weinzierl, Stefan

2011-10-01

This article discusses the occurrence of one-loop amplitudes within a next-to-next-to-leading-order calculation. In a next-to-next-to-leading-order calculation, the one-loop amplitude enters squared and one would therefore naively expect that the O({epsilon})- and O({epsilon}{sup 2})-terms of the one-loop amplitudes are required. I show that the calculation of these terms can be avoided if a method is known, which computes the O({epsilon}{sup 0})-terms of the finite remainder function of the two-loop amplitude.

How to share underground reservoirs

NASA Astrophysics Data System (ADS)

Schrenk, K. J.; Araújo, N. A. M.; Herrmann, H. J.

2012-10-01

Many resources, such as oil, gas, or water, are extracted from porous soils and their exploration is often shared among different companies or nations. We show that the effective shares can be obtained by invading the porous medium simultaneously with various fluids. Partitioning a volume in two parts requires one division surface while the simultaneous boundary between three parts consists of lines. We identify and characterize these lines, showing that they form a fractal set consisting of a single thread spanning the medium and a surrounding cloud of loops. While the spanning thread has fractal dimension 1.55 +/- 0.03, the set of all lines has dimension 1.69 +/- 0.02. The size distribution of the loops follows a power law and the evolution of the set of lines exhibits a tricritical point described by a crossover with a negative dimension at criticality.

Submembranous recruitment of creatine kinase B supports formation of dynamic actin-based protrusions of macrophages and relies on its C-terminal flexible loop.

PubMed

Venter, Gerda; Polling, Saskia; Pluk, Helma; Venselaar, Hanka; Wijers, Mietske; Willemse, Marieke; Fransen, Jack A M; Wieringa, Bé

2015-02-01

Subcellular partitioning of creatine kinase contributes to the formation of patterns in intracellular ATP distribution and the fuelling of cellular processes with a high and sudden energy demand. We have previously shown that brain-type creatine kinase (CK-B) accumulates at the phagocytic cup in macrophages where it is involved in the compartmentalized generation of ATP for actin remodeling. Here, we report that CK-B catalytic activity also helps in the formation of protrusive ruffle structures which are actin-dependent and abundant on the surface of both unstimulated and LPS-activated macrophages. Recruitment of CK-B to these structures occurred transiently and inhibition of the enzyme's catalytic activity with cyclocreatine led to a general smoothening of surface morphology as visualized by scanning electron microscopy. Comparison of the dynamics of distribution of YFP-tagged CK-mutants and isoforms by live imaging revealed that amino acid residues in the C-terminal segment (aa positions 323-330) that forms one of the protein's two mobile loops are involved in partitioning over inner regions of the cytosol and nearby sites where membrane protrusions occur during induction of phagocytic cup formation. Although wt CK-B, muscle-type CK (CK-M), and a catalytically dead CK-B-E232Q mutant with intact loop region were normally recruited from the cytosolic pool, no dynamic transition to the phagocytic cup area was seen for the CK-homologue arginine kinase and a CK-B-D326A mutant protein. Bioinformatics analysis helped us to predict that conformational flexibility of the C-terminal loop, independent of conformational changes induced by substrate binding or catalytic activity, is likely involved in exposing the enzyme for binding at or near the sites of membrane protrusion formation. Copyright © 2014 Elsevier GmbH. All rights reserved.

Asymptotics of quantum weighted Hurwitz numbers

NASA Astrophysics Data System (ADS)

Harnad, J.; Ortmann, Janosch

2018-06-01

This work concerns both the semiclassical and zero temperature asymptotics of quantum weighted double Hurwitz numbers. The partition function for quantum weighted double Hurwitz numbers can be interpreted in terms of the energy distribution of a quantum Bose gas with vanishing fugacity. We compute the leading semiclassical term of the partition function for three versions of the quantum weighted Hurwitz numbers, as well as lower order semiclassical corrections. The classical limit is shown to reproduce the simple single and double Hurwitz numbers studied by Okounkov and Pandharipande (2000 Math. Res. Lett. 7 447–53, 2000 Lett. Math. Phys. 53 59–74). The KP-Toda τ-function that serves as generating function for the quantum Hurwitz numbers is shown to have the τ-function of Okounkov and Pandharipande (2000 Math. Res. Lett. 7 447–53, 2000 Lett. Math. Phys. 53 59–74) as its leading term in the classical limit, and, with suitable scaling, the same holds for the partition function, the weights and expectations of Hurwitz numbers. We also compute the zero temperature limit of the partition function and quantum weighted Hurwitz numbers. The KP or Toda τ-function serving as generating function for the quantum Hurwitz numbers are shown to give the one for Belyi curves in the zero temperature limit and, with suitable scaling, the same holds true for the partition function, the weights and the expectations of Hurwitz numbers.

Marginal Consistency: Upper-Bounding Partition Functions over Commutative Semirings.

PubMed

Werner, Tomás

2015-07-01

Many inference tasks in pattern recognition and artificial intelligence lead to partition functions in which addition and multiplication are abstract binary operations forming a commutative semiring. By generalizing max-sum diffusion (one of convergent message passing algorithms for approximate MAP inference in graphical models), we propose an iterative algorithm to upper bound such partition functions over commutative semirings. The iteration of the algorithm is remarkably simple: change any two factors of the partition function such that their product remains the same and their overlapping marginals become equal. In many commutative semirings, repeating this iteration for different pairs of factors converges to a fixed point when the overlapping marginals of every pair of factors coincide. We call this state marginal consistency. During that, an upper bound on the partition function monotonically decreases. This abstract algorithm unifies several existing algorithms, including max-sum diffusion and basic constraint propagation (or local consistency) algorithms in constraint programming. We further construct a hierarchy of marginal consistencies of increasingly higher levels and show than any such level can be enforced by adding identity factors of higher arity (order). Finally, we discuss instances of the framework for several semirings, including the distributive lattice and the max-sum and sum-product semirings.

One-loop matching and running with covariant derivative expansion

DOE PAGES

Henning, Brian; Lu, Xiaochuan; Murayama, Hitoshi

2018-01-24

We develop tools for performing effective field theory (EFT) calculations in a manifestly gauge-covariant fashion. We clarify how functional methods account for one-loop diagrams resulting from the exchange of both heavy and light fields, as some confusion has recently arisen in the literature. To efficiently evaluate functional traces containing these “mixed” one-loop terms, we develop a new covariant derivative expansion (CDE) technique that is capable of evaluating a much wider class of traces than previous methods. The technique is detailed in an appendix, so that it can be read independently from the rest of this work. We review the well-knownmore » matching procedure to one-loop order with functional methods. What we add to this story is showing how to isolate one-loop terms coming from diagrams involving only heavy propagators from diagrams with mixed heavy and light propagators. This is done using a non-local effective action, which physically connects to the notion of “integrating out” heavy fields. Lastly, we show how to use a CDE to do running analyses in EFTs, i.e. to obtain the anomalous dimension matrix. We demonstrate the methodologies by several explicit example calculations.« less

One-loop matching and running with covariant derivative expansion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Henning, Brian; Lu, Xiaochuan; Murayama, Hitoshi

We develop tools for performing effective field theory (EFT) calculations in a manifestly gauge-covariant fashion. We clarify how functional methods account for one-loop diagrams resulting from the exchange of both heavy and light fields, as some confusion has recently arisen in the literature. To efficiently evaluate functional traces containing these “mixed” one-loop terms, we develop a new covariant derivative expansion (CDE) technique that is capable of evaluating a much wider class of traces than previous methods. The technique is detailed in an appendix, so that it can be read independently from the rest of this work. We review the well-knownmore » matching procedure to one-loop order with functional methods. What we add to this story is showing how to isolate one-loop terms coming from diagrams involving only heavy propagators from diagrams with mixed heavy and light propagators. This is done using a non-local effective action, which physically connects to the notion of “integrating out” heavy fields. Lastly, we show how to use a CDE to do running analyses in EFTs, i.e. to obtain the anomalous dimension matrix. We demonstrate the methodologies by several explicit example calculations.« less

One-loop matching and running with covariant derivative expansion

NASA Astrophysics Data System (ADS)

Henning, Brian; Lu, Xiaochuan; Murayama, Hitoshi

2018-01-01

We develop tools for performing effective field theory (EFT) calculations in a manifestly gauge-covariant fashion. We clarify how functional methods account for one-loop diagrams resulting from the exchange of both heavy and light fields, as some confusion has recently arisen in the literature. To efficiently evaluate functional traces containing these "mixed" one-loop terms, we develop a new covariant derivative expansion (CDE) technique that is capable of evaluating a much wider class of traces than previous methods. The technique is detailed in an appendix, so that it can be read independently from the rest of this work. We review the well-known matching procedure to one-loop order with functional methods. What we add to this story is showing how to isolate one-loop terms coming from diagrams involving only heavy propagators from diagrams with mixed heavy and light propagators. This is done using a non-local effective action, which physically connects to the notion of "integrating out" heavy fields. Lastly, we show how to use a CDE to do running analyses in EFTs, i.e. to obtain the anomalous dimension matrix. We demonstrate the methodologies by several explicit example calculations.

Asymptotic One-Point Functions in Gauge-String Duality with Defects.

PubMed

Buhl-Mortensen, Isak; de Leeuw, Marius; Ipsen, Asger C; Kristjansen, Charlotte; Wilhelm, Matthias

2017-12-29

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. Furthermore, when applied to the Berenstein-Maldacena-Nastase vacuum state, the asymptotic formula gives a result for the one-point function which in a certain double-scaling limit agrees with that obtained in the dual string theory up to wrapping order.

Stability of coefficients in the Kronecker product of a hook and a rectangle

NASA Astrophysics Data System (ADS)

Ballantine, Cristina M.; Hallahan, William T.

2016-02-01

We use recent work of Jonah Blasiak (2012 arXiv:1209.2018) to prove a stability result for the coefficients in the Kronecker product of two Schur functions: one indexed by a hook partition and one indexed by a rectangle partition. We also give nearly sharp bounds for the size of the partition starting with which the Kronecker coefficients are stable. Moreover, we show that once the bound is reached, no new Schur functions appear in the decomposition of Kronecker product. We call this property superstability. Thus, one can recover the Schur decomposition of the Kronecker product from the smallest case in which the superstability holds. The bound for superstability is sharp. Our study of this particular case of the Kronecker product is motivated by its usefulness for the understanding of the quantum Hall effect (Scharf T et al 1994 J. Phys. A: Math. Gen 27 4211-9).

Comparison of Transverse Intraosseous Loop Technique and Pull Out Suture for Reinsertion of the Flexor Digitorum Profundus tendon. A Retrospective Study.

PubMed

Rigó, István Zoltán; Røkkum, Magne

2013-12-01

We compared the results of two methods for reinsertion of flexor digitorum profundus tendons retrospectively. In 35 fingers of 29 patients pull-out suture and in 13 fingers of 11 patients transverse intraosseous loop technique was performed with a mean follow-up of 8 and 6 months, respectively. Eleven and nine fingers achieved "excellent" or "good" function according to Strickland and Glogovac at 8 weeks; 20 and ten at the last control in the pull-out and transverse intraosseous loop groups, respectively. The difference at 8 weeks was statistically significant in favour of the transverse intraosseous loop group. Ten patients underwent 12 complications in the pull-out group (four superficial infections; one rerupture, one PIP and one DIP joint contracture, one adhesion, two granulomas, one nail deformity and one carpal tunnel syndrome) and four of them were reoperated (one carpal tunnel release, one teno-arthrolysis and two resections of granuloma). There was no complication and no reoperation in the transverse intraosseous loop group, the difference being statistically significant for the former. In our study the transverse intraosseous loop technique seemed to be a safe alternative with possibly better functional results compared to the pull-out suture.

A statistical mechanical approach to restricted integer partition functions

NASA Astrophysics Data System (ADS)

Zhou, Chi-Chun; Dai, Wu-Sheng

2018-05-01

The main aim of this paper is twofold: (1) suggesting a statistical mechanical approach to the calculation of the generating function of restricted integer partition functions which count the number of partitions—a way of writing an integer as a sum of other integers under certain restrictions. In this approach, the generating function of restricted integer partition functions is constructed from the canonical partition functions of various quantum gases. (2) Introducing a new type of restricted integer partition functions corresponding to general statistics which is a generalization of Gentile statistics in statistical mechanics; many kinds of restricted integer partition functions are special cases of this restricted integer partition function. Moreover, with statistical mechanics as a bridge, we reveal a mathematical fact: the generating function of restricted integer partition function is just the symmetric function which is a class of functions being invariant under the action of permutation groups. Using this approach, we provide some expressions of restricted integer partition functions as examples.

Extending the Universal One-Loop Effective Action: heavy-light coefficients

DOE PAGES

Ellis, Sebastian A. R.; Quevillon, Jérémie; You, Tevong; ...

2017-08-16

The Universal One-Loop Effective Action (UOLEA) is a general expression for the effective action obtained by evaluating in a model-independent way the one-loop expansion of a functional path integral. It can also be used to match UV theories to their low-energy EFTs more efficiently by avoiding redundant steps in the application of functional methods, simplifying the process of obtaining Wilson coefficients of operators up to dimension six. In addition to loops involving only heavy fields, matching may require the inclusion of loops containing both heavy and light particles. Here we use the recently-developed covariant diagram technique to extend the UOLEAmore » to include heavy-light terms which retain the same universal structure as the previously-derived heavy-only terms. As an example of its application, we integrate out a heavy singlet scalar with a linear coupling to a light doublet Higgs. The extension presented here is a first step towards completing the UOLEA to incorporate all possible structures encountered in a covariant derivative expansion of the one-loop path integral.« less

Extending the Universal One-Loop Effective Action: heavy-light coefficients

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ellis, Sebastian A. R.; Quevillon, Jérémie; You, Tevong

The Universal One-Loop Effective Action (UOLEA) is a general expression for the effective action obtained by evaluating in a model-independent way the one-loop expansion of a functional path integral. It can also be used to match UV theories to their low-energy EFTs more efficiently by avoiding redundant steps in the application of functional methods, simplifying the process of obtaining Wilson coefficients of operators up to dimension six. In addition to loops involving only heavy fields, matching may require the inclusion of loops containing both heavy and light particles. Here we use the recently-developed covariant diagram technique to extend the UOLEAmore » to include heavy-light terms which retain the same universal structure as the previously-derived heavy-only terms. As an example of its application, we integrate out a heavy singlet scalar with a linear coupling to a light doublet Higgs. The extension presented here is a first step towards completing the UOLEA to incorporate all possible structures encountered in a covariant derivative expansion of the one-loop path integral.« less

Two independent modes of chromatin organization revealed by cohesin removal.

PubMed

Schwarzer, Wibke; Abdennur, Nezar; Goloborodko, Anton; Pekowska, Aleksandra; Fudenberg, Geoffrey; Loe-Mie, Yann; Fonseca, Nuno A; Huber, Wolfgang; H Haering, Christian; Mirny, Leonid; Spitz, Francois

2017-11-02

Imaging and chromosome conformation capture studies have revealed several layers of chromosome organization, including segregation into megabase-sized active and inactive compartments, and partitioning into sub-megabase domains (TADs). It remains unclear, however, how these layers of organization form, interact with one another and influence genome function. Here we show that deletion of the cohesin-loading factor Nipbl in mouse liver leads to a marked reorganization of chromosomal folding. TADs and associated Hi-C peaks vanish globally, even in the absence of transcriptional changes. By contrast, compartmental segregation is preserved and even reinforced. Strikingly, the disappearance of TADs unmasks a finer compartment structure that accurately reflects the underlying epigenetic landscape. These observations demonstrate that the three-dimensional organization of the genome results from the interplay of two independent mechanisms: cohesin-independent segregation of the genome into fine-scale compartments, defined by chromatin state; and cohesin-dependent formation of TADs, possibly by loop extrusion, which helps to guide distant enhancers to their target genes.

Distributed memory compiler methods for irregular problems: Data copy reuse and runtime partitioning

NASA Technical Reports Server (NTRS)

Das, Raja; Ponnusamy, Ravi; Saltz, Joel; Mavriplis, Dimitri

1991-01-01

Outlined here are two methods which we believe will play an important role in any distributed memory compiler able to handle sparse and unstructured problems. We describe how to link runtime partitioners to distributed memory compilers. In our scheme, programmers can implicitly specify how data and loop iterations are to be distributed between processors. This insulates users from having to deal explicitly with potentially complex algorithms that carry out work and data partitioning. We also describe a viable mechanism for tracking and reusing copies of off-processor data. In many programs, several loops access the same off-processor memory locations. As long as it can be verified that the values assigned to off-processor memory locations remain unmodified, we show that we can effectively reuse stored off-processor data. We present experimental data from a 3-D unstructured Euler solver run on iPSC/860 to demonstrate the usefulness of our methods.

NNLO splitting and coefficient functions with time-like kinematics

NASA Astrophysics Data System (ADS)

Mitov, A.; Moch, S.; Vogt, A.

2006-10-01

We discuss recent results on the three-loop (next-to-next-to-leading order, NNLO) time-like splitting functions of QCD and the two-loop (NNLO) coefficient functions in one-particle inclusive e+e--annihilation. These results form the basis for extracting fragmentation functions for light and heavy flavors with NNLO accuracy that will be needed at the LHC and ILC. The two-loop calculations have been performed in Mellin space based on a new method, the main features of which we also describe briefly.

Comments on "The multisynapse neural network and its application to fuzzy clustering".

PubMed

Yu, Jian; Hao, Pengwei

2005-05-01

In the above-mentioned paper, Wei and Fahn proposed a neural architecture, the multisynapse neural network, to solve constrained optimization problems including high-order, logarithmic, and sinusoidal forms, etc. As one of its main applications, a fuzzy bidirectional associative clustering network (FBACN) was proposed for fuzzy-partition clustering according to the objective-functional method. The connection between the objective-functional-based fuzzy c-partition algorithms and FBACN is the Lagrange multiplier approach. Unfortunately, the Lagrange multiplier approach was incorrectly applied so that FBACN does not equivalently minimize its corresponding constrained objective-function. Additionally, Wei and Fahn adopted traditional definition of fuzzy c-partition, which is not satisfied by FBACN. Therefore, FBACN can not solve constrained optimization problems, either.

On supersymmetry anomalies

NASA Astrophysics Data System (ADS)

Howe, P. S.; Parkes, A. J.; West, P. C.

1985-01-01

It is shown analytically that there are no one-loop supersymmetry anomalies in N = 2 and N = 4 supersymmetric Yang-Mills theories. This implies that the two-loop β functions in these theories are in accord with supersymmetry when the one-loop finite local counter terms required by supersymmetry are correctly taken into account. Permanent address: Department of Mathematics, King's College, London, UK.

Hexagonalization of correlation functions II: two-particle contributions

NASA Astrophysics Data System (ADS)

Fleury, Thiago; Komatsu, Shota

2018-02-01

In this work, we compute one-loop planar five-point functions in N=4 super-Yang-Mills using integrability. As in the previous work, we decompose the correlation functions into hexagon form factors and glue them using the weight factors which depend on the cross-ratios. The main new ingredient in the computation, as compared to the four-point functions studied in the previous paper, is the two-particle mirror contribution. We develop techniques to evaluate it and find agreement with the perturbative results in all the cases we analyzed. In addition, we consider next-to-extremal four-point functions, which are known to be protected, and show that the sum of one-particle and two-particle contributions at one loop adds up to zero as expected. The tools developed in this work would be useful for computing higher-particle contributions which would be relevant for more complicated quantities such as higher-loop corrections and non-planar correlators.

SU-E-J-85: Leave-One-Out Perturbation (LOOP) Fitting Algorithm for Absolute Dose Film Calibration

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chu, A; Ahmad, M; Chen, Z

2014-06-01

Purpose: To introduce an outliers-recognition fitting routine for film dosimetry. It cannot only be flexible with any linear and non-linear regression but also can provide information for the minimal number of sampling points, critical sampling distributions and evaluating analytical functions for absolute film-dose calibration. Methods: The technique, leave-one-out (LOO) cross validation, is often used for statistical analyses on model performance. We used LOO analyses with perturbed bootstrap fitting called leave-one-out perturbation (LOOP) for film-dose calibration . Given a threshold, the LOO process detects unfit points (“outliers”) compared to other cohorts, and a bootstrap fitting process follows to seek any possibilitiesmore » of using perturbations for further improvement. After that outliers were reconfirmed by a traditional t-test statistics and eliminated, then another LOOP feedback resulted in the final. An over-sampled film-dose- calibration dataset was collected as a reference (dose range: 0-800cGy), and various simulated conditions for outliers and sampling distributions were derived from the reference. Comparisons over the various conditions were made, and the performance of fitting functions, polynomial and rational functions, were evaluated. Results: (1) LOOP can prove its sensitive outlier-recognition by its statistical correlation to an exceptional better goodness-of-fit as outliers being left-out. (2) With sufficient statistical information, the LOOP can correct outliers under some low-sampling conditions that other “robust fits”, e.g. Least Absolute Residuals, cannot. (3) Complete cross-validated analyses of LOOP indicate that the function of rational type demonstrates a much superior performance compared to the polynomial. Even with 5 data points including one outlier, using LOOP with rational function can restore more than a 95% value back to its reference values, while the polynomial fitting completely failed under the same conditions. Conclusion: LOOP can cooperate with any fitting routine functioning as a “robust fit”. In addition, it can be set as a benchmark for film-dose calibration fitting performance.« less

Conical twist fields and null polygonal Wilson loops

NASA Astrophysics Data System (ADS)

Castro-Alvaredo, Olalla A.; Doyon, Benjamin; Fioravanti, Davide

2018-06-01

Using an extension of the concept of twist field in QFT to space-time (external) symmetries, we study conical twist fields in two-dimensional integrable QFT. These create conical singularities of arbitrary excess angle. We show that, upon appropriate identification between the excess angle and the number of sheets, they have the same conformal dimension as branch-point twist fields commonly used to represent partition functions on Riemann surfaces, and that both fields have closely related form factors. However, we show that conical twist fields are truly different from branch-point twist fields. They generate different operator product expansions (short distance expansions) and form factor expansions (large distance expansions). In fact, we verify in free field theories, by re-summing form factors, that the conical twist fields operator product expansions are correctly reproduced. We propose that conical twist fields are the correct fields in order to understand null polygonal Wilson loops/gluon scattering amplitudes of planar maximally supersymmetric Yang-Mills theory.

Kinetic energy partition method applied to ground state helium-like atoms.

PubMed

Chen, Yu-Hsin; Chao, Sheng D

2017-03-28

We have used the recently developed kinetic energy partition (KEP) method to solve the quantum eigenvalue problems for helium-like atoms and obtain precise ground state energies and wave-functions. The key to treating properly the electron-electron (repulsive) Coulomb potential energies for the KEP method to be applied is to introduce a "negative mass" term into the partitioned kinetic energy. A Hartree-like product wave-function from the subsystem wave-functions is used to form the initial trial function, and the variational search for the optimized adiabatic parameters leads to a precise ground state energy. This new approach sheds new light on the all-important problem of solving many-electron Schrödinger equations and hopefully opens a new way to predictive quantum chemistry. The results presented here give very promising evidence that an effective one-electron model can be used to represent a many-electron system, in the spirit of density functional theory.

Diagrammatic expansion for positive density-response spectra: Application to the electron gas

NASA Astrophysics Data System (ADS)

Uimonen, A.-M.; Stefanucci, G.; Pavlyukh, Y.; van Leeuwen, R.

2015-03-01

In a recent paper [Phys. Rev. B 90, 115134 (2014), 10.1103/PhysRevB.90.115134] we put forward a diagrammatic expansion for the self-energy which guarantees the positivity of the spectral function. In this work we extend the theory to the density-response function. We write the generic diagram for the density-response spectrum as the sum of "partitions." In a partition the original diagram is evaluated using time-ordered Green's functions on the left half of the diagram, antitime-ordered Green's functions on the right half of the diagram, and lesser or greater Green's function gluing the two halves. As there exists more than one way to cut a diagram in two halves, to every diagram corresponds more than one partition. We recognize that the most convenient diagrammatic objects for constructing a theory of positive spectra are the half-diagrams. Diagrammatic approximations obtained by summing the squares of half-diagrams do indeed correspond to a combination of partitions which, by construction, yield a positive spectrum. We develop the theory using bare Green's functions and subsequently extend it to dressed Green's functions. We further prove a connection between the positivity of the spectral function and the analytic properties of the polarizability. The general theory is illustrated with several examples and then applied to solve the long-standing problem of including vertex corrections without altering the positivity of the spectrum. In fact already the first-order vertex diagram, relevant to the study of gradient expansion, Friedel oscillations, etc., leads to spectra which are negative in certain frequency domain. We find that the simplest approximation to cure this deficiency is given by the sum of the zeroth-order bubble diagram, the first-order vertex diagram, and a partition of the second-order ladder diagram. We evaluate this approximation in the three-dimensional homogeneous electron gas and show the positivity of the spectrum for all frequencies and densities.

Aspects of hot Galilean field theory

NASA Astrophysics Data System (ADS)

Jensen, Kristan

2015-04-01

We reconsider general aspects of Galilean-invariant thermal field theory. Using the proposal of our companion paper, we recast non-relativistic hydrodynamics in a manifestly covariant way and couple it to a background spacetime. We examine the concomitant consequences for the thermal partition functions of Galilean theories on a time-independent, but weakly curved background. We work out both the hydrodynamics and partition functions in detail for the example of parity-violating normal fluids in two dimensions to first order in the gradient expansion, finding results that differ from those previously reported in the literature. As for relativistic field theories, the equality-type constraints imposed by the existence of an entropy current appear to be in one-to-one correspondence with those arising from the existence of a hydrostatic partition function. Along the way, we obtain a number of useful results about non-relativistic hydrodynamics, including a manifestly boost-invariant presentation thereof, simplified Ward identities, the systematics of redefinitions of the fluid variables, and the positivity of entropy production.

Instantons on ALE spaces and orbifold partitions

NASA Astrophysics Data System (ADS)

Dijkgraaf, Robbert; Sułkowski, Piotr

2008-03-01

We consider Script N = 4 theories on ALE spaces of Ak-1 type. As is well known, their partition functions coincide with Ak-1 affine characters. We show that these partition functions are equal to the generating functions of some peculiar classes of partitions which we introduce under the name 'orbifold partitions'. These orbifold partitions turn out to be related to the generalized Frobenius partitions introduced by G. E. Andrews some years ago. We relate the orbifold partitions to the blended partitions and interpret explicitly in terms of a free fermion system.

One-loop effects of a heavy Higgs boson: A functional approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dittmaier, S.; Grosse-Knetter, C.

1995-11-01

We integrate out the Higgs boson in the electroweak standard model at one loop, assuming that it is very heavy. We construct a low-energy effective Lagrangian, which parametrizes the one-loop effect of the heavy Higgs boson at {O}({ital M}{sup O}{sup -}{sub {ital H}}). Instead of applying conventional diagrammatical techniques, we integrate out the Higgs boson directly in the path integral. {copyright} 1995 American Institute of Physics

Holographic calculation for large interval Rényi entropy at high temperature

NASA Astrophysics Data System (ADS)

Chen, Bin; Wu, Jie-qiang

2015-11-01

In this paper, we study the holographic Rényi entropy of a large interval on a circle at high temperature for the two-dimensional conformal field theory (CFT) dual to pure AdS3 gravity. In the field theory, the Rényi entropy is encoded in the CFT partition function on n -sheeted torus connected with each other by a large branch cut. As proposed by Chen and Wu [Large interval limit of Rényi entropy at high temperature, arXiv:1412.0763], the effective way to read the entropy in the large interval limit is to insert a complete set of state bases of the twist sector at the branch cut. Then the calculation transforms into an expansion of four-point functions in the twist sector with respect to e-2/π T R n . By using the operator product expansion of the twist operators at the branch points, we read the first few terms of the Rényi entropy, including the leading and next-to-leading contributions in the large central charge limit. Moreover, we show that the leading contribution is actually captured by the twist vacuum module. In this case by the Ward identity the four-point functions can be derived from the correlation function of four twist operators, which is related to double interval entanglement entropy. Holographically, we apply the recipe in [T. Faulkner, The entanglement Rényi entropies of disjoint intervals in AdS/CFT, arXiv:1303.7221] and [T. Barrella et al., Holographic entanglement beyond classical gravity, J. High Energy Phys. 09 (2013) 109] to compute the classical Rényi entropy and its one-loop quantum correction, after imposing a new set of monodromy conditions. The holographic classical result matches exactly with the leading contribution in the field theory up to e-4 π T R and l6, while the holographical one-loop contribution is in exact agreement with next-to-leading results in field theory up to e-6/π T R n and l4 as well.

Closed-loop, pilot/vehicle analysis of the approach and landing task

NASA Technical Reports Server (NTRS)

Anderson, M. R.; Schmidt, D. K.

1986-01-01

In the case of approach and landing, it is universally accepted that the pilot uses more than one vehicle response, or output, to close his control loops. Therefore, to model this task, a multi-loop analysis technique is required. The analysis problem has been in obtaining reasonable analytic estimates of the describing functions representing the pilot's loop compensation. Once these pilot describing functions are obtained, appropriate performance and workload metrics must then be developed for the landing task. The optimal control approach provides a powerful technique for obtaining the necessary describing functions, once the appropriate task objective is defined in terms of a quadratic objective function. An approach is presented through the use of a simple, reasonable objective function and model-based metrics to evaluate loop performance and pilot workload. The results of an analysis of the LAHOS (Landing and Approach of Higher Order Systems) study performed by R.E. Smith is also presented.

Discrete wavelet approach to multifractality

NASA Astrophysics Data System (ADS)

Isaacson, Susana I.; Gabbanelli, Susana C.; Busch, Jorge R.

2000-12-01

The use of wavelet techniques for the multifractal analysis generalizes the box counting approach, and in addition provides information on eventual deviations of multifractal behavior. By the introduction of a wavelet partition function Wq and its corresponding free energy (beta) (q), the discrepancies between (beta) (q) and the multifractal free energy r(q) are shown to be indicative of these deviations. We study with Daubechies wavelets (D4) some 1D examples previously treated with Haar wavelets, and we apply the same ideas to some 2D Monte Carlo configurations, that simulate a solution under the action of an attractive potential. In this last case, we study the influence in the multifractal spectra and partition functions of four physical parameters: the intensity of the pairwise potential, the temperature, the range of the model potential, and the concentration of the solution. The wavelet partition function Wq carries more information about the cluster statistics than the multifractal partition function Zq, and the location of its peaks contributes to the determination of characteristic sales of the measure. In our experiences, the information provided by Daubechies wavelet sis slightly more accurate than the one obtained by Haar wavelets.

Improving predicted protein loop structure ranking using a Pareto-optimality consensus method.

PubMed

Li, Yaohang; Rata, Ionel; Chiu, See-wing; Jakobsson, Eric

2010-07-20

Accurate protein loop structure models are important to understand functions of many proteins. Identifying the native or near-native models by distinguishing them from the misfolded ones is a critical step in protein loop structure prediction. We have developed a Pareto Optimal Consensus (POC) method, which is a consensus model ranking approach to integrate multiple knowledge- or physics-based scoring functions. The procedure of identifying the models of best quality in a model set includes: 1) identifying the models at the Pareto optimal front with respect to a set of scoring functions, and 2) ranking them based on the fuzzy dominance relationship to the rest of the models. We apply the POC method to a large number of decoy sets for loops of 4- to 12-residue in length using a functional space composed of several carefully-selected scoring functions: Rosetta, DOPE, DDFIRE, OPLS-AA, and a triplet backbone dihedral potential developed in our lab. Our computational results show that the sets of Pareto-optimal decoys, which are typically composed of approximately 20% or less of the overall decoys in a set, have a good coverage of the best or near-best decoys in more than 99% of the loop targets. Compared to the individual scoring function yielding best selection accuracy in the decoy sets, the POC method yields 23%, 37%, and 64% less false positives in distinguishing the native conformation, indentifying a near-native model (RMSD < 0.5A from the native) as top-ranked, and selecting at least one near-native model in the top-5-ranked models, respectively. Similar effectiveness of the POC method is also found in the decoy sets from membrane protein loops. Furthermore, the POC method outperforms the other popularly-used consensus strategies in model ranking, such as rank-by-number, rank-by-rank, rank-by-vote, and regression-based methods. By integrating multiple knowledge- and physics-based scoring functions based on Pareto optimality and fuzzy dominance, the POC method is effective in distinguishing the best loop models from the other ones within a loop model set.

Improving predicted protein loop structure ranking using a Pareto-optimality consensus method

PubMed Central

2010-01-01

Background Accurate protein loop structure models are important to understand functions of many proteins. Identifying the native or near-native models by distinguishing them from the misfolded ones is a critical step in protein loop structure prediction. Results We have developed a Pareto Optimal Consensus (POC) method, which is a consensus model ranking approach to integrate multiple knowledge- or physics-based scoring functions. The procedure of identifying the models of best quality in a model set includes: 1) identifying the models at the Pareto optimal front with respect to a set of scoring functions, and 2) ranking them based on the fuzzy dominance relationship to the rest of the models. We apply the POC method to a large number of decoy sets for loops of 4- to 12-residue in length using a functional space composed of several carefully-selected scoring functions: Rosetta, DOPE, DDFIRE, OPLS-AA, and a triplet backbone dihedral potential developed in our lab. Our computational results show that the sets of Pareto-optimal decoys, which are typically composed of ~20% or less of the overall decoys in a set, have a good coverage of the best or near-best decoys in more than 99% of the loop targets. Compared to the individual scoring function yielding best selection accuracy in the decoy sets, the POC method yields 23%, 37%, and 64% less false positives in distinguishing the native conformation, indentifying a near-native model (RMSD < 0.5A from the native) as top-ranked, and selecting at least one near-native model in the top-5-ranked models, respectively. Similar effectiveness of the POC method is also found in the decoy sets from membrane protein loops. Furthermore, the POC method outperforms the other popularly-used consensus strategies in model ranking, such as rank-by-number, rank-by-rank, rank-by-vote, and regression-based methods. Conclusions By integrating multiple knowledge- and physics-based scoring functions based on Pareto optimality and fuzzy dominance, the POC method is effective in distinguishing the best loop models from the other ones within a loop model set. PMID:20642859

Poisson equation for the three-loop ladder diagram in string theory at genus one

NASA Astrophysics Data System (ADS)

Basu, Anirban

2016-11-01

The three-loop ladder diagram is a graph with six links and four cubic vertices that contributes to the D12ℛ4 amplitude at genus one in type II string theory. The vertices represent the insertion points of vertex operators on the toroidal worldsheet and the links represent scalar Green functions connecting them. By using the properties of the Green function and manipulating the various expressions, we obtain a modular invariant Poisson equation satisfied by this diagram, with source terms involving one-, two- and three-loop diagrams. Unlike the source terms in the Poisson equations for diagrams at lower orders in the momentum expansion or the Mercedes diagram, a particular source term involves a five-point function containing a holomorphic and a antiholomorphic worldsheet derivative acting on different Green functions. We also obtain simple equalities between topologically distinct diagrams, and consider some elementary examples.

Pinch technique and the Batalin-Vilkovisky formalism

NASA Astrophysics Data System (ADS)

Binosi, Daniele; Papavassiliou, Joannis

2002-07-01

In this paper we take the first step towards a nondiagrammatic formulation of the pinch technique. In particular we proceed into a systematic identification of the parts of the one-loop and two-loop Feynman diagrams that are exchanged during the pinching process in terms of unphysical ghost Green's functions; the latter appear in the standard Slavnov-Taylor identity satisfied by the tree-level and one-loop three-gluon vertex. This identification allows for the consistent generalization of the intrinsic pinch technique to two loops, through the collective treatment of entire sets of diagrams, instead of the laborious algebraic manipulation of individual graphs, and sets up the stage for the generalization of the method to all orders. We show that the task of comparing the effective Green's functions obtained by the pinch technique with those computed in the background field method Feynman gauge is significantly facilitated when employing the powerful quantization framework of Batalin and Vilkovisky. This formalism allows for the derivation of a set of useful nonlinear identities, which express the background field method Green's functions in terms of the conventional (quantum) ones and auxiliary Green's functions involving the background source and the gluonic antifield; these latter Green's functions are subsequently related by means of a Schwinger-Dyson type of equation to the ghost Green's functions appearing in the aforementioned Slavnov-Taylor identity.

A small modified hammerhead ribozyme and its conformational characteristics determined by mutagenesis and lattice calculation.

PubMed Central

Lustig, B; Lin, N H; Smith, S M; Jernigan, R L; Jeang, K T

1995-01-01

A prototypic hammerhead ribozyme has three helices that surround an asymmetrical central core loop. We have mutagenized a hammerhead type ribozyme. In agreement with previous studies, progressive removal of stem-loop II from a three stemmed ribozyme showed that this region is not absolutely critical for catalysis. However, complete elimination of stem II and its loop did reduce, but did not eliminate, function. In a stem-loop II-deleted ribozyme, activity was best preserved when a purine, preferably a G, was present at position 10.1. This G contributed to catalysis irregardless of its role as either one part of a canonical pair with a C residue at 11.1 or a lone nucleotide with C (11.1) deleted. Computational methods using lattices generated 87 million three-dimensional chain forms for a stem-loop II-deleted RNA complex that preserved one potential G.C base pair at positions 10.1 and 11.1. This exhaustive set of chain forms included one major class of structures with G(10.1) being spatially proximal to the GUCX cleavage site of the substrate strand. Strong correlations were observed between colinear arrangement of stems I and III, constraints of base-pairing in the central core loop, and one particular placement of G(10.1) relative to the cleavage site. Our calculations of a stem-loop II-deleted ribozyme indicate that without needing to invoke any other constraints, the inherent asymmetry in the lengths of the two loop strands (3 nt in one and 7 nt in the other) that compose the core and flank G10.1-C11.1 stipulated strongly this particular G placement. This suggests that the hammerhead ribozyme maintains an asymmetry in its internal loop for a necessary structure/function reason. Images PMID:7567466

An efficient sampling approach for variance-based sensitivity analysis based on the law of total variance in the successive intervals without overlapping

NASA Astrophysics Data System (ADS)

Yun, Wanying; Lu, Zhenzhou; Jiang, Xian

2018-06-01

To efficiently execute the variance-based global sensitivity analysis, the law of total variance in the successive intervals without overlapping is proved at first, on which an efficient space-partition sampling-based approach is subsequently proposed in this paper. Through partitioning the sample points of output into different subsets according to different inputs, the proposed approach can efficiently evaluate all the main effects concurrently by one group of sample points. In addition, there is no need for optimizing the partition scheme in the proposed approach. The maximum length of subintervals is decreased by increasing the number of sample points of model input variables in the proposed approach, which guarantees the convergence condition of the space-partition approach well. Furthermore, a new interpretation on the thought of partition is illuminated from the perspective of the variance ratio function. Finally, three test examples and one engineering application are employed to demonstrate the accuracy, efficiency and robustness of the proposed approach.

Conformal partition functions of critical percolation from D 3 thermodynamic Bethe Ansatz equations

NASA Astrophysics Data System (ADS)

Morin-Duchesne, Alexi; Klümper, Andreas; Pearce, Paul A.

2017-08-01

Using the planar Temperley-Lieb algebra, critical bond percolation on the square lattice can be reformulated as a loop model. In this form, it is incorporated as {{ L}}{{ M}}(2, 3) in the Yang-Baxter integrable family of logarithmic minimal models {{ L}}{{ M}}( p, p\\prime) . We consider this model of percolation in the presence of boundaries and with periodic boundary conditions. Inspired by Kuniba, Sakai and Suzuki, we rewrite the recently obtained infinite Y-system of functional equations. In this way, we obtain nonlinear integral equations in the form of a closed finite set of TBA equations described by a D 3 Dynkin diagram. Following the methods of Klümper and Pearce, we solve the TBA equations for the conformal finite-size corrections. For the ground states of the standard modules on the strip, these agree with the known central charge c  =  0 and conformal weights Δ1, s for \\renewcommand≥≥slant} s\\in {{ Z}≥slant 1} with Δr, s=\\big((3r-2s){\\hspace{0pt}}^2-1\\big)/24 . For the periodic case, the finite-size corrections agree with the conformal weights Δ0, s , Δ1, s with \\renewcommand{≥{≥slant} s\\in\\frac{1}{2}{{ Z}≥slant 0} . These are obtained analytically using Rogers dilogarithm identities. We incorporate all finite excitations by formulating empirical selection rules for the patterns of zeros of all the eigenvalues of the standard modules. We thus obtain the conformal partition functions on the cylinder and the modular invariant partition function (MIPF) on the torus. By applying q-binomial and q-Narayana identities, it is shown that our refined finitized characters on the strip agree with those of Pearce, Rasmussen and Zuber. For percolation on the torus, the MIPF is a non-diagonal sesquilinear form in affine u(1) characters given by the u(1) partition function Z2, 3(q)=Z2, 3{Circ}(q) . The u(1) operator content is {{ N}}Δ, \\barΔ=1 for Δ=\\barΔ=-\\frac{1}{24}, \\frac{35}{24} and {{ N}}Δ, \\barΔ=2 for Δ=\\barΔ=\\frac{1}{8}, \\frac{1}{3}, \\frac{5}{8} and (Δ, \\barΔ)=(0, 1), (1, 0) . This result is compatible with the general conjecture of Pearce and Rasmussen, namely Zp, p\\prime(q)=Z{Proj}p, p\\prime(q)+np, p\\prime Z{Min}p, p\\prime(q) with np, p\\prime\\in {{ Z}} , where the minimal partition function is Z{Min}2, 3(q)=1 and the lattice derivation fixes n 2,3  =  -1.

S-HARP: A parallel dynamic spectral partitioner

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sohn, A.; Simon, H.

1998-01-01

Computational science problems with adaptive meshes involve dynamic load balancing when implemented on parallel machines. This dynamic load balancing requires fast partitioning of computational meshes at run time. The authors present in this report a fast parallel dynamic partitioner, called S-HARP. The underlying principles of S-HARP are the fast feature of inertial partitioning and the quality feature of spectral partitioning. S-HARP partitions a graph from scratch, requiring no partition information from previous iterations. Two types of parallelism have been exploited in S-HARP, fine grain loop level parallelism and coarse grain recursive parallelism. The parallel partitioner has been implemented in Messagemore » Passing Interface on Cray T3E and IBM SP2 for portability. Experimental results indicate that S-HARP can partition a mesh of over 100,000 vertices into 256 partitions in 0.2 seconds on a 64 processor Cray T3E. S-HARP is much more scalable than other dynamic partitioners, giving over 15 fold speedup on 64 processors while ParaMeTiS1.0 gives a few fold speedup. Experimental results demonstrate that S-HARP is three to 10 times faster than the dynamic partitioners ParaMeTiS and Jostle on six computational meshes of size over 100,000 vertices.« less

An iterative network partition algorithm for accurate identification of dense network modules

PubMed Central

Sun, Siqi; Dong, Xinran; Fu, Yao; Tian, Weidong

2012-01-01

A key step in network analysis is to partition a complex network into dense modules. Currently, modularity is one of the most popular benefit functions used to partition network modules. However, recent studies suggested that it has an inherent limitation in detecting dense network modules. In this study, we observed that despite the limitation, modularity has the advantage of preserving the primary network structure of the undetected modules. Thus, we have developed a simple iterative Network Partition (iNP) algorithm to partition a network. The iNP algorithm provides a general framework in which any modularity-based algorithm can be implemented in the network partition step. Here, we tested iNP with three modularity-based algorithms: multi-step greedy (MSG), spectral clustering and Qcut. Compared with the original three methods, iNP achieved a significant improvement in the quality of network partition in a benchmark study with simulated networks, identified more modules with significantly better enrichment of functionally related genes in both yeast protein complex network and breast cancer gene co-expression network, and discovered more cancer-specific modules in the cancer gene co-expression network. As such, iNP should have a broad application as a general method to assist in the analysis of biological networks. PMID:22121225

α1-Antitrypsin Portland, a bioengineered serpin highly selective for furin: Application as an antipathogenic agent

PubMed Central

Jean, François; Stella, Kori; Thomas, Laurel; Liu, Gseping; Xiang, Yang; Reason, Andrew J.; Thomas, Gary

1998-01-01

The important role of furin in the proteolytic activation of many pathogenic molecules has made this endoprotease a target for the development of potent and selective antiproteolytic agents. Here, we demonstrate the utility of the protein-based inhibitor α1-antitrypsin Portland (α1-PDX) as an antipathogenic agent that can be used prophylactically to block furin-dependent cell killing by Pseudomonas exotoxin A. Biochemical analysis of the specificity of a bacterially expressed His- and FLAG-tagged α1-PDX (α1-PDX/hf) revealed the selectivity of the α1-PDX/hf reactive site loop for furin (Ki, 600 pM) but not for other proprotein convertase family members or other unrelated endoproteases. Kinetic studies show that α1-PDX/hf inhibits furin by a slow tight-binding mechanism characteristic of serpin molecules and functions as a suicide substrate inhibitor. Once bound to furin’s active site, α1-PDX/hf partitions with equal probability to undergo proteolysis by furin at the C-terminal side of the reactive center -Arg355-Ile-Pro-Arg358-↓ or to form a kinetically trapped SDS-stable complex with the enzyme. This partitioning between the complex-forming and proteolytic pathways contributes to the ability of α1-PDX/hf to differentially inhibit members of the proprotein convertase family. Finally, we propose a structural model of the α1-PDX-reactive site loop that explains the high degree of enzyme selectivity of this serpin and which can be used to generate small molecule furin inhibitors. PMID:9636142

Anharmonic effects in the quantum cluster equilibrium method

NASA Astrophysics Data System (ADS)

von Domaros, Michael; Perlt, Eva

2017-03-01

The well-established quantum cluster equilibrium (QCE) model provides a statistical thermodynamic framework to apply high-level ab initio calculations of finite cluster structures to macroscopic liquid phases using the partition function. So far, the harmonic approximation has been applied throughout the calculations. In this article, we apply an important correction in the evaluation of the one-particle partition function and account for anharmonicity. Therefore, we implemented an analytical approximation to the Morse partition function and the derivatives of its logarithm with respect to temperature, which are required for the evaluation of thermodynamic quantities. This anharmonic QCE approach has been applied to liquid hydrogen chloride and cluster distributions, and the molar volume, the volumetric thermal expansion coefficient, and the isobaric heat capacity have been calculated. An improved description for all properties is observed if anharmonic effects are considered.

Universality, twisted fans, and the Ising model. [Renormalization, two-loop calculations, scale

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dash, J.W.; Harrington, S.J.

1975-06-24

Critical exponents are evaluated for the Ising model using universality in the form of ''twisted fans'' previously introduced in Reggeon field theory. The universality is with respect to scales induced through renormalization. Exact twists are obtained at ..beta.. = 0 in one loop for D = 2,3 with ..nu.. = 0.75 and 0.60 respectively. In two loops one obtains ..nu.. approximately 1.32 and 0.68. No twists are obtained for eta, however. The results for the standard two loop calculations are also presented as functions of a scale.

A Meinardus Theorem with Multiple Singularities

NASA Astrophysics Data System (ADS)

Granovsky, Boris L.; Stark, Dudley

2012-09-01

Meinardus proved a general theorem about the asymptotics of the number of weighted partitions, when the Dirichlet generating function for weights has a single pole on the positive real axis. Continuing (Granovsky et al., Adv. Appl. Math. 41:307-328, 2008), we derive asymptotics for the numbers of three basic types of decomposable combinatorial structures (or, equivalently, ideal gas models in statistical mechanics) of size n, when their Dirichlet generating functions have multiple simple poles on the positive real axis. Examples to which our theorem applies include ones related to vector partitions and quantum field theory. Our asymptotic formula for the number of weighted partitions disproves the belief accepted in the physics literature that the main term in the asymptotics is determined by the rightmost pole.

From r-spin intersection numbers to Hodge integrals

NASA Astrophysics Data System (ADS)

Ding, Xiang-Mao; Li, Yuping; Meng, Lingxian

2016-01-01

Generalized Kontsevich Matrix Model (GKMM) with a certain given potential is the partition function of r-spin intersection numbers. We represent this GKMM in terms of fermions and expand it in terms of the Schur polynomials by boson-fermion correspondence, and link it with a Hurwitz partition function and a Hodge partition by operators in a widehat{GL}(∞) group. Then, from a W 1+∞ constraint of the partition function of r-spin intersection numbers, we get a W 1+∞ constraint for the Hodge partition function. The W 1+∞ constraint completely determines the Schur polynomials expansion of the Hodge partition function.

Bypassing Evolutionary Roadblocks: Phenotypic Diversity in Isogenic Population Bridges Tradeoff in Evolution of a New Function

NASA Astrophysics Data System (ADS)

Petrie, K. L.; Meyer, J. R.

2017-07-01

A novel mechanism of innovation bridges fitness valleys by violating the one gene-one phenotype dogma. Protein products of a single gene partition into populations, some of which carry out a new function and some the old, avoiding tradeoffs.

Witten index for noncompact dynamics

NASA Astrophysics Data System (ADS)

Lee, Seung-Joo; Yi, Piljin

2016-06-01

Among gauged dynamics motivated by string theory, we find many with gapless asymptotic directions. Although the natural boundary condition for ground states is L 2, one often turns on chemical potentials or supersymmetric mass terms to regulate the infrared issues, instead, and computes the twisted partition function. We point out how this procedure generically fails to capture physical L 2 Witten index with often misleading results. We also explore how, nevertheless, the Witten index is sometimes intricately embedded in such twisted partition functions. For d = 1 theories with gapless continuum sector from gauge multiplets, such as non-primitive quivers and pure Yang-Mills, a further subtlety exists, leading to fractional expressions. Quite unexpectedly, however, the integral L 2 Witten index can be extracted directly and easily from the twisted partition function of such theories. This phenomenon is tied to the notion of the rational invariant that appears naturally in the wall-crossing formulae, and offers a general mechanism of reading off Witten index directly from the twisted partition function. Along the way, we correct early numerical results for some of mathcal{N} = 4 , 8 , 16 pure Yang-Mills quantum mechanics, and count threshold bound states for general gauge groups beyond SU( N ).

Bounds for the Eventual Positivity of Difference Functions of Partitions

NASA Astrophysics Data System (ADS)

Woodford, Roger

2007-01-01

In this paper we specialize work done by Bateman and Erdos concerning difference functions of partition functions. In particular, we are concerned with partitions into fixed powers of the primes. We show that any difference function of these partition functions is eventually increasing, and derive explicit bounds for when it will attain strictly positive values. From these bounds an asymptotic result is derived.

Parameter estimation in a human operator describing function model for a two-dimensional tracking task

NASA Technical Reports Server (NTRS)

Vanlunteren, A.

1977-01-01

A previously described parameter estimation program was applied to a number of control tasks, each involving a human operator model consisting of more than one describing function. One of these experiments is treated in more detail. It consisted of a two dimensional tracking task with identical controlled elements. The tracking errors were presented on one display as two vertically moving horizontal lines. Each loop had its own manipulator. The two forcing functions were mutually independent and consisted each of 9 sine waves. A human operator model was chosen consisting of 4 describing functions, thus taking into account possible linear cross couplings. From the Fourier coefficients of the relevant signals the model parameters were estimated after alignment, averaging over a number of runs and decoupling. The results show that for the elements in the main loops the crossover model applies. A weak linear cross coupling existed with the same dynamics as the elements in the main loops but with a negative sign.

One-loop corrections to light cone wave functions: The dipole picture DIS cross section

NASA Astrophysics Data System (ADS)

Hänninen, H.; Lappi, T.; Paatelainen, R.

2018-06-01

We develop methods to perform loop calculations in light cone perturbation theory using a helicity basis, refining the method introduced in our earlier work. In particular this includes implementing a consistent way to contract the four-dimensional tensor structures from the helicity vectors with d-dimensional tensors arising from loop integrals, in a way that can be fully automatized. We demonstrate this explicitly by calculating the one-loop correction to the virtual photon to quark-antiquark dipole light cone wave function. This allows us to calculate the deep inelastic scattering cross section in the dipole formalism to next-to-leading order accuracy. Our results, obtained using the four dimensional helicity scheme, agree with the recent calculation by Beuf using conventional dimensional regularization, confirming the regularization scheme independence of this cross section.

Effects of two-loop contributions in the pseudofermion functional renormalization group method for quantum spin systems

NASA Astrophysics Data System (ADS)

Rück, Marlon; Reuther, Johannes

2018-04-01

We implement an extension of the pseudofermion functional renormalization group method for quantum spin systems that takes into account two-loop diagrammatic contributions. An efficient numerical treatment of the additional terms is achieved within a nested graph construction which recombines different one-loop interaction channels. In order to be fully self-consistent with respect to self-energy corrections, we also include certain three-loop terms of Katanin type. We first apply this formalism to the antiferromagnetic J1-J2 Heisenberg model on the square lattice and benchmark our results against the previous one-loop plus Katanin approach. Even though the renormalization group (RG) equations undergo significant modifications when including the two-loop terms, the magnetic phase diagram, comprising Néel ordered and collinear ordered phases separated by a magnetically disordered regime, remains remarkably unchanged. Only the boundary position between the disordered and the collinear phases is found to be moderately affected by two-loop terms. On the other hand, critical RG scales, which we associate with critical temperatures Tc, are reduced by a factor of ˜2 indicating that the two-loop diagrams play a significant role in enforcing the Mermin-Wagner theorem. Improved estimates for critical temperatures are also obtained for the Heisenberg ferromagnet on the three-dimensional simple cubic lattice where errors in Tc are reduced by ˜34 % . These findings have important implications for the quantum phase diagrams calculated within the previous one-loop plus Katanin approach which turn out to be already well converged.

Partitioned key-value store with atomic memory operations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bent, John M.; Faibish, Sorin; Grider, Gary

A partitioned key-value store is provided that supports atomic memory operations. A server performs a memory operation in a partitioned key-value store by receiving a request from an application for at least one atomic memory operation, the atomic memory operation comprising a memory address identifier; and, in response to the atomic memory operation, performing one or more of (i) reading a client-side memory location identified by the memory address identifier and storing one or more key-value pairs from the client-side memory location in a local key-value store of the server; and (ii) obtaining one or more key-value pairs from themore » local key-value store of the server and writing the obtained one or more key-value pairs into the client-side memory location identified by the memory address identifier. The server can perform functions obtained from a client-side memory location and return a result to the client using one or more of the atomic memory operations.« less

Confinement and Mayer cluster expansions

NASA Astrophysics Data System (ADS)

Bourgine, Jean-Emile

2014-05-01

In this paper, we study a class of grand-canonical partition functions with a kernel depending on a small parameter ɛ. This class is directly relevant to Nekrasov partition functions of 𝒩 = 2 SUSY gauge theories on the 4d Ω-background, for which ɛ is identified with one of the equivariant deformation parameter. In the Nekrasov-Shatashvili limit ɛ→0, we show that the free energy is given by an on-shell effective action. The equations of motion take the form of a TBA equation. The free energy is identified with the Yang-Yang functional of the corresponding system of Bethe roots. We further study the associated canonical model that takes the form of a generalized matrix model. Confinement of the eigenvalues by the short-range potential is observed. In the limit where this confining potential becomes weak, the collective field theory formulation is recovered. Finally, we discuss the connection with the alternative expression of instanton partition functions as sums over Young tableaux.

Interaction-induced partitioning and magnetization jumps in the mixed-spin oxide FeTiO3-Fe2O3.

PubMed

Charilaou, M; Sahu, K K; Zhao, S; Löffler, J F; Gehring, A U

2011-07-29

In this study we report on jumps in the magnetic moment of the hemo-ilmenite solid solution (x)FeTiO(3)-(1-x)Fe(2)O(3) above Fe(III) percolation at low temperature (T<3 K). The first jumps appear at 2.5 K, one at each side of the magnetization loop, and their number increases with decreasing temperature and reaches 5 at T=0.5 K. The jumps occur after field reversal from a saturated state and are symmetrical in the trigger field and intensity with respect to the field axis. Moreover, an increase of the sample temperature by 2.8% at T=2.0 K indicates the energy released after the ignition of the magnetization jump, as the spin-currents generated by the event are dissipated in the lattice. The magnetization jumps are further investigated by Monte Carlo simulations, which show that these effects are a result of magnetic interaction-induced partitioning on a sublattice level. © 2011 American Physical Society

P-HARP: A parallel dynamic spectral partitioner

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sohn, A.; Biswas, R.; Simon, H.D.

1997-05-01

Partitioning unstructured graphs is central to the parallel solution of problems in computational science and engineering. The authors have introduced earlier the sequential version of an inertial spectral partitioner called HARP which maintains the quality of recursive spectral bisection (RSB) while forming the partitions an order of magnitude faster than RSB. The serial HARP is known to be the fastest spectral partitioner to date, three to four times faster than similar partitioners on a variety of meshes. This paper presents a parallel version of HARP, called P-HARP. Two types of parallelism have been exploited: loop level parallelism and recursive parallelism.more » P-HARP has been implemented in MPI on the SGI/Cray T3E and the IBM SP2. Experimental results demonstrate that P-HARP can partition a mesh of over 100,000 vertices into 256 partitions in 0.25 seconds on a 64-processor T3E. Experimental results further show that P-HARP can give nearly a 20-fold speedup on 64 processors. These results indicate that graph partitioning is no longer a major bottleneck that hinders the advancement of computational science and engineering for dynamically-changing real-world applications.« less

Implementation of spectral clustering with partitioning around medoids (PAM) algorithm on microarray data of carcinoma

NASA Astrophysics Data System (ADS)

Cahyaningrum, Rosalia D.; Bustamam, Alhadi; Siswantining, Titin

2017-03-01

Technology of microarray became one of the imperative tools in life science to observe the gene expression levels, one of which is the expression of the genes of people with carcinoma. Carcinoma is a cancer that forms in the epithelial tissue. These data can be analyzed such as the identification expressions hereditary gene and also build classifications that can be used to improve diagnosis of carcinoma. Microarray data usually served in large dimension that most methods require large computing time to do the grouping. Therefore, this study uses spectral clustering method which allows to work with any object for reduces dimension. Spectral clustering method is a method based on spectral decomposition of the matrix which is represented in the form of a graph. After the data dimensions are reduced, then the data are partitioned. One of the famous partition method is Partitioning Around Medoids (PAM) which is minimize the objective function with exchanges all the non-medoid points into medoid point iteratively until converge. Objectivity of this research is to implement methods spectral clustering and partitioning algorithm PAM to obtain groups of 7457 genes with carcinoma based on the similarity value. The result in this study is two groups of genes with carcinoma.

Determinant representation of the domain-wall boundary condition partition function of a Richardson-Gaudin model containing one arbitrary spin

NASA Astrophysics Data System (ADS)

Faribault, Alexandre; Tschirhart, Hugo; Muller, Nicolas

2016-05-01

In this work we present a determinant expression for the domain-wall boundary condition partition function of rational (XXX) Richardson-Gaudin models which, in addition to N-1 spins \\frac{1}{2}, contains one arbitrarily large spin S. The proposed determinant representation is written in terms of a set of variables which, from previous work, are known to define eigenstates of the quantum integrable models belonging to this class as solutions to quadratic Bethe equations. Such a determinant can be useful numerically since systems of quadratic equations are much simpler to solve than the usual highly nonlinear Bethe equations. It can therefore offer significant gains in stability and computation speed.

Partitioning in Avionics Architectures: Requirements, Mechanisms, and Assurance

NASA Technical Reports Server (NTRS)

Rushby, John

1999-01-01

Automated aircraft control has traditionally been divided into distinct "functions" that are implemented separately (e.g., autopilot, autothrottle, flight management); each function has its own fault-tolerant computer system, and dependencies among different functions are generally limited to the exchange of sensor and control data. A by-product of this "federated" architecture is that faults are strongly contained within the computer system of the function where they occur and cannot readily propagate to affect the operation of other functions. More modern avionics architectures contemplate supporting multiple functions on a single, shared, fault-tolerant computer system where natural fault containment boundaries are less sharply defined. Partitioning uses appropriate hardware and software mechanisms to restore strong fault containment to such integrated architectures. This report examines the requirements for partitioning, mechanisms for their realization, and issues in providing assurance for partitioning. Because partitioning shares some concerns with computer security, security models are reviewed and compared with the concerns of partitioning.

Diagrammatic analysis of correlations in polymer fluids: Cluster diagrams via Edwards' field theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Morse, David C.

2006-10-15

Edwards' functional integral approach to the statistical mechanics of polymer liquids is amenable to a diagrammatic analysis in which free energies and correlation functions are expanded as infinite sums of Feynman diagrams. This analysis is shown to lead naturally to a perturbative cluster expansion that is closely related to the Mayer cluster expansion developed for molecular liquids by Chandler and co-workers. Expansion of the functional integral representation of the grand-canonical partition function yields a perturbation theory in which all quantities of interest are expressed as functionals of a monomer-monomer pair potential, as functionals of intramolecular correlation functions of non-interacting molecules,more » and as functions of molecular activities. In different variants of the theory, the pair potential may be either a bare or a screened potential. A series of topological reductions yields a renormalized diagrammatic expansion in which collective correlation functions are instead expressed diagrammatically as functionals of the true single-molecule correlation functions in the interacting fluid, and as functions of molecular number density. Similar renormalized expansions are also obtained for a collective Ornstein-Zernicke direct correlation function, and for intramolecular correlation functions. A concise discussion is given of the corresponding Mayer cluster expansion, and of the relationship between the Mayer and perturbative cluster expansions for liquids of flexible molecules. The application of the perturbative cluster expansion to coarse-grained models of dense multi-component polymer liquids is discussed, and a justification is given for the use of a loop expansion. As an example, the formalism is used to derive a new expression for the wave-number dependent direct correlation function and recover known expressions for the intramolecular two-point correlation function to first-order in a renormalized loop expansion for coarse-grained models of binary homopolymer blends and diblock copolymer melts.« less

Implementation of MPEG-2 encoder to multiprocessor system using multiple MVPs (TMS320C80)

NASA Astrophysics Data System (ADS)

Kim, HyungSun; Boo, Kenny; Chung, SeokWoo; Choi, Geon Y.; Lee, YongJin; Jeon, JaeHo; Park, Hyun Wook

1997-05-01

This paper presents the efficient algorithm mapping for the real-time MPEG-2 encoding on the KAIST image computing system (KICS), which has a parallel architecture using five multimedia video processors (MVPs). The MVP is a general purpose digital signal processor (DSP) of Texas Instrument. It combines one floating-point processor and four fixed- point DSPs on a single chip. The KICS uses the MVP as a primary processing element (PE). Two PEs form a cluster, and there are two processing clusters in the KICS. Real-time MPEG-2 encoder is implemented through the spatial and the functional partitioning strategies. Encoding process of spatially partitioned half of the video input frame is assigned to ne processing cluster. Two PEs perform the functionally partitioned MPEG-2 encoding tasks in the pipelined operation mode. One PE of a cluster carries out the transform coding part and the other performs the predictive coding part of the MPEG-2 encoding algorithm. One MVP among five MVPs is used for system control and interface with host computer. This paper introduces an implementation of the MPEG-2 algorithm with a parallel processing architecture.

FeynArts model file for MSSM transition counterterms from DREG to DRED

NASA Astrophysics Data System (ADS)

Stöckinger, Dominik; Varšo, Philipp

2012-02-01

The FeynArts model file MSSMdreg2dred implements MSSM transition counterterms which can convert one-loop Green functions from dimensional regularization to dimensional reduction. They correspond to a slight extension of the well-known Martin/Vaughn counterterms, specialized to the MSSM, and can serve also as supersymmetry-restoring counterterms. The paper provides full analytic results for the counterterms and gives one- and two-loop usage examples. The model file can simplify combining MS¯-parton distribution functions with supersymmetric renormalization or avoiding the renormalization of ɛ-scalars in dimensional reduction. Program summaryProgram title:MSSMdreg2dred.mod Catalogue identifier: AEKR_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEKR_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: LGPL-License [1] No. of lines in distributed program, including test data, etc.: 7600 No. of bytes in distributed program, including test data, etc.: 197 629 Distribution format: tar.gz Programming language: Mathematica, FeynArts Computer: Any, capable of running Mathematica and FeynArts Operating system: Any, with running Mathematica, FeynArts installation Classification: 4.4, 5, 11.1 Subprograms used: Cat Id Title Reference ADOW_v1_0 FeynArts CPC 140 (2001) 418 Nature of problem: The computation of one-loop Feynman diagrams in the minimal supersymmetric standard model (MSSM) requires regularization. Two schemes, dimensional regularization and dimensional reduction are both common but have different pros and cons. In order to combine the advantages of both schemes one would like to easily convert existing results from one scheme into the other. Solution method: Finite counterterms are constructed which correspond precisely to the one-loop scheme differences for the MSSM. They are provided as a FeynArts [2] model file. Using this model file together with FeynArts, the (ultra-violet) regularization of any MSSM one-loop Green function is switched automatically from dimensional regularization to dimensional reduction. In particular the counterterms serve as supersymmetry-restoring counterterms for dimensional regularization. Restrictions: The counterterms are restricted to the one-loop level and the MSSM. Running time: A few seconds to generate typical Feynman graphs with FeynArts.

Gluon and Wilson loop TMDs for hadrons of spin ≤ 1

NASA Astrophysics Data System (ADS)

Boer, Daniël; Cotogno, Sabrina; van Daal, Tom; Mulders, Piet J.; Signori, Andrea; Zhou, Ya-Jin

2016-10-01

In this paper we consider the parametrizations of gluon transverse momentum dependent (TMD) correlators in terms of TMD parton distribution functions (PDFs). These functions, referred to as TMDs, are defined as the Fourier transforms of hadronic matrix elements of nonlocal combinations of gluon fields. The nonlocality is bridged by gauge links, which have characteristic paths (future or past pointing), giving rise to a process dependence that breaks universality. For gluons, the specific correlator with one future and one past pointing gauge link is, in the limit of small x, related to a correlator of a single Wilson loop. We present the parametrization of Wilson loop correlators in terms of Wilson loop TMDs and discuss the relation between these functions and the small- x `dipole' gluon TMDs. This analysis shows which gluon TMDs are leading or suppressed in the small- x limit. We discuss hadronic targets that are unpolarized, vector polarized (relevant for spin-1 /2 and spin-1 hadrons), and tensor polarized (relevant for spin-1 hadrons). The latter are of interest for studies with a future Electron-Ion Collider with polarized deuterons.

Canonical partition functions: ideal quantum gases, interacting classical gases, and interacting quantum gases

NASA Astrophysics Data System (ADS)

Zhou, Chi-Chun; Dai, Wu-Sheng

2018-02-01

In statistical mechanics, for a system with a fixed number of particles, e.g. a finite-size system, strictly speaking, the thermodynamic quantity needs to be calculated in the canonical ensemble. Nevertheless, the calculation of the canonical partition function is difficult. In this paper, based on the mathematical theory of the symmetric function, we suggest a method for the calculation of the canonical partition function of ideal quantum gases, including ideal Bose, Fermi, and Gentile gases. Moreover, we express the canonical partition functions of interacting classical and quantum gases given by the classical and quantum cluster expansion methods in terms of the Bell polynomial in mathematics. The virial coefficients of ideal Bose, Fermi, and Gentile gases are calculated from the exact canonical partition function. The virial coefficients of interacting classical and quantum gases are calculated from the canonical partition function by using the expansion of the Bell polynomial, rather than calculated from the grand canonical potential.

Two-loop renormalization of the quark propagator in the light-cone gauge

NASA Astrophysics Data System (ADS)

Williams, James Daniel

The divergent parts of the five two-loop quark self- energy diagrams of quantum chromodynamics are evaluated in the noncovariant light-cone gauge. Most of the Feynman integrals are computed by means of the powerful matrix integration method, originally developed for the author's Master's thesis. From the results of the integrations, it is shown how to renormalize the quark mass and wave function in such a way that the effective quark propagator is rendered finite at two-loop order. The required counterterms turn out to be local functions of the quark momentum, due to cancellation of the nonlocal divergent parts of the two-loop integrals with equal and opposite contributions from one-loop counterterm subtraction diagrams. The final form of the counterterms is seen to be consistent with the renormalization framework proposed by Bassetto, Dalbosco, and Soldati, in which all noncovariant divergences are absorbed into the wave function normalizations. It also turns out that the mass renormalization d m is the same in the light-cone gauge as it is in a general covariant gauge, at least up to two-loop order.

An approach toward the numerical evaluation of multi-loop Feynman diagrams

NASA Astrophysics Data System (ADS)

Passarino, Giampiero

2001-12-01

A scheme for systematically achieving accurate numerical evaluation of multi-loop Feynman diagrams is developed. This shows the feasibility of a project aimed to produce a complete calculation for two-loop predictions in the Standard Model. As a first step an algorithm, proposed by F.V. Tkachov and based on the so-called generalized Bernstein functional relation, is applied to one-loop multi-leg diagrams with particular emphasis to the presence of infrared singularities, to the problem of tensorial reduction and to the classification of all singularities of a given diagram. Successively, the extension of the algorithm to two-loop diagrams is examined. The proposed solution consists in applying the functional relation to the one-loop sub-diagram which has the largest number of internal lines. In this way the integrand can be made smooth, a part from a factor which is a polynomial in xS, the vector of Feynman parameters needed for the complementary sub-diagram with the smallest number of internal lines. Since the procedure does not introduce new singularities one can distort the xS-integration hyper-contour into the complex hyper-plane, thus achieving numerical stability. The algorithm is then modified to deal with numerical evaluation around normal thresholds. Concise and practical formulas are assembled and presented, numerical results and comparisons with the available literature are shown and discussed for the so-called sunset topology.

Beyond Poisson-Boltzmann: Fluctuation effects and correlation functions

NASA Astrophysics Data System (ADS)

Netz, R. R.; Orland, H.

2000-02-01

We formulate the exact non-linear field theory for a fluctuating counter-ion distribution in the presence of a fixed, arbitrary charge distribution. The Poisson-Boltzmann equation is obtained as the saddle-point of the field-theoretic action, and the effects of counter-ion fluctuations are included by a loop-wise expansion around this saddle point. The Poisson equation is obeyed at each order in this loop expansion. We explicitly give the expansion of the Gibbs potential up to two loops. We then apply our field-theoretic formalism to the case of a single impenetrable wall with counter ions only (in the absence of salt ions). We obtain the fluctuation corrections to the electrostatic potential and the counter-ion density to one-loop order without further approximations. The relative importance of fluctuation corrections is controlled by a single parameter, which is proportional to the cube of the counter-ion valency and to the surface charge density. The effective interactions and correlation functions between charged particles close to the charged wall are obtained on the one-loop level.

Correspondence between spanning trees and the Ising model on a square lattice

NASA Astrophysics Data System (ADS)

Viswanathan, G. M.

2017-06-01

An important problem in statistical physics concerns the fascinating connections between partition functions of lattice models studied in equilibrium statistical mechanics on the one hand and graph theoretical enumeration problems on the other hand. We investigate the nature of the relationship between the number of spanning trees and the partition function of the Ising model on the square lattice. The spanning tree generating function T (z ) gives the spanning tree constant when evaluated at z =1 , while giving the lattice green function when differentiated. It is known that for the infinite square lattice the partition function Z (K ) of the Ising model evaluated at the critical temperature K =Kc is related to T (1 ) . Here we show that this idea in fact generalizes to all real temperatures. We prove that [Z(K ) s e c h 2 K ] 2=k exp[T (k )] , where k =2 tanh(2 K )s e c h (2 K ) . The identical Mahler measure connects the two seemingly disparate quantities T (z ) and Z (K ) . In turn, the Mahler measure is determined by the random walk structure function. Finally, we show that the the above correspondence does not generalize in a straightforward manner to nonplanar lattices.

Multi-loop positivity of the planar $$ \\mathcal{N} $$ = 4 SYM six-point amplitude

DOE PAGES

Dixon, Lance J.; von Hippel, Matt; McLeod, Andrew J.; ...

2017-02-22

We study the six-point NMHV ratio function in planarmore » $$ \\mathcal{N} $$ = 4 SYM theory in the context of positive geometry. The Amplituhedron construction of the integrand for the amplitudes provides a kinematical region in which the integrand was observed to be positive. It is natural to conjecture that this property survives integration, i.e. that the final result for the ratio function is also positive in this region. Establishing such a result would imply that preserving positivity is a surprising property of the Minkowski contour of integration and it might indicate some deeper underlying structure. We find that the ratio function is positive everywhere we have tested it, including analytic results for special kinematical regions at one and two loops, as well as robust numerical evidence through five loops. There is also evidence for not just positivity, but monotonicity in a “radial” direction. We also investigate positivity of the MHV six-gluon amplitude. While the remainder function ceases to be positive at four loops, the BDS-like normalized MHV amplitude appears to be positive through five loops.« less

The solution structure of the prototype foamy virus RNase H domain indicates an important role of the basic loop in substrate binding.

PubMed

Leo, Berit; Schweimer, Kristian; Rösch, Paul; Hartl, Maximilian J; Wöhrl, Birgitta M

2012-09-10

The ribonuclease H (RNase H) domains of retroviral reverse transcriptases play an essential role in the replication cycle of retroviruses. During reverse transcription of the viral genomic RNA, an RNA/DNA hybrid is created whose RNA strand needs to be hydrolyzed by the RNase H to enable synthesis of the second DNA strand by the DNA polymerase function of the reverse transcriptase. Here, we report the solution structure of the separately purified RNase H domain from prototype foamy virus (PFV) revealing the so-called C-helix and the adjacent basic loop, which both were suggested to be important in substrate binding and activity. The solution structure of PFV RNase H shows that it contains a mixed five-stranded β-sheet, which is sandwiched by four α-helices (A-D), including the C-helix, on one side and one α-helix (helix E) on the opposite side. NMR titration experiments demonstrate that upon substrate addition signal changes can be detected predominantly in the basic loop as well as in the C-helix. All these regions are oriented towards the bound substrate. In addition, signal intensities corresponding to residues in the B-helix and the active site decrease, while only minor or no changes of the overall structure of the RNase H are detectable upon substrate binding. Dynamic studies confirm the monomeric state of the RNase H domain. Structure comparisons with HIV-1 RNase H, which lacks the basic protrusion, indicate that the basic loop is relevant for substrate interaction, while the C-helix appears to fulfill mainly structural functions, i.e. positioning the basic loop in the correct orientation for substrate binding. The structural data of PFV RNase H demonstrate the importance of the basic loop, which contains four positively charged lysines, in substrate binding and the function of the C-helix in positioning of the loop. In the dimeric full length HIV-1 RT, the function of the basic loop is carried out by a different loop, which also harbors basic residues, derived from the connection domain of the p66 subunit. Our results suggest that RNases H which are also active as separate domains might need a functional basic loop for proper substrate binding.

Scaled lattice fermion fields, stability bounds, and regularity

NASA Astrophysics Data System (ADS)

O'Carroll, Michael; Faria da Veiga, Paulo A.

2018-02-01

We consider locally gauge-invariant lattice quantum field theory models with locally scaled Wilson-Fermi fields in d = 1, 2, 3, 4 spacetime dimensions. The use of scaled fermions preserves Osterwalder-Seiler positivity and the spectral content of the models (the decay rates of correlations are unchanged in the infinite lattice). In addition, it also results in less singular, more regular behavior in the continuum limit. Precisely, we treat general fermionic gauge and purely fermionic lattice models in an imaginary-time functional integral formulation. Starting with a hypercubic finite lattice Λ ⊂(aZ ) d, a ∈ (0, 1], and considering the partition function of non-Abelian and Abelian gauge models (the free fermion case is included) neglecting the pure gauge interactions, we obtain stability bounds uniformly in the lattice spacing a ∈ (0, 1]. These bounds imply, at least in the subsequential sense, the existence of the thermodynamic (Λ ↗ (aZ ) d) and the continuum (a ↘ 0) limits. Specializing to the U(1) gauge group, the known non-intersecting loop expansion for the d = 2 partition function is extended to d = 3 and the thermodynamic limit of the free energy is shown to exist with a bound independent of a ∈ (0, 1]. In the case of scaled free Fermi fields (corresponding to a trivial gauge group with only the identity element), spectral representations are obtained for the partition function, free energy, and correlations. The thermodynamic and continuum limits of the free fermion free energy are shown to exist. The thermodynamic limit of n-point correlations also exist with bounds independent of the point locations and a ∈ (0, 1], and with no n! dependence. Also, a time-zero Hilbert-Fock space is constructed, as well as time-zero, spatially pointwise scaled fermion creation operators which are shown to be norm bounded uniformly in a ∈ (0, 1]. The use of our scaled fields since the beginning allows us to extract and isolate the singularities of the free energy when a ↘ 0.

Higgs boson self-coupling from two-loop analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alhendi, H. A.; National Center for Mathematics and Physics, KACST P. O. Box 6086, Riyadh 11442; Barakat, T.

2010-09-01

The scale invariant of the effective potential of the standard model at two loop is used as a boundary condition under the assumption that the two-loop effective potential approximates the full effective potential. This condition leads with the help of the renormalization-group functions of the model at two loop to an algebraic equation of the scalar self-coupling with coefficients that depend on the gauge and the top quark couplings. It admits only two real positive solutions. One of them, in the absence of the gauge and top quark couplings, corresponds to the nonperturbative ultraviolet fixed point of the scalar renormalization-groupmore » function and the other corresponds to the perturbative infrared fixed point. The dependence of the scalar coupling on the top quark and the strong couplings at two-loop radiative corrections is analyzed.« less

Loop transfer recovery for general nonminimum phase discrete time systems. I - Analysis

NASA Technical Reports Server (NTRS)

Chen, Ben M.; Saberi, Ali; Sannuti, Peddapullaiah; Shamash, Yacov

1992-01-01

A complete analysis of loop transfer recovery (LTR) for general nonstrictly proper, not necessarily minimum phase discrete time systems is presented. Three different observer-based controllers, namely, `prediction estimator' and full or reduced-order type `current estimator' based controllers, are used. The analysis corresponding to all these three controllers is unified into a single mathematical framework. The LTR analysis given here focuses on three fundamental issues: (1) the recoverability of a target loop when it is arbitrarily given, (2) the recoverability of a target loop while taking into account its specific characteristics, and (3) the establishment of necessary and sufficient conditions on the given system so that it has at least one recoverable target loop transfer function or sensitivity function. Various differences that arise in LTR analysis of continuous and discrete systems are pointed out.

Electrostatic correlations in inhomogeneous charged fluids beyond loop expansion

NASA Astrophysics Data System (ADS)

Buyukdagli, Sahin; Achim, C. V.; Ala-Nissila, T.

2012-09-01

Electrostatic correlation effects in inhomogeneous symmetric electrolytes are investigated within a previously developed electrostatic self-consistent theory [R. R. Netz and H. Orland, Eur. Phys. J. E 11, 301 (2003)], 10.1140/epje/i2002-10159-0. To this aim, we introduce two computational approaches that allow to solve the self-consistent equations beyond the loop expansion. The first method is based on a perturbative Green's function technique, and the second one is an extension of a previously introduced semiclassical approximation for single dielectric interfaces to the case of slit nanopores. Both approaches can handle the case of dielectrically discontinuous boundaries where the one-loop theory is known to fail. By comparing the theoretical results obtained from these schemes with the results of the Monte Carlo simulations that we ran for ions at neutral single dielectric interfaces, we first show that the weak coupling Debye-Huckel theory remains quantitatively accurate up to the bulk ion density ρb ≃ 0.01 M, whereas the self-consistent theory exhibits a good quantitative accuracy up to ρb ≃ 0.2 M, thus improving the accuracy of the Debye-Huckel theory by one order of magnitude in ionic strength. Furthermore, we compare the predictions of the self-consistent theory with previous Monte Carlo simulation data for charged dielectric interfaces and show that the proposed approaches can also accurately handle the correlation effects induced by the surface charge in a parameter regime where the mean-field result significantly deviates from the Monte Carlo data. Then, we derive from the perturbative self-consistent scheme the one-loop theory of asymmetrically partitioned salt systems around a dielectrically homogeneous charged surface. It is shown that correlation effects originate in these systems from a competition between the salt screening loss at the interface driving the ions to the bulk region, and the interfacial counterion screening excess attracting them towards the surface. This competition can be quantified in terms of the characteristic surface charge σ _s^*=√{2ρ _b/(π ℓ _B)}, where ℓB = 7 Å is the Bjerrum length. In the case of weak surface charges σ _s≪ σ _s^* where counterions form a diffuse layer, the interfacial salt screening loss is the dominant effect. As a result, correlation effects decrease the mean-field density of both coions and counterions. With an increase of the surface charge towards σ _s^*, the surface-attractive counterion screening excess starts to dominate, and correlation effects amplify in this regime the mean-field density of both type of ions. However, in the regime σ _s>σ _s^*, the same counterion screening excess also results in a significant decrease of the electrostatic mean-field potential. This reduces in turn the mean-field counterion density far from the charged surface. We also show that for σ _s≫ σ _s^*, electrostatic correlations result in a charge inversion effect. However, the electrostatic coupling regime where this phenomenon takes place should be verified with Monte Carlo simulations since this parameter regime is located beyond the validity range of the one-loop theory.

Electrostatic correlations in inhomogeneous charged fluids beyond loop expansion.

PubMed

Buyukdagli, Sahin; Achim, C V; Ala-Nissila, T

2012-09-14

Electrostatic correlation effects in inhomogeneous symmetric electrolytes are investigated within a previously developed electrostatic self-consistent theory [R. R. Netz and H. Orland, Eur. Phys. J. E 11, 301 (2003)]. To this aim, we introduce two computational approaches that allow to solve the self-consistent equations beyond the loop expansion. The first method is based on a perturbative Green's function technique, and the second one is an extension of a previously introduced semiclassical approximation for single dielectric interfaces to the case of slit nanopores. Both approaches can handle the case of dielectrically discontinuous boundaries where the one-loop theory is known to fail. By comparing the theoretical results obtained from these schemes with the results of the Monte Carlo simulations that we ran for ions at neutral single dielectric interfaces, we first show that the weak coupling Debye-Huckel theory remains quantitatively accurate up to the bulk ion density ρ(b) ≃ 0.01 M, whereas the self-consistent theory exhibits a good quantitative accuracy up to ρ(b) ≃ 0.2 M, thus improving the accuracy of the Debye-Huckel theory by one order of magnitude in ionic strength. Furthermore, we compare the predictions of the self-consistent theory with previous Monte Carlo simulation data for charged dielectric interfaces and show that the proposed approaches can also accurately handle the correlation effects induced by the surface charge in a parameter regime where the mean-field result significantly deviates from the Monte Carlo data. Then, we derive from the perturbative self-consistent scheme the one-loop theory of asymmetrically partitioned salt systems around a dielectrically homogeneous charged surface. It is shown that correlation effects originate in these systems from a competition between the salt screening loss at the interface driving the ions to the bulk region, and the interfacial counterion screening excess attracting them towards the surface. This competition can be quantified in terms of the characteristic surface charge σ(s)*=√(2ρ(b)/(πl(B)), where l(B) = 7 Å is the Bjerrum length. In the case of weak surface charges σ(s)≪σ(s)* where counterions form a diffuse layer, the interfacial salt screening loss is the dominant effect. As a result, correlation effects decrease the mean-field density of both coions and counterions. With an increase of the surface charge towards σ(s)*, the surface-attractive counterion screening excess starts to dominate, and correlation effects amplify in this regime the mean-field density of both type of ions. However, in the regime σ(s)>σ(s)*, the same counterion screening excess also results in a significant decrease of the electrostatic mean-field potential. This reduces in turn the mean-field counterion density far from the charged surface. We also show that for σ(s)≫σ(s)*, electrostatic correlations result in a charge inversion effect. However, the electrostatic coupling regime where this phenomenon takes place should be verified with Monte Carlo simulations since this parameter regime is located beyond the validity range of the one-loop theory.

Cylindric partitions, {{\\boldsymbol{ W }}}_{r} characters and the Andrews-Gordon-Bressoud identities

NASA Astrophysics Data System (ADS)

Foda, O.; Welsh, T. A.

2016-04-01

We study the Andrews-Gordon-Bressoud (AGB) generalisations of the Rogers-Ramanujan q-series identities in the context of cylindric partitions. We recall the definition of r-cylindric partitions, and provide a simple proof of Borodin’s product expression for their generating functions, that can be regarded as a limiting case of an unpublished proof by Krattenthaler. We also recall the relationships between the r-cylindric partition generating functions, the principal characters of {\\hat{{sl}}}r algebras, the {{\\boldsymbol{ M }}}r r,r+d minimal model characters of {{\\boldsymbol{ W }}}r algebras, and the r-string abaci generating functions, providing simple proofs for each. We then set r = 2, and use two-cylindric partitions to re-derive the AGB identities as follows. Firstly, we use Borodin’s product expression for the generating functions of the two-cylindric partitions with infinitely long parts, to obtain the product sides of the AGB identities, times a factor {(q;q)}∞ -1, which is the generating function of ordinary partitions. Next, we obtain a bijection from the two-cylindric partitions, via two-string abaci, into decorated versions of Bressoud’s restricted lattice paths. Extending Bressoud’s method of transforming between restricted paths that obey different restrictions, we obtain sum expressions with manifestly non-negative coefficients for the generating functions of the two-cylindric partitions which contains a factor {(q;q)}∞ -1. Equating the product and sum expressions of the same two-cylindric partitions, and canceling a factor of {(q;q)}∞ -1 on each side, we obtain the AGB identities.

A Study of the Thermal Environment Developed by a Traveling Slipper at High Velocity

DTIC Science & Technology

2013-03-01

Power Partition Function The next partition function takes the same formulation as the powered function but now the exponent is squared. The...function and note the squared term in the exponent . 66 Equation 4.27 (4.36) Thus far the three partition functions each give a predicted...hypothesized that the function would fall somewhere between the first exponential decay function and the power function. However, by squaring the exponent

Application of an integrated flight/propulsion control design methodology to a STOVL aircraft

NASA Technical Reports Server (NTRS)

Garg, Sanjay; Mattern, Duane L.

1991-01-01

Results are presented from the application of an emerging Integrated Flight/Propulsion Control (IFPC) design methodology to a Short Take Off and Vertical Landing (STOVL) aircraft in transition flight. The steps in the methodology consist of designing command shaping prefilters to provide the overall desired response to pilot command inputs. A previously designed centralized controller is first validated for the integrated airframe/engine plant used. This integrated plant is derived from a different model of the engine subsystem than the one used for the centralized controller design. The centralized controller is then partitioned in a decentralized, hierarchical structure comprising of airframe lateral and longitudinal subcontrollers and an engine subcontroller. Command shaping prefilters from the pilot control effector inputs are then designed and time histories of the closed loop IFPC system response to simulated pilot commands are compared to desired responses based on handling qualities requirements. Finally, the propulsion system safety and nonlinear limited protection logic is wrapped around the engine subcontroller and the response of the closed loop integrated system is evaluated for transients that encounter the propulsion surge margin limit.

Multivariate Hermite interpolation on scattered point sets using tensor-product expo-rational B-splines

NASA Astrophysics Data System (ADS)

Dechevsky, Lubomir T.; Bang, Børre; Laksa˚, Arne; Zanaty, Peter

2011-12-01

At the Seventh International Conference on Mathematical Methods for Curves and Surfaces, To/nsberg, Norway, in 2008, several new constructions for Hermite interpolation on scattered point sets in domains in Rn,n∈N, combined with smooth convex partition of unity for several general types of partitions of these domains were proposed in [1]. All of these constructions were based on a new type of B-splines, proposed by some of the authors several years earlier: expo-rational B-splines (ERBS) [3]. In the present communication we shall provide more details about one of these constructions: the one for the most general class of domain partitions considered. This construction is based on the use of two separate families of basis functions: one which has all the necessary Hermite interpolation properties, and another which has the necessary properties of a smooth convex partition of unity. The constructions of both of these two bases are well-known; the new part of the construction is the combined use of these bases for the derivation of a new basis which enjoys having all above-said interpolation and unity partition properties simultaneously. In [1] the emphasis was put on the use of radial basis functions in the definitions of the two initial bases in the construction; now we shall put the main emphasis on the case when these bases consist of tensor-product B-splines. This selection provides two useful advantages: (A) it is easier to compute higher-order derivatives while working in Cartesian coordinates; (B) it becomes clear that this construction becomes a far-going extension of tensor-product constructions. We shall provide 3-dimensional visualization of the resulting bivariate bases, using tensor-product ERBS. In the main tensor-product variant, we shall consider also replacement of ERBS with simpler generalized ERBS (GERBS) [2], namely, their simplified polynomial modifications: the Euler Beta-function B-splines (BFBS). One advantage of using BFBS instead of ERBS is the simplified computation, since BFBS are piecewise polynomial, which ERBS are not. One disadvantage of using BFBS in the place of ERBS in this construction is that the necessary selection of the degree of BFBS imposes constraints on the maximal possible multiplicity of the Hermite interpolation.

Droplet motion in microfluidic networks: Hydrodynamic interactions and pressure-drop measurements

NASA Astrophysics Data System (ADS)

Sessoms, D. A.; Belloul, M.; Engl, W.; Roche, M.; Courbin, L.; Panizza, P.

2009-07-01

We present experimental, numerical, and theoretical studies of droplet flows in hydrodynamic networks. Using both millifluidic and microfluidic devices, we study the partitioning of monodisperse droplets in an asymmetric loop. In both cases, we show that droplet traffic results from the hydrodynamic feedback due to the presence of droplets in the outlet channels. We develop a recently-introduced phenomenological model [W. Engl , Phys. Rev. Lett. 95, 208304 (2005)] and successfully confront its predictions to our experimental results. This approach offers a simple way to measure the excess hydrodynamic resistance of a channel filled with droplets. We discuss the traffic behavior and the variations in the corresponding hydrodynamic resistance length Ld and of the droplet mobility β , as a function of droplet interdistance and confinement for channels having circular or rectangular cross sections.

Refined 3d-3d correspondence

NASA Astrophysics Data System (ADS)

Alday, Luis F.; Genolini, Pietro Benetti; Bullimore, Mathew; van Loon, Mark

2017-04-01

We explore aspects of the correspondence between Seifert 3-manifolds and 3d N = 2 supersymmetric theories with a distinguished abelian flavour symmetry. We give a prescription for computing the squashed three-sphere partition functions of such 3d N = 2 theories constructed from boundary conditions and interfaces in a 4d N = 2∗ theory, mirroring the construction of Seifert manifold invariants via Dehn surgery. This is extended to include links in the Seifert manifold by the insertion of supersymmetric Wilson-'t Hooft loops in the 4d N = 2∗ theory. In the presence of a mass parameter cfor the distinguished flavour symmetry, we recover aspects of refined Chern-Simons theory with complex gauge group, and in particular construct an analytic continuation of the S-matrix of refined Chern-Simons theory.

JTRS/SCA and Custom/SDR Waveform Comparison

NASA Technical Reports Server (NTRS)

Oldham, Daniel R.; Scardelletti, Maximilian C.

2007-01-01

This paper compares two waveform implementations generating the same RF signal using the same SDR development system. Both waveforms implement a satellite modem using QPSK modulation at 1M BPS data rates with one half rate convolutional encoding. Both waveforms are partitioned the same across the general purpose processor (GPP) and the field programmable gate array (FPGA). Both waveforms implement the same equivalent set of radio functions on the GPP and FPGA. The GPP implements the majority of the radio functions and the FPGA implements the final digital RF modulator stage. One waveform is implemented directly on the SDR development system and the second waveform is implemented using the JTRS/SCA model. This paper contrasts the amount of resources to implement both waveforms and demonstrates the importance of waveform partitioning across the SDR development system.

A Special Golden Curve in Human Upper Limbs' Length Proportion: A Functional Partition Which Is Different from Anatomy.

PubMed

Wang, Nan; Ma, Jie; Jin, Dan; Yu, Bin

2017-01-01

Aim . The purpose of this study was to investigate the relationship between upper limbs' three functional partitions and the golden curve. Materials and Methods . We measured 30 subjects' right or left upper limb data and investigate the relationship between them and the golden curve by use of SPSS version 20.0 statistical software (SPSS, Inc., Chicago, Illinois), one-sample t -test. Results . There are four points on human's upper limbs which have no difference with the four points on the golden curve. And there is one point of which the difference is obvious. But we still could draw the conclusion that human upper limbs are accordant with the golden curve. Conclusion . Human upper limbs are accordant with the golden curve.

Fully probabilistic control design in an adaptive critic framework.

PubMed

Herzallah, Randa; Kárný, Miroslav

2011-12-01

Optimal stochastic controller pushes the closed-loop behavior as close as possible to the desired one. The fully probabilistic design (FPD) uses probabilistic description of the desired closed loop and minimizes Kullback-Leibler divergence of the closed-loop description to the desired one. Practical exploitation of the fully probabilistic design control theory continues to be hindered by the computational complexities involved in numerically solving the associated stochastic dynamic programming problem; in particular, very hard multivariate integration and an approximate interpolation of the involved multivariate functions. This paper proposes a new fully probabilistic control algorithm that uses the adaptive critic methods to circumvent the need for explicitly evaluating the optimal value function, thereby dramatically reducing computational requirements. This is a main contribution of this paper. Copyright © 2011 Elsevier Ltd. All rights reserved.

Task-specific image partitioning.

PubMed

Kim, Sungwoong; Nowozin, Sebastian; Kohli, Pushmeet; Yoo, Chang D

2013-02-01

Image partitioning is an important preprocessing step for many of the state-of-the-art algorithms used for performing high-level computer vision tasks. Typically, partitioning is conducted without regard to the task in hand. We propose a task-specific image partitioning framework to produce a region-based image representation that will lead to a higher task performance than that reached using any task-oblivious partitioning framework and existing supervised partitioning framework, albeit few in number. The proposed method partitions the image by means of correlation clustering, maximizing a linear discriminant function defined over a superpixel graph. The parameters of the discriminant function that define task-specific similarity/dissimilarity among superpixels are estimated based on structured support vector machine (S-SVM) using task-specific training data. The S-SVM learning leads to a better generalization ability while the construction of the superpixel graph used to define the discriminant function allows a rich set of features to be incorporated to improve discriminability and robustness. We evaluate the learned task-aware partitioning algorithms on three benchmark datasets. Results show that task-aware partitioning leads to better labeling performance than the partitioning computed by the state-of-the-art general-purpose and supervised partitioning algorithms. We believe that the task-specific image partitioning paradigm is widely applicable to improving performance in high-level image understanding tasks.

Intersecting surface defects and instanton partition functions

NASA Astrophysics Data System (ADS)

Pan, Yiwen; Peelaers, Wolfger

2017-07-01

We analyze intersecting surface defects inserted in interacting four-dimensional N=2 supersymmetric quantum field theories. We employ the realization of a class of such systems as the infrared fixed points of renormalization group flows from larger theories, triggered by perturbed Seiberg-Witten monopole-like configurations, to compute their partition functions. These results are cast into the form of a partition function of 4d/2d/0d coupled systems. Our computations provide concrete expressions for the instanton partition function in the presence of intersecting defects and we study the corresponding ADHM model.

Off-diagonal series expansion for quantum partition functions

NASA Astrophysics Data System (ADS)

Hen, Itay

2018-05-01

We derive an integral-free thermodynamic perturbation series expansion for quantum partition functions which enables an analytical term-by-term calculation of the series. The expansion is carried out around the partition function of the classical component of the Hamiltonian with the expansion parameter being the strength of the off-diagonal, or quantum, portion. To demonstrate the usefulness of the technique we analytically compute to third order the partition functions of the 1D Ising model with longitudinal and transverse fields, and the quantum 1D Heisenberg model.

A non-planar two-loop three-point function beyond multiple polylogarithms

NASA Astrophysics Data System (ADS)

von Manteuffel, Andreas; Tancredi, Lorenzo

2017-06-01

We consider the analytic calculation of a two-loop non-planar three-point function which contributes to the two-loop amplitudes for t\\overline{t} production and γγ production in gluon fusion through a massive top-quark loop. All subtopology integrals can be written in terms of multiple polylogarithms over an irrational alphabet and we employ a new method for the integration of the differential equations which does not rely on the rationalization of the latter. The top topology integrals, instead, in spite of the absence of a massive three-particle cut, cannot be evaluated in terms of multiple polylogarithms and require the introduction of integrals over complete elliptic integrals and polylogarithms. We provide one-fold integral representations for the solutions and continue them analytically to all relevant regions of the phase space in terms of real functions, extracting all imaginary parts explicitly. The numerical evaluation of our expressions becomes straightforward in this way.

Optical phase-locked loop (OPLL) for free-space laser communications with heterodyne detection

NASA Technical Reports Server (NTRS)

Win, Moe Z.; Chen, Chien-Chung; Scholtz, Robert A.

1991-01-01

Several advantages of coherent free-space optical communications are outlined. Theoretical analysis is formulated for an OPLL disturbed by shot noise, modulation noise, and frequency noise consisting of a white component, a 1/f component, and a 1/f-squared component. Each of the noise components is characterized by its associated power spectral density. It is shown that the effect of modulation depends only on the ratio of loop bandwidth and data rate, and is negligible for an OPLL with loop bandwidth smaller than one fourth the data rate. Total phase error variance as a function of loop bandwidth is displayed for several values of carrier signal to noise ratio. Optimal loop bandwidth is also calculated as a function of carrier signal to noise ratio. An OPLL experiment is performed, where it is shown that the measured phase error variance closely matches the theoretical predictions.

Control of a flexible link by shaping the closed loop frequency response function through optimised feedback filters

NASA Astrophysics Data System (ADS)

Del Vescovo, D.; D'Ambrogio, W.

1995-01-01

A frequency domain method is presented to design a closed-loop control for vibration reduction flexible mechanisms. The procedure is developed on a single-link flexible arm, driven by one rotary degree of freedom servomotor, although the same technique may be applied to similar systems such as supports for aerospace antennae or solar panels. The method uses the structural frequency response functions (FRFs), thus avoiding system identification, that produces modeling uncertainties. Two closed-loops are implemented: the inner loop uses acceleration feedback with the aim of making the FRF similar to that of an equivalent rigid link; the outer loop feeds back displacements to achieve a fast positioning response and null steady state error. In both cases, the controller type is established a priori, while actual characteristics are defined by an optimisation procedure in which the relevant FRF is constrained into prescribed bounds and stability is taken into account.

Quantum corrections to Bekenstein-Hawking black hole entropy and gravity partition functions

NASA Astrophysics Data System (ADS)

Bytsenko, A. A.; Tureanu, A.

2013-08-01

Algebraic aspects of the computation of partition functions for quantum gravity and black holes in AdS3 are discussed. We compute the sub-leading quantum corrections to the Bekenstein-Hawking entropy. It is shown that the quantum corrections to the classical result can be included systematically by making use of the comparison with conformal field theory partition functions, via the AdS3/CFT2 correspondence. This leads to a better understanding of the role of modular and spectral functions, from the point of view of the representation theory of infinite-dimensional Lie algebras. Besides, the sum of known quantum contributions to the partition function can be presented in a closed form, involving the Patterson-Selberg spectral function. These contributions can be reproduced in a holomorphically factorized theory whose partition functions are associated with the formal characters of the Virasoro modules. We propose a spectral function formulation for quantum corrections to the elliptic genus from supergravity states.

Spinning AdS loop diagrams: two point functions

NASA Astrophysics Data System (ADS)

Giombi, Simone; Sleight, Charlotte; Taronna, Massimo

2018-06-01

We develop a systematic approach to evaluating AdS loop amplitudes with spinning legs based on the spectral (or "split") representation of bulk-to-bulk propagators, which re-expresses loop diagrams in terms of spectral integrals and higher-point tree diagrams. In this work we focus on 2pt one-loop Witten diagrams involving totally symmetric fields of arbitrary mass and integer spin. As an application of this framework, we study the contribution to the anomalous dimension of higher-spin currents generated by bubble diagrams in higher-spin gauge theories on AdS.

Loop-quantum-gravity vertex amplitude.

PubMed

Engle, Jonathan; Pereira, Roberto; Rovelli, Carlo

2007-10-19

Spin foam models are hoped to provide the dynamics of loop-quantum gravity. However, the most popular of these, the Barrett-Crane model, does not have the good boundary state space and there are indications that it fails to yield good low-energy n-point functions. We present an alternative dynamics that can be derived as a quantization of a Regge discretization of Euclidean general relativity, where second class constraints are imposed weakly. Its state space matches the SO(3) loop gravity one and it yields an SO(4)-covariant vertex amplitude for Euclidean loop gravity.

Unitarity violation in noninteger dimensional Gross-Neveu-Yukawa model

NASA Astrophysics Data System (ADS)

Ji, Yao; Kelly, Michael

2018-05-01

We construct an explicit example of unitarity violation in fermionic quantum field theories in noninteger dimensions. We study the two-point correlation function of four-fermion operators. We compute the one-loop anomalous dimensions of these operators in the Gross-Neveu-Yukawa model. We find that at one-loop order, the four-fermion operators split into three classes with one class having negative norms. This implies that the theory violates unitarity, following the definition in Ref. [1].

Exact Path Integral for 3D Quantum Gravity.

PubMed

Iizuka, Norihiro; Tanaka, Akinori; Terashima, Seiji

2015-10-16

Three-dimensional Euclidean pure gravity with a negative cosmological constant can be formulated in terms of the Chern-Simons theory, classically. This theory can be written in a supersymmetric way by introducing auxiliary gauginos and scalars. We calculate the exact partition function of this Chern-Simons theory by using the localization technique. Thus, we obtain the quantum gravity partition function, assuming that it can be obtained nonperturbatively by summing over partition functions of the Chern-Simons theory on topologically different manifolds. The resultant partition function is modular invariant, and, in the case in which the central charge is expected to be 24, it is the J function, predicted by Witten.

New approach to canonical partition functions computation in Nf=2 lattice QCD at finite baryon density

NASA Astrophysics Data System (ADS)

Bornyakov, V. G.; Boyda, D. L.; Goy, V. A.; Molochkov, A. V.; Nakamura, Atsushi; Nikolaev, A. A.; Zakharov, V. I.

2017-05-01

We propose and test a new approach to computation of canonical partition functions in lattice QCD at finite density. We suggest a few steps procedure. We first compute numerically the quark number density for imaginary chemical potential i μq I . Then we restore the grand canonical partition function for imaginary chemical potential using the fitting procedure for the quark number density. Finally we compute the canonical partition functions using high precision numerical Fourier transformation. Additionally we compute the canonical partition functions using the known method of the hopping parameter expansion and compare results obtained by two methods in the deconfining as well as in the confining phases. The agreement between two methods indicates the validity of the new method. Our numerical results are obtained in two flavor lattice QCD with clover improved Wilson fermions.

An improved method of renal tissue engineering, by combining renal dissociation and reaggregation with a low-volume culture technique, results in development of engineered kidneys complete with loops of Henle.

PubMed

Chang, C-Hong; Davies, Jamie A

2012-01-01

Tissue engineering of functional kidney tissue is an important goal for clinical restoration of renal function in patients damaged by infectious, toxicological, or genetic disease. One promising approach is the use of the self-organizing abilities of embryonic kidney cells to arrange themselves, from a simply reaggregated cell suspension, into engineered organs similar to fetal kidneys. The previous state-of-the-art method for this results in the formation of a branched collecting duct tree, immature nephrons (S-shaped bodies) beside and connected to it, and supportive stroma. It does not, though, result in the significant formation of morphologically detectable loops of Henle - anatomical features of the nephron that are critical to physiological function. We have combined the best existing technique for renal tissue engineering from cell suspensions with a low-volume culture technique that allows intact kidney rudiments to make loops of Henle to test whether engineered kidneys can produce these loops. The result is the formation of loops of Henle in engineered cultured 'fetal kidneys', very similar in both morphology and in number to those formed by intact organ rudiments. This brings the engineering technique one important step closer to production of a fully realistic organ. Copyright © 2012 S. Karger AG, Basel.

An investigation into closed-loop treatment of neurological disorders based on sensing mitochondrial dysfunction.

PubMed

Adams, Scott D; Kouzani, Abbas Z; Tye, Susannah J; Bennet, Kevin E; Berk, Michael

2018-02-13

Dynamic feedback based closed-loop medical devices offer a number of advantages for treatment of heterogeneous neurological conditions. Closed-loop devices integrate a level of neurobiological feedback, which allows for real-time adjustments to be made with the overarching aim of improving treatment efficacy and minimizing risks for adverse events. One target which has not been extensively explored as a potential feedback component in closed-loop therapies is mitochondrial function. Several neurodegenerative and psychiatric disorders including Parkinson's disease, Major Depressive disorder and Bipolar disorder have been linked to perturbations in the mitochondrial respiratory chain. This paper investigates the potential to monitor this mitochondrial function as a method of feedback for closed-loop neuromodulation treatments. A generic model of the closed-loop treatment is developed to describe the high-level functions of any system designed to control neural function based on mitochondrial response to stimulation, simplifying comparison and future meta-analysis. This model has four key functional components including: a sensor, signal manipulator, controller and effector. Each of these components are described and several potential technologies for each are investigated. While some of these candidate technologies are quite mature, there are still technological gaps remaining. The field of closed-loop medical devices is rapidly evolving, and whilst there is a lot of interest in this area, widespread adoption has not yet been achieved due to several remaining technological hurdles. However, the significant therapeutic benefits offered by this technology mean that this will be an active area for research for years to come.

Intersecting surface defects and instanton partition functions

DOE PAGES

Pan, Yiwen; Peelaers, Wolfger

2017-07-14

We analyze intersecting surface defects inserted in interacting four-dimensional N = 2 supersymmetric quantum field theories. We employ the realization of a class of such systems as the infrared xed points of renormalization group flows from larger theories, triggered by perturbed Seiberg-Witten monopole-like con gurations, to compute their partition functions. These results are cast into the form of a partition function of 4d/2d/0d coupled systems. In conclusion, our computations provide concrete expressions for the instanton partition function in the presence of intersecting defects and we study the corresponding ADHM model.

Intersecting surface defects and instanton partition functions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pan, Yiwen; Peelaers, Wolfger

We analyze intersecting surface defects inserted in interacting four-dimensional N = 2 supersymmetric quantum field theories. We employ the realization of a class of such systems as the infrared xed points of renormalization group flows from larger theories, triggered by perturbed Seiberg-Witten monopole-like con gurations, to compute their partition functions. These results are cast into the form of a partition function of 4d/2d/0d coupled systems. In conclusion, our computations provide concrete expressions for the instanton partition function in the presence of intersecting defects and we study the corresponding ADHM model.

Smeared quasidistributions in perturbation theory

NASA Astrophysics Data System (ADS)

Monahan, Christopher

2018-03-01

Quasi- and pseudodistributions provide a new approach to determining parton distribution functions from first principles' calculations of QCD. Here, I calculate the flavor nonsinglet unpolarized quasidistribution at one loop in perturbation theory, using the gradient flow to remove ultraviolet divergences. I demonstrate that, as expected, the gradient flow does not change the infrared structure of the quasidistribution at one loop and use the results to match the smeared matrix elements to those in the MS ¯ scheme. This matching calculation is required to relate numerical results obtained from nonperturbative lattice QCD computations to light-front parton distribution functions extracted from global analyses of experimental data.

Derivative expansion of one-loop effective energy of stiff membranes with tension

NASA Astrophysics Data System (ADS)

Borelli, M. E. S.; Kleinert, H.; Schakel, Adriaan M. J.

1999-03-01

With help of a derivative expansion, the one-loop corrections to the energy functional of a nearly flat, stiff membrane with tension due to thermal fluctuations are calculated in the Monge parametrization. Contrary to previous studies, an arbitrary tilt of the surface is allowed to exhibit the nontrivial relations between the different, highly nonlinear terms accompanying the ultraviolet divergences. These terms are shown to have precisely the same form as those in the original energy functional, as necessary for renormalizability. Also infrared divergences arise. These, however, are shown to cancel in a nontrivial way.

Regulation of the demographic structure in isomorphic biphasic life cycles at the spatial fine scale.

PubMed

Vieira, Vasco Manuel Nobre de Carvalho da Silva; Mateus, Marcos Duarte

2014-01-01

Isomorphic biphasic algal life cycles often occur in the environment at ploidy abundance ratios (Haploid:Diploid) different from 1. Its spatial variability occurs within populations related to intertidal height and hydrodynamic stress, possibly reflecting the niche partitioning driven by their diverging adaptation to the environment argued necessary for their prevalence (evolutionary stability). Demographic models based in matrix algebra were developed to investigate which vital rates may efficiently generate an H:D variability at a fine spatial resolution. It was also taken into account time variation and type of life strategy. Ploidy dissimilarities in fecundity rates set an H:D spatial structure miss-fitting the ploidy fitness ratio. The same happened with ploidy dissimilarities in ramet growth whenever reproductive output dominated the population demography. Only through ploidy dissimilarities in looping rates (stasis, breakage and clonal growth) did the life cycle respond to a spatially heterogeneous environment efficiently creating a niche partition. Marginal locations were more sensitive than central locations. Related results have been obtained experimentally and numerically for widely different life cycles from the plant and animal kingdoms. Spore dispersal smoothed the effects of ploidy dissimilarities in fertility and enhanced the effects of ploidy dissimilarities looping rates. Ploidy dissimilarities in spore dispersal could also create the necessary niche partition, both over the space and time dimensions, even in spatial homogeneous environments and without the need for conditional differentiation of the ramets. Fine scale spatial variability may be the key for the prevalence of isomorphic biphasic life cycles, which has been neglected so far.

Regulation of the Demographic Structure in Isomorphic Biphasic Life Cycles at the Spatial Fine Scale

PubMed Central

Vieira, Vasco Manuel Nobre de Carvalho da Silva; Mateus, Marcos Duarte

2014-01-01

Isomorphic biphasic algal life cycles often occur in the environment at ploidy abundance ratios (Haploid:Diploid) different from 1. Its spatial variability occurs within populations related to intertidal height and hydrodynamic stress, possibly reflecting the niche partitioning driven by their diverging adaptation to the environment argued necessary for their prevalence (evolutionary stability). Demographic models based in matrix algebra were developed to investigate which vital rates may efficiently generate an H:D variability at a fine spatial resolution. It was also taken into account time variation and type of life strategy. Ploidy dissimilarities in fecundity rates set an H:D spatial structure miss-fitting the ploidy fitness ratio. The same happened with ploidy dissimilarities in ramet growth whenever reproductive output dominated the population demography. Only through ploidy dissimilarities in looping rates (stasis, breakage and clonal growth) did the life cycle respond to a spatially heterogeneous environment efficiently creating a niche partition. Marginal locations were more sensitive than central locations. Related results have been obtained experimentally and numerically for widely different life cycles from the plant and animal kingdoms. Spore dispersal smoothed the effects of ploidy dissimilarities in fertility and enhanced the effects of ploidy dissimilarities looping rates. Ploidy dissimilarities in spore dispersal could also create the necessary niche partition, both over the space and time dimensions, even in spatial homogeneous environments and without the need for conditional differentiation of the ramets. Fine scale spatial variability may be the key for the prevalence of isomorphic biphasic life cycles, which has been neglected so far. PMID:24658603

The partition function of the Bures ensemble as the τ-function of BKP and DKP hierarchies: continuous and discrete

NASA Astrophysics Data System (ADS)

Hu, Xing-Biao; Li, Shi-Hao

2017-07-01

The relationship between matrix integrals and integrable systems was revealed more than 20 years ago. As is known, matrix integrals over a Gaussian ensemble used in random matrix theory could act as the τ-function of several hierarchies of integrable systems. In this article, we will show that the time-dependent partition function of the Bures ensemble, whose measure has many interesting geometric properties, could act as the τ-function of BKP and DKP hierarchies. In addition, if discrete time variables are introduced, then this partition function could act as the τ-function of discrete BKP and DKP hierarchies. In particular, there are some links between the partition function of the Bures ensemble and Toda-type equations.

Noncommutative Jackiw-Pi model: One-loop renormalization

NASA Astrophysics Data System (ADS)

Bufalo, R.; Ghasemkhani, M.; Alipour, M.

2018-06-01

In this paper, we study the quantum behavior of the noncommutative Jackiw-Pi model. After establishing the Becchi-Rouet-Store-Tyutin (BRST) invariant action, the perturbative renormalizability is discussed, allowing us to introduce the renormalized mass and gauge coupling. We then proceed to compute the one-loop correction to the basic 1PI functions, necessary to determine the renormalized parameters (mass and charge), next we discuss the physical behavior of these parameters.

One-Loop One-Point Functions in Gauge-Gravity Dualities with Defects.

PubMed

Buhl-Mortensen, Isak; de Leeuw, Marius; Ipsen, Asger C; Kristjansen, Charlotte; Wilhelm, Matthias

2016-12-02

We initiate the calculation of loop corrections to correlation functions in 4D defect conformal field theories (dCFTs). More precisely, we consider N=4 SYM theory with a codimension-one defect separating two regions of space, x_{3}>0 and x_{3}<0, where the gauge group is SU(N) and SU(N-k), respectively. This setup is made possible by some of the real scalar fields acquiring a nonvanishing and x_{3}-dependent vacuum expectation value for x_{3}>0. The holographic dual is the D3-D5 probe brane system where the D5-brane geometry is AdS_{4}×S^{2} and a background gauge field has k units of flux through the S^{2}. We diagonalize the mass matrix of the dCFT making use of fuzzy-sphere coordinates and we handle the x_{3} dependence of the mass terms in the 4D Minkowski space propagators by reformulating these as standard massive AdS_{4} propagators. Furthermore, we show that only two Feynman diagrams contribute to the one-loop correction to the one-point function of any single-trace operator and we explicitly calculate this correction in the planar limit for the simplest chiral primary. The result of this calculation is compared to an earlier string-theory computation in a certain double scaling limit and perfect agreement is found. Finally, we discuss how to generalize our calculation to any single-trace operator, to finite N, and to other types of observables such as Wilson loops.

Refrigerator with anti-sweat hot liquid loop

DOE Office of Scientific and Technical Information (OSTI.GOV)

Woolley, S.J.; Cushing, D.S.; Jenkins, T.E.

A cabinet assembly for a refrigerator having a freezer compartment ontop with two top front corners, a fresh food compartment on the bottom, a mullion partition between the compartments and a hot liquid anti-sweat loop is described comprising; an outer sheet metal shell having a top panel, side panels and a front face, a brace located at each of the two top front corners of the cabinet and having two formed sections at right angles to each other and each section is formed as an inwardly open U-shaped channel having a base, a first leg and a second leg spacedmore » apart and integrally joined to the base, fastening means for rigidly attaching each of the second leg of the corner braces to the flange of the third wall of the front face, and means to secure a portion of the hot liquid anti-sweat loop to the braces.« less

T -odd correlations in polarized top quark decays in the sequential decay t (↑)→Xb+W+(→ℓ++νℓ) and in the quasi-three-body decay t (↑)→ Xb+ℓ++νℓ

NASA Astrophysics Data System (ADS)

Fischer, M.; Groote, S.; Körner, J. G.

2018-05-01

We identify the T -odd structure functions that appear in the description of polarized top quark decays in the sequential decay t (↑)→Xb+W+(→ℓ++νℓ) (two structure functions) and the quasi-three-body decay t (↑)→X b+ℓ++νℓ (one structure function). A convenient measure of the magnitude of the T -odd structure functions is the contribution of the imaginary part Im gR of the right-chiral tensor coupling gR to the T -odd structure functions which we work out. Contrary to the case of QCD, the NLO electroweak corrections to polarized top quark decays admit absorptive one-loop vertex contributions. We analytically calculate the imaginary parts of the relevant four electroweak one-loop triangle vertex diagrams and determine their contributions to the T -odd helicity structure functions that appear in the description of polarized top quark decays.

Covariant diagrams for one-loop matching

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Zhengkang

Here, we present a diagrammatic formulation of recently-revived covariant functional approaches to one-loop matching from an ultraviolet (UV) theory to a low-energy effective field theory. Various terms following from a covariant derivative expansion (CDE) are represented by diagrams which, unlike conventional Feynman diagrams, involve gauge-covariant quantities and are thus dubbed "covariant diagrams." The use of covariant diagrams helps organize and simplify one-loop matching calculations, which we illustrate with examples. Of particular interest is the derivation of UV model-independent universal results, which reduce matching calculations of specific UV models to applications of master formulas. We also show how such derivation canmore » be done in a more concise manner than the previous literature, and discuss how additional structures that are not directly captured by existing universal results, including mixed heavy-light loops, open covariant derivatives, and mixed statistics, can be easily accounted for.« less

Covariant diagrams for one-loop matching

DOE PAGES

Zhang, Zhengkang

2017-05-30

Here, we present a diagrammatic formulation of recently-revived covariant functional approaches to one-loop matching from an ultraviolet (UV) theory to a low-energy effective field theory. Various terms following from a covariant derivative expansion (CDE) are represented by diagrams which, unlike conventional Feynman diagrams, involve gauge-covariant quantities and are thus dubbed "covariant diagrams." The use of covariant diagrams helps organize and simplify one-loop matching calculations, which we illustrate with examples. Of particular interest is the derivation of UV model-independent universal results, which reduce matching calculations of specific UV models to applications of master formulas. We also show how such derivation canmore » be done in a more concise manner than the previous literature, and discuss how additional structures that are not directly captured by existing universal results, including mixed heavy-light loops, open covariant derivatives, and mixed statistics, can be easily accounted for.« less

Quantifying the equilibrium partitioning of substituted polycyclic aromatic hydrocarbons in aerosols and clouds using COSMOtherm.

PubMed

Awonaike, Boluwatife; Wang, Chen; Goss, Kai-Uwe; Wania, Frank

2017-03-22

Functional groups attached to polycyclic aromatic hydrocarbons (PAHs) can significantly modify the environmental fate of the parent compound. Equilibrium partition coefficients, which are essential for describing the environmental phase distribution of a compound, are largely unavailable for substituted PAHs (SPAHs). Here, COSMOtherm, a software based on quantum-chemical calculations is used to estimate the atmospherically relevant partition coefficients between the gas phase, the aqueous bulk phase, the water surface and the water insoluble organic matter phase, as well as the salting-out coefficients, for naphthalene, anthracene, phenanthrene, benz(a)anthracene, benzo(a)pyrene and dibenz(a,h)anthracene and 62 of their substituted counterparts. They serve as input parameters for the calculation of equilibrium phase distribution of these compounds in aerosols and clouds. Our results, which were compared with available experimental data, show that the effect of salts, the adsorption to the water surface and the dissolution in a bulk aqueous phase can be safely neglected when estimating the gas-particle partitioning of SPAHs in aerosols. However, for small PAHs with more than one polar functional group the aqueous phase can be the dominant reservoir in a cloud.

One-loop calculations in Supersymmetric Lattice QCD

NASA Astrophysics Data System (ADS)

Costa, M.; Panagopoulos, H.

2017-03-01

We study the self energies of all particles which appear in a lattice regularization of supersymmetric QCD (N = 1). We compute, perturbatively to one-loop, the relevant two-point Green's functions using both the dimensional and the lattice regularizations. Our lattice formulation employs the Wilson fermion acrion for the gluino and quark fields. The gauge group that we consider is SU(Nc) while the number of colors, Nc and the number of flavors, Nf , are kept as generic parameters. We have also searched for relations among the propagators which are computed from our one-loop results. We have obtained analytic expressions for the renormalization functions of the quark field (Zψ), gluon field (Zu), gluino field (Zλ) and squark field (ZA±). We present here results from dimensional regularization, relegating to a forthcoming publication [1] our results along with a more complete list of references. Part of the lattice study regards also the renormalization of quark bilinear operators which, unlike the nonsupersymmetric case, exhibit a rich pattern of operator mixing at the quantum level.

Use of JANAF Tables in Equilibrium Calculations and Partition Function Calculations for an Undergraduate Physical Chemistry Course

ERIC Educational Resources Information Center

Cleary, David A.

2014-01-01

The usefulness of the JANAF tables is demonstrated with specific equilibrium calculations. An emphasis is placed on the nature of standard chemical potential calculations. Also, the use of the JANAF tables for calculating partition functions is examined. In the partition function calculations, the importance of the zero of energy is highlighted.

Partition functions of thermally dissociating diatomic molecules and related momentum problem

NASA Astrophysics Data System (ADS)

Buchowiecki, Marcin

2017-11-01

The anharmonicity and ro-vibrational coupling in ro-vibrational partition functions of diatomic molecules are analyzed for the high temperatures of the thermal dissociation regime. The numerically exact partition functions and thermal energies are calculated. At the high temperatures the proper integration of momenta is important if the partition function of the molecule, understood as bounded system, is to be obtained. The problem of proper treatment of momentum is crucial for correctness of high temperature molecular simulations as the decomposition of simulated molecule have to be avoided; the analysis of O2, H2+, and NH3 molecules allows to show importance of βDe value.

Effective field theory dimensional regularization

NASA Astrophysics Data System (ADS)

Lehmann, Dirk; Prézeau, Gary

2002-01-01

A Lorentz-covariant regularization scheme for effective field theories with an arbitrary number of propagating heavy and light particles is given. This regularization scheme leaves the low-energy analytic structure of Greens functions intact and preserves all the symmetries of the underlying Lagrangian. The power divergences of regularized loop integrals are controlled by the low-energy kinematic variables. Simple diagrammatic rules are derived for the regularization of arbitrary one-loop graphs and the generalization to higher loops is discussed.

Orientifolding of the ABJ Fermi gas

NASA Astrophysics Data System (ADS)

Okuyama, Kazumi

2016-03-01

The grand partition functions of ABJ theory can be factorized into even and odd parts under the reflection of fermion coordinate in the Fermi gas approach. In some cases, the even/odd part of ABJ grand partition function is equal to that of {N}=5O(n)× USp({n}^') theory, hence it is natural to think of the even/odd projection of grand partition function as an orientifolding of ABJ Fermi gas system. By a systematic WKB analysis, we determine the coefficients in the perturbative part of grand potential of such orientifold ABJ theory. We also find the exact form of the first few "half-instanton" corrections coming from the twisted sector of the reflection of fermion coordinate. For the Chern-Simons level k = 2 ,4 ,8 we find closed form expressions of the grand partition functions of orientifold ABJ theory, and for k = 2 , 4 we prove the functional relations among the grand partition functions conjectured in arXiv:1410.7658.

Data approximation using a blending type spline construction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dalmo, Rune; Bratlie, Jostein

2014-11-18

Generalized expo-rational B-splines (GERBS) is a blending type spline construction where local functions at each knot are blended together by C{sup k}-smooth basis functions. One way of approximating discrete regular data using GERBS is by partitioning the data set into subsets and fit a local function to each subset. Partitioning and fitting strategies can be devised such that important or interesting data points are interpolated in order to preserve certain features. We present a method for fitting discrete data using a tensor product GERBS construction. The method is based on detection of feature points using differential geometry. Derivatives, which aremore » necessary for feature point detection and used to construct local surface patches, are approximated from the discrete data using finite differences.« less

Acquisition and Tracking Behavior of Phase-Locked Loops

NASA Technical Reports Server (NTRS)

Viterbi, A. J.

1958-01-01

Phase-locked or APC loops have found increasing applications in recent years as tracking filters, synchronizing devices, and narrowband FM discriminators. Considerable work has been performed to determine the noise-squelching properties of the loop when it is operating in or near phase lock and is functioning as a linear coherent detector. However, insufficient consideration has been devoted to the non-linear behavior of the loop when it is out of lock and in the process of pulling in. Experimental evidence has indicated that there is a strong tendency for phase-locked loops to achieve lock under most circumstances. However, the analysis which has appeared in the literature iis limited to the acquisition of a constant frequency reference signal with only one phase-locked loop filter configuration. This work represents an investigation of frequency acquisition properties of phase-locked loops for a variety of reference-signal behavior and loop configurations

One-loop corrections from higher dimensional tree amplitudes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cachazo, Freddy; He, Song; Yuan, Ellis Ye

We show how one-loop corrections to scattering amplitudes of scalars and gauge bosons can be obtained from tree amplitudes in one higher dimension. Starting with a complete tree-level scattering amplitude of n + 2 particles in five dimensions, one assumes that two of them cannot be “detected” and therefore an integration over their LIPS is carried out. The resulting object, function of the remaining n particles, is taken to be four-dimensional by restricting the corresponding momenta. We perform this procedure in the context of the tree-level CHY formulation of amplitudes. The scattering equations obtained in the procedure coincide with thosemore » derived by Geyer et al. from ambitwistor constructions and recently studied by two of the authors for bi-adjoint scalars. They have two sectors of solutions: regular and singular. We prove that the contribution from regular solutions generically gives rise to unphysical poles. However, using a BCFW argument we prove that the unphysical contributions are always homogeneous functions of the loop momentum and can be discarded. We also show that the contribution from singular solutions turns out to be homogeneous as well.« less

One-loop corrections from higher dimensional tree amplitudes

DOE PAGES

Cachazo, Freddy; He, Song; Yuan, Ellis Ye

2016-08-01

We show how one-loop corrections to scattering amplitudes of scalars and gauge bosons can be obtained from tree amplitudes in one higher dimension. Starting with a complete tree-level scattering amplitude of n + 2 particles in five dimensions, one assumes that two of them cannot be “detected” and therefore an integration over their LIPS is carried out. The resulting object, function of the remaining n particles, is taken to be four-dimensional by restricting the corresponding momenta. We perform this procedure in the context of the tree-level CHY formulation of amplitudes. The scattering equations obtained in the procedure coincide with thosemore » derived by Geyer et al. from ambitwistor constructions and recently studied by two of the authors for bi-adjoint scalars. They have two sectors of solutions: regular and singular. We prove that the contribution from regular solutions generically gives rise to unphysical poles. However, using a BCFW argument we prove that the unphysical contributions are always homogeneous functions of the loop momentum and can be discarded. We also show that the contribution from singular solutions turns out to be homogeneous as well.« less

Quantum properties of supersymmetric theories regularized by higher covariant derivatives

NASA Astrophysics Data System (ADS)

Stepanyantz, Konstantin

2018-02-01

We investigate quantum corrections in \\mathscr{N} = 1 non-Abelian supersymmetric gauge theories, regularized by higher covariant derivatives. In particular, by the help of the Slavnov-Taylor identities we prove that the vertices with two ghost legs and one leg of the quantum gauge superfield are finite in all orders. This non-renormalization theorem is confirmed by an explicit one-loop calculation. By the help of this theorem we rewrite the exact NSVZ β-function in the form of the relation between the β-function and the anomalous dimensions of the matter superfields, of the quantum gauge superfield, and of the Faddeev-Popov ghosts. Such a relation has simple qualitative interpretation and allows suggesting a prescription producing the NSVZ scheme in all loops for the theories regularized by higher derivatives. This prescription is verified by the explicit three-loop calculation for the terms quartic in the Yukawa couplings.

Schwannoma of the descending loop of the hypoglossal nerve: Case report.

PubMed

Illuminati, Giulio; Pizzardi, Giulia; Pasqua, Rocco; Palumbo, Piergaspare; Vietri, Francesco

2017-01-01

Schwannomas of the descending loop of the hypoglossal nerve are very rare. They are slow-growing tumors that may masquerade a carotid body tumor. A 60-year-old female was referred for a latero-cervical mass appearing as a chemodectoma at CT-scan. At operation, a 2cm mass arising from the descending loop of the hypoglossal nerve was resected en bloc with the loop itself and a functional lymphadenectomy was associated. Post-operative course was uneventful and the patient is free from disease recurrence at one year follow-up. En bloc resection remains the real curative treatment of Schwannomas, ensuring unlimited freedom from disease, although causing functional impairment which may be significant. Nonetheless recurrence should be prevented as, beside requiring reintervention, it may harbor a malignant evolution towards sarcoma. Schwannomas of the descending lop of the hypoglossal nerve may masquerade a chemodectoma of the carotid bifurcation and can be curatively resected without any functional impairment. Copyright © 2017 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Computational Prediction of Kinetic Rate Constants

DTIC Science & Technology

2006-11-30

without requiring additional data. Zero-point energy ( ZPE ) anharmonicity has a large effect on the accuracy of approximate partition function estimates. If...the accurate ZPE is taken into account, separable approximation partition functions using the most accurate torsion treatment and harmonic treatments...for the remaining degrees of freedom agree with accurate QM partition functions to within a mean accuracy of 9%. If no ZPE anharmonicity correction

Space and Time Partitioning with Hardware Support for Space Applications

NASA Astrophysics Data System (ADS)

Pinto, S.; Tavares, A.; Montenegro, S.

2016-08-01

Complex and critical systems like airplanes and spacecraft implement a very fast growing amount of functions. Typically, those systems were implemented with fully federated architectures, but the number and complexity of desired functions of todays systems led aerospace industry to follow another strategy. Integrated Modular Avionics (IMA) arose as an attractive approach for consolidation, by combining several applications into one single generic computing resource. Current approach goes towards higher integration provided by space and time partitioning (STP) of system virtualization. The problem is existent virtualization solutions are not ready to fully provide what the future of aerospace are demanding: performance, flexibility, safety, security while simultaneously containing Size, Weight, Power and Cost (SWaP-C).This work describes a real time hypervisor for space applications assisted by commercial off-the-shell (COTS) hardware. ARM TrustZone technology is exploited to implement a secure virtualization solution with low overhead and low memory footprint. This is demonstrated by running multiple guest partitions of RODOS operating system on a Xilinx Zynq platform.

Graph coarse-graining reveals differences in the module-level structure of functional brain networks.

PubMed

Kujala, Rainer; Glerean, Enrico; Pan, Raj Kumar; Jääskeläinen, Iiro P; Sams, Mikko; Saramäki, Jari

2016-11-01

Networks have become a standard tool for analyzing functional magnetic resonance imaging (fMRI) data. In this approach, brain areas and their functional connections are mapped to the nodes and links of a network. Even though this mapping reduces the complexity of the underlying data, it remains challenging to understand the structure of the resulting networks due to the large number of nodes and links. One solution is to partition networks into modules and then investigate the modules' composition and relationship with brain functioning. While this approach works well for single networks, understanding differences between two networks by comparing their partitions is difficult and alternative approaches are thus necessary. To this end, we present a coarse-graining framework that uses a single set of data-driven modules as a frame of reference, enabling one to zoom out from the node- and link-level details. As a result, differences in the module-level connectivity can be understood in a transparent, statistically verifiable manner. We demonstrate the feasibility of the method by applying it to networks constructed from fMRI data recorded from 13 healthy subjects during rest and movie viewing. While independently partitioning the rest and movie networks is shown to yield little insight, the coarse-graining framework enables one to pinpoint differences in the module-level structure, such as the increased number of intra-module links within the visual cortex during movie viewing. In addition to quantifying differences due to external stimuli, the approach could also be applied in clinical settings, such as comparing patients with healthy controls. © 2016 Federation of European Neuroscience Societies and John Wiley & Sons Ltd.

Partitioning of Nb, Mo, Ba, Ce, Pb, Th and U between immiscible carbonate and silicate liquids: Evaluating the effects of P2O5,F, and carbonate composition

NASA Technical Reports Server (NTRS)

Jones, J. H.; Walker, D.

1993-01-01

Previously we have reported carbonate liq./silicate liq. partition coefficients (D) for a standard suite of trace elements (Nb, Mo, Ba, Ce, Pb, Th, and U) and Ra and Pa as well. In brief, we have found that immiscible liquid partitioning is a strong function of temperature. As the critical temperature of the carbonate-silicate solvus is approached, all partition coefficients approach unity. Additionally, for the overwhelming majority of the partitioning elements, InD is a linear function of 'ionic field strength,' z/r, where z is the charge of the partitioned cation and r is its ionic radius.

Optimal steering for kinematic vehicles with applications to spatially distributed agents

NASA Astrophysics Data System (ADS)

Brown, Scott; Praeger, Cheryl E.; Giudici, Michael

While there is no universal method to address control problems involving networks of autonomous vehicles, there exist a few promising schemes that apply to different specific classes of problems, which have attracted the attention of many researchers from different fields. In particular, one way to extend techniques that address problems involving a single autonomous vehicle to those involving teams of autonomous vehicles is to use the concept of Voronoi diagram. The Voronoi diagram provides a spatial partition of the environment the team of vehicles operate in, where each element of this partition is associated with a unique vehicle from the team. The partition induces a graph abstraction of the operating space that is in an one-to-one correspondence with the network abstraction of the team of autonomous vehicles; a fact that can provide both conceptual and analytical advantages during mission planning and execution. In this dissertation, we propose the use of a new class of Voronoi-like partitioning schemes with respect to state-dependent proximity (pseudo-) metrics rather than the Euclidean distance or other generalized distance functions, which are typically used in the literature. An important nuance here is that, in contrast to the Euclidean distance, state-dependent metrics can succinctly capture system theoretic features of each vehicle from the team (e.g., vehicle kinematics), as well as the environment-vehicle interactions, which are induced, for example, by local winds/currents. We subsequently illustrate how the proposed concept of state-dependent Voronoi-like partition can induce local control schemes for problems involving networks of spatially distributed autonomous vehicles by examining a sequential pursuit problem of a maneuvering target by a group of pursuers distributed in the plane. The construction of generalized Voronoi diagrams with respect to state-dependent metrics poses some significant challenges. First, the generalized distance metric may be a function of the direction of motion of the vehicle (anisotropic pseudo-distance function) and/or may not be expressible in closed form. Second, such problems fall under the general class of partitioning problems for which the vehicles' dynamics must be taken into account. The topology of the vehicle's configuration space may be non-Euclidean, for example, it may be a manifold embedded in a Euclidean space. In other words, these problems may not be reducible to generalized Voronoi diagram problems for which efficient construction schemes, analytical and/or computational, exist in the literature. This research effort pursues three main objectives. First, we present the complete solution of different steering problems involving a single vehicle in the presence of motion constraints imposed by the maneuverability envelope of the vehicle and/or the presence of a drift field induced by winds/currents in its vicinity. The analysis of each steering problem involving a single vehicle provides us with a state-dependent generalized metric, such as the minimum time-to-go/come. We subsequently use these state-dependent generalized distance functions as the proximity metrics in the formulation of generalized Voronoi-like partitioning problems. The characterization of the solutions of these state-dependent Voronoi-like partitioning problems using either analytical or computational techniques constitutes the second main objective of this dissertation. The third objective of this research effort is to illustrate the use of the proposed concept of state-dependent Voronoi-like partition as a means for passing from control techniques that apply to problems involving a single vehicle to problems involving networks of spatially distributed autonomous vehicles. To this aim, we formulate the problem of sequential/relay pursuit of a maneuvering target by a group of spatially distributed pursuers and subsequently propose a distributed group pursuit strategy that directly derives from the solution of a state-dependent Voronoi-like partitioning problem. (Abstract shortened by UMI.)

In the Loop: The Organization of Team-Based Communication in a Patient-Centered Clinical Collaboration System.

PubMed

Kurahashi, Allison M; Weinstein, Peter B; Jamieson, Trevor; Stinson, Jennifer N; Cafazzo, Joseph A; Lokuge, Bhadra; Morita, Plinio P; Cohen, Eyal; Rapoport, Adam; Bezjak, Andrea; Husain, Amna

2016-03-24

We describe the development and evaluation of a secure Web-based system for the purpose of collaborative care called Loop. Loop assembles the team of care with the patient as an integral member of the team in a secure space. The objectives of this paper are to present the iterative design of the separate views for health care providers (HCPs) within each patient's secure space and examine patients', caregivers', and HCPs' perspectives on this separate view for HCP-only communication. The overall research program includes cycles of ethnography, prototyping, usability testing, and pilot testing. This paper describes the usability testing phase that directly informed development. A descriptive qualitative approach was used to analyze participant perspectives that emerged during usability testing. During usability testing, we sampled 89 participants from three user groups: 23 patients, 19 caregivers, and 47 HCPs. Almost all perspectives from the three user groups supported the need for an HCP-only communication view. In an earlier prototype, the visual presentation caused confusion among HCPs when reading and composing messages about whether a message was visible to the patient. Usability testing guided us to design a more deliberate distinction between posting in the Patient and Team view and the Health Care Provider Only view at the time of composing a message, which once posted is distinguished by an icon. The team made a decision to incorporate an HCP-only communication view based on findings during earlier phases of work. During usability testing we tested the separate communication views, and all groups supported this partition. We spent considerable effort designing the partition; however, preliminary findings from the next phase of evaluation, pilot testing, show that the Patient and Team communication is predominantly being used. This demonstrates the importance of a subsequent phase of the clinical trial of Loop to validate the concept and design.

The Performance of A Sampled Data Delay Lock Loop Implemented with a Kalman Loop Filter.

DTIC Science & Technology

1980-01-01

que for analysis is computer simulation. Other techniques include state variable techniques and z-transform methods. Since the Kalman filter is linear...LOGIC NOT SHOWN Figure 2. Block diagram of the sampled data delay lock loop (SDDLL) Es A/ A 3/A/ Figure 3. Sampled error voltage ( Es ) as a function of...from a sum of two components. The first component is the previous filtered es - timate advanced one step forward by the state transition matrix. The 8

3d expansions of 5d instanton partition functions

NASA Astrophysics Data System (ADS)

Nieri, Fabrizio; Pan, Yiwen; Zabzine, Maxim

2018-04-01

We propose a set of novel expansions of Nekrasov's instanton partition functions. Focusing on 5d supersymmetric pure Yang-Mills theory with unitary gauge group on C_{q,{t}^{-1}}^2× S^1 , we show that the instanton partition function admits expansions in terms of partition functions of unitary gauge theories living on the 3d subspaces C_q× S^1 , C_{t^{-1}}× S^1 and their intersection along S^1 . These new expansions are natural from the BPS/CFT viewpoint, as they can be matched with W q,t correlators involving an arbitrary number of screening charges of two kinds. Our constructions generalize and interpolate existing results in the literature.

Equivalence of several descriptions for 6d SCFT

NASA Astrophysics Data System (ADS)

Hayashi, Hirotaka; Kim, Sung-Soo; Lee, Kimyeong; Yagi, Futoshi

2017-01-01

We show that the three different looking BPS partition functions, namely the elliptic genus of the 6d N=(1, 0) Sp(1) gauge theory with 10 flavors and a tensor multiplet, the Nekrasov partition function of the 5d N=1 Sp(2) gauge theory with 10 flavors, and the Nekrasov partition function of the 5d N=1 SU(3) gauge theory with 10 flavors, are all equal to each other under specific maps among gauge theory parameters. This result strongly suggests that the three gauge theories have an identical UV fixed point. Type IIB 5-brane web diagrams play an essential role to compute the SU(3) Nekrasov partition function as well as establishing the maps.

Computation offloading for real-time health-monitoring devices.

PubMed

Kalantarian, Haik; Sideris, Costas; Tuan Le; Hosseini, Anahita; Sarrafzadeh, Majid

2016-08-01

Among the major challenges in the development of real-time wearable health monitoring systems is to optimize battery life. One of the major techniques with which this objective can be achieved is computation offloading, in which portions of computation can be partitioned between the device and other resources such as a server or cloud. In this paper, we describe a novel dynamic computation offloading scheme for real-time wearable health monitoring devices that adjusts the partitioning of data between the wearable device and mobile application as a function of desired classification accuracy.

On N = 1 partition functions without R-symmetry

DOE PAGES

Knodel, Gino; Liu, James T.; Zayas, Leopoldo A. Pando

2015-03-25

Here, we examine the dependence of four-dimensional Euclidean N = 1 partition functions on coupling constants. In particular, we focus on backgrounds without R-symmetry, which arise in the rigid limit of old minimal supergravity. Backgrounds preserving a single supercharge may be classified as having either trivial or SU(2) structure, with the former including S 4. We show that, in the absence of additional symmetries, the partition function depends non-trivially on all couplings in the trivial structure case, and (anti)-holomorphically on couplings in the SU(2) structure case. In both cases, this allows for ambiguities in the form of finite counterterms, whichmore » in principle render the partition function unphysical. However, we argue that on dimensional grounds, ambiguities are restricted to finite powers in relevant couplings, and can therefore be kept under control. On the other hand, for backgrounds preserving supercharges of opposite chiralities, the partition function is completely independent of all couplings. In this case, the background admits an R-symmetry, and the partition function is physical, in agreement with the results obtained in the rigid limit of new minimal supergravity. Based on a systematic analysis of supersymmetric invariants, we also demonstrate that N = 1 localization is not possible for backgrounds without R-symmetry.« less

Boundary perimeter Bethe ansatz

NASA Astrophysics Data System (ADS)

Frassek, Rouven

2017-06-01

We study the partition function of the six-vertex model in the rational limit on arbitrary Baxter lattices with reflecting boundary. Every such lattice is interpreted as an invariant of the twisted Yangian. This identification allows us to relate the partition function of the vertex model to the Bethe wave function of an open spin chain. We obtain the partition function in terms of creation operators on a reference state from the algebraic Bethe ansatz and as a sum of permutations and reflections from the coordinate Bethe ansatz.

Nontrivial thermodynamics in 't Hooft's large-N limit

NASA Astrophysics Data System (ADS)

Cubero, Axel Cortés

2015-05-01

We study the finite volume/temperature correlation functions of the (1 +1 )-dimensional SU (N ) principal chiral sigma model in the planar limit. The exact S-matrix of the sigma model is known to simplify drastically at large N , and this leads to trivial thermodynamic Bethe ansatz (TBA) equations. The partition function, if derived using the TBA, can be shown to be that of free particles. We show that the correlation functions and expectation values of operators at finite volume/temperature are not those of the free theory, and that the TBA does not give enough information to calculate them. Our analysis is done using the Leclair-Mussardo formula for finite-volume correlators, and knowledge of the exact infinite-volume form factors. We present analytical results for the one-point function of the energy-momentum tensor, and the two-point function of the renormalized field operator. The results for the energy-momentum tensor can be used to define a nontrivial partition function.

Capillary Limit in a Loop Heat Pipe with Dual Evaporators

NASA Technical Reports Server (NTRS)

Ku, Jentung; Birur, Gajanana; Obenschain, Arthur F. (Technical Monitor)

2002-01-01

This paper describes a study on the capillary limit of a loop heat pipe (LHP) with two evaporators and two condensers. Both theoretical analysis and experimental investigation are conducted. Tests include heat load to one evaporator only, even heat loads to both evaporators and uneven heat load to both evaporators. Results show that after the capillary limit is exceeded, vapor will penetrate through the wick of the weaker evaporator and the compensation chamber (CC) of that evaporator will control the loop operating temperature regardless of which CC has been in control prior to the event Because the evaporator can tolerate vapor bubbles, the loop may continue to work and reach a new steady state at a higher operating temperature. The loop may even function with a modest increase in the heat load past the capillary limit With a heat load to only one evaporator, the capillary limit can be identified by rapid increases in the operating temperature and in the temperature difference between the evaporator and the CC. However, it is more difficult to tell when the capillary limit is exceeded if heat loads are applied to both evaporators. In all cases, the loop can recover by reducing the heat load to the loop.

Elliptic supersymmetric integrable model and multivariable elliptic functions

NASA Astrophysics Data System (ADS)

Motegi, Kohei

2017-12-01

We investigate the elliptic integrable model introduced by Deguchi and Martin [Int. J. Mod. Phys. A 7, Suppl. 1A, 165 (1992)], which is an elliptic extension of the Perk-Schultz model. We introduce and study a class of partition functions of the elliptic model by using the Izergin-Korepin analysis. We show that the partition functions are expressed as a product of elliptic factors and elliptic Schur-type symmetric functions. This result resembles recent work by number theorists in which the correspondence between the partition functions of trigonometric models and the product of the deformed Vandermonde determinant and Schur functions were established.

The effective χ parameter in polarizable polymeric systems: One-loop perturbation theory and field-theoretic simulations.

PubMed

Grzetic, Douglas J; Delaney, Kris T; Fredrickson, Glenn H

2018-05-28

We derive the effective Flory-Huggins parameter in polarizable polymeric systems, within a recently introduced polarizable field theory framework. The incorporation of bead polarizabilities in the model self-consistently embeds dielectric response, as well as van der Waals interactions. The latter generate a χ parameter (denoted χ̃) between any two species with polarizability contrast. Using one-loop perturbation theory, we compute corrections to the structure factor Sk and the dielectric function ϵ^(k) for a polarizable binary homopolymer blend in the one-phase region of the phase diagram. The electrostatic corrections to S(k) can be entirely accounted for by a renormalization of the excluded volume parameter B into three van der Waals-corrected parameters B AA , B AB , and B BB , which then determine χ̃. The one-loop theory not only enables the quantitative prediction of χ̃ but also provides useful insight into the dependence of χ̃ on the electrostatic environment (for example, its sensitivity to electrostatic screening). The unapproximated polarizable field theory is amenable to direct simulation via complex Langevin sampling, which we employ here to test the validity of the one-loop results. From simulations of S(k) and ϵ^(k) for a system of polarizable homopolymers, we find that the one-loop theory is best suited to high concentrations, where it performs very well. Finally, we measure χ̃N in simulations of a polarizable diblock copolymer melt and obtain excellent agreement with the one-loop theory. These constitute the first fully fluctuating simulations conducted within the polarizable field theory framework.

The effective χ parameter in polarizable polymeric systems: One-loop perturbation theory and field-theoretic simulations

NASA Astrophysics Data System (ADS)

Grzetic, Douglas J.; Delaney, Kris T.; Fredrickson, Glenn H.

2018-05-01

We derive the effective Flory-Huggins parameter in polarizable polymeric systems, within a recently introduced polarizable field theory framework. The incorporation of bead polarizabilities in the model self-consistently embeds dielectric response, as well as van der Waals interactions. The latter generate a χ parameter (denoted χ ˜ ) between any two species with polarizability contrast. Using one-loop perturbation theory, we compute corrections to the structure factor S (k ) and the dielectric function ɛ ^ (k ) for a polarizable binary homopolymer blend in the one-phase region of the phase diagram. The electrostatic corrections to S(k) can be entirely accounted for by a renormalization of the excluded volume parameter B into three van der Waals-corrected parameters BAA, BAB, and BBB, which then determine χ ˜ . The one-loop theory not only enables the quantitative prediction of χ ˜ but also provides useful insight into the dependence of χ ˜ on the electrostatic environment (for example, its sensitivity to electrostatic screening). The unapproximated polarizable field theory is amenable to direct simulation via complex Langevin sampling, which we employ here to test the validity of the one-loop results. From simulations of S(k) and ɛ ^ (k ) for a system of polarizable homopolymers, we find that the one-loop theory is best suited to high concentrations, where it performs very well. Finally, we measure χ ˜ N in simulations of a polarizable diblock copolymer melt and obtain excellent agreement with the one-loop theory. These constitute the first fully fluctuating simulations conducted within the polarizable field theory framework.

On program restructuring, scheduling, and communication for parallel processor systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Polychronopoulos, Constantine D.

1986-08-01

This dissertation discusses several software and hardware aspects of program execution on large-scale, high-performance parallel processor systems. The issues covered are program restructuring, partitioning, scheduling and interprocessor communication, synchronization, and hardware design issues of specialized units. All this work was performed focusing on a single goal: to maximize program speedup, or equivalently, to minimize parallel execution time. Parafrase, a Fortran restructuring compiler was used to transform programs in a parallel form and conduct experiments. Two new program restructuring techniques are presented, loop coalescing and subscript blocking. Compile-time and run-time scheduling schemes are covered extensively. Depending on the program construct, thesemore » algorithms generate optimal or near-optimal schedules. For the case of arbitrarily nested hybrid loops, two optimal scheduling algorithms for dynamic and static scheduling are presented. Simulation results are given for a new dynamic scheduling algorithm. The performance of this algorithm is compared to that of self-scheduling. Techniques for program partitioning and minimization of interprocessor communication for idealized program models and for real Fortran programs are also discussed. The close relationship between scheduling, interprocessor communication, and synchronization becomes apparent at several points in this work. Finally, the impact of various types of overhead on program speedup and experimental results are presented.« less

Closed-loop spontaneous baroreflex transfer function is inappropriate for system identification of neural arc but partly accurate for peripheral arc: predictability analysis

PubMed Central

Kamiya, Atsunori; Kawada, Toru; Shimizu, Shuji; Sugimachi, Masaru

2011-01-01

Abstract Although the dynamic characteristics of the baroreflex system have been described by baroreflex transfer functions obtained from open-loop analysis, the predictability of time-series output dynamics from input signals, which should confirm the accuracy of system identification, remains to be elucidated. Moreover, despite theoretical concerns over closed-loop system identification, the accuracy and the predictability of the closed-loop spontaneous baroreflex transfer function have not been evaluated compared with the open-loop transfer function. Using urethane and α-chloralose anaesthetized, vagotomized and aortic-denervated rabbits (n = 10), we identified open-loop baroreflex transfer functions by recording renal sympathetic nerve activity (SNA) while varying the vascularly isolated intracarotid sinus pressure (CSP) according to a binary random (white-noise) sequence (operating pressure ± 20 mmHg), and using a simplified equation to calculate closed-loop-spontaneous baroreflex transfer function while matching CSP with systemic arterial pressure (AP). Our results showed that the open-loop baroreflex transfer functions for the neural and peripheral arcs predicted the time-series SNA and AP outputs from measured CSP and SNA inputs, with r2 of 0.8 ± 0.1 and 0.8 ± 0.1, respectively. In contrast, the closed-loop-spontaneous baroreflex transfer function for the neural arc was markedly different from the open-loop transfer function (enhanced gain increase and a phase lead), and did not predict the time-series SNA dynamics (r2; 0.1 ± 0.1). However, the closed-loop-spontaneous baroreflex transfer function of the peripheral arc partially matched the open-loop transfer function in gain and phase functions, and had limited but reasonable predictability of the time-series AP dynamics (r2, 0.7 ± 0.1). A numerical simulation suggested that a noise predominantly in the neural arc under resting conditions might be a possible mechanism responsible for our findings. Furthermore, the predictabilities of the neural arc transfer functions obtained in open-loop and closed-loop conditions were validated by closed-loop pharmacological (phenylephrine and nitroprusside infusions) pressure interventions. Time-series SNA responses to drug-induced AP changes predicted by the open-loop transfer function matched closely the measured responses (r2, 0.9 ± 0.1), whereas SNA responses predicted by closed-loop-spontaneous transfer function deviated greatly and were the inverse of measured responses (r, −0.8 ± 0.2). These results indicate that although the spontaneous baroreflex transfer function obtained by closed-loop analysis has been believed to represent the neural arc function, it is inappropriate for system identification of the neural arc but is essentially appropriate for the peripheral arc under resting conditions, when compared with open-loop analysis. PMID:21486839

On the Casimir scaling violation in the cusp anomalous dimension at small angle

NASA Astrophysics Data System (ADS)

Grozin, Andrey; Henn, Johannes; Stahlhofen, Maximilian

2017-10-01

We compute the four-loop n f contribution proportional to the quartic Casimir of the QCD cusp anomalous dimension as an expansion for small cusp angle ϕ. This piece is gauge invariant, violates Casimir scaling, and first appears at four loops. It requires the evaluation of genuine non-planar four-loop Feynman integrals. We present results up to O({φ}^4) . One motivation for our calculation is to probe a recent conjecture on the all-order structure of the cusp anomalous dimension. As a byproduct we obtain the four-loop HQET wave function anomalous dimension for this color structure.

Compressible fluids with Maxwell-type equations, the minimal coupling with electromagnetic field and the Stefan–Boltzmann law

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mendes, Albert C.R., E-mail: albert@fisica.ufjf.br; Takakura, Flavio I., E-mail: takakura@fisica.ufjf.br; Abreu, Everton M.C., E-mail: evertonabreu@ufrrj.br

In this work we have obtained a higher-derivative Lagrangian for a charged fluid coupled with the electromagnetic fluid and the Dirac’s constraints analysis was discussed. A set of first-class constraints fixed by noncovariant gauge condition were obtained. The path integral formalism was used to obtain the partition function for the corresponding higher-derivative Hamiltonian and the Faddeev–Popov ansatz was used to construct an effective Lagrangian. Through the partition function, a Stefan–Boltzmann type law was obtained. - Highlights: • Higher-derivative Lagrangian for a charged fluid. • Electromagnetic coupling and Dirac’s constraint analysis. • Partition function through path integral formalism. • Stefan–Boltzmann-kind lawmore » through the partition function.« less

Binary partition tree analysis based on region evolution and its application to tree simplification.

PubMed

Lu, Huihai; Woods, John C; Ghanbari, Mohammed

2007-04-01

Pyramid image representations via tree structures are recognized methods for region-based image analysis. Binary partition trees can be applied which document the merging process with small details found at the bottom levels and larger ones close to the root. Hindsight of the merging process is stored within the tree structure and provides the change histories of an image property from the leaf to the root node. In this work, the change histories are modelled by evolvement functions and their second order statistics are analyzed by using a knee function. Knee values show the reluctancy of each merge. We have systematically formulated these findings to provide a novel framework for binary partition tree analysis, where tree simplification is demonstrated. Based on an evolvement function, for each upward path in a tree, the tree node associated with the first reluctant merge is considered as a pruning candidate. The result is a simplified version providing a reduced solution space and still complying with the definition of a binary tree. The experiments show that image details are preserved whilst the number of nodes is dramatically reduced. An image filtering tool also results which preserves object boundaries and has applications for segmentation.

Noncommutative QED+QCD and the {beta} function for QED

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ettefaghi, M. M.; Haghighat, M.; Mohammadi, R.

2010-11-15

QED based on {theta}-unexpanded noncomutative space-time in contrast with the noncommutative QED based on {theta}-expanded U(1) gauge theory via the Seiberg-Witten map is one-loop renormalizable. Meanwhile it suffers from asymptotic freedom that is not in agreement with the experiment. We show that the QED part of the U{sub *}(3)xU{sub *}(1) gauge group as an appropriate gauge group for the noncommutative QED+QCD is not only one-loop renormalizable but also has a {beta} function that can be positive, negative and even zero. In fact the {beta} function depends on the mixing parameter {delta}{sub 13} as a free parameter and it will bemore » equal to its counterpart in the ordinary QED for {delta}{sub 13}=0.367{pi}.« less

On the bispectra of very massive tracers in the Effective Field Theory of Large-Scale Structure

DOE PAGES

Nadler, Ethan O.; Perko, Ashley; Senatore, Leonardo

2018-02-01

The Effective Field Theory of Large-Scale Structure (EFTofLSS) provides a consistent perturbative framework for describing the statistical distribution of cosmological large-scale structure. In a previous EFTofLSS calculation that involved the one-loop power spectra and tree-level bispectra, it was shown that the k-reach of the prediction for biased tracers is comparable for all investigated masses if suitable higher-derivative biases, which are less suppressed for more massive tracers, are added. However, it is possible that the non-linear biases grow faster with tracer mass than the linear bias, implying that loop contributions could be the leading correction to the bispectra. To check this,more » we include the one-loop contributions in a fit to numerical data in the limit of strongly enhanced higher-order biases. Here, we show that the resulting one-loop power spectra and higher-derivative plus leading one-loop bispectra fit the two- and three-point functions respectively up to k≃0.19 h Mpc -1 and ksime 0.14 h Mpc -1 at the percent level. We find that the higher-order bias coefficients are not strongly enhanced, and we argue that the gain in perturbative reach due to the leading one-loop contributions to the bispectra is relatively small. Thus, we conclude that higher-derivative biases provide the leading correction to the bispectra for tracers of a very wide range of masses.« less

On the bispectra of very massive tracers in the Effective Field Theory of Large-Scale Structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nadler, Ethan O.; Perko, Ashley; Senatore, Leonardo

The Effective Field Theory of Large-Scale Structure (EFTofLSS) provides a consistent perturbative framework for describing the statistical distribution of cosmological large-scale structure. In a previous EFTofLSS calculation that involved the one-loop power spectra and tree-level bispectra, it was shown that the k-reach of the prediction for biased tracers is comparable for all investigated masses if suitable higher-derivative biases, which are less suppressed for more massive tracers, are added. However, it is possible that the non-linear biases grow faster with tracer mass than the linear bias, implying that loop contributions could be the leading correction to the bispectra. To check this,more » we include the one-loop contributions in a fit to numerical data in the limit of strongly enhanced higher-order biases. Here, we show that the resulting one-loop power spectra and higher-derivative plus leading one-loop bispectra fit the two- and three-point functions respectively up to k≃0.19 h Mpc -1 and ksime 0.14 h Mpc -1 at the percent level. We find that the higher-order bias coefficients are not strongly enhanced, and we argue that the gain in perturbative reach due to the leading one-loop contributions to the bispectra is relatively small. Thus, we conclude that higher-derivative biases provide the leading correction to the bispectra for tracers of a very wide range of masses.« less

Architectural roles of multiple chromatin insulators at the human apolipoprotein gene cluster

PubMed Central

Mishiro, Tsuyoshi; Ishihara, Ko; Hino, Shinjiro; Tsutsumi, Shuichi; Aburatani, Hiroyuki; Shirahige, Katsuhiko; Kinoshita, Yoshikazu; Nakao, Mitsuyoshi

2009-01-01

Long-range regulatory elements and higher-order chromatin structure coordinate the expression of multiple genes in cluster, and CTCF/cohesin-mediated chromatin insulator may be a key in this regulation. The human apolipoprotein (APO) A1/C3/A4/A5 gene region, whose alterations increase the risk of dyslipidemia and atherosclerosis, is partitioned at least by three CTCF-enriched sites and three cohesin protein RAD21-enriched sites (two overlap with the CTCF sites), resulting in the formation of two transcribed chromatin loops by interactions between insulators. The C3 enhancer and APOC3/A4/A5 promoters reside in the same loop, where the APOC3/A4 promoters are pointed towards the C3 enhancer, whereas the APOA1 promoter is present in the different loop. The depletion of either CTCF or RAD21 disrupts the chromatin loop structure, together with significant changes in the APO expression and the localization of transcription factor hepatocyte nuclear factor (HNF)-4α and transcriptionally active form of RNA polymerase II at the APO promoters. Thus, CTCF/cohesin-mediated insulators maintain the chromatin loop formation and the localization of transcriptional apparatus at the promoters, suggesting an essential role of chromatin insulation in controlling the expression of clustered genes. PMID:19322193

Comparative analysis of local spin definitions.

PubMed

Herrmann, Carmen; Reiher, Markus; Hess, Bernd A

2005-01-15

This work provides a survey of the definition of electron spin as a local property and its dependence on several parameters in actual calculations. We analyze one-determinant wave functions constructed from Hartree-Fock and, in particular, from Kohn-Sham orbitals within the collinear approach to electron spin. The scalar total spin operators S2 and Sz are partitioned by projection operators, as introduced by Clark and Davidson, in order to obtain local spin operators SASB and SzA, respectively. To complement the work of Davidson and co-workers, we analyze some features of local spins which have not yet been discussed in sufficient depth. The dependence of local spin on the choice of basis set, density functional, and projector is studied. We also discuss the results of Sz partitioning and show that SzA values depend less on these parameters than SASB values. Furthermore, we demonstrate that for small organic test molecules, a partitioning of Sz with preorthogonalized Lowdin projectors yields nearly the same results as one obtains using atoms-in-molecules projectors. In addition, the physical significance of nonzero SASB values for closed-shell molecules is investigated. It is shown that due to this problem, SASB values are useful for calculations of relative spin values, but not for absolute local spins, where SzA values appear to be better suited.

Infrared propagators of Yang-Mills theory from perturbation theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tissier, Matthieu; Wschebor, Nicolas

2010-11-15

We show that the correlation functions of ghosts and gluons for the pure Yang-Mills theory in Landau gauge can be accurately reproduced for all momenta by a one-loop calculation. The key point is to use a massive extension of the Faddeev-Popov action. The agreement with lattice simulation is excellent in d=4. The one-loop calculation also reproduces all the characteristic features of the lattice simulations in d=3 and naturally explains the peculiarities of the propagators in d=2.

Adaptive Fuzzy Tracking Control for a Class of MIMO Nonlinear Systems in Nonstrict-Feedback Form.

PubMed

Chen, Bing; Lin, Chong; Liu, Xiaoping; Liu, Kefu

2015-12-01

This paper focuses on the problem of fuzzy adaptive control for a class of multiinput and multioutput (MIMO) nonlinear systems in nonstrict-feedback form, which contains the strict-feedback form as a special case. By the condition of variable partition, a new fuzzy adaptive backstepping is proposed for such a class of nonlinear MIMO systems. The suggested fuzzy adaptive controller guarantees that the proposed control scheme can guarantee that all the signals in the closed-loop system are semi-globally uniformly ultimately bounded and the tracking errors eventually converge to a small neighborhood around the origin. The main advantage of this paper is that a control approach is systematically derived for nonlinear systems with strong interconnected terms which are the functions of all states of the whole system. Simulation results further illustrate the effectiveness of the suggested approach.

CLOSED-FIELD CORONAL HEATING DRIVEN BY WAVE TURBULENCE

DOE Office of Scientific and Technical Information (OSTI.GOV)

Downs, Cooper; Lionello, Roberto; Mikić, Zoran

To simulate the energy balance of coronal plasmas on macroscopic scales, we often require the specification of the coronal heating mechanism in some functional form. To go beyond empirical formulations and to build a more physically motivated heating function, we investigate the wave-turbulence-driven (WTD) phenomenology for the heating of closed coronal loops. Our implementation is designed to capture the large-scale propagation, reflection, and dissipation of wave turbulence along a loop. The parameter space of this model is explored by solving the coupled WTD and hydrodynamic evolution in 1D for an idealized loop. The relevance to a range of solar conditionsmore » is also established by computing solutions for over one hundred loops extracted from a realistic 3D coronal field. Due to the implicit dependence of the WTD heating model on loop geometry and plasma properties along the loop and at the footpoints, we find that this model can significantly reduce the number of free parameters when compared to traditional empirical heating models, and still robustly describe a broad range of quiet-Sun and active region conditions. The importance of the self-reflection term in producing relatively short heating scale heights and thermal nonequilibrium cycles is also discussed.« less

Closed-field Coronal Heating Driven by Wave Turbulence

NASA Astrophysics Data System (ADS)

Downs, Cooper; Lionello, Roberto; Mikić, Zoran; Linker, Jon A.; Velli, Marco

2016-12-01

To simulate the energy balance of coronal plasmas on macroscopic scales, we often require the specification of the coronal heating mechanism in some functional form. To go beyond empirical formulations and to build a more physically motivated heating function, we investigate the wave-turbulence-driven (WTD) phenomenology for the heating of closed coronal loops. Our implementation is designed to capture the large-scale propagation, reflection, and dissipation of wave turbulence along a loop. The parameter space of this model is explored by solving the coupled WTD and hydrodynamic evolution in 1D for an idealized loop. The relevance to a range of solar conditions is also established by computing solutions for over one hundred loops extracted from a realistic 3D coronal field. Due to the implicit dependence of the WTD heating model on loop geometry and plasma properties along the loop and at the footpoints, we find that this model can significantly reduce the number of free parameters when compared to traditional empirical heating models, and still robustly describe a broad range of quiet-Sun and active region conditions. The importance of the self-reflection term in producing relatively short heating scale heights and thermal nonequilibrium cycles is also discussed.

Wigner expansions for partition functions of nonrelativistic and relativistic oscillator systems

NASA Technical Reports Server (NTRS)

Zylka, Christian; Vojta, Guenter

1993-01-01

The equilibrium quantum statistics of various anharmonic oscillator systems including relativistic systems is considered within the Wigner phase space formalism. For this purpose the Wigner series expansion for the partition function is generalized to include relativistic corrections. The new series for partition functions and all thermodynamic potentials yield quantum corrections in terms of powers of h(sup 2) and relativistic corrections given by Kelvin functions (modified Hankel functions) K(sub nu)(mc(sup 2)/kT). As applications, the symmetric Toda oscillator, isotonic and singular anharmonic oscillators, and hindered rotators, i.e. oscillators with cosine potential, are addressed.

Non-supersymmetric Wilson loop in N = 4 SYM and defect 1d CFT

NASA Astrophysics Data System (ADS)

Beccaria, Matteo; Giombi, Simone; Tseytlin, Arkady A.

2018-03-01

Following Polchinski and Sully (arXiv:1104.5077), we consider a generalized Wilson loop operator containing a constant parameter ζ in front of the scalar coupling term, so that ζ = 0 corresponds to the standard Wilson loop, while ζ = 1 to the locally supersymmetric one. We compute the expectation value of this operator for circular loop as a function of ζ to second order in the planar weak coupling expansion in N = 4 SYM theory. We then explain the relation of the expansion near the two conformal points ζ = 0 and ζ = 1 to the correlators of scalar operators inserted on the loop. We also discuss the AdS5 × S 5 string 1-loop correction to the strong-coupling expansion of the standard circular Wilson loop, as well as its generalization to the case of mixed boundary conditions on the five-sphere coordinates, corresponding to general ζ. From the point of view of the defect CFT1 defined on the Wilson line, the ζ-dependent term can be seen as a perturbation driving a RG flow from the standard Wilson loop in the UV to the supersymmetric Wilson loop in the IR. Both at weak and strong coupling we find that the logarithm of the expectation value of the standard Wilson loop for the circular contour is larger than that of the supersymmetric one, which appears to be in agreement with the 1d analog of the F-theorem.

Integrated flight/propulsion control system design based on a centralized approach

NASA Technical Reports Server (NTRS)

Garg, Sanjay; Mattern, Duane L.; Bullard, Randy E.

1989-01-01

An integrated flight/propulsion control system design is presented for the piloted longitudinal landing task with a modern, statically unstable, fighter aircraft. A centralized compensator based on the Linear Quadratic Gaussian/Loop Transfer Recovery methodology is first obtained to satisfy the feedback loop performance and robustness specificiations. This high-order centralized compensator is then partitioned into airframe and engine sub-controllers based on modal controllability/observability for the compensator modes. The order of the sub-controllers is then reduced using internally-balanced realization techniques and the sub-controllers are simplified by neglecting the insignificant feedbacks. These sub-controllers have the advantage that they can be implemented as separate controllers on the airframe and the engine while still retaining the important performance and stability characteristics of the full-order centralized compensator. Command prefilters are then designed for the closed-loop system with the simplified sub-controllers to obtain the desired system response to airframe and engine command inputs, and the overall system performance evaluation results are presented.

Non-polynomial closed string field theory: loops and conformal maps

NASA Astrophysics Data System (ADS)

Hua, Long; Kaku, Michio

1990-11-01

Recently, we proposed the complete classical action for the non-polynomial closed string field theory, which succesfully reproduced all closed string tree amplitudes. (The action was simultaneously proposed by the Kyoto group). In this paper, we analyze the structure of the theory. We (a) compute the explicit conformal map for all g-loop, p-puncture diagrams, (b) compute all one-loop, two-puncture maps in terms of hyper-elliptic functions, and (c) analyze their modular structure. We analyze, but do not resolve, the question of modular invariance.

Detection of no-model input-output pairs in closed-loop systems.

PubMed

Potts, Alain Segundo; Alvarado, Christiam Segundo Morales; Garcia, Claudio

2017-11-01

The detection of no-model input-output (IO) pairs is important because it can speed up the multivariable system identification process, since all the pairs with null transfer functions are previously discarded and it can also improve the identified model quality, thus improving the performance of model based controllers. In the available literature, the methods focus just on the open-loop case, since in this case there is not the effect of the controller forcing the main diagonal in the transfer matrix to one and all the other terms to zero. In this paper, a modification of a previous method able to detect no-model IO pairs in open-loop systems is presented, but adapted to perform this duty in closed-loop systems. Tests are performed by using the traditional methods and the proposed one to show its effectiveness. Copyright © 2017 ISA. Published by Elsevier Ltd. All rights reserved.

VizieR Online Data Catalog: Partition functions for molecules and atoms (Barklem+, 2016)

NASA Astrophysics Data System (ADS)

Barklem, P. S.; Collet, R.

2016-02-01

The results and input data are presented in the following files. Table 1 contains dissociation energies from the literature, and final adopted values, for 291 molecules. The literature values are from the compilations of Huber & Herzberg (1979, Constants of Diatomic Molecules (Van Nostrand Reinhold), Luo (2007, Comprehensive Handbook of Chemical Bond Energies (CRC Press)) and G2 theory calculations of Curtiss et al. (1991, J. Chem. Phys., 94, 7221). Table 2 contains the input data for the molecular calculations including adopted dissociation energy, nuclear spins, molecular spectroscopic constants and their sources. There are 291 files, one for each molecule, labelled by the molecule name. The various molecular spectroscopic constants are as defined in the paper. Table 4 contains the first, second and third ionisation energies for all chemical elements from H to U. The data comes from the CRC Handbook of Chemistry and Physics (Haynes, W.M. 2010, CRC Handbook of Chemistry and Physics, 91st edn. (CRC Press, Taylor and Francis Group)). Table 5a contains a list of keys to bibliographic references for the atomic energy level data that was extracted from NIST Atomic Spectra Database and used in the present work to compute atomic partition functions. The citation keys are abbreviations of the full bibliographic references which are made available in Table 5b in BibTeX format. Table 5b contains the full bibliographic references for the atomic energy level data that was extracted from the NIST Atomic Spectra Database. Table 6 contains tabulated partition function data as a function of temperature for 291 molecules. Table 7 contains tabulated equilibrium constant data as a function of temperature for 291 molecules. Table 8 contains tabulated partition function data as a function of temperature for 284 atoms and ions. The paper should be consulted for further details. (10 data files).

Calculation of site affinity constants and cooperativity coefficients for binding of ligands and/or protons to macromolecules. II. Relationships between chemical model and partition function algorithm.

PubMed

Fisicaro, E; Braibanti, A; Lamb, J D; Oscarson, J L

1990-05-01

The relationships between the chemical properties of a system and the partition function algorithm as applied to the description of multiple equilibria in solution are explained. The partition functions ZM, ZA, and ZH are obtained from powers of the binary generating functions Jj = (1 + kappa j gamma j,i[Y])i tau j, where i tau j = p tau j, q tau j, or r tau j represent the maximum number of sites in sites in class j, for Y = M, A, or H, respectively. Each term of the generating function can be considered an element (ij) of a vector Jj and each power of the cooperativity factor gamma ij,i can be considered an element of a diagonal cooperativity matrix gamma j. The vectors Jj are combined in tensor product matrices L tau = (J1) [J2]...[Jj]..., thus representing different receptor-ligand combinations. The partition functions are obtained by summing elements of the tensor matrices. The relationship of the partition functions with the total chemical amounts TM, TA, and TH has been found. The aim is to describe the total chemical amounts TM, TA, and TH as functions of the site affinity constants kappa j and cooperativity coefficients bj. The total amounts are calculated from the sum of elements of tensor matrices Ll. Each set of indices (pj..., qj..., rj...) represents one element of a tensor matrix L tau and defines each term of the summation. Each term corresponds to the concentration of a chemical microspecies. The distinction between microspecies MpjAqjHrj with ligands bound on specific sites and macrospecies MpAqHR corresponding to a chemical stoichiometric composition is shown. The translation of the properties of chemical model schemes into the algorithms for the generation of partition functions is illustrated with reference to a series of examples of gradually increasing complexity. The equilibria examined concern: (1) a unique class of sites; (2) the protonation of a base with two classes of sites; (3) the simultaneous binding of ligand A and proton H to a macromolecule or receptor M with four classes of sites; and (4) the binding to a macromolecule M of ligand A which is in turn a receptor for proton H. With reference to a specific example, it is shown how a computer program for least-squares refinement of variables kappa j and bj can be organized. The chemical model from the free components M, A, and H to the saturated macrospecies MpAQHR, with possible complex macrospecies MpAq and AHR, is defined first.(ABSTRACT TRUNCATED AT 250 WORDS)

Multilevel Green's function interpolation method for scattering from composite metallic and dielectric objects.

PubMed

Shi, Yan; Wang, Hao Gang; Li, Long; Chan, Chi Hou

2008-10-01

A multilevel Green's function interpolation method based on two kinds of multilevel partitioning schemes--the quasi-2D and the hybrid partitioning scheme--is proposed for analyzing electromagnetic scattering from objects comprising both conducting and dielectric parts. The problem is formulated using the surface integral equation for homogeneous dielectric and conducting bodies. A quasi-2D multilevel partitioning scheme is devised to improve the efficiency of the Green's function interpolation. In contrast to previous multilevel partitioning schemes, noncubic groups are introduced to discretize the whole EM structure in this quasi-2D multilevel partitioning scheme. Based on the detailed analysis of the dimension of the group in this partitioning scheme, a hybrid quasi-2D/3D multilevel partitioning scheme is proposed to effectively handle objects with fine local structures. Selection criteria for some key parameters relating to the interpolation technique are given. The proposed algorithm is ideal for the solution of problems involving objects such as missiles, microstrip antenna arrays, photonic bandgap structures, etc. Numerical examples are presented to show that CPU time is between O(N) and O(N log N) while the computer memory requirement is O(N).

Communication: Hilbert-space partitioning of the molecular one-electron density matrix with orthogonal projectors

NASA Astrophysics Data System (ADS)

Vanfleteren, Diederik; Van Neck, Dimitri; Bultinck, Patrick; Ayers, Paul W.; Waroquier, Michel

2010-12-01

A double-atom partitioning of the molecular one-electron density matrix is used to describe atoms and bonds. All calculations are performed in Hilbert space. The concept of atomic weight functions (familiar from Hirshfeld analysis of the electron density) is extended to atomic weight matrices. These are constructed to be orthogonal projection operators on atomic subspaces, which has significant advantages in the interpretation of the bond contributions. In close analogy to the iterative Hirshfeld procedure, self-consistency is built in at the level of atomic charges and occupancies. The method is applied to a test set of about 67 molecules, representing various types of chemical binding. A close correlation is observed between the atomic charges and the Hirshfeld-I atomic charges.

One-loop gravitational wave spectrum in de Sitter spacetime

NASA Astrophysics Data System (ADS)

Fröb, Markus B.; Roura, Albert; Verdaguer, Enric

2012-08-01

The two-point function for tensor metric perturbations around de Sitter spacetime including one-loop corrections from massless conformally coupled scalar fields is calculated exactly. We work in the Poincaré patch (with spatially flat sections) and employ dimensional regularization for the renormalization process. Unlike previous studies we obtain the result for arbitrary time separations rather than just equal times. Moreover, in contrast to existing results for tensor perturbations, ours is manifestly invariant with respect to the subgroup of de Sitter isometries corresponding to a simultaneous time translation and rescaling of the spatial coordinates. Having selected the right initial state for the interacting theory via an appropriate iepsilon prescription is crucial for that. Finally, we show that although the two-point function is a well-defined spacetime distribution, the equal-time limit of its spatial Fourier transform is divergent. Therefore, contrary to the well-defined distribution for arbitrary time separations, the power spectrum is strictly speaking ill-defined when loop corrections are included.

Galileo attitude and articulation control subsystem closed loop testing

NASA Technical Reports Server (NTRS)

Lembeck, M. F.; Pignatano, N. D.

1983-01-01

In order to ensure the reliable operation of the Attitude and Articulation Control Subsystem (AACS) which will guide the Galileo spacecraft on its two and one-half year journey to Jupiter, the AACS is being rigorously tested. The primary objectives of the test program are the verification of the AACS's form, fit, and function, especially with regard to subsystem external interfaces and the functional operation of the flight software. Attention is presently given to the Galileo Closed Loop Test System, which simulates the dynamic and 'visual' flight environment for AACS components in the laboratory.

Dual-Level Method for Estimating Multistructural Partition Functions with Torsional Anharmonicity.

PubMed

Bao, Junwei Lucas; Xing, Lili; Truhlar, Donald G

2017-06-13

For molecules with multiple torsions, an accurate evaluation of the molecular partition function requires consideration of multiple structures and their torsional-potential anharmonicity. We previously developed a method called MS-T for this problem, and it requires an exhaustive conformational search with frequency calculations for all the distinguishable conformers; this can become expensive for molecules with a large number of torsions (and hence a large number of structures) if it is carried out with high-level methods. In the present work, we propose a cost-effective method to approximate the MS-T partition function when there are a large number of structures, and we test it on a transition state that has eight torsions. This new method is a dual-level method that combines an exhaustive conformer search carried out by a low-level electronic structure method (for instance, AM1, which is very inexpensive) and selected calculations with a higher-level electronic structure method (for example, density functional theory with a functional that is suitable for conformational analysis and thermochemistry). To provide a severe test of the new method, we consider a transition state structure that has 8 torsional degrees of freedom; this transition state structure is formed along one of the reaction pathways of the hydrogen abstraction reaction (at carbon-1) of ketohydroperoxide (KHP; its IUPAC name is 4-hydroperoxy-2-pentanone) by OH radical. We find that our proposed dual-level method is able to significantly reduce the computational cost for computing MS-T partition functions for this test case with a large number of torsions and with a large number of conformers because we carry out high-level calculations for only a fraction of the distinguishable conformers found by the low-level method. In the example studied here, the dual-level method with 40 high-level optimizations (1.8% of the number of optimizations in a coarse-grained full search and 0.13% of the number of optimizations in a fine-grained full search) reproduces the full calculation of the high-level partition function within a factor of 1.0 to 2.0 from 200 to 1000 K. The error in the dual-level method can be further reduced to factors of 0.6 to 1.1 over the whole temperature interval from 200 to 2400 K by optimizing 128 structures (5.9% of the number of optimizations in a fine-grained full search and 0.41% of the number of optimizations in a fine-grained full search). These factor-of-two or better errors are small compared to errors up to a factor of 1.0 × 10 3 if one neglects multistructural effects for the case under study.

Perturbed generalized multicritical one-matrix models

NASA Astrophysics Data System (ADS)

Ambjørn, J.; Chekhov, L.; Makeenko, Y.

2018-03-01

We study perturbations around the generalized Kazakov multicritical one-matrix model. The multicritical matrix model has a potential where the coefficients of zn only fall off as a power 1 /n s + 1. This implies that the potential and its derivatives have a cut along the real axis, leading to technical problems when one performs perturbations away from the generalized Kazakov model. Nevertheless it is possible to relate the perturbed partition function to the tau-function of a KdV hierarchy and solve the model by a genus expansion in the double scaling limit.

New method of computing the contributions of graphs without lepton loops to the electron anomalous magnetic moment in QED

NASA Astrophysics Data System (ADS)

Volkov, Sergey

2017-11-01

This paper presents a new method of numerical computation of the mass-independent QED contributions to the electron anomalous magnetic moment which arise from Feynman graphs without closed electron loops. The method is based on a forestlike subtraction formula that removes all ultraviolet and infrared divergences in each Feynman graph before integration in Feynman-parametric space. The integration is performed by an importance sampling Monte-Carlo algorithm with the probability density function that is constructed for each Feynman graph individually. The method is fully automated at any order of the perturbation series. The results of applying the method to 2-loop, 3-loop, 4-loop Feynman graphs, and to some individual 5-loop graphs are presented, as well as the comparison of this method with other ones with respect to Monte Carlo convergence speed.

Coordinated gripping of substrate by subunits of a AAA+ proteolytic machine

PubMed Central

Iosefson, Ohad; Nager, Andrew R.; Baker, Tania A.; Sauer, Robert T.

2014-01-01

Hexameric AAA+ unfoldases of ATP-dependent proteases and protein-remodeling machines use conserved loops that line the axial pore to apply force to substrates during the mechanical processes of protein unfolding and translocation. Whether loops from multiple subunits act independently or coordinately in these processes is a critical aspect of mechanism but is currently unknown for any AAA+ machine. By studying covalently linked hexamers of the E. coli ClpX unfoldase bearing different numbers and configurations of wild-type and mutant pore loops, we show that loops function synergistically, with the number of wild-type loops required for efficient degradation depending upon the stability of the protein substrate. Our results support a mechanism in which a power stroke initiated in one subunit of the ClpX hexamer results in the concurrent movement of all six pore loops, which coordinately grip and apply force to the substrate. PMID:25599533

A comparative approach to closed-loop computation.

PubMed

Roth, E; Sponberg, S; Cowan, N J

2014-04-01

Neural computation is inescapably closed-loop: the nervous system processes sensory signals to shape motor output, and motor output consequently shapes sensory input. Technological advances have enabled neuroscientists to close, open, and alter feedback loops in a wide range of experimental preparations. The experimental capability of manipulating the topology-that is, how information can flow between subsystems-provides new opportunities to understand the mechanisms and computations underlying behavior. These experiments encompass a spectrum of approaches from fully open-loop, restrained preparations to the fully closed-loop character of free behavior. Control theory and system identification provide a clear computational framework for relating these experimental approaches. We describe recent progress and new directions for translating experiments at one level in this spectrum to predictions at another level. Operating across this spectrum can reveal new understanding of how low-level neural mechanisms relate to high-level function during closed-loop behavior. Copyright © 2013 Elsevier Ltd. All rights reserved.

The 1-loop effective potential for the Standard Model in curved spacetime

NASA Astrophysics Data System (ADS)

Markkanen, Tommi; Nurmi, Sami; Rajantie, Arttu; Stopyra, Stephen

2018-06-01

The renormalisation group improved Standard Model effective potential in an arbitrary curved spacetime is computed to one loop order in perturbation theory. The loop corrections are computed in the ultraviolet limit, which makes them independent of the choice of the vacuum state and allows the derivation of the complete set of β-functions. The potential depends on the spacetime curvature through the direct non-minimal Higgs-curvature coupling, curvature contributions to the loop diagrams, and through the curvature dependence of the renormalisation scale. Together, these lead to significant curvature dependence, which needs to be taken into account in cosmological applications, which is demonstrated with the example of vacuum stability in de Sitter space.

Joint multifractal analysis based on the partition function approach: analytical analysis, numerical simulation and empirical application

NASA Astrophysics Data System (ADS)

Xie, Wen-Jie; Jiang, Zhi-Qiang; Gu, Gao-Feng; Xiong, Xiong; Zhou, Wei-Xing

2015-10-01

Many complex systems generate multifractal time series which are long-range cross-correlated. Numerous methods have been proposed to characterize the multifractal nature of these long-range cross correlations. However, several important issues about these methods are not well understood and most methods consider only one moment order. We study the joint multifractal analysis based on partition function with two moment orders, which was initially invented to investigate fluid fields, and derive analytically several important properties. We apply the method numerically to binomial measures with multifractal cross correlations and bivariate fractional Brownian motions without multifractal cross correlations. For binomial multifractal measures, the explicit expressions of mass function, singularity strength and multifractal spectrum of the cross correlations are derived, which agree excellently with the numerical results. We also apply the method to stock market indexes and unveil intriguing multifractality in the cross correlations of index volatilities.

Shrunk loop theorem for the topology probabilities of closed Brownian (or Feynman) paths on the twice punctured plane

NASA Astrophysics Data System (ADS)

Giraud, O.; Thain, A.; Hannay, J. H.

2004-02-01

The shrunk loop theorem proved here is an integral identity which facilitates the calculation of the relative probability (or probability amplitude) of any given topology that a free, closed Brownian (or Feynman) path of a given 'duration' might have on the twice punctured plane (plane with two marked points). The result is expressed as a 'scattering' series of integrals of increasing dimensionality based on the maximally shrunk version of the path. Physically, this applies in different contexts: (i) the topology probability of a closed ideal polymer chain on a plane with two impassable points, (ii) the trace of the Schrödinger Green function, and thence spectral information, in the presence of two Aharonov-Bohm fluxes and (iii) the same with two branch points of a Riemann surface instead of fluxes. Our theorem starts from the Stovicek scattering expansion for the Green function in the presence of two Aharonov-Bohm flux lines, which itself is based on the famous Sommerfeld one puncture point solution of 1896 (the one puncture case has much easier topology, just one winding number). Stovicek's expansion itself can supply the results at the expense of choosing a base point on the loop and then integrating it away. The shrunk loop theorem eliminates this extra two-dimensional integration, distilling the topology from the geometry.

Reconstructing a missing link in the evolution of a recently diverged phosphotriesterase by active-site loop remodeling.

PubMed

Afriat-Jurnou, Livnat; Jackson, Colin J; Tawfik, Dan S

2012-08-07

Only decades after the introduction of organophosphate pesticides, bacterial phosphotriesterases (PTEs) have evolved to catalyze their degradation with remarkable efficiency. Their closest known relatives, lactonases, with promiscuous phosphotriasterase activity, dubbed PTE-like lactonases (PLLs), share only 30% sequence identity and also differ in the configuration of their active-site loops. PTE was therefore presumed to have evolved from a yet unknown PLL whose primary activity was the hydrolysis of quorum sensing homoserine lactones (HSLs) (Afriat et al. (2006) Biochemistry 45, 13677-13686). However, how PTEs diverged from this presumed PLL remains a mystery. In this study we investigated loop remodeling as a means of reconstructing a homoserine lactonase ancestor that relates to PTE by few mutational steps. Although, in nature, loop remodeling is a common mechanism of divergence of enzymatic functions, reproducing this process in the laboratory is a challenge. Structural and phylogenetic analyses enabled us to remodel one of PTE's active-site loops into a PLL-like configuration. A deletion in loop 7, combined with an adjacent, highly epistatic, point mutation led to the emergence of an HSLase activity that is undetectable in PTE (k(cat)/K(M) values of up to 2 × 10(4)). The appearance of the HSLase activity was accompanied by only a minor decrease in PTE's paraoxonase activity. This specificity change demonstrates the potential role of bifunctional intermediates in the divergence of new enzymatic functions and highlights the critical contribution of loop remodeling to the rapid divergence of new enzyme functions.

Adaptive Neural Output-Feedback Control for a Class of Nonlower Triangular Nonlinear Systems With Unmodeled Dynamics.

PubMed

Wang, Huanqing; Liu, Peter Xiaoping; Li, Shuai; Wang, Ding

2017-08-29

This paper presents the development of an adaptive neural controller for a class of nonlinear systems with unmodeled dynamics and immeasurable states. An observer is designed to estimate system states. The structure consistency of virtual control signals and the variable partition technique are combined to overcome the difficulties appearing in a nonlower triangular form. An adaptive neural output-feedback controller is developed based on the backstepping technique and the universal approximation property of the radial basis function (RBF) neural networks. By using the Lyapunov stability analysis, the semiglobally and uniformly ultimate boundedness of all signals within the closed-loop system is guaranteed. The simulation results show that the controlled system converges quickly, and all the signals are bounded. This paper is novel at least in the two aspects: 1) an output-feedback control strategy is developed for a class of nonlower triangular nonlinear systems with unmodeled dynamics and 2) the nonlinear disturbances and their bounds are the functions of all states, which is in a more general form than existing results.

Spider toxin inhibits gating pore currents underlying periodic paralysis.

PubMed

Männikkö, Roope; Shenkarev, Zakhar O; Thor, Michael G; Berkut, Antonina A; Myshkin, Mikhail Yu; Paramonov, Alexander S; Kulbatskii, Dmitrii S; Kuzmin, Dmitry A; Sampedro Castañeda, Marisol; King, Louise; Wilson, Emma R; Lyukmanova, Ekaterina N; Kirpichnikov, Mikhail P; Schorge, Stephanie; Bosmans, Frank; Hanna, Michael G; Kullmann, Dimitri M; Vassilevski, Alexander A

2018-04-24

Gating pore currents through the voltage-sensing domains (VSDs) of the skeletal muscle voltage-gated sodium channel Na V 1.4 underlie hypokalemic periodic paralysis (HypoPP) type 2. Gating modifier toxins target ion channels by modifying the function of the VSDs. We tested the hypothesis that these toxins could function as blockers of the pathogenic gating pore currents. We report that a crab spider toxin Hm-3 from Heriaeus melloteei can inhibit gating pore currents due to mutations affecting the second arginine residue in the S4 helix of VSD-I that we have found in patients with HypoPP and describe here. NMR studies show that Hm-3 partitions into micelles through a hydrophobic cluster formed by aromatic residues and reveal complex formation with VSD-I through electrostatic and hydrophobic interactions with the S3b helix and the S3-S4 extracellular loop. Our data identify VSD-I as a specific binding site for neurotoxins on sodium channels. Gating modifier toxins may constitute useful hits for the treatment of HypoPP. Copyright © 2018 the Author(s). Published by PNAS.

Uncertain Henry's law constants compromise equilibrium partitioning calculations of atmospheric oxidation products

NASA Astrophysics Data System (ADS)

Wang, Chen; Yuan, Tiange; Wood, Stephen A.; Goss, Kai-Uwe; Li, Jingyi; Ying, Qi; Wania, Frank

2017-06-01

Gas-particle partitioning governs the distribution, removal, and transport of organic compounds in the atmosphere and the formation of secondary organic aerosol (SOA). The large variety of atmospheric species and their wide range of properties make predicting this partitioning equilibrium challenging. Here we expand on earlier work and predict gas-organic and gas-aqueous phase partitioning coefficients for 3414 atmospherically relevant molecules using COSMOtherm, SPARC Performs Automated Reasoning in Chemistry (SPARC), and poly-parameter linear free-energy relationships. The Master Chemical Mechanism generated the structures by oxidizing primary emitted volatile organic compounds. Predictions for gas-organic phase partitioning coefficients (KWIOM/G) by different methods are on average within 1 order of magnitude of each other, irrespective of the numbers of functional groups, except for predictions by COSMOtherm and SPARC for compounds with more than three functional groups, which have a slightly higher discrepancy. Discrepancies between predictions of gas-aqueous partitioning (KW/G) are much larger and increase with the number of functional groups in the molecule. In particular, COSMOtherm often predicts much lower KW/G for highly functionalized compounds than the other methods. While the quantum-chemistry-based COSMOtherm accounts for the influence of intra-molecular interactions on conformation, highly functionalized molecules likely fall outside of the applicability domain of the other techniques, which at least in part rely on empirical data for calibration. Further analysis suggests that atmospheric phase distribution calculations are sensitive to the partitioning coefficient estimation method, in particular to the estimated value of KW/G. The large uncertainty in KW/G predictions for highly functionalized organic compounds needs to be resolved to improve the quantitative treatment of SOA formation.

Methods for selecting fixed-effect models for heterogeneous codon evolution, with comments on their application to gene and genome data.

PubMed

Bao, Le; Gu, Hong; Dunn, Katherine A; Bielawski, Joseph P

2007-02-08

Models of codon evolution have proven useful for investigating the strength and direction of natural selection. In some cases, a priori biological knowledge has been used successfully to model heterogeneous evolutionary dynamics among codon sites. These are called fixed-effect models, and they require that all codon sites are assigned to one of several partitions which are permitted to have independent parameters for selection pressure, evolutionary rate, transition to transversion ratio or codon frequencies. For single gene analysis, partitions might be defined according to protein tertiary structure, and for multiple gene analysis partitions might be defined according to a gene's functional category. Given a set of related fixed-effect models, the task of selecting the model that best fits the data is not trivial. In this study, we implement a set of fixed-effect codon models which allow for different levels of heterogeneity among partitions in the substitution process. We describe strategies for selecting among these models by a backward elimination procedure, Akaike information criterion (AIC) or a corrected Akaike information criterion (AICc). We evaluate the performance of these model selection methods via a simulation study, and make several recommendations for real data analysis. Our simulation study indicates that the backward elimination procedure can provide a reliable method for model selection in this setting. We also demonstrate the utility of these models by application to a single-gene dataset partitioned according to tertiary structure (abalone sperm lysin), and a multi-gene dataset partitioned according to the functional category of the gene (flagellar-related proteins of Listeria). Fixed-effect models have advantages and disadvantages. Fixed-effect models are desirable when data partitions are known to exhibit significant heterogeneity or when a statistical test of such heterogeneity is desired. They have the disadvantage of requiring a priori knowledge for partitioning sites. We recommend: (i) selection of models by using backward elimination rather than AIC or AICc, (ii) use a stringent cut-off, e.g., p = 0.0001, and (iii) conduct sensitivity analysis of results. With thoughtful application, fixed-effect codon models should provide a useful tool for large scale multi-gene analyses.

Thermodynamics and statistical mechanics. [thermodynamic properties of gases

NASA Technical Reports Server (NTRS)

1976-01-01

The basic thermodynamic properties of gases are reviewed and the relations between them are derived from the first and second laws. The elements of statistical mechanics are then formulated and the partition function is derived. The classical form of the partition function is used to obtain the Maxwell-Boltzmann distribution of kinetic energies in the gas phase and the equipartition of energy theorem is given in its most general form. The thermodynamic properties are all derived as functions of the partition function. Quantum statistics are reviewed briefly and the differences between the Boltzmann distribution function for classical particles and the Fermi-Dirac and Bose-Einstein distributions for quantum particles are discussed.

Choosing the best partition of the output from a large-scale simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Challacombe, Chelsea Jordan; Casleton, Emily Michele

Data partitioning becomes necessary when a large-scale simulation produces more data than can be feasibly stored. The goal is to partition the data, typically so that every element belongs to one and only one partition, and store summary information about the partition, either a representative value plus an estimate of the error or a distribution. Once the partitions are determined and the summary information stored, the raw data is discarded. This process can be performed in-situ; meaning while the simulation is running. When creating the partitions there are many decisions that researchers must make. For instance, how to determine oncemore » an adequate number of partitions have been created, how are the partitions created with respect to dividing the data, or how many variables should be considered simultaneously. In addition, decisions must be made for how to summarize the information within each partition. Because of the combinatorial number of possible ways to partition and summarize the data, a method of comparing the different possibilities will help guide researchers into choosing a good partitioning and summarization scheme for their application.« less

Quantum speedup of Monte Carlo methods.

PubMed

Montanaro, Ashley

2015-09-08

Monte Carlo methods use random sampling to estimate numerical quantities which are hard to compute deterministically. One important example is the use in statistical physics of rapidly mixing Markov chains to approximately compute partition functions. In this work, we describe a quantum algorithm which can accelerate Monte Carlo methods in a very general setting. The algorithm estimates the expected output value of an arbitrary randomized or quantum subroutine with bounded variance, achieving a near-quadratic speedup over the best possible classical algorithm. Combining the algorithm with the use of quantum walks gives a quantum speedup of the fastest known classical algorithms with rigorous performance bounds for computing partition functions, which use multiple-stage Markov chain Monte Carlo techniques. The quantum algorithm can also be used to estimate the total variation distance between probability distributions efficiently.

Spheres, charges, instantons, and bootstrap: A five-dimensional odyssey

NASA Astrophysics Data System (ADS)

Chang, Chi-Ming; Fluder, Martin; Lin, Ying-Hsuan; Wang, Yifan

2018-03-01

We combine supersymmetric localization and the conformal bootstrap to study five-dimensional superconformal field theories. To begin, we classify the admissible counter-terms and derive a general relation between the five-sphere partition function and the conformal and flavor central charges. Along the way, we discover a new superconformal anomaly in five dimensions. We then propose a precise triple factorization formula for the five-sphere partition function, that incorporates instantons and is consistent with flavor symmetry enhancement. We numerically evaluate the central charges for the rank-one Seiberg and Morrison-Seiberg theories, and find strong evidence for their saturation of bootstrap bounds, thereby determining the spectra of long multiplets in these theories. Lastly, our results provide new evidence for the F-theorem and possibly a C-theorem in five-dimensional superconformal theories.

Quantum speedup of Monte Carlo methods

PubMed Central

Montanaro, Ashley

2015-01-01

Monte Carlo methods use random sampling to estimate numerical quantities which are hard to compute deterministically. One important example is the use in statistical physics of rapidly mixing Markov chains to approximately compute partition functions. In this work, we describe a quantum algorithm which can accelerate Monte Carlo methods in a very general setting. The algorithm estimates the expected output value of an arbitrary randomized or quantum subroutine with bounded variance, achieving a near-quadratic speedup over the best possible classical algorithm. Combining the algorithm with the use of quantum walks gives a quantum speedup of the fastest known classical algorithms with rigorous performance bounds for computing partition functions, which use multiple-stage Markov chain Monte Carlo techniques. The quantum algorithm can also be used to estimate the total variation distance between probability distributions efficiently. PMID:26528079

Random Partition Distribution Indexed by Pairwise Information

PubMed Central

Dahl, David B.; Day, Ryan; Tsai, Jerry W.

2017-01-01

We propose a random partition distribution indexed by pairwise similarity information such that partitions compatible with the similarities are given more probability. The use of pairwise similarities, in the form of distances, is common in some clustering algorithms (e.g., hierarchical clustering), but we show how to use this type of information to define a prior partition distribution for flexible Bayesian modeling. A defining feature of the distribution is that it allocates probability among partitions within a given number of subsets, but it does not shift probability among sets of partitions with different numbers of subsets. Our distribution places more probability on partitions that group similar items yet keeps the total probability of partitions with a given number of subsets constant. The distribution of the number of subsets (and its moments) is available in closed-form and is not a function of the similarities. Our formulation has an explicit probability mass function (with a tractable normalizing constant) so the full suite of MCMC methods may be used for posterior inference. We compare our distribution with several existing partition distributions, showing that our formulation has attractive properties. We provide three demonstrations to highlight the features and relative performance of our distribution. PMID:29276318

Additional support for Afrotheria and Paenungulata, the performance of mitochondrial versus nuclear genes, and the impact of data partitions with heterogeneous base composition.

PubMed

Springer, M S; Amrine, H M; Burk, A; Stanhope, M J

1999-03-01

We concatenated sequences for four mitochondrial genes (12S rRNA, tRNA valine, 16S rRNA, cytochrome b) and four nuclear genes [aquaporin, alpha 2B adrenergic receptor (A2AB), interphotoreceptor retinoid-binding protein (IRBP), von Willebrand factor (vWF)] into a multigene data set representing 11 eutherian orders (Artiodactyla, Hyracoidea, Insectivora, Lagomorpha, Macroscelidea, Perissodactyla, Primates, Proboscidea, Rodentia, Sirenia, Tubulidentata). Within this data set, we recognized nine mitochondrial partitions (both stems and loops, for each of 12S rRNA, tRNA valine, and 16S rRNA; and first, second, and third codon positions of cytochrome b) and 12 nuclear partitions (first, second, and third codon positions, respectively, of each of the four nuclear genes). Four of the 21 partitions (third positions of cytochrome b, A2AB, IRBP, and vWF) showed significant heterogeneity in base composition across taxa. Phylogenetic analyses (parsimony, minimum evolution, maximum likelihood) based on sequences for all 21 partitions provide 99-100% bootstrap support for Afrotheria and Paenungulata. With the elimination of the four partitions exhibiting heterogeneity in base composition, there is also high bootstrap support (89-100%) for cow + horse. Statistical tests reject Altungulata, Anagalida, and Ungulata. Data set heterogeneity between mitochondrial and nuclear genes is most evident when all partitions are included in the phylogenetic analyses. Mitochondrial-gene trees associate cow with horse, whereas nuclear-gene trees associate cow with hedgehog and these two with horse. However, after eliminating third positions of A2AB, IRBP, and vWF, nuclear data agree with mitochondrial data in supporting cow + horse. Nuclear genes provide stronger support for both Afrotheria and Paenungulata. Removal of third positions of cytochrome b results in improved performance for the mitochondrial genes in recovering these clades.

Language in the brain at rest: new insights from resting state data and graph theoretical analysis

PubMed Central

Muller, Angela M.; Meyer, Martin

2014-01-01

In humans, the most obvious functional lateralization is the specialization of the left hemisphere for language. Therefore, the involvement of the right hemisphere in language is one of the most remarkable findings during the last two decades of fMRI research. However, the importance of this finding continues to be underestimated. We examined the interaction between the two hemispheres and also the role of the right hemisphere in language. From two seeds representing Broca's area, we conducted a seed correlation analysis (SCA) of resting state fMRI data and could identify a resting state network (RSN) overlapping to significant extent with a language network that was generated by an automated meta-analysis tool. To elucidate the relationship between the clusters of this RSN, we then performed graph theoretical analyses (GTA) using the same resting state dataset. We show that the right hemisphere is clearly involved in language. A modularity analysis revealed that the interaction between the two hemispheres is mediated by three partitions: A bilateral frontal partition consists of nodes representing the classical left sided language regions as well as two right-sided homologs. The second bilateral partition consists of nodes from the right frontal, the left inferior parietal cortex as well as of two nodes within the posterior cerebellum. The third partition is also bilateral and comprises five regions from the posterior midline parts of the brain to the temporal and frontal cortex, two of the nodes are prominent default mode nodes. The involvement of this last partition in a language relevant function is a novel finding. PMID:24808843

Phase transitions in single macromolecules: Loop-stretch transition versus loop adsorption transition in end-grafted polymer chains

NASA Astrophysics Data System (ADS)

Zhang, Shuangshuang; Qi, Shuanhu; Klushin, Leonid I.; Skvortsov, Alexander M.; Yan, Dadong; Schmid, Friederike

2018-01-01

We use Brownian dynamics simulations and analytical theory to compare two prominent types of single molecule transitions. One is the adsorption transition of a loop (a chain with two ends bound to an attractive substrate) driven by an attraction parameter ɛ and the other is the loop-stretch transition in a chain with one end attached to a repulsive substrate, driven by an external end-force F applied to the free end. Specifically, we compare the behavior of the respective order parameters of the transitions, i.e., the mean number of surface contacts in the case of the adsorption transition and the mean position of the chain end in the case of the loop-stretch transition. Close to the transition points, both the static behavior and the dynamic behavior of chains with different length N are very well described by a scaling ansatz with the scaling parameters (ɛ - ɛ*)Nϕ (adsorption transition) and (F - F*)Nν (loop-stretch transition), respectively, where ϕ is the crossover exponent of the adsorption transition and ν is the Flory exponent. We show that both the loop-stretch and the loop adsorption transitions provide an exceptional opportunity to construct explicit analytical expressions for the crossover functions which perfectly describe all simulation results on static properties in the finite-size scaling regime. Explicit crossover functions are based on the ansatz for the analytical form of the order parameter distributions at the respective transition points. In contrast to the close similarity in equilibrium static behavior, the dynamic relaxation at the two transitions shows qualitative differences, especially in the strongly ordered regimes. This is attributed to the fact that the surface contact dynamics in a strongly adsorbed chain is governed by local processes, whereas the end height relaxation of a strongly stretched chain involves the full spectrum of Rouse modes.

Leading singularities and off-shell conformal integrals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Drummond, James; Duhr, Claude; Eden, Burkhard

2013-08-29

The three-loop four-point function of stress-tensor multiplets in N=4 super Yang-Mills theory contains two so far unknown, off-shell, conformal integrals, in addition to the known, ladder-type integrals. In our paper we evaluate the unknown integrals, thus obtaining the three-loop correlation function analytically. The integrals have the generic structure of rational functions multiplied by (multiple) polylogarithms. We use the idea of leading singularities to obtain the rational coefficients, the symbol — with an appropriate ansatz for its structure — as a means of characterising multiple polylogarithms, and the technique of asymptotic expansion of Feynman integrals to obtain the integrals in certainmore » limits. The limiting behaviour uniquely fixes the symbols of the integrals, which we then lift to find the corresponding polylogarithmic functions. The final formulae are numerically confirmed. Furthermore, we develop techniques that can be applied more generally, and we illustrate this by analytically evaluating one of the integrals contributing to the same four-point function at four loops. This example shows a connection between the leading singularities and the entries of the symbol.« less

Matrix models and stochastic growth in Donaldson-Thomas theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Szabo, Richard J.; Tierz, Miguel; Departamento de Analisis Matematico, Facultad de Ciencias Matematicas, Universidad Complutense de Madrid, Plaza de Ciencias 3, 28040 Madrid

We show that the partition functions which enumerate Donaldson-Thomas invariants of local toric Calabi-Yau threefolds without compact divisors can be expressed in terms of specializations of the Schur measure. We also discuss the relevance of the Hall-Littlewood and Jack measures in the context of BPS state counting and study the partition functions at arbitrary points of the Kaehler moduli space. This rewriting in terms of symmetric functions leads to a unitary one-matrix model representation for Donaldson-Thomas theory. We describe explicitly how this result is related to the unitary matrix model description of Chern-Simons gauge theory. This representation is used tomore » show that the generating functions for Donaldson-Thomas invariants are related to tau-functions of the integrable Toda and Toeplitz lattice hierarchies. The matrix model also leads to an interpretation of Donaldson-Thomas theory in terms of non-intersecting paths in the lock-step model of vicious walkers. We further show that these generating functions can be interpreted as normalization constants of a corner growth/last-passage stochastic model.« less

On the subsystem formulation of linear-response time-dependent DFT.

PubMed

Pavanello, Michele

2013-05-28

A new and thorough derivation of linear-response subsystem time-dependent density functional theory (TD-DFT) is presented and analyzed in detail. Two equivalent derivations are presented and naturally yield self-consistent subsystem TD-DFT equations. One reduces to the subsystem TD-DFT formalism of Neugebauer [J. Chem. Phys. 126, 134116 (2007)]. The other yields Dyson type equations involving three types of subsystem response functions: coupled, uncoupled, and Kohn-Sham. The Dyson type equations for subsystem TD-DFT are derived here for the first time. The response function formalism reveals previously hidden qualities and complications of subsystem TD-DFT compared with the regular TD-DFT of the supersystem. For example, analysis of the pole structure of the subsystem response functions shows that each function contains information about the electronic spectrum of the entire supersystem. In addition, comparison of the subsystem and supersystem response functions shows that, while the correlated response is subsystem additive, the Kohn-Sham response is not. Comparison with the non-subjective partition DFT theory shows that this non-additivity is largely an artifact introduced by the subjective nature of the density partitioning in subsystem DFT.

Structure of the beta 2 homodimer of bacterial luciferase from Vibrio harveyi: X-ray analysis of a kinetic protein folding trap.

PubMed Central

Thoden, J. B.; Holden, H. M.; Fisher, A. J.; Sinclair, J. F.; Wesenberg, G.; Baldwin, T. O.; Rayment, I.

1997-01-01

Luciferase, as isolated from Vibrio harveyi, is an alpha beta heterodimer. When allowed to fold in the absence of the alpha subunit, either in vitro or in vivo, the beta subunit of enzyme will form a kinetically stable homodimer that does not unfold even after prolonged incubation in 5 M urea at pH 7.0 and 18 degrees C. This form of the beta subunit, arising via kinetic partitioning on the folding pathway, appears to constitute a kinetically trapped alternative to the heterodimeric enzyme (Sinclair JF, Ziegler MM, Baldwin TO. 1994. Kinetic partitioning during protein folding yields multiple native states. Nature Struct Biol 1: 320-326). Here we describe the X-ray crystal structure of the beta 2 homodimer of luciferase from V. harveyi determined and refined at 1.95 A resolution. Crystals employed in the investigational belonged to the orthorhombic space group P2(1)2(1)2(1) with unit cell dimensions of a = 58.8 A, b = 62.0 A, and c = 218.2 A and contained one dimer per asymmetric unit. Like that observed in the functional luciferase alpha beta heterodimer, the major tertiary structural motif of each beta subunit consists of an (alpha/beta)8 barrel (Fisher AJ, Raushel FM, Baldwin TO, Rayment I. 1995. Three-dimensional structure of bacterial luciferase from Vibrio harveyi at 2.4 A resolution. Biochemistry 34: 6581-6586). The root-mean-square deviation of the alpha-carbon coordinates between the beta subunits of the hetero- and homodimers is 0.7 A. This high resolution X-ray analysis demonstrated that "domain" or "loop" swapping has not occurred upon formation of the beta 2 homodimer and thus the stability of the beta 2 species to denaturation cannot be explained in such simple terms. In fact, the subunit:subunit interfaces observed in both the beta 2 homodimer and alpha beta heterodimer are remarkably similar in hydrogen-bonding patterns and buried surface areas. PMID:9007973

Interactions among resource partitioning, sampling effect, and facilitation on the biodiversity effect: a modeling approach.

PubMed

Flombaum, Pedro; Sala, Osvaldo E; Rastetter, Edward B

2014-02-01

Resource partitioning, facilitation, and sampling effect are the three mechanisms behind the biodiversity effect, which is depicted usually as the effect of plant-species richness on aboveground net primary production. These mechanisms operate simultaneously but their relative importance and interactions are difficult to unravel experimentally. Thus, niche differentiation and facilitation have been lumped together and separated from the sampling effect. Here, we propose three hypotheses about interactions among the three mechanisms and test them using a simulation model. The model simulated water movement through soil and vegetation, and net primary production mimicking the Patagonian steppe. Using the model, we created grass and shrub monocultures and mixtures, controlled root overlap and grass water-use efficiency (WUE) to simulate gradients of biodiversity, resource partitioning and facilitation. The presence of shrubs facilitated grass growth by increasing its WUE and in turn increased the sampling effect, whereas root overlap (resource partitioning) had, on average, no effect on sampling effect. Interestingly, resource partitioning and facilitation interacted so the effect of facilitation on sampling effect decreased as resource partitioning increased. Sampling effect was enhanced by the difference between the two functional groups in their efficiency in using resources. Morphological and physiological differences make one group outperform the other; once these differences were established further differences did not enhance the sampling effect. In addition, grass WUE and root overlap positively influence the biodiversity effect but showed no interactions.

A dynamic re-partitioning strategy based on the distribution of key in Spark

NASA Astrophysics Data System (ADS)

Zhang, Tianyu; Lian, Xin

2018-05-01

Spark is a memory-based distributed data processing framework, has the ability of processing massive data and becomes a focus in Big Data. But the performance of Spark Shuffle depends on the distribution of data. The naive Hash partition function of Spark can not guarantee load balancing when data is skewed. The time of job is affected by the node which has more data to process. In order to handle this problem, dynamic sampling is used. In the process of task execution, histogram is used to count the key frequency distribution of each node, and then generate the global key frequency distribution. After analyzing the distribution of key, load balance of data partition is achieved. Results show that the Dynamic Re-Partitioning function is better than the default Hash partition, Fine Partition and the Balanced-Schedule strategy, it can reduce the execution time of the task and improve the efficiency of the whole cluster.

MELiSSA Pilot Plant: A facility for ground demonstration of a closed life support system

NASA Astrophysics Data System (ADS)

Godia, Francesc; Fossen, Arnaud; Peiro, Enrique; Gerbi, Olivier; Dussap, Gilles; Leys, Natalie; Arnau, Carolina; Milian, Ernest

MELiSSA (Micro Ecological Life Support System Alternative) is an international collaborative effort focused on the development of a Life Support System for long-term Space missions. The goals of the MELiSSA loop are the recovery of food, water and oxygen from wastes, i.e. CO2 and organic wastes, using light as a source of energy. It is conceived as a series of compartments, each one performing a specific function within this cycle, inspired in the terrestrial ecological systems. Each one of the compartments is colonized with specific bacteria or higher plants depending on its dedicated function. Therefore, its design and operational conditions should guarantee that only a given specific biological activity takes place in each compartment. Moreover, this has to be done in a controlled manner, both at the subsystems level (i.e., compartments) and at the overall system level (i.e., complete loop). In order to achieve the complete operation of such a Closed Ecological System, in a first step each compartment has to be developed at individual level, and its operation demonstrated under its associated control law. In a second step, the complete loop needs to be integrated by the connection of the different compartments in the gas, loop and solid phases. An extensive demonstration of MELiSSA loop under terrestrial conditions is a mandatory step in the process of its adaptation to space. This is the main goal of the MPP. The demonstration scenario for the MPP is the respiration equivalent of a human being, and production of 20 percent of the diet of one person. To serve this goal, the different compartments of the MELiSSA loop have been designed and sized at the pilot scale level, and further characterized. Nowadays, the focus of the MELiSSA Pilot Plant is on the integration of its compartments. To this end, the integration challenge is concentrated in three compartments devoted to the following functions: nitrification (Compartment 3, an axenic co-culture of Nitrosomonas europaea and Nitrobacter winogradskyi), edible biomass and oxygen production (Compartment 4a, an axenic co-culture of Arthrospira platensis) and oxygen consumers (Compartment 5, rats isolator). The presentation will focus on all the necessary elements to achieve this integration, particularly in the start-up of continuous operation of the bioreactors and on the key challenges addressed in the integration of the gas phase of two compartments, 4a and 5, one producing O2 and one consuming it. The design of the integration conditions to ensure the functionality of all the elements will also be discussed. Keywords:, MELiSSA, Pilot Plant, Integration, Arthrospira platensis, Nitrosomonas europaea, Nitrobacter winogradskyi

Looping probabilities of elastic chains: a path integral approach.

PubMed

Cotta-Ramusino, Ludovica; Maddocks, John H

2010-11-01

We consider an elastic chain at thermodynamic equilibrium with a heat bath, and derive an approximation to the probability density function, or pdf, governing the relative location and orientation of the two ends of the chain. Our motivation is to exploit continuum mechanics models for the computation of DNA looping probabilities, but here we focus on explaining the novel analytical aspects in the derivation of our approximation formula. Accordingly, and for simplicity, the current presentation is limited to the illustrative case of planar configurations. A path integral formalism is adopted, and, in the standard way, the first approximation to the looping pdf is obtained from a minimal energy configuration satisfying prescribed end conditions. Then we compute an additional factor in the pdf which encompasses the contributions of quadratic fluctuations about the minimum energy configuration along with a simultaneous evaluation of the partition function. The original aspects of our analysis are twofold. First, the quadratic Lagrangian describing the fluctuations has cross-terms that are linear in first derivatives. This, seemingly small, deviation from the structure of standard path integral examples complicates the necessary analysis significantly. Nevertheless, after a nonlinear change of variable of Riccati type, we show that the correction factor to the pdf can still be evaluated in terms of the solution to an initial value problem for the linear system of Jacobi ordinary differential equations associated with the second variation. The second novel aspect of our analysis is that we show that the Hamiltonian form of these linear Jacobi equations still provides the appropriate correction term in the inextensible, unshearable limit that is commonly adopted in polymer physics models of, e.g. DNA. Prior analyses of the inextensible case have had to introduce nonlinear and nonlocal integral constraints to express conditions on the relative displacement of the end points. Our approximation formula for the looping pdf is of quite general applicability as, in contrast to most prior approaches, no assumption is made of either uniformity of the elastic chain, nor of a straight intrinsic shape. If the chain is uniform the Jacobi system evaluated at certain minimum energy configurations has constant coefficients. In such cases our approximate pdf can be evaluated in an entirely explicit, closed form. We illustrate our analysis with a planar example of this type and compute an approximate probability of cyclization, i.e., of forming a closed loop, from a uniform elastic chain whose intrinsic shape is an open circular arc.

Mining protein loops using a structural alphabet and statistical exceptionality

PubMed Central

2010-01-01

Background Protein loops encompass 50% of protein residues in available three-dimensional structures. These regions are often involved in protein functions, e.g. binding site, catalytic pocket... However, the description of protein loops with conventional tools is an uneasy task. Regular secondary structures, helices and strands, have been widely studied whereas loops, because they are highly variable in terms of sequence and structure, are difficult to analyze. Due to data sparsity, long loops have rarely been systematically studied. Results We developed a simple and accurate method that allows the description and analysis of the structures of short and long loops using structural motifs without restriction on loop length. This method is based on the structural alphabet HMM-SA. HMM-SA allows the simplification of a three-dimensional protein structure into a one-dimensional string of states, where each state is a four-residue prototype fragment, called structural letter. The difficult task of the structural grouping of huge data sets is thus easily accomplished by handling structural letter strings as in conventional protein sequence analysis. We systematically extracted all seven-residue fragments in a bank of 93000 protein loops and grouped them according to the structural-letter sequence, named structural word. This approach permits a systematic analysis of loops of all sizes since we consider the structural motifs of seven residues rather than complete loops. We focused the analysis on highly recurrent words of loops (observed more than 30 times). Our study reveals that 73% of loop-lengths are covered by only 3310 highly recurrent structural words out of 28274 observed words). These structural words have low structural variability (mean RMSd of 0.85 Å). As expected, half of these motifs display a flanking-region preference but interestingly, two thirds are shared by short (less than 12 residues) and long loops. Moreover, half of recurrent motifs exhibit a significant level of amino-acid conservation with at least four significant positions and 87% of long loops contain at least one such word. We complement our analysis with the detection of statistically over-represented patterns of structural letters as in conventional DNA sequence analysis. About 30% (930) of structural words are over-represented, and cover about 40% of loop lengths. Interestingly, these words exhibit lower structural variability and higher sequential specificity, suggesting structural or functional constraints. Conclusions We developed a method to systematically decompose and study protein loops using recurrent structural motifs. This method is based on the structural alphabet HMM-SA and not on structural alignment and geometrical parameters. We extracted meaningful structural motifs that are found in both short and long loops. To our knowledge, it is the first time that pattern mining helps to increase the signal-to-noise ratio in protein loops. This finding helps to better describe protein loops and might permit to decrease the complexity of long-loop analysis. Detailed results are available at http://www.mti.univ-paris-diderot.fr/publication/supplementary/2009/ACCLoop/. PMID:20132552

Mining protein loops using a structural alphabet and statistical exceptionality.

PubMed

Regad, Leslie; Martin, Juliette; Nuel, Gregory; Camproux, Anne-Claude

2010-02-04

Protein loops encompass 50% of protein residues in available three-dimensional structures. These regions are often involved in protein functions, e.g. binding site, catalytic pocket... However, the description of protein loops with conventional tools is an uneasy task. Regular secondary structures, helices and strands, have been widely studied whereas loops, because they are highly variable in terms of sequence and structure, are difficult to analyze. Due to data sparsity, long loops have rarely been systematically studied. We developed a simple and accurate method that allows the description and analysis of the structures of short and long loops using structural motifs without restriction on loop length. This method is based on the structural alphabet HMM-SA. HMM-SA allows the simplification of a three-dimensional protein structure into a one-dimensional string of states, where each state is a four-residue prototype fragment, called structural letter. The difficult task of the structural grouping of huge data sets is thus easily accomplished by handling structural letter strings as in conventional protein sequence analysis. We systematically extracted all seven-residue fragments in a bank of 93000 protein loops and grouped them according to the structural-letter sequence, named structural word. This approach permits a systematic analysis of loops of all sizes since we consider the structural motifs of seven residues rather than complete loops. We focused the analysis on highly recurrent words of loops (observed more than 30 times). Our study reveals that 73% of loop-lengths are covered by only 3310 highly recurrent structural words out of 28274 observed words). These structural words have low structural variability (mean RMSd of 0.85 A). As expected, half of these motifs display a flanking-region preference but interestingly, two thirds are shared by short (less than 12 residues) and long loops. Moreover, half of recurrent motifs exhibit a significant level of amino-acid conservation with at least four significant positions and 87% of long loops contain at least one such word. We complement our analysis with the detection of statistically over-represented patterns of structural letters as in conventional DNA sequence analysis. About 30% (930) of structural words are over-represented, and cover about 40% of loop lengths. Interestingly, these words exhibit lower structural variability and higher sequential specificity, suggesting structural or functional constraints. We developed a method to systematically decompose and study protein loops using recurrent structural motifs. This method is based on the structural alphabet HMM-SA and not on structural alignment and geometrical parameters. We extracted meaningful structural motifs that are found in both short and long loops. To our knowledge, it is the first time that pattern mining helps to increase the signal-to-noise ratio in protein loops. This finding helps to better describe protein loops and might permit to decrease the complexity of long-loop analysis. Detailed results are available at http://www.mti.univ-paris-diderot.fr/publication/supplementary/2009/ACCLoop/.

A Data-Driven Approach to Reverse Engineering Customer Engagement Models: Towards Functional Constructs

PubMed Central

de Vries, Natalie Jane; Carlson, Jamie; Moscato, Pablo

2014-01-01

Online consumer behavior in general and online customer engagement with brands in particular, has become a major focus of research activity fuelled by the exponential increase of interactive functions of the internet and social media platforms and applications. Current research in this area is mostly hypothesis-driven and much debate about the concept of Customer Engagement and its related constructs remains existent in the literature. In this paper, we aim to propose a novel methodology for reverse engineering a consumer behavior model for online customer engagement, based on a computational and data-driven perspective. This methodology could be generalized and prove useful for future research in the fields of consumer behaviors using questionnaire data or studies investigating other types of human behaviors. The method we propose contains five main stages; symbolic regression analysis, graph building, community detection, evaluation of results and finally, investigation of directed cycles and common feedback loops. The ‘communities’ of questionnaire items that emerge from our community detection method form possible ‘functional constructs’ inferred from data rather than assumed from literature and theory. Our results show consistent partitioning of questionnaire items into such ‘functional constructs’ suggesting the method proposed here could be adopted as a new data-driven way of human behavior modeling. PMID:25036766

A data-driven approach to reverse engineering customer engagement models: towards functional constructs.

PubMed

de Vries, Natalie Jane; Carlson, Jamie; Moscato, Pablo

2014-01-01

Online consumer behavior in general and online customer engagement with brands in particular, has become a major focus of research activity fuelled by the exponential increase of interactive functions of the internet and social media platforms and applications. Current research in this area is mostly hypothesis-driven and much debate about the concept of Customer Engagement and its related constructs remains existent in the literature. In this paper, we aim to propose a novel methodology for reverse engineering a consumer behavior model for online customer engagement, based on a computational and data-driven perspective. This methodology could be generalized and prove useful for future research in the fields of consumer behaviors using questionnaire data or studies investigating other types of human behaviors. The method we propose contains five main stages; symbolic regression analysis, graph building, community detection, evaluation of results and finally, investigation of directed cycles and common feedback loops. The 'communities' of questionnaire items that emerge from our community detection method form possible 'functional constructs' inferred from data rather than assumed from literature and theory. Our results show consistent partitioning of questionnaire items into such 'functional constructs' suggesting the method proposed here could be adopted as a new data-driven way of human behavior modeling.

Does a String-Particle Dualism Indicate the Uncertainty Principle's Philosophical Dichotomy?

NASA Astrophysics Data System (ADS)

Mc Leod, David; Mc Leod, Roger

2007-04-01

String theory may allow resonances of neutrino-wave-strings to account for all experimentally detected phenomena. Particle theory logically, and physically, provides an alternate, contradictory dualism. Is it contradictory to symbolically and simultaneously state that λp = h, but, the product of position and momentum must be greater than, or equal to, the same (scaled) Plank's constant? Our previous electron and positron models require `membrane' vibrations of string-linked neutrinos, in closed loops, to behave like traveling waves, Tws, intermittently metamorphosing into alternately ascending and descending standing waves, Sws, between the nodes, which advance sequentially through 360 degrees. Accumulated time passages as Tws detail required ``loop currents'' supplying magnetic moments. Remaining time partitions into the Sws' alternately ascending and descending phases: the physical basis of the experimentally established 3D modes of these ``particles.'' Waves seem to indicate that point mass cannot be required to exist instantaneously at one point; Mott's and Sneddon's Wave Mechanics says that a constant, [mass], is present. String-like resonances may also account for homeopathy's efficacy, dark matter, and constellations' ``stick-figure projections,'' as indicated by some traditional cultures, all possibly involving neutrino strings. To cite this abstract, use the following reference: http://meetings.aps.org/link/BAPS.2007.NES07.C2.5

Research on the Automatic Fusion Strategy of Fixed Value Boundary Based on the Weak Coupling Condition of Grid Partition

NASA Astrophysics Data System (ADS)

Wang, X. Y.; Dou, J. M.; Shen, H.; Li, J.; Yang, G. S.; Fan, R. Q.; Shen, Q.

2018-03-01

With the continuous strengthening of power grids, the network structure is becoming more and more complicated. An open and regional data modeling is used to complete the calculation of the protection fixed value based on the local region. At the same time, a high precision, quasi real-time boundary fusion technique is needed to seamlessly integrate the various regions so as to constitute an integrated fault computing platform which can conduct transient stability analysis of covering the whole network with high accuracy and multiple modes, deal with the impact results of non-single fault, interlocking fault and build “the first line of defense” of the power grid. The boundary fusion algorithm in this paper is an automatic fusion algorithm based on the boundary accurate coupling of the networking power grid partition, which takes the actual operation mode for qualification, complete the boundary coupling algorithm of various weak coupling partition based on open-loop mode, improving the fusion efficiency, truly reflecting its transient stability level, and effectively solving the problems of too much data, too many difficulties of partition fusion, and no effective fusion due to mutually exclusive conditions. In this paper, the basic principle of fusion process is introduced firstly, and then the method of boundary fusion customization is introduced by scene description. Finally, an example is given to illustrate the specific algorithm on how it effectively implements the boundary fusion after grid partition and to verify the accuracy and efficiency of the algorithm.

Integrated Modular Avionics for Spacecraft: Earth Observation Use Case Demonstrator

NASA Astrophysics Data System (ADS)

Deredempt, Marie-Helene; Rossignol, Alain; Hyounet, Philippe

2013-08-01

Integrated Modular Avionics (IMA) for Space, as European Space Agency initiative, aimed to make applicable to space domain the time and space partitioning concepts and particularly the ARINC 653 standard [1][2]. Expected benefits of such an approach are development flexibility, capability to provide differential V&V for different criticality level functionalities and to integrate late or In-Orbit delivery. This development flexibility could improve software subcontracting, industrial organization and software reuse. Time and space partitioning technique facilitates integration of software functions as black boxes and integration of decentralized function such as star tracker in On Board Computer to save mass and power by limiting electronics resources. In aeronautical domain, Integrated Modular Avionics architecture is based on a network of LRU (Line Replaceable Unit) interconnected by AFDX (Avionic Full DupleX). Time and Space partitioning concept is applicable to LRU and provides independent partitions which inter communicate using ARINC 653 communication ports. Using End System (LRU component) intercommunication between LRU is managed in the same way than intercommunication between partitions in LRU. In such architecture an application developed using only communication port can be integrated in an LRU or another one without impacting the global architecture. In space domain, a redundant On Board Computer controls (ground monitoring TM) and manages the platform (ground command TC) in terms of power, solar array deployment, attitude, orbit, thermal, maintenance, failure detection and recovery isolation. In addition, Payload units and platform units such as RIU, PCDU, AOCS units (Star tracker, Reaction wheels) are considered in this architecture. Interfaces are mainly realized through MIL-STD-1553B busses and SpaceWire and this could be considered as the main constraint for IMA implementation in space domain. During the first phase of IMA SP project, ARINC653 impact was analyzed. Requirements and architecture for space domain were defined [3][4] and System Executive platforms (based on Xtratum, Pike OS, and AIR) were developed with RTEMS as Guest OS. This paper focuses on the demonstrator developed by Astrium as part of IMA SP project. This demonstrator has the objective to confirm operational software partitioning feasibility above Xtratum System Executive Platform with acceptable CPU overhead.

Partition functions for heterotic WZW conformal field theories

NASA Astrophysics Data System (ADS)

Gannon, Terry

1993-08-01

Thus far in the search for, and classification of, "physical" modular invariant partition functions ΣN LRχ Lχ R∗ the attention has been focused on the symmetric case where the holomorphic and anti-holomorphic sectors, and hence the characters χLand χR, are associated with the same Kac-Moody algebras ĝL = ĝR and levels κ L = κ R. In this paper we consider the more general possibility where ( ĝL, κ L) may not equal ( ĝR, κ R). We discuss which choices of algebras and levels may correspond to well-defined conformal field theories, we find the "smallest" such heterotic (i.e. asymmetric) partition functions, and we give a method, generalizing the Roberts-Terao-Warner lattice method, for explicitly constructing many other modular invariants. We conclude the paper by proving that this new lattice method will succeed in generating all the heterotic partition functions, for all choices of algebras and levels.

Closed-loop model identification of cooperative manipulators holding deformable objects

NASA Astrophysics Data System (ADS)

Alkathiri, A. A.; Akmeliawati, R.; Azlan, N. Z.

2017-11-01

This paper presents system identification to obtain the closed-loop models of a couple of cooperative manipulators in a system, which function to hold deformable objects. The system works using the master-slave principle. In other words, one of the manipulators is position-controlled through encoder feedback, while a force sensor gives feedback to the other force-controlled manipulator. Using the closed-loop input and output data, the closed-loop models, which are useful for model-based control design, are estimated. The criteria for model validation are a 95% fit between the measured and simulated output of the estimated models and residual analysis. The results show that for both position and force control respectively, the fits are 95.73% and 95.88%.

Finding and testing network communities by lumped Markov chains.

PubMed

Piccardi, Carlo

2011-01-01

Identifying communities (or clusters), namely groups of nodes with comparatively strong internal connectivity, is a fundamental task for deeply understanding the structure and function of a network. Yet, there is a lack of formal criteria for defining communities and for testing their significance. We propose a sharp definition that is based on a quality threshold. By means of a lumped Markov chain model of a random walker, a quality measure called "persistence probability" is associated to a cluster, which is then defined as an "α-community" if such a probability is not smaller than α. Consistently, a partition composed of α-communities is an "α-partition." These definitions turn out to be very effective for finding and testing communities. If a set of candidate partitions is available, setting the desired α-level allows one to immediately select the α-partition with the finest decomposition. Simultaneously, the persistence probabilities quantify the quality of each single community. Given its ability in individually assessing each single cluster, this approach can also disclose single well-defined communities even in networks that overall do not possess a definite clusterized structure.

Periodic, Quasi-periodic and Chaotic Dynamics in Simple Gene Elements with Time Delays

PubMed Central

Suzuki, Yoko; Lu, Mingyang; Ben-Jacob, Eshel; Onuchic, José N.

2016-01-01

Regulatory gene circuit motifs play crucial roles in performing and maintaining vital cellular functions. Frequently, theoretical studies of gene circuits focus on steady-state behaviors and do not include time delays. In this study, the inclusion of time delays is shown to entirely change the time-dependent dynamics for even the simplest possible circuits with one and two gene elements with self and cross regulations. These elements can give rise to rich behaviors including periodic, quasi-periodic, weak chaotic, strong chaotic and intermittent dynamics. We introduce a special power-spectrum-based method to characterize and discriminate these dynamical modes quantitatively. Our simulation results suggest that, while a single negative feedback loop of either one- or two-gene element can only have periodic dynamics, the elements with two positive/negative feedback loops are the minimalist elements to have chaotic dynamics. These elements typically have one negative feedback loop that generates oscillations, and another unit that allows frequent switches among multiple steady states or between oscillatory and non-oscillatory dynamics. Possible dynamical features of several simple one- and two-gene elements are presented in details. Discussion is presented for possible roles of the chaotic behavior in the robustness of cellular functions and diseases, for example, in the context of cancer. PMID:26876008

Periodic, Quasi-periodic and Chaotic Dynamics in Simple Gene Elements with Time Delays

NASA Astrophysics Data System (ADS)

Suzuki, Yoko; Lu, Mingyang; Ben-Jacob, Eshel; Onuchic, José N.

2016-02-01

Regulatory gene circuit motifs play crucial roles in performing and maintaining vital cellular functions. Frequently, theoretical studies of gene circuits focus on steady-state behaviors and do not include time delays. In this study, the inclusion of time delays is shown to entirely change the time-dependent dynamics for even the simplest possible circuits with one and two gene elements with self and cross regulations. These elements can give rise to rich behaviors including periodic, quasi-periodic, weak chaotic, strong chaotic and intermittent dynamics. We introduce a special power-spectrum-based method to characterize and discriminate these dynamical modes quantitatively. Our simulation results suggest that, while a single negative feedback loop of either one- or two-gene element can only have periodic dynamics, the elements with two positive/negative feedback loops are the minimalist elements to have chaotic dynamics. These elements typically have one negative feedback loop that generates oscillations, and another unit that allows frequent switches among multiple steady states or between oscillatory and non-oscillatory dynamics. Possible dynamical features of several simple one- and two-gene elements are presented in details. Discussion is presented for possible roles of the chaotic behavior in the robustness of cellular functions and diseases, for example, in the context of cancer.

Lorentz covariance of loop quantum gravity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rovelli, Carlo; Speziale, Simone

2011-05-15

The kinematics of loop gravity can be given a manifestly Lorentz-covariant formulation: the conventional SU(2)-spin-network Hilbert space can be mapped to a space K of SL(2,C) functions, where Lorentz covariance is manifest. K can be described in terms of a certain subset of the projected spin networks studied by Livine, Alexandrov and Dupuis. It is formed by SL(2,C) functions completely determined by their restriction on SU(2). These are square-integrable in the SU(2) scalar product, but not in the SL(2,C) one. Thus, SU(2)-spin-network states can be represented by Lorentz-covariant SL(2,C) functions, as two-component photons can be described in the Lorentz-covariant Gupta-Bleulermore » formalism. As shown by Wolfgang Wieland in a related paper, this manifestly Lorentz-covariant formulation can also be directly obtained from canonical quantization. We show that the spinfoam dynamics of loop quantum gravity is locally SL(2,C)-invariant in the bulk, and yields states that are precisely in K on the boundary. This clarifies how the SL(2,C) spinfoam formalism yields an SU(2) theory on the boundary. These structures define a tidy Lorentz-covariant formalism for loop gravity.« less

Beta-diversity of ectoparasites at two spatial scales: nested hierarchy, geography and habitat type.

PubMed

Warburton, Elizabeth M; van der Mescht, Luther; Stanko, Michal; Vinarski, Maxim V; Korallo-Vinarskaya, Natalia P; Khokhlova, Irina S; Krasnov, Boris R

2017-06-01

Beta-diversity of biological communities can be decomposed into (a) dissimilarity of communities among units of finer scale within units of broader scale and (b) dissimilarity of communities among units of broader scale. We investigated compositional, phylogenetic/taxonomic and functional beta-diversity of compound communities of fleas and gamasid mites parasitic on small Palearctic mammals in a nested hierarchy at two spatial scales: (a) continental scale (across the Palearctic) and (b) regional scale (across sites within Slovakia). At each scale, we analyzed beta-diversity among smaller units within larger units and among larger units with partitioning based on either geography or ecology. We asked (a) whether compositional, phylogenetic/taxonomic and functional dissimilarities of flea and mite assemblages are scale dependent; (b) how geographical (partitioning of sites according to geographic position) or ecological (partitioning of sites according to habitat type) characteristics affect phylogenetic/taxonomic and functional components of dissimilarity of ectoparasite assemblages and (c) whether assemblages of fleas and gamasid mites differ in their degree of dissimilarity, all else being equal. We found that compositional, phylogenetic/taxonomic, or functional beta-diversity was greater on a continental rather than a regional scale. Compositional and phylogenetic/taxonomic components of beta-diversity were greater among larger units than among smaller units within larger units, whereas functional beta-diversity did not exhibit any consistent trend regarding site partitioning. Geographic partitioning resulted in higher values of beta-diversity of ectoparasites than ecological partitioning. Compositional and phylogenetic components of beta-diversity were higher in fleas than mites but the opposite was true for functional beta-diversity in some, but not all, traits.

Partitioning of K, U, and Th between sulfide and silicate liquids - Implications for radioactive heating of planetary cores

NASA Technical Reports Server (NTRS)

Murrell, M. T.; Burnett, D. S.

1986-01-01

Experimental partitioning studies are reported of K, U, and Th between silicate and FeFeS liquids designed to test the proposal that actinide partitioning into sulfide liquids is more important then K partitioning in the radioactive heating of planetary cores. For a basaltic liquid at 1450 C and 1.5 GPa, U partitioning into FeFeS liquids is five times greater than K partitioning. A typical value for the liquid partition coefficient for U from a granitic silicate liquid at one atmosphere at 1150 C and low fO2 is about 0.02; the coefficient for Th is similar. At low fO2 and higher temperature, experiments with basaltic liquids produce strong Ca and U partitioning into the sulfide liquid with U coefficient greater than one. The Th coefficient is less strongly affected.

A New Spinel-Olivine Oxybarometer: Near-Liquidus Partitioning of V between Olivine-Melt, Spinel-Melt, and Spinel-Olivine in Martian Basalt Composition Y980459 as a Function of Oxygen Fugacity

NASA Technical Reports Server (NTRS)

Papike, J. J.; Le, L.; Burger, P. V.; Shearer, C. K.; Bell, A. S.; Jones, J.

2013-01-01

Our research on valence state partitioning began in 2005 with a review of Cr, Fe, Ti, and V partitioning among crystallographic sites in olivine, pyroxene, and spinel [1]. That paper was followed by several on QUE94201 melt composition and specifically on Cr, V, and Eu partitioning between pyroxene and melt [2-5]. This paper represents the continuation of our examination of the partitioning of multivalent V between olivine, spinel, and melt in martian olivine-phyric basalts of Y980459 composition [6, 7]. Here we introduce a new, potentially powerful oxybarometer, V partitioning between spinel and olivine, which can be used when no melt is preserved in the meteorite. The bulk composition of QUE94201 was ideal for our study of martian pyroxene-phyric basalts and specifically the partitioning between pyroxene-melt for Cr, V, and Eu. Likewise, bulk composition Y980459 is ideal for the study of martian olivine-phyric basalts and specifically for olivine-melt, spinel-melt, and spinel-olivine partitioning of V as a function of oxygen fugacity.

Octanol-Water Partition Coefficient from 3D-RISM-KH Molecular Theory of Solvation with Partial Molar Volume Correction.

PubMed

Huang, WenJuan; Blinov, Nikolay; Kovalenko, Andriy

2015-04-30

The octanol-water partition coefficient is an important physical-chemical characteristic widely used to describe hydrophobic/hydrophilic properties of chemical compounds. The partition coefficient is related to the transfer free energy of a compound from water to octanol. Here, we introduce a new protocol for prediction of the partition coefficient based on the statistical-mechanical, 3D-RISM-KH molecular theory of solvation. It was shown recently that with the compound-solvent correlation functions obtained from the 3D-RISM-KH molecular theory of solvation, the free energy functional supplemented with the correction linearly related to the partial molar volume obtained from the Kirkwood-Buff/3D-RISM theory, also called the "universal correction" (UC), provides accurate prediction of the hydration free energy of small compounds, compared to explicit solvent molecular dynamics [ Palmer , D. S. ; J. Phys.: Condens. Matter 2010 , 22 , 492101 ]. Here we report that with the UC reparametrized accordingly this theory also provides an excellent agreement with the experimental data for the solvation free energy in nonpolar solvent (1-octanol) and so accurately predicts the octanol-water partition coefficient. The performance of the Kovalenko-Hirata (KH) and Gaussian fluctuation (GF) functionals of the solvation free energy, with and without UC, is tested on a large library of small compounds with diverse functional groups. The best agreement with the experimental data for octanol-water partition coefficients is obtained with the KH-UC solvation free energy functional.

A Recursive Method for Calculating Certain Partition Functions.

ERIC Educational Resources Information Center

Woodrum, Luther; And Others

1978-01-01

Describes a simple recursive method for calculating the partition function and average energy of a system consisting of N electrons and L energy levels. Also, presents an efficient APL computer program to utilize the recursion relation. (Author/GA)

Partitioning of functional gene expression data using principal points.

PubMed

Kim, Jaehee; Kim, Haseong

2017-10-12

DNA microarrays offer motivation and hope for the simultaneous study of variations in multiple genes. Gene expression is a temporal process that allows variations in expression levels with a characterized gene function over a period of time. Temporal gene expression curves can be treated as functional data since they are considered as independent realizations of a stochastic process. This process requires appropriate models to identify patterns of gene functions. The partitioning of the functional data can find homogeneous subgroups of entities for the massive genes within the inherent biological networks. Therefor it can be a useful technique for the analysis of time-course gene expression data. We propose a new self-consistent partitioning method of functional coefficients for individual expression profiles based on the orthonormal basis system. A principal points based functional partitioning method is proposed for time-course gene expression data. The method explores the relationship between genes using Legendre coefficients as principal points to extract the features of gene functions. Our proposed method provides high connectivity in connectedness after clustering for simulated data and finds a significant subsets of genes with the increased connectivity. Our approach has comparative advantages that fewer coefficients are used from the functional data and self-consistency of principal points for partitioning. As real data applications, we are able to find partitioned genes through the gene expressions found in budding yeast data and Escherichia coli data. The proposed method benefitted from the use of principal points, dimension reduction, and choice of orthogonal basis system as well as provides appropriately connected genes in the resulting subsets. We illustrate our method by applying with each set of cell-cycle-regulated time-course yeast genes and E. coli genes. The proposed method is able to identify highly connected genes and to explore the complex dynamics of biological systems in functional genomics.

Standoff Sensing of Electronic Systems

DTIC Science & Technology

2011-03-12

74<�/M!N��./!!M/!N’ AR@’!017!1.Q617921.S!󈨘.17< 6M !N’ AA@’!017!1.Q617921.S!’./01.2’ 756>/.M!N’ A+@󈧫!2.9>52917Q8?89;8>9;92<’!282/6/72’ AB...called the value function. Sondik (1978) showed that, for a finite- transient deterministic policy 1, there exists a Markov partition B = B1 ∪ B2... transient deterministic policy. Sondik noted that an arbitrary policy Π is not likely to be finite- transient , and for it one can only construct a partition

Surveillance system and method having parameter estimation and operating mode partitioning

NASA Technical Reports Server (NTRS)

Bickford, Randall L. (Inventor)

2005-01-01

A system and method for monitoring an apparatus or process asset including creating a process model comprised of a plurality of process submodels each correlative to at least one training data subset partitioned from an unpartitioned training data set and each having an operating mode associated thereto; acquiring a set of observed signal data values from the asset; determining an operating mode of the asset for the set of observed signal data values; selecting a process submodel from the process model as a function of the determined operating mode of the asset; calculating a set of estimated signal data values from the selected process submodel for the determined operating mode; and determining asset status as a function of the calculated set of estimated signal data values for providing asset surveillance and/or control.

Temperature extrapolation of multicomponent grand canonical free energy landscapes

NASA Astrophysics Data System (ADS)

Mahynski, Nathan A.; Errington, Jeffrey R.; Shen, Vincent K.

2017-08-01

We derive a method for extrapolating the grand canonical free energy landscape of a multicomponent fluid system from one temperature to another. Previously, we introduced this statistical mechanical framework for the case where kinetic energy contributions to the classical partition function were neglected for simplicity [N. A. Mahynski et al., J. Chem. Phys. 146, 074101 (2017)]. Here, we generalize the derivation to admit these contributions in order to explicitly illustrate the differences that result. Specifically, we show how factoring out kinetic energy effects a priori, in order to consider only the configurational partition function, leads to simpler mathematical expressions that tend to produce more accurate extrapolations than when these effects are included. We demonstrate this by comparing and contrasting these two approaches for the simple cases of an ideal gas and a non-ideal, square-well fluid.

Hydraulic geometry of the Platte River in south-central Nebraska

USGS Publications Warehouse

Eschner, T.R.

1982-01-01

At-a-station hydraulic-geometry of the Platte River in south-central Nebraska is complex. The range of exponents of simple power-function relations is large, both between different reaches of the river, and among different sections within a given reach. The at-a-station exponents plot in several fields of the b-f-m diagram, suggesting that morphologic and hydraulic changes with increasing discharge vary considerably. Systematic changes in the plotting positions of the exponents with time indicate that in general, the width exponent has decreased, although trends are not readily apparent in the other exponents. Plots of the hydraulic-geometry relations indicate that simple power functions are not the proper model in all instances. For these sections, breaks in the slopes of the hydraulic geometry relations serve to partition the data sets. Power functions fit separately to the partitioned data described the width-, depth-, and velocity-discharge relations more accurately than did a single power function. Plotting positions of the exponents from hydraulic geometry relations of partitioned data sets on b-f-m diagrams indicate that much of the apparent variations of plotting positions of single power functions results because the single power functions compromise both subsets of partitioned data. For several sections, the shape of the channel primarily accounts for the better fit of two-power functions to partitioned data than a single power function over the entire range of data. These non-log linear relations may have significance for channel maintenance. (USGS)

A strategy to load balancing for non-connectivity MapReduce job

NASA Astrophysics Data System (ADS)

Zhou, Huaping; Liu, Guangzong; Gui, Haixia

2017-09-01

MapReduce has been widely used in large scale and complex datasets as a kind of distributed programming model. Original Hash partitioning function in MapReduce often results the problem of data skew when data distribution is uneven. To solve the imbalance of data partitioning, we proposes a strategy to change the remaining partitioning index when data is skewed. In Map phase, we count the amount of data which will be distributed to each reducer, then Job Tracker monitor the global partitioning information and dynamically modify the original partitioning function according to the data skew model, so the Partitioner can change the index of these partitioning which will cause data skew to the other reducer that has less load in the next partitioning process, and can eventually balance the load of each node. Finally, we experimentally compare our method with existing methods on both synthetic and real datasets, the experimental results show our strategy can solve the problem of data skew with better stability and efficiency than Hash method and Sampling method for non-connectivity MapReduce task.

Evaluating Feynman integrals by the hypergeometry

NASA Astrophysics Data System (ADS)

Feng, Tai-Fu; Chang, Chao-Hsi; Chen, Jian-Bin; Gu, Zhi-Hua; Zhang, Hai-Bin

2018-02-01

The hypergeometric function method naturally provides the analytic expressions of scalar integrals from concerned Feynman diagrams in some connected regions of independent kinematic variables, also presents the systems of homogeneous linear partial differential equations satisfied by the corresponding scalar integrals. Taking examples of the one-loop B0 and massless C0 functions, as well as the scalar integrals of two-loop vacuum and sunset diagrams, we verify our expressions coinciding with the well-known results of literatures. Based on the multiple hypergeometric functions of independent kinematic variables, the systems of homogeneous linear partial differential equations satisfied by the mentioned scalar integrals are established. Using the calculus of variations, one recognizes the system of linear partial differential equations as stationary conditions of a functional under some given restrictions, which is the cornerstone to perform the continuation of the scalar integrals to whole kinematic domains numerically with the finite element methods. In principle this method can be used to evaluate the scalar integrals of any Feynman diagrams.

Parallel file system with metadata distributed across partitioned key-value store c

DOEpatents

Bent, John M.; Faibish, Sorin; Grider, Gary; Torres, Aaron

2017-09-19

Improved techniques are provided for storing metadata associated with a plurality of sub-files associated with a single shared file in a parallel file system. The shared file is generated by a plurality of applications executing on a plurality of compute nodes. A compute node implements a Parallel Log Structured File System (PLFS) library to store at least one portion of the shared file generated by an application executing on the compute node and metadata for the at least one portion of the shared file on one or more object storage servers. The compute node is also configured to implement a partitioned data store for storing a partition of the metadata for the shared file, wherein the partitioned data store communicates with partitioned data stores on other compute nodes using a message passing interface. The partitioned data store can be implemented, for example, using Multidimensional Data Hashing Indexing Middleware (MDHIM).

A static data flow simulation study at Ames Research Center

NASA Technical Reports Server (NTRS)

Barszcz, Eric; Howard, Lauri S.

1987-01-01

Demands in computational power, particularly in the area of computational fluid dynamics (CFD), led NASA Ames Research Center to study advanced computer architectures. One architecture being studied is the static data flow architecture based on research done by Jack B. Dennis at MIT. To improve understanding of this architecture, a static data flow simulator, written in Pascal, has been implemented for use on a Cray X-MP/48. A matrix multiply and a two-dimensional fast Fourier transform (FFT), two algorithms used in CFD work at Ames, have been run on the simulator. Execution times can vary by a factor of more than 2 depending on the partitioning method used to assign instructions to processing elements. Service time for matching tokens has proved to be a major bottleneck. Loop control and array address calculation overhead can double the execution time. The best sustained MFLOPS rates were less than 50% of the maximum capability of the machine.

The four-loop six-gluon NMHV ratio function

DOE PAGES

Dixon, Lance J.; von Hippel, Matt; McLeod, Andrew J.

2016-01-11

We use the hexagon function bootstrap to compute the ratio function which characterizes the next-to-maximally-helicity-violating (NMHV) six-point amplitude in planar N=4 super-Yang-Mills theory at four loops. A powerful constraint comes from dual superconformal invariance, in the form of a Q¯ differential equation, which heavily constrains the first derivatives of the transcendental functions entering the ratio function. At four loops, it leaves only a 34-parameter space of functions. Constraints from the collinear limits, and from the multi-Regge limit at the leading-logarithmic (LL) and next-to-leading-logarithmic (NLL) order, suffice to fix these parameters and obtain a unique result. We test the result againstmore » multi-Regge predictions at NNLL and N 3LL, and against predictions from the operator product expansion involving one and two flux-tube excitations; all cross-checks are satisfied. We study the analytical and numerical behavior of the parity-even and parity-odd parts on various lines and surfaces traversing the three-dimensional space of cross ratios. As part of this program, we characterize all irreducible hexagon functions through weight eight in terms of their coproduct. As a result, we also provide representations of the ratio function in particular kinematic regions in terms of multiple polylogarithms.« less

The four-loop six-gluon NMHV ratio function

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dixon, Lance J.; von Hippel, Matt; McLeod, Andrew J.

2016-01-11

We use the hexagon function bootstrap to compute the ratio function which characterizes the next-to-maximally-helicity-violating (NMHV) six-point amplitude in planar N = 4 super-Yang-Mills theory at four loops. A powerful constraint comes from dual superconformal invariance, in the form of a Q - differential equation, which heavily constrains the first derivatives of the transcendental functions entering the ratio function. At four loops, it leaves only a 34-parameter space of functions. Constraints from the collinear limits, and from the multi-Regge limit at the leading-logarithmic (LL) and next-to-leading-logarithmic (NLL) order, suffice to fix these parameters and obtain a unique result. We testmore » the result against multi- Regge predictions at NNLL and N 3LL, and against predictions from the operator product expansion involving one and two flux-tube excitations; all cross-checks are satisfied. We also study the analytical and numerical behavior of the parity-even and parity-odd parts on various lines and surfaces traversing the three-dimensional space of cross ratios. As part of this program, we characterize all irreducible hexagon functions through weight eight in terms of their coproduct. Furthermore, we provide representations of the ratio function in particular kinematic regions in terms of multiple polylogarithms.« less

Evidence for an RNA pseudoknot loop-helix interaction essential for efficient -1 ribosomal frameshifting.

PubMed

Liphardt, J; Napthine, S; Kontos, H; Brierley, I

1999-05-07

RNA pseudoknots are structural elements that participate in a variety of biological processes. At -1 ribosomal frameshifting sites, several types of pseudoknot have been identified which differ in their organisation and functionality. The pseudoknot found in infectious bronchitis virus (IBV) is typical of those that possess a long stem 1 of 11-12 bp and a long loop 2 (30-164 nt). A second group of pseudoknots are distinguishable that contain stems of only 5 to 7 bp and shorter loops. The NMR structure of one such pseudoknot, that of mouse mammary tumor virus (MMTV), has revealed that it is kinked at the stem 1-stem 2 junction, and that this kinked conformation is essential for efficient frameshifting. We recently investigated the effect on frameshifting of modulating stem 1 length and stability in IBV-based pseudoknots, and found that a stem 1 with at least 11 bp was needed for efficient frameshifting. Here, we describe the sequence manipulations that are necessary to bypass the requirement for an 11 bp stem 1 and to convert a short non-functional IBV-derived pseudoknot into a highly efficient, kinked frameshifter pseudoknot. Simple insertion of an adenine residue at the stem 1-stem 2 junction (an essential feature of a kinked pseudoknot) was not sufficient to create a functional pseudoknot. An additional change was needed: efficient frameshifting was recovered only when the last nucleotide of loop 2 was changed from a G to an A. The requirement for an A at the end of loop 2 is consistent with a loop-helix contact similar to those described in other RNA tertiary structures. A mutational analysis of both partners of the proposed interaction, the loop 2 terminal adenine residue and two G.C pairs near the top of stem 1, revealed that the interaction was essential for efficient frameshifting. The specific requirement for a 3'-terminal A residue was lost when loop 2 was increased from 8 to 14 nt, suggesting that the loop-helix contact may be required only in those pseudoknots with a short loop 2. Copyright 1999 Academic Press.

Protein loop modeling using a new hybrid energy function and its application to modeling in inaccurate structural environments.

PubMed

Park, Hahnbeom; Lee, Gyu Rie; Heo, Lim; Seok, Chaok

2014-01-01

Protein loop modeling is a tool for predicting protein local structures of particular interest, providing opportunities for applications involving protein structure prediction and de novo protein design. Until recently, the majority of loop modeling methods have been developed and tested by reconstructing loops in frameworks of experimentally resolved structures. In many practical applications, however, the protein loops to be modeled are located in inaccurate structural environments. These include loops in model structures, low-resolution experimental structures, or experimental structures of different functional forms. Accordingly, discrepancies in the accuracy of the structural environment assumed in development of the method and that in practical applications present additional challenges to modern loop modeling methods. This study demonstrates a new strategy for employing a hybrid energy function combining physics-based and knowledge-based components to help tackle this challenge. The hybrid energy function is designed to combine the strengths of each energy component, simultaneously maintaining accurate loop structure prediction in a high-resolution framework structure and tolerating minor environmental errors in low-resolution structures. A loop modeling method based on global optimization of this new energy function is tested on loop targets situated in different levels of environmental errors, ranging from experimental structures to structures perturbed in backbone as well as side chains and template-based model structures. The new method performs comparably to force field-based approaches in loop reconstruction in crystal structures and better in loop prediction in inaccurate framework structures. This result suggests that higher-accuracy predictions would be possible for a broader range of applications. The web server for this method is available at http://galaxy.seoklab.org/loop with the PS2 option for the scoring function.

Loop system for creating jet fuel vapor standards used in the calibration of infrared spectrophotometers and gas chromatographs.

PubMed

Reboulet, James; Cunningham, Robert; Gunasekar, Palur G; Chapman, Gail D; Stevens, Sean C

2009-02-01

A whole body inhalation study of mixed jet fuel vapor and its aerosol necessitated the development of a method for preparing vapor only standards from the neat fuel. Jet fuel is a complex mixture of components which partitions between aerosol and vapor when aspirated based on relative volatility of the individual compounds. A method was desired which could separate the vapor portion from the aerosol component to prepare standards for the calibration of infrared spectrophotometers and a head space gas chromatography system. A re-circulating loop system was developed which provided vapor only standards whose composition matched those seen in an exposure system. Comparisons of nominal concentrations in the exposure system to those determined by infrared spectrophotometry were in 92-95% agreement. Comparison of jet fuel vapor concentrations determined by infrared spectrophotometry compared to head space gas chromatography yielded a 93% overall agreement in trial runs. These levels of agreement show the loop system to be a viable method for creating jet fuel vapor standards for calibrating instruments.

QCD Resummation for Single Spin Asymmetries

NASA Astrophysics Data System (ADS)

Kang, Zhong-Bo; Xiao, Bo-Wen; Yuan, Feng

2011-10-01

We study the transverse momentum dependent factorization for single spin asymmetries in Drell-Yan and semi-inclusive deep inelastic scattering processes at one-loop order. The next-to-leading order hard factors are calculated in the Ji-Ma-Yuan factorization scheme. We further derive the QCD resummation formalisms for these observables following the Collins-Soper-Sterman method. The results are expressed in terms of the collinear correlation functions from initial and/or final state hadrons coupled with the Sudakov form factor containing all order soft-gluon resummation effects. The scheme-independent coefficients are calculated up to one-loop order.

QCD Resummation for Single Spin Asymmetries

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kang Z.; Xiao, Bo-Wen; Yuan, Feng

We study the transverse momentum dependent factorization for single spin asymmetries in Drell-Yan and semi-inclusive deep inelastic scattering processes at one-loop order. The next-to-leading order hard factors are calculated in the Ji-Ma-Yuan factorization scheme. We further derive the QCD resummation formalisms for these observables following the Collins-Soper-Sterman method. The results are expressed in terms of the collinear correlation functions from initial and/or final state hadrons coupled with the Sudakov form factor containing all order soft-gluon resummation effects. The scheme-independent coefficients are calculated up to one-loop order.

The spin-partitioned total position-spread tensor: An application to Heisenberg spin chains

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fertitta, Edoardo; Paulus, Beate; El Khatib, Muammar

2015-12-28

The spin partition of the Total Position-Spread (TPS) tensor has been performed for one-dimensional Heisenberg chains with open boundary conditions. Both the cases of a ferromagnetic (high-spin) and an anti-ferromagnetic (low-spin) ground-state have been considered. In the case of a low-spin ground-state, the use of alternating magnetic couplings allowed to investigate the effect of spin-pairing. The behavior of the spin-partitioned TPS (SP-TPS) tensor as a function of the number of sites turned to be closely related to the presence of an energy gap between the ground-state and the first excited-state at the thermodynamic limit. Indeed, a gapped energy spectrum ismore » associated to a linear growth of the SP-TPS tensor with the number of sites. On the other hand, in gapless situations, the spread presents a faster-than-linear growth, resulting in the divergence of its per-site value. Finally, for the case of a high-spin wave function, an analytical expression of the dependence of the SP-TPS on the number of sites n and the total spin-projection S{sub z} has been derived.« less

Determination of octanol-air partition coefficients and supercooled liquid vapor pressures of PAHs as a function of temperature: Application to gas-particle partitioning in an urban atmosphere

NASA Astrophysics Data System (ADS)

Odabasi, Mustafa; Cetin, Eylem; Sofuoglu, Aysun

Octanol-air partition coefficients ( KOA) for 14 polycyclic aromatic hydrocarbons (PAHs) were determined as a function of temperature using the gas chromatographic retention time method. log KOA values at 25° ranged over six orders of magnitude, between 6.34 (acenaphthylene) and 12.59 (dibenz[ a,h]anthracene). The determined KOA values were within factor of 0.7 (dibenz[ a,h]anthracene) to 15.1 (benz[ a]anthracene) of values calculated as the ratio of octanol-water partition coefficient to dimensionless Henry's law constant. Supercooled liquid vapor pressures ( PL) of 13 PAHs were also determined using the gas chromatographic retention time technique. Activity coefficients in octanol calculated using KOA and PL ranged between 3.2 and 6.2 indicating near-ideal solution behavior. Atmospheric concentrations measured in this study in Izmir, Turkey were used to investigate the partitioning of PAHs between particle and gas-phases. Experimental gas-particle partition coefficients ( Kp) were compared to the predictions of KOA absorption and KSA (soot-air partition coefficient) models. Octanol-based absorptive partitioning model predicted lower partition coefficients especially for relatively volatile PAHs. Ratios of measured/modeled partition coefficients ranged between 1.1 and 15.5 (4.5±6.0, average±SD) for KOA model. KSA model predictions were relatively better and measured to modeled ratios ranged between 0.6 and 5.6 (2.3±2.7, average±SD).

Potent Mechanism-Based Inactivation Of Cytochrome P450 2B4 By 9-Ethynylphenanthrene: Implications For Allosteric Modulation Of Cytochrome P450 Catalysis1

PubMed Central

Zhang, Haoming; Gay, Sean C.; Shah, Manish; Foroozesh, Maryam; Liu, Jiawang; Osawa, Yoichi; Zhang, Qinghai; Stout, C. David; Halpert, James R.; Hollenberg, Paul F.

2013-01-01

The mechanism-based inactivation of cytochrome P450 2B4 (CYP2B4) by 9-ethynylphenanthrene (9EP) has been investigated. The partition ratio and kinact are 0.2 and 0.25 min−1, respectively. Intriguingly, the inactivation exhibits sigmoidal kinetics with a Hill coefficient of 2.5 and S50 of 4.5 μM indicative of homotropic cooperativity. Enzyme inactivation led to an increase in mass of the apo-CYP2B4 by 218 Da as determined by ESI-LC/MS, consistent with covalent protein modification. The modified CYP2B4 was purified to homogeneity and its structure determined by X-ray crystallography. The structure showed that 9EP is covalently attached to the Oγ of Thr 302 via an ester bond, which is consistent with the increased mass of the protein. The presence of the bulky phenanthrenyl ring resulted in inward rotations of Phe 297 and Phe 206 leading to a compact active site. Thus, binding of another molecule of 9EP in the active site is prohibited. However, results from the quenching of 9EP fluorescence by unmodified or 9EP-modified CYP2B4 revealed at least two binding sites with distinct affinities, with the low affinity site being the catalytic site and the high affinity site on the protein periphery. Computer-aided docking and MD simulations with one or two ligands bound revealed that the high affinity site is situated at the entrance of a substrate access channel surrounded by the F’ helix, β1/β2 loop and β4 loop and functions as an allosteric site to enhance the efficiency of activation of the acetylenic group of 9EP and subsequent covalent modification of Thr 302. PMID:23276288

Caustics, counting maps and semi-classical asymptotics

NASA Astrophysics Data System (ADS)

Ercolani, N. M.

2011-02-01

This paper develops a deeper understanding of the structure and combinatorial significance of the partition function for Hermitian random matrices. The coefficients of the large N expansion of the logarithm of this partition function, also known as the genus expansion (and its derivatives), are generating functions for a variety of graphical enumeration problems. The main results are to prove that these generating functions are, in fact, specific rational functions of a distinguished irrational (algebraic) function, z0(t). This distinguished function is itself the generating function for the Catalan numbers (or generalized Catalan numbers, depending on the choice of weight of the parameter t). It is also a solution of the inviscid Burgers equation for certain initial data. The shock formation, or caustic, of the Burgers characteristic solution is directly related to the poles of the rational forms of the generating functions. As an intriguing application, one gains new insights into the relation between certain derivatives of the genus expansion, in a double-scaling limit, and the asymptotic expansion of the first Painlevé transcendent. This provides a precise expression of the Painlevé asymptotic coefficients directly in terms of the coefficients of the partial fractions expansion of the rational form of the generating functions established in this paper. Moreover, these insights point towards a more general program relating the first Painlevé hierarchy to the higher order structure of the double-scaling limit through the specific rational structure of generating functions in the genus expansion. The paper closes with a discussion of the relation of this work to recent developments in understanding the asymptotics of graphical enumeration. As a by-product, these results also yield new information about the asymptotics of recurrence coefficients for orthogonal polynomials with respect to exponential weights, the calculation of correlation functions for certain tied random walks on a 1D lattice, and the large time asymptotics of random matrix partition functions.

Computer code for controller partitioning with IFPC application: A user's manual

NASA Technical Reports Server (NTRS)

Schmidt, Phillip H.; Yarkhan, Asim

1994-01-01

A user's manual for the computer code for partitioning a centralized controller into decentralized subcontrollers with applicability to Integrated Flight/Propulsion Control (IFPC) is presented. Partitioning of a centralized controller into two subcontrollers is described and the algorithm on which the code is based is discussed. The algorithm uses parameter optimization of a cost function which is described. The major data structures and functions are described. Specific instructions are given. The user is led through an example of an IFCP application.

Hearing the shape of the Ising model with a programmable superconducting-flux annealer.

PubMed

Vinci, Walter; Markström, Klas; Boixo, Sergio; Roy, Aidan; Spedalieri, Federico M; Warburton, Paul A; Severini, Simone

2014-07-16

Two objects can be distinguished if they have different measurable properties. Thus, distinguishability depends on the Physics of the objects. In considering graphs, we revisit the Ising model as a framework to define physically meaningful spectral invariants. In this context, we introduce a family of refinements of the classical spectrum and consider the quantum partition function. We demonstrate that the energy spectrum of the quantum Ising Hamiltonian is a stronger invariant than the classical one without refinements. For the purpose of implementing the related physical systems, we perform experiments on a programmable annealer with superconducting flux technology. Departing from the paradigm of adiabatic computation, we take advantage of a noisy evolution of the device to generate statistics of low energy states. The graphs considered in the experiments have the same classical partition functions, but different quantum spectra. The data obtained from the annealer distinguish non-isomorphic graphs via information contained in the classical refinements of the functions but not via the differences in the quantum spectra.

Analytical and experimental investigation on transmission loss of clamped double panels: implication of boundary effects.

PubMed

Xin, F X; Lu, T J

2009-03-01

The air-borne sound insulation performance of a rectangular double-panel partition clamp mounted on an infinite acoustic rigid baffle is investigated both analytically and experimentally and compared with that of a simply supported one. With the clamped (or simply supported) boundary accounted for by using the method of modal function, a double series solution for the sound transmission loss (STL) of the structure is obtained by employing the weighted residual (Galerkin) method. Experimental measurements with Al double-panel partitions having air cavity are subsequently carried out to validate the theoretical model for both types of the boundary condition, and good overall agreement is achieved. A consistency check of the two different models (based separately on clamped modal function and simply supported modal function) is performed by extending the panel dimensions to infinite where no boundaries exist. The significant discrepancies between the two different boundary conditions are demonstrated in terms of the STL versus frequency plots as well as the panel deflection mode shapes.

An Investigation of Document Partitions.

ERIC Educational Resources Information Center

Shaw, W. M., Jr.

1986-01-01

Empirical significance of document partitions is investigated as a function of index term-weight and similarity thresholds. Results show the same empirically preferred partitions can be detected by two independent strategies: an analysis of cluster-based retrieval analysis and an analysis of regularities in the underlying structure of the document…

ESTIMATING DISSOLVED ORGANIC CARBON PARTITION COEFFICIENTS FOR NONIONIC ORGANIC CHEMICALS

EPA Science Inventory

A literature search was performed for dissolved organic carbon/water partition coefficients for nonionic chemicals (Kdoc) and Kdoc data was taken from more than sixty references. The Kdoc data were evaluated as a function of the n-octanol/water partition coefficients (Kow). A pre...

Evolution and development of model membranes for physicochemical and functional studies of the membrane lateral heterogeneity.

PubMed

Morigaki, Kenichi; Tanimoto, Yasushi

2018-03-14

One of the main questions in the membrane biology is the functional roles of membrane heterogeneity and molecular localization. Although segregation and local enrichment of protein/lipid components (rafts) have been extensively studied, the presence and functions of such membrane domains still remain elusive. Along with biochemical, cell observation, and simulation studies, model membranes are emerging as an important tool for understanding the biological membrane, providing quantitative information on the physicochemical properties of membrane proteins and lipids. Segregation of fluid lipid bilayer into liquid-ordered (Lo) and liquid-disordered (Ld) phases has been studied as a simplified model of raft in model membranes, including giant unilamellar vesicles (GUVs), giant plasma membrane vesicles (GPMVs), and supported lipid bilayers (SLB). Partition coefficients of membrane proteins between Lo and Ld phases were measured to gauze their affinities to lipid rafts (raftophilicity). One important development in model membrane is patterned SLB based on the microfabrication technology. Patterned Lo/Ld phases have been applied to study the partition and function of membrane-bound molecules. Quantitative information of individual molecular species attained by model membranes is critical for elucidating the molecular functions in the complex web of molecular interactions. The present review gives a short account of the model membranes developed for studying the lateral heterogeneity, especially focusing on patterned model membranes on solid substrates. Copyright © 2018 Elsevier B.V. All rights reserved.

Effects of Gas-Wall Partitioning in Teflon Tubing, Instrumentation and Other Materials on Time-Resolved Measurements of Gas-Phase Organic Compounds

NASA Astrophysics Data System (ADS)

Pagonis, D.; Deming, B.; Krechmer, J. E.; De Gouw, J. A.; Jimenez, J. L.; Ziemann, P. J.

2017-12-01

Recently it has been shown that gas-phase organic compounds partition to and from the walls of Teflon environmental chambers. This process is fast, reversible, and can be modeled as absorptive partitioning. Here these studies were extended to investigate gas-wall partitioning inside Teflon tubing by introducing step function changes in the concentration of compounds being sampled and measuring the delay in the response of a proton transfer reaction-mass spectrometer (PTR-MS). We find that these delays are significant for compounds with a saturation vapor concentration (c*) below 106 μg m-3, and that the Teflon tubing and the PTR-MS both contribute to the delays. Tubing delays range from minutes to hours under common sampling conditions and can be accurately predicted by a simple chromatography model across a range of tubing lengths and diameters, flow rates, compound functional groups, and c*. This method also allows one to determine the volatility-dependent response function of an instrument, which can be convolved with the output of the tubing model to correct for delays in instrument response time for these "sticky" compounds. This correction is expected to be of particular interest to researchers utilizing and developing chemical ionization mass spectrometry (CIMS) techniques, since many of the multifunctional organic compounds detected by CIMS show significant tubing and instrument delays. These results also enable better design of sampling systems, in particular when fast instrument response is needed, such as for rapid transients, aircraft, or eddy covariance measurements. Additional results presented here extend this method to quantify the relative sorptive capacities for other commonly used tubing materials, including PFA, FEP, PTFE, PEEK, glass, copper, stainless steel, and passivated steel.

Quantum Probability Cancellation Due to a Single-Photon State

NASA Technical Reports Server (NTRS)

Ou, Z. Y.

1996-01-01

When an N-photon state enters a lossless symmetric beamsplitter from one input port, the photon distribution for the two output ports has the form of Bernouli Binormial, with highest probability at equal partition (N/2 at one outport and N/2 at the other). However, injection of a single photon state at the other input port can dramatically change the photon distribution at the outputs, resulting in zero probability at equal partition. Such a strong deviation from classical particle theory stems from quantum probability amplitude cancellation. The effect persists even if the N-photon state is replaced by an arbitrary state of light. A special case is the coherent state which corresponds to homodyne detection of a single photon state and can lead to the measurement of the wave function of a single photon state.

Responses of microbial community functional structures to pilot-scale uranium in situ bioremediation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, M.; Wu, W.-M.; Wu, L.

2010-02-15

A pilot-scale field test system with an inner loop nested within an outer loop was constructed for in situ U(VI) bioremediation at a US Department of Energy site, Oak Ridge, TN. The outer loop was used for hydrological protection of the inner loop where ethanol was injected for biostimulation of microorganisms for U(VI) reduction/immobilization. After 2 years of biostimulation with ethanol, U(VI) levels were reduced to below drinking water standard (<30 {micro}gl{sup -1}) in the inner loop monitoring wells. To elucidate the microbial community structure and functions under in situ uranium bioremediation conditions, we used a comprehensive functional gene arraymore » (GeoChip) to examine the microbial functional gene composition of the sediment samples collected from both inner and outer loop wells. Our study results showed that distinct microbial communities were established in the inner loop wells. Also, higher microbial functional gene number, diversity and abundance were observed in the inner loop wells than the outer loop wells. In addition, metal-reducing bacteria, such as Desulfovibrio, Geobacter, Anaeromyxobacter and Shewanella, and other bacteria, for example, Rhodopseudomonas and Pseudomonas, are highly abundant in the inner loop wells. Finally, the richness and abundance of microbial functional genes were highly correlated with the mean travel time of groundwater from the inner loop injection well, pH and sulfate concentration in groundwater. These results suggest that the indigenous microbial communities can be successfully stimulated for U bioremediation in the groundwater ecosystem, and their structure and performance can be manipulated or optimized by adjusting geochemical and hydrological conditions.« less

Complex Chern-Simons Theory at Level k via the 3d-3d Correspondence

NASA Astrophysics Data System (ADS)

Dimofte, Tudor

2015-10-01

We use the 3d-3d correspondence together with the DGG construction of theories T n [ M] labelled by 3-manifolds M to define a non-perturbative state-integral model for Chern-Simons theory at any level k, based on ideal triangulations. The resulting partition functions generalize a widely studied k = 1 state-integral, as well as the 3d index, which is k = 0. The Chern-Simons partition functions correspond to partition functions of T n [ M] on squashed lens spaces L( k, 1). At any k, they admit a holomorphic-antiholomorphic factorization, corresponding to the decomposition of L( k, 1) into two solid tori, and the associated holomorphic block decomposition of the partition functions of T n [ M]. A generalization to L( k, p) is also presented. Convergence of the state integrals, for any k, requires triangulations to admit a positive angle structure; we propose that this is also necessary for the DGG gauge theory T n [ M] to flow to a desired IR SCFT.

Model‐based analysis of the influence of catchment properties on hydrologic partitioning across five mountain headwater subcatchments

PubMed Central

Wagener, Thorsten; McGlynn, Brian

2015-01-01

Abstract Ungauged headwater basins are an abundant part of the river network, but dominant influences on headwater hydrologic response remain difficult to predict. To address this gap, we investigated the ability of a physically based watershed model (the Distributed Hydrology‐Soil‐Vegetation Model) to represent controls on metrics of hydrologic partitioning across five adjacent headwater subcatchments. The five study subcatchments, located in Tenderfoot Creek Experimental Forest in central Montana, have similar climate but variable topography and vegetation distribution. This facilitated a comparative hydrology approach to interpret how parameters that influence partitioning, detected via global sensitivity analysis, differ across catchments. Model parameters were constrained a priori using existing regional information and expert knowledge. Influential parameters were compared to perceptions of catchment functioning and its variability across subcatchments. Despite between‐catchment differences in topography and vegetation, hydrologic partitioning across all metrics and all subcatchments was sensitive to a similar subset of snow, vegetation, and soil parameters. Results also highlighted one subcatchment with low certainty in parameter sensitivity, indicating that the model poorly represented some complexities in this subcatchment likely because an important process is missing or poorly characterized in the mechanistic model. For use in other basins, this method can assess parameter sensitivities as a function of the specific ungauged system to which it is applied. Overall, this approach can be employed to identify dominant modeled controls on catchment response and their agreement with system understanding. PMID:27642197

An approach to the analysis of performance of quasi-optimum digital phase-locked loops.

NASA Technical Reports Server (NTRS)

Polk, D. R.; Gupta, S. C.

1973-01-01

An approach to the analysis of performance of quasi-optimum digital phase-locked loops (DPLL's) is presented. An expression for the characteristic function of the prior error in the state estimate is derived, and from this expression an infinite dimensional equation for the prior error variance is obtained. The prior error-variance equation is a function of the communication system model and the DPLL gain and is independent of the method used to derive the DPLL gain. Two approximations are discussed for reducing the prior error-variance equation to finite dimension. The effectiveness of one approximation in analyzing DPLL performance is studied.

Renormalization of QCD in the interpolating momentum subtraction scheme at three loops

NASA Astrophysics Data System (ADS)

Gracey, J. A.; Simms, R. M.

2018-04-01

We introduce a more general set of kinematic renormalization schemes than the original momentum subtraction schemes of Celmaster and Gonsalves. These new schemes will depend on a parameter ω , which tags the external momentum of one of the legs of the three-point vertex functions in QCD. In each of the three new schemes, we renormalize QCD in the Landau and maximal Abelian gauges and establish the three-loop renormalization group functions in each gauge. For an application, we evaluate two critical exponents at the Banks-Zaks fixed point and demonstrate that their values appear to be numerically scheme independent in a subrange of the conformal window.

A semi-automatic computer-aided method for surgical template design

NASA Astrophysics Data System (ADS)

Chen, Xiaojun; Xu, Lu; Yang, Yue; Egger, Jan

2016-02-01

This paper presents a generalized integrated framework of semi-automatic surgical template design. Several algorithms were implemented including the mesh segmentation, offset surface generation, collision detection, ruled surface generation, etc., and a special software named TemDesigner was developed. With a simple user interface, a customized template can be semi- automatically designed according to the preoperative plan. Firstly, mesh segmentation with signed scalar of vertex is utilized to partition the inner surface from the input surface mesh based on the indicated point loop. Then, the offset surface of the inner surface is obtained through contouring the distance field of the inner surface, and segmented to generate the outer surface. Ruled surface is employed to connect inner and outer surfaces. Finally, drilling tubes are generated according to the preoperative plan through collision detection and merging. It has been applied to the template design for various kinds of surgeries, including oral implantology, cervical pedicle screw insertion, iliosacral screw insertion and osteotomy, demonstrating the efficiency, functionality and generality of our method.

A semi-automatic computer-aided method for surgical template design

PubMed Central

Chen, Xiaojun; Xu, Lu; Yang, Yue; Egger, Jan

2016-01-01

This paper presents a generalized integrated framework of semi-automatic surgical template design. Several algorithms were implemented including the mesh segmentation, offset surface generation, collision detection, ruled surface generation, etc., and a special software named TemDesigner was developed. With a simple user interface, a customized template can be semi- automatically designed according to the preoperative plan. Firstly, mesh segmentation with signed scalar of vertex is utilized to partition the inner surface from the input surface mesh based on the indicated point loop. Then, the offset surface of the inner surface is obtained through contouring the distance field of the inner surface, and segmented to generate the outer surface. Ruled surface is employed to connect inner and outer surfaces. Finally, drilling tubes are generated according to the preoperative plan through collision detection and merging. It has been applied to the template design for various kinds of surgeries, including oral implantology, cervical pedicle screw insertion, iliosacral screw insertion and osteotomy, demonstrating the efficiency, functionality and generality of our method. PMID:26843434

A semi-automatic computer-aided method for surgical template design.

PubMed

Chen, Xiaojun; Xu, Lu; Yang, Yue; Egger, Jan

2016-02-04

This paper presents a generalized integrated framework of semi-automatic surgical template design. Several algorithms were implemented including the mesh segmentation, offset surface generation, collision detection, ruled surface generation, etc., and a special software named TemDesigner was developed. With a simple user interface, a customized template can be semi- automatically designed according to the preoperative plan. Firstly, mesh segmentation with signed scalar of vertex is utilized to partition the inner surface from the input surface mesh based on the indicated point loop. Then, the offset surface of the inner surface is obtained through contouring the distance field of the inner surface, and segmented to generate the outer surface. Ruled surface is employed to connect inner and outer surfaces. Finally, drilling tubes are generated according to the preoperative plan through collision detection and merging. It has been applied to the template design for various kinds of surgeries, including oral implantology, cervical pedicle screw insertion, iliosacral screw insertion and osteotomy, demonstrating the efficiency, functionality and generality of our method.

Drug Distribution. Part 1. Models to Predict Membrane Partitioning.

PubMed

Nagar, Swati; Korzekwa, Ken

2017-03-01

Tissue partitioning is an important component of drug distribution and half-life. Protein binding and lipid partitioning together determine drug distribution. Two structure-based models to predict partitioning into microsomal membranes are presented. An orientation-based model was developed using a membrane template and atom-based relative free energy functions to select drug conformations and orientations for neutral and basic drugs. The resulting model predicts the correct membrane positions for nine compounds tested, and predicts the membrane partitioning for n = 67 drugs with an average fold-error of 2.4. Next, a more facile descriptor-based model was developed for acids, neutrals and bases. This model considers the partitioning of neutral and ionized species at equilibrium, and can predict membrane partitioning with an average fold-error of 2.0 (n = 92 drugs). Together these models suggest that drug orientation is important for membrane partitioning and that membrane partitioning can be well predicted from physicochemical properties.

Statistical mechanics of free particles on space with Lie-type noncommutativity

NASA Astrophysics Data System (ADS)

Shariati, Ahmad; Khorrami, Mohammad; Fatollahi, Amir H.

2010-07-01

Effects of Lie-type noncommutativity on thermodynamic properties of a system of free identical particles are investigated. A definition for finite volume of the configuration space is given, and the grandcanonical partition function in the thermodynamic limit is calculated. Two possible definitions for the pressure are discussed, which are equivalent when the noncommutativity vanishes. The thermodynamic observables are extracted from the partition function. Different limits are discussed where either the noncommutativity or the quantum effects are important. Finally, specific cases are discussed where the group is SU(2) or SO(3), and the partition function of a nondegenerate gas is calculated.

Force-field functor theory: classical force-fields which reproduce equilibrium quantum distributions

PubMed Central

Babbush, Ryan; Parkhill, John; Aspuru-Guzik, Alán

2013-01-01

Feynman and Hibbs were the first to variationally determine an effective potential whose associated classical canonical ensemble approximates the exact quantum partition function. We examine the existence of a map between the local potential and an effective classical potential which matches the exact quantum equilibrium density and partition function. The usefulness of such a mapping rests in its ability to readily improve Born-Oppenheimer potentials for use with classical sampling. We show that such a map is unique and must exist. To explore the feasibility of using this result to improve classical molecular mechanics, we numerically produce a map from a library of randomly generated one-dimensional potential/effective potential pairs then evaluate its performance on independent test problems. We also apply the map to simulate liquid para-hydrogen, finding that the resulting radial pair distribution functions agree well with path integral Monte Carlo simulations. The surprising accessibility and transferability of the technique suggest a quantitative route to adapting Born-Oppenheimer potentials, with a motivation similar in spirit to the powerful ideas and approximations of density functional theory. PMID:24790954

Hierarchical Partitioning of Metazoan Protein Conservation Profiles Provides New Functional Insights

PubMed Central

Witztum, Jonathan; Persi, Erez; Horn, David; Pasmanik-Chor, Metsada; Chor, Benny

2014-01-01

The availability of many complete, annotated proteomes enables the systematic study of the relationships between protein conservation and functionality. We explore this question based solely on the presence or absence of protein homologues (a.k.a. conservation profiles). We study 18 metazoans, from two distinct points of view: the human's and the fly's. Using the GOrilla gene ontology (GO) analysis tool, we explore functional enrichment of the “universal proteins”, those with homologues in all 17 other species, and of the “non-universal proteins”. A large number of GO terms are strongly enriched in both human and fly universal proteins. Most of these functions are known to be essential. A smaller number of GO terms, exhibiting markedly different properties, are enriched in both human and fly non-universal proteins. We further explore the non-universal proteins, whose conservation profiles are consistent with the “tree of life” (TOL consistent), as well as the TOL inconsistent proteins. Finally, we applied Quantum Clustering to the conservation profiles of the TOL consistent proteins. Each cluster is strongly associated with one or a small number of specific monophyletic clades in the tree of life. The proteins in many of these clusters exhibit strong functional enrichment associated with the “life style” of the related clades. Most previous approaches for studying function and conservation are “bottom up”, studying protein families one by one, and separately assessing the conservation of each. By way of contrast, our approach is “top down”. We globally partition the set of all proteins hierarchically, as described above, and then identify protein families enriched within different subdivisions. While supporting previous findings, our approach also provides a tool for discovering novel relations between protein conservation profiles, functionality, and evolutionary history as represented by the tree of life. PMID:24594619

Soft Clustering Criterion Functions for Partitional Document Clustering

DTIC Science & Technology

2004-05-26

in the clus- ter that it already belongs to. The refinement phase ends, as soon as we perform an iteration in which no documents moved between...for failing to comply with a collection of information if it does not display a currently valid OMB control number. 1. REPORT DATE 26 MAY 2004 2... it with the one obtained by the hard criterion functions. We present a comprehensive experimental evaluation involving twelve differ- ent datasets

Partitioning of electron flux between the respiratory chains of the yeast Candida parapsilosis: parallel working of the two chains.

PubMed

Guerin, M G; Camougrand, N M

1994-02-08

Partitioning of the electron flux between the classical and the alternative respiratory chains of the yeast Candida parapsilosis, was measured as a function of the oxidation rate and of the Q-pool redox poise. At low respiration rate, electrons from external NADH travelled preferentially through the alternative pathway as indicated by the antimycin A-insensitivity of electron flow. Inhibition of the alternative pathway by SHAM restored full antimycin A-sensitivity to the remaining electro flow. The dependence of the respiratory rate on the redox poise of the quinone pool was investigated when the electron flux was mediated either by the main respiratory chain (growth in the absence of antimycin A) or by the second respiratory chain (growth in the presence of antimycin A). In the former case, a linear relationship was found between these two parameters. In contrast, in the latter case, the relationship between Q-pool reduction level and electron flux was non-linear, but it could be resolved into two distinct curves. This second quinone is not reducible in the presence of antimycin A but only in the presence of high concentrations of myxothiazol or cyanide. Since two quinone species exist in C. parapsilosis, UQ9 and Qx (C33H54O4), we hypothesized that these two curves could correspond to the functioning of the second quinone engaged during the alternative pathway activity. Partitioning of electrons between both respiratory chains could occur upstream of complex III with the second chain functioning in parallel to the main one, and with the additional possibility of merging into the main one at the complex IV level.

Single amino acid insertions in extracellular loop 2 of Bombyx mori ABCC2 disrupt its receptor function for Bacillus thuringiensis Cry1Ab and Cry1Ac but not Cry1Aa toxins.

PubMed

Tanaka, Shiho; Miyamoto, Kazuhisa; Noda, Hiroaki; Endo, Haruka; Kikuta, Shingo; Sato, Ryoichi

2016-04-01

In a previous report, seven Cry1Ab-resistant strains were identified in the silkworm, Bombyx mori; these strains were shown to have a tyrosine insertion at position 234 in extracellular loop 2 of the ABC transporter C2 (BmABCC2). This insertion was confirmed to destroy the receptor function of BmABCC2 and confer the strains resistance against Cry1Ab and Cry1Ac. However, these strains were susceptible to Cry1Aa. In this report, we examined the mechanisms of the loss of receptor function of the transporter by expressing mutations in Sf9 cells. After replacement of one or two of the five amino acid residues in loop 2 of the susceptible BmABCC2 gene [BmABCC2_S] with alanine, cells still showed susceptibility, retaining the receptor function. Five mutants with single amino acid insertions at position 234 in BmABCC2 were also generated, resulting in loop 2 having six amino acids, which corresponds to replacing the tyrosine insertion in the resistant BmABCC2 gene [BmABCC2_R(+(234)Y)] with another amino acid. All five mutants exhibited loss of function against Cry1Ab and Cry1Ac. These results suggest that the amino acid sequence in loop 2 is less important than the loop size (five vs. six amino acids) or loop structure for Cry1Ab and Cry1Ac activity. Several domain-swapped mutant toxins were then generated among Cry1Aa, Cry1Ab, and Cry1Ac, which are composed of three domains. Swapped mutants containing domain II of Cry1Ab or Cry1Ac did not kill Sf9 cells expressing BmABCC2_R(+(234)Y), suggesting that domain II of the Cry toxin is related to the interaction with the receptor function of BmABCC2. This also suggests that different reactions against Bt-toxins in some B. mori strains, that is, Cry1Ab resistance or Cry1Aa susceptibility, are attributable to structural differences in domain II of Cry1A toxins. Copyright © 2016. Published by Elsevier Inc.

Surveillance system and method having parameter estimation and operating mode partitioning

NASA Technical Reports Server (NTRS)

Bickford, Randall L. (Inventor)

2003-01-01

A system and method for monitoring an apparatus or process asset including partitioning an unpartitioned training data set into a plurality of training data subsets each having an operating mode associated thereto; creating a process model comprised of a plurality of process submodels each trained as a function of at least one of the training data subsets; acquiring a current set of observed signal data values from the asset; determining an operating mode of the asset for the current set of observed signal data values; selecting a process submodel from the process model as a function of the determined operating mode of the asset; calculating a current set of estimated signal data values from the selected process submodel for the determined operating mode; and outputting the calculated current set of estimated signal data values for providing asset surveillance and/or control.

Fast de novo discovery of low-energy protein loop conformations.

PubMed

Wong, Samuel W K; Liu, Jun S; Kou, S C

2017-08-01

In the prediction of protein structure from amino acid sequence, loops are challenging regions for computational methods. Since loops are often located on the protein surface, they can have significant roles in determining protein functions and binding properties. Loop prediction without the aid of a structural template requires extensive conformational sampling and energy minimization, which are computationally difficult. In this article we present a new de novo loop sampling method, the Parallely filtered Energy Targeted All-atom Loop Sampler (PETALS) to rapidly locate low energy conformations. PETALS explores both backbone and side-chain positions of the loop region simultaneously according to the energy function selected by the user, and constructs a nonredundant ensemble of low energy loop conformations using filtering criteria. The method is illustrated with the DFIRE potential and DiSGro energy function for loops, and shown to be highly effective at discovering conformations with near-native (or better) energy. Using the same energy function as the DiSGro algorithm, PETALS samples conformations with both lower RMSDs and lower energies. PETALS is also useful for assessing the accuracy of different energy functions. PETALS runs rapidly, requiring an average time cost of 10 minutes for a length 12 loop on a single 3.2 GHz processor core, comparable to the fastest existing de novo methods for generating an ensemble of conformations. Proteins 2017; 85:1402-1412. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Partitioning taxonomic diversity of aquatic insect assemblages and functional feeding groups in Neotropical Savanna headwater streams

EPA Science Inventory

Biological diversity can be divided into: alpha (α, local), beta (β, difference in assemblage composition among locals), and gamma (γ, total diversity). We assessed the partitioning of taxonomic diversity of Ephemeroptera, Plecoptera and Trichoptera (EPT) and of functional feedin...

Movement Forms: A Graph-Dynamic Perspective

PubMed Central

Saltzman, Elliot; Holt, Ken

2014-01-01

The focus of this paper is on characterizing the physical movement forms (e.g., walk, crawl, roll, etc.) that can be used to actualize abstract, functionally-specified behavioral goals (e.g., locomotion). Emphasis is placed on how such forms are distinguished from one another, in part, by the set of topological patterns of physical contact between agent and environment (i.e., the set of physical graphs associated with each form) and the transitions among these patterns displayed over the course of performance (i.e., the form’s physical graph dynamics). Crucial in this regard is the creation and dissolution of loops in these graphs, which can be related to the distinction between open and closed kinematic chains. Formal similarities are described within the theoretical framework of task-dynamics between physically-closed kinematic chains (physical loops) that are created during various movement forms and functionally-closed kinematic chains (functional loops) that are associated with task-space control of end-effectors; it is argued that both types of loop must be flexibly incorporated into the coordinative structures that govern skilled action. Final speculation is focused on the role of graphs and their dynamics, not only in processes of coordination and control for individual agents, but also in processes of inter-agent coordination and the coupling of agents with (non-sentient) environmental objects. PMID:24910507

Movement Forms: A Graph-Dynamic Perspective.

PubMed

Saltzman, Elliot; Holt, Ken

2014-01-01

The focus of this paper is on characterizing the physical movement forms (e.g., walk, crawl, roll, etc.) that can be used to actualize abstract, functionally-specified behavioral goals (e.g., locomotion). Emphasis is placed on how such forms are distinguished from one another, in part, by the set of topological patterns of physical contact between agent and environment (i.e., the set of physical graphs associated with each form) and the transitions among these patterns displayed over the course of performance (i.e., the form's physical graph dynamics ). Crucial in this regard is the creation and dissolution of loops in these graphs, which can be related to the distinction between open and closed kinematic chains. Formal similarities are described within the theoretical framework of task-dynamics between physically-closed kinematic chains (physical loops) that are created during various movement forms and functionally-closed kinematic chains (functional loops) that are associated with task-space control of end-effectors; it is argued that both types of loop must be flexibly incorporated into the coordinative structures that govern skilled action. Final speculation is focused on the role of graphs and their dynamics, not only in processes of coordination and control for individual agents, but also in processes of inter-agent coordination and the coupling of agents with (non-sentient) environmental objects.

Plasticity of 150-loop in influenza neuraminidase explored by Hamiltonian replica exchange molecular dynamics simulations.

PubMed

Han, Nanyu; Mu, Yuguang

2013-01-01

Neuraminidase (NA) of influenza is a key target for antiviral inhibitors, and the 150-cavity in group-1 NA provides new insight in treating this disease. However, NA of 2009 pandemic influenza (09N1) was found lacking this cavity in a crystal structure. To address the issue of flexibility of the 150-loop, Hamiltonian replica exchange molecular dynamics simulations were performed on different groups of NAs. Free energy landscape calculated based on the volume of 150-cavity indicates that 09N1 prefers open forms of 150-loop. The turn A (residues 147-150) of the 150-loop is discovered as the most dynamical motif which induces the inter-conversion of this loop among different conformations. In the turn A, the backbone dynamic of residue 149 is highly related with the shape of 150-loop, thus can function as a marker for the conformation of 150-loop. As a contrast, the closed conformation of 150-loop is more energetically favorable in N2, one of group-2 NAs. The D147-H150 salt bridge is found having no correlation with the conformation of 150-loop. Instead the intimate salt bridge interaction between the 150 and 430 loops in N2 variant contributes the stabilizing factor for the closed form of 150-loop. The clustering analysis elaborates the structural plasticity of the loop. This enhanced sampling simulation provides more information in further structural-based drug discovery on influenza virus.

Plasticity of 150-Loop in Influenza Neuraminidase Explored by Hamiltonian Replica Exchange Molecular Dynamics Simulations

PubMed Central

Han, Nanyu; Mu, Yuguang

2013-01-01

Neuraminidase (NA) of influenza is a key target for antiviral inhibitors, and the 150-cavity in group-1 NA provides new insight in treating this disease. However, NA of 2009 pandemic influenza (09N1) was found lacking this cavity in a crystal structure. To address the issue of flexibility of the 150-loop, Hamiltonian replica exchange molecular dynamics simulations were performed on different groups of NAs. Free energy landscape calculated based on the volume of 150-cavity indicates that 09N1 prefers open forms of 150-loop. The turn A (residues 147–150) of the 150-loop is discovered as the most dynamical motif which induces the inter-conversion of this loop among different conformations. In the turn A, the backbone dynamic of residue 149 is highly related with the shape of 150-loop, thus can function as a marker for the conformation of 150-loop. As a contrast, the closed conformation of 150-loop is more energetically favorable in N2, one of group-2 NAs. The D147-H150 salt bridge is found having no correlation with the conformation of 150-loop. Instead the intimate salt bridge interaction between the 150 and 430 loops in N2 variant contributes the stabilizing factor for the closed form of 150-loop. The clustering analysis elaborates the structural plasticity of the loop. This enhanced sampling simulation provides more information in further structural-based drug discovery on influenza virus. PMID:23593372

OPERATOR NORM INEQUALITIES BETWEEN TENSOR UNFOLDINGS ON THE PARTITION LATTICE

PubMed Central

Wang, Miaoyan; Duc, Khanh Dao; Fischer, Jonathan; Song, Yun S.

2017-01-01

Interest in higher-order tensors has recently surged in data-intensive fields, with a wide range of applications including image processing, blind source separation, community detection, and feature extraction. A common paradigm in tensor-related algorithms advocates unfolding (or flattening) the tensor into a matrix and applying classical methods developed for matrices. Despite the popularity of such techniques, how the functional properties of a tensor changes upon unfolding is currently not well understood. In contrast to the body of existing work which has focused almost exclusively on matricizations, we here consider all possible unfoldings of an order-k tensor, which are in one-to-one correspondence with the set of partitions of {1, …, k}. We derive general inequalities between the lp-norms of arbitrary unfoldings defined on the partition lattice. In particular, we demonstrate how the spectral norm (p = 2) of a tensor is bounded by that of its unfoldings, and obtain an improved upper bound on the ratio of the Frobenius norm to the spectral norm of an arbitrary tensor. For specially-structured tensors satisfying a generalized definition of orthogonal decomposability, we prove that the spectral norm remains invariant under specific subsets of unfolding operations. PMID:28286347

OPERATOR NORM INEQUALITIES BETWEEN TENSOR UNFOLDINGS ON THE PARTITION LATTICE.

PubMed

Wang, Miaoyan; Duc, Khanh Dao; Fischer, Jonathan; Song, Yun S

2017-05-01

Interest in higher-order tensors has recently surged in data-intensive fields, with a wide range of applications including image processing, blind source separation, community detection, and feature extraction. A common paradigm in tensor-related algorithms advocates unfolding (or flattening) the tensor into a matrix and applying classical methods developed for matrices. Despite the popularity of such techniques, how the functional properties of a tensor changes upon unfolding is currently not well understood. In contrast to the body of existing work which has focused almost exclusively on matricizations, we here consider all possible unfoldings of an order- k tensor, which are in one-to-one correspondence with the set of partitions of {1, …, k }. We derive general inequalities between the l p -norms of arbitrary unfoldings defined on the partition lattice. In particular, we demonstrate how the spectral norm ( p = 2) of a tensor is bounded by that of its unfoldings, and obtain an improved upper bound on the ratio of the Frobenius norm to the spectral norm of an arbitrary tensor. For specially-structured tensors satisfying a generalized definition of orthogonal decomposability, we prove that the spectral norm remains invariant under specific subsets of unfolding operations.

Gauge-free cluster variational method by maximal messages and moment matching.

PubMed

Domínguez, Eduardo; Lage-Castellanos, Alejandro; Mulet, Roberto; Ricci-Tersenghi, Federico

2017-04-01

We present an implementation of the cluster variational method (CVM) as a message passing algorithm. The kind of message passing algorithm used for CVM, usually named generalized belief propagation (GBP), is a generalization of the belief propagation algorithm in the same way that CVM is a generalization of the Bethe approximation for estimating the partition function. However, the connection between fixed points of GBP and the extremal points of the CVM free energy is usually not a one-to-one correspondence because of the existence of a gauge transformation involving the GBP messages. Our contribution is twofold. First, we propose a way of defining messages (fields) in a generic CVM approximation, such that messages arrive on a given region from all its ancestors, and not only from its direct parents, as in the standard parent-to-child GBP. We call this approach maximal messages. Second, we focus on the case of binary variables, reinterpreting the messages as fields enforcing the consistency between the moments of the local (marginal) probability distributions. We provide a precise rule to enforce all consistencies, avoiding any redundancy, that would otherwise lead to a gauge transformation on the messages. This moment matching method is gauge free, i.e., it guarantees that the resulting GBP is not gauge invariant. We apply our maximal messages and moment matching GBP to obtain an analytical expression for the critical temperature of the Ising model in general dimensions at the level of plaquette CVM. The values obtained outperform Bethe estimates, and are comparable with loop corrected belief propagation equations. The method allows for a straightforward generalization to disordered systems.

Gauge-free cluster variational method by maximal messages and moment matching

NASA Astrophysics Data System (ADS)

Domínguez, Eduardo; Lage-Castellanos, Alejandro; Mulet, Roberto; Ricci-Tersenghi, Federico

2017-04-01

We present an implementation of the cluster variational method (CVM) as a message passing algorithm. The kind of message passing algorithm used for CVM, usually named generalized belief propagation (GBP), is a generalization of the belief propagation algorithm in the same way that CVM is a generalization of the Bethe approximation for estimating the partition function. However, the connection between fixed points of GBP and the extremal points of the CVM free energy is usually not a one-to-one correspondence because of the existence of a gauge transformation involving the GBP messages. Our contribution is twofold. First, we propose a way of defining messages (fields) in a generic CVM approximation, such that messages arrive on a given region from all its ancestors, and not only from its direct parents, as in the standard parent-to-child GBP. We call this approach maximal messages. Second, we focus on the case of binary variables, reinterpreting the messages as fields enforcing the consistency between the moments of the local (marginal) probability distributions. We provide a precise rule to enforce all consistencies, avoiding any redundancy, that would otherwise lead to a gauge transformation on the messages. This moment matching method is gauge free, i.e., it guarantees that the resulting GBP is not gauge invariant. We apply our maximal messages and moment matching GBP to obtain an analytical expression for the critical temperature of the Ising model in general dimensions at the level of plaquette CVM. The values obtained outperform Bethe estimates, and are comparable with loop corrected belief propagation equations. The method allows for a straightforward generalization to disordered systems.

A multiscale restriction-smoothed basis method for high contrast porous media represented on unstructured grids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Møyner, Olav, E-mail: olav.moyner@sintef.no; Lie, Knut-Andreas, E-mail: knut-andreas.lie@sintef.no

2016-01-01

A wide variety of multiscale methods have been proposed in the literature to reduce runtime and provide better scaling for the solution of Poisson-type equations modeling flow in porous media. We present a new multiscale restricted-smoothed basis (MsRSB) method that is designed to be applicable to both rectilinear grids and unstructured grids. Like many other multiscale methods, MsRSB relies on a coarse partition of the underlying fine grid and a set of local prolongation operators (multiscale basis functions) that map unknowns associated with the fine grid cells to unknowns associated with blocks in the coarse partition. These mappings are constructedmore » by restricted smoothing: Starting from a constant, a localized iterative scheme is applied directly to the fine-scale discretization to compute prolongation operators that are consistent with the local properties of the differential operators. The resulting method has three main advantages: First of all, both the coarse and the fine grid can have general polyhedral geometry and unstructured topology. This means that partitions and good prolongation operators can easily be constructed for complex models involving high media contrasts and unstructured cell connections introduced by faults, pinch-outs, erosion, local grid refinement, etc. In particular, the coarse partition can be adapted to geological or flow-field properties represented on cells or faces to improve accuracy. Secondly, the method is accurate and robust when compared to existing multiscale methods and does not need expensive recomputation of local basis functions to account for transient behavior: Dynamic mobility changes are incorporated by continuing to iterate a few extra steps on existing basis functions. This way, the cost of updating the prolongation operators becomes proportional to the amount of change in fluid mobility and one reduces the need for expensive, tolerance-based updates. Finally, since the MsRSB method is formulated on top of a cell-centered, conservative, finite-volume method, it is applicable to any flow model in which one can isolate a pressure equation. Herein, we only discuss single and two-phase incompressible models. Compressible flow, e.g., as modeled by the black-oil equations, is discussed in a separate paper.« less

Novel methods for predicting gas-particle partitioning during the formation of secondary organic aerosol

NASA Astrophysics Data System (ADS)

Wania, F.; Lei, Y. D.; Wang, C.; Abbatt, J. P. D.; Goss, K.-U.

2014-12-01

Several methods have been presented in the literature to predict an organic chemical's equilibrium partitioning between the water insoluble organic matter (WIOM) component of aerosol and the gas phase, Ki,WIOM, as a function of temperature. They include (i) polyparameter linear free energy relationships calibrated with empirical aerosol sorption data, as well as (ii) the solvation models implemented in SPARC and (iii) the quantum-chemical software COSMOtherm, which predict solvation equilibria from molecular structure alone. We demonstrate that these methods can be used to predict Ki,WIOM for large numbers of individual molecules implicated in secondary organic aerosol (SOA) formation, including those with multiple functional groups. Although very different in their theoretical foundations, these methods give remarkably consistent results for the products of the reaction of normal alkanes with OH, i.e. their partition coefficients Ki,WIOM generally agree within one order of magnitude over a range of more than ten orders of magnitude. This level of agreement is much better than that achieved by different vapour pressure estimation methods that are more commonly used in the SOA community. Also, in contrast to the agreement between vapour pressure estimates, the agreement between the Ki,WIOM estimates does not deteriorate with increasing number of functional groups. Furthermore, these partitioning coefficients Ki,WIOM predicted SOA mass yields in agreement with those measured in chamber experiments of the oxidation of normal alkanes. If a Ki,WIOM prediction method was based on one or more surrogate molecules representing the solvation properties of the mixed OM phase of SOA, the choice of those molecule(s) was found to have a relatively minor effect on the predicted Ki,WIOM, as long as the molecule(s) are not very polar. This suggests that a single surrogate molecule, such as 1-octanol or a hypothetical SOA structure proposed by Kalberer et al. (2004), may often be sufficient to represent the WIOM component of the SOA phase, greatly simplifying the prediction. The presented methods could substitute for vapour-pressure-based methods in studies such as the explicit modelling of SOA formation from single precursor molecules in chamber experiments.

A brief history of partitions of numbers, partition functions and their modern applications

NASA Astrophysics Data System (ADS)

Debnath, Lokenath

2016-04-01

'Number rules the universe.' The Pythagoras 'If you wish to forsee the future of mathematics our course is to study the history and present conditions of the science.' Henri Poincaré 'The primary source (Urqell) of all mathematics are integers.' Hermann Minkowski This paper is written to commemorate the centennial anniversary of the Mathematical Association of America. It deals with a short history of different kinds of natural numbers including triangular, square, pentagonal, hexagonal and k-gonal numbers, and their simple properties and their geometrical representations. Included are Euclid's and Pythagorean's main contributions to elementary number theory with the main contents of the Euclid Elements of the 13-volume masterpiece of mathematical work. This is followed by Euler's new discovery of the additive number theory based on partitions of numbers. Special attention is given to many examples, Euler's theorems on partitions of numbers with geometrical representations of Ferrers' graphs, Young's diagrams, Lagrange's four-square theorem and the celebrated Waring problem. Included are Euler's generating functions for the partitions of numbers, Euler's pentagonal number theorem, Gauss' triangular and square number theorems and the Jacobi triple product identity. Applications of the theory of partitions of numbers to different statistics such as the Bose- Einstein, Fermi- Dirac, Gentile, and Maxwell- Boltzmann statistics are briefly discussed. Special attention is given to pedagogical information through historical approach to number theory so that students and teachers at the school, college and university levels can become familiar with the basic concepts of partitions of numbers, partition functions and their modern applications, and can pursue advanced study and research in analytical and computational number theory.

Trace element partitioning between plagioclase and melt: An investigation of the impact of experimental and analytical procedures

NASA Astrophysics Data System (ADS)

Nielsen, Roger L.; Ustunisik, Gokce; Weinsteiger, Allison B.; Tepley, Frank J.; Johnston, A. Dana; Kent, Adam J. R.

2017-09-01

Quantitative models of petrologic processes require accurate partition coefficients. Our ability to obtain accurate partition coefficients is constrained by their dependence on pressure temperature and composition, and on the experimental and analytical techniques we apply. The source and magnitude of error in experimental studies of trace element partitioning may go unrecognized if one examines only the processed published data. The most important sources of error are relict crystals, and analyses of more than one phase in the analytical volume. Because we have typically published averaged data, identification of compromised data is difficult if not impossible. We addressed this problem by examining unprocessed data from plagioclase/melt partitioning experiments, by comparing models based on that data with existing partitioning models, and evaluated the degree to which the partitioning models are dependent on the calibration data. We found that partitioning models are dependent on the calibration data in ways that result in erroneous model values, and that the error will be systematic and dependent on the value of the partition coefficient. In effect, use of different calibration datasets will result in partitioning models whose results are systematically biased, and that one can arrive at different and conflicting conclusions depending on how a model is calibrated, defeating the purpose of applying the models. Ultimately this is an experimental data problem, which can be solved if we publish individual analyses (not averages) or use a projection method wherein we use an independent compositional constraint to identify and estimate the uncontaminated composition of each phase.

Horizontal Running Mattress Suture Modified with Intermittent Simple Loops

PubMed Central

Chacon, Anna H; Shiman, Michael I; Strozier, Narissa; Zaiac, Martin N

2013-01-01

Using the combination of a horizontal running mattress suture with intermittent loops achieves both good eversion with the horizontal running mattress plus the ease of removal of the simple loops. This combination technique also avoids the characteristic railroad track marks that result from prolonged non-absorbable suture retention. The unique feature of our technique is the incorporation of one simple running suture after every two runs of the horizontal running mattress suture. To demonstrate its utility, we used the suturing technique on several patients and analyzed the cosmetic outcome with post-operative photographs in comparison to other suturing techniques. In summary, the combination of running horizontal mattress suture with simple intermittent loops demonstrates functional and cosmetic benefits that can be readily taught, comprehended, and employed, leading to desirable aesthetic results and wound edge eversion. PMID:23723610

Epitopes in α8β1 and other RGD-binding integrins delineate classes of integrin-blocking antibodies and major binding loops in α subunits.

PubMed

Nishimichi, Norihisa; Kawashima, Nagako; Yokosaki, Yasuyuki

2015-09-09

Identification of epitopes for integrin-blocking monoclonal antibodies (mAbs) has aided our understanding of structure-function relationship of integrins. We mapped epitopes of chicken anti-integrin-α8-subunit-blocking mAbs by mutational analyses, examining regions that harboured all mapped epitopes recognized by mAbs against other α-subunits in the RGD-binding-integrin subfamily. Six mAbs exhibited blocking function, and these mAbs recognized residues on the same W2:41-loop on the top-face of the β-propeller. Loop-tips sufficiently close to W2:41 (<25 Å) contained within a footprint of the mAbs were mutated, and the loop W3:34 on the bottom face was identified as an additional component of the epitope of one antibody, clone YZ5. Binding sequences on the two loops were conserved in virtually all mammals, and that on W3:34 was also conserved in chickens. These indicate 1) YZ5 binds both top and bottom loops, and the binding to W3:34 is by interactions to conserved residues between immunogen and host species, 2) five other blocking mAbs solely bind to W2:41 and 3) the α8 mAbs would cross-react with most mammals. Comparing with the mAbs against the other α-subunits of RGD-integrins, two classes were delineated; those binding to "W3:34 and an top-loop", and "solely W2:41", accounting for 82% of published RGD-integrin-mAbs.

Solution NMR analyses of the anticodon arms of proteinogenic and non-proteinogenic tRNAGly

PubMed Central

Chang, Andrew T.; Nikonowicz, Edward P.

2012-01-01

Although the fate of most tRNA molecules in the cell is aminoacylation and delivery to the ribosome, some tRNAs are destined to fulfill other functional roles. In addition to their central role in translation, tRNA molecules participate in processes such as regulation of gene expression, bacterial cell wall biosynthesis, viral replication, antibiotic biosynthesis, and suppression of alternative splicing. In bacteria, glycyl-tRNA molecules with anticodon sequences GCC and UCC exhibit multiple extra-translational functions including transcriptional regulation and cell wall biosynthesis. We have determined the high-resolution structures of three glycyl-tRNA anticodon arms with anticodon sequences GCC and UCC. Two of the tRNA molecules are proteinogenic (tRNAGly,GCC and tRNAGly,UCC) and the third is non-proteinogenic (np-tRNAGly,UCC) and participates in cell wall biosynthesis. The UV-monitored thermal melting curves show that the anticodon arm of tRNAGly,UCC with a loop-closing C-A+ base pair melts at a 10 °C lower temperature than those of tRNAGly,GCC or np-tRNAGly,UCC. U-A and C-G pairs close the loops of the later two molecules and enhance stem stability. Mg2+ stabilizes the tRNAGly,UCC anticodon arm and lessens the Tm differential. The structures of the three tRNAGly anticodon arms exhibit small differences between one another, but none of them form the classical U-turn motif. The anticodon loop of tRNAGly,GCC becomes more dynamic and disordered in the presence of multivalent cations, whereas metal ion coordination in the anticodon loops of tRNAGly,UCC and np-tRNAGly,UCC establishes conformational homogeneity. The conformational similarity of the molecules is greater than their functional differences might suggest. Because aminoacylation of the full-length tRNA molecules is accomplished by one tRNA synthetase, the similar structural context of the loop may facilitate efficient recognition of each of the anticodon sequences. PMID:22468768

Thumb-loops up for catalysis: a structure/function investigation of a functional loop movement in a GH11 xylanase

PubMed Central

Paës, Gabriel; Cortés, Juan; Siméon, Thierry; O'Donohue, Michael J.; Tran, Vinh

2012-01-01

Dynamics is a key feature of enzyme catalysis. Unfortunately, current experimental and computational techniques do not yet provide a comprehensive understanding and description of functional macromolecular motions. In this work, we have extended a novel computational technique, which combines molecular modeling methods and robotics algorithms, to investigate functional motions of protein loops. This new approach has been applied to study the functional importance of the so-called thumb-loop in the glycoside hydrolase family 11 xylanase from Thermobacillus xylanilyticus (Tx-xyl). The results obtained provide new insight into the role of the loop in the glycosylation/deglycosylation catalytic cycle, and underline the key importance of the nature of the residue located at the tip of the thumb-loop. The effect of mutations predicted in silico has been validated by in vitro site-directed mutagenesis experiments. Overall, we propose a comprehensive model of Tx-xyl catalysis in terms of substrate and product dynamics by identifying the action of the thumb-loop motion during catalysis. PMID:24688637

Dynamics driving function: new insights from electron transferring flavoproteins and partner complexes.

PubMed

Toogood, Helen S; Leys, David; Scrutton, Nigel S

2007-11-01

Electron transferring flavoproteins (ETFs) are soluble heterodimeric FAD-containing proteins that function primarily as soluble electron carriers between various flavoprotein dehydrogenases. ETF is positioned at a key metabolic branch point, responsible for transferring electrons from up to 10 primary dehydrogenases to the membrane-bound respiratory chain. Clinical mutations of ETF result in the often fatal disease glutaric aciduria type II. Structural and biophysical studies of ETF in complex with partner proteins have shown that ETF partitions the functions of partner binding and electron transfer between (a) a 'recognition loop', which acts as a static anchor at the ETF-partner interface, and (b) a highly mobile redox-active FAD domain. Together, this enables the FAD domain of ETF to sample a range of conformations, some compatible with fast interprotein electron transfer. This 'conformational sampling' enables ETF to recognize structurally distinct partners, whilst also maintaining a degree of specificity. Complex formation triggers mobility of the FAD domain, an 'induced disorder' mechanism contrasting with the more generally accepted models of protein-protein interaction by induced fit mechanisms. We discuss the implications of the highly dynamic nature of ETFs in biological interprotein electron transfer. ETF complexes point to mechanisms of electron transfer in which 'dynamics drive function', a feature that is probably widespread in biology given the modular assembly and flexible nature of biological electron transfer systems.

Effect of supercoiling on formation of protein-mediated DNA loops

NASA Astrophysics Data System (ADS)

Purohit, P. K.; Nelson, P. C.

2006-12-01

DNA loop formation is one of several mechanisms used by organisms to regulate genes. The free energy of forming a loop is an important factor in determining whether the associated gene is switched on or off. In this paper we use an elastic rod model of DNA to determine the free energy of forming short (50-100 basepair), protein mediated DNA loops. Superhelical stress in the DNA of living cells is a critical factor determining the energetics of loop formation, and we explicitly account for it in our calculations. The repressor protein itself is regarded as a rigid coupler; its geometry enters the problem through the boundary conditions it applies on the DNA. We show that a theory with these ingredients is sufficient to explain certain features observed in modulation of in vivo gene activity as a function of the distance between operator sites for the lac repressor. We also use our theory to make quantitative predictions for the dependence of looping on superhelical stress, which may be testable both in vivo and in single-molecule experiments such as the tethered particle assay and the magnetic bead assay.

Connected, disconnected and strange quark contributions to HVP

NASA Astrophysics Data System (ADS)

Bijnens, Johan; Relefors, Johan

2016-11-01

We calculate all neutral vector two-point functions in Chiral Perturbation Theory (ChPT) to two-loop order and use these to estimate the ratio of disconnected to connected contributions as well as contributions involving the strange quark. We extend the ratio of -1/10 derived earlier in two flavour ChPT at one-loop order to a large part of the higher order contributions and discuss corrections to it. Our final estimate of the ratio disconnected to connected is negative and a few % in magnitude.

PREFERENTIAL PARTITIONING OF A PAH AND PCB TO A MARINE SEDIMENT AMENDED WITH SEVERAL SOURCES OF SOOT CARBON

EPA Science Inventory

Over the last decade, several studies reported that the partitioning of PAHs to sediments, in some cases, did not follow predictions based on equilibrium partitioning theory. One explanation for these differences is the presence of a second sedimentary phase with partitioning cha...

High Throughput Analyses of Budding Yeast ARSs Reveal New DNA Elements Capable of Conferring Centromere-Independent Plasmid Propagation

PubMed Central

Hoggard, Timothy; Liachko, Ivan; Burt, Cassaundra; Meikle, Troy; Jiang, Katherine; Craciun, Gheorghe; Dunham, Maitreya J.; Fox, Catherine A.

2016-01-01

The ability of plasmids to propagate in Saccharomyces cerevisiae has been instrumental in defining eukaryotic chromosomal control elements. Stable propagation demands both plasmid replication, which requires a chromosomal replication origin (i.e., an ARS), and plasmid distribution to dividing cells, which requires either a chromosomal centromere for segregation or a plasmid-partitioning element. While our knowledge of yeast ARSs and centromeres is relatively advanced, we know less about chromosomal regions that can function as plasmid partitioning elements. The Rap1 protein-binding site (RAP1) present in transcriptional silencers and telomeres of budding yeast is a known plasmid-partitioning element that functions to anchor a plasmid to the inner nuclear membrane (INM), which in turn facilitates plasmid distribution to daughter cells. This Rap1-dependent INM-anchoring also has an important chromosomal role in higher-order chromosomal structures that enhance transcriptional silencing and telomere stability. Thus, plasmid partitioning can reflect fundamental features of chromosome structure and biology, yet a systematic screen for plasmid partitioning elements has not been reported. Here, we couple deep sequencing with competitive growth experiments of a plasmid library containing thousands of short ARS fragments to identify new plasmid partitioning elements. Competitive growth experiments were performed with libraries that differed only in terms of the presence or absence of a centromere. Comparisons of the behavior of ARS fragments in the two experiments allowed us to identify sequences that were likely to drive plasmid partitioning. In addition to the silencer RAP1 site, we identified 74 new putative plasmid-partitioning motifs predicted to act as binding sites for DNA binding proteins enriched for roles in negative regulation of gene expression and G2/M-phase associated biology. These data expand our knowledge of chromosomal elements that may function in plasmid partitioning and suggest underlying biological roles shared by such elements. PMID:26865697

Modeling the Lac repressor-operator assembly: The influence of DNA looping on Lac repressor conformation

PubMed Central

Swigon, David; Coleman, Bernard D.; Olson, Wilma K.

2006-01-01

Repression of transcription of the Escherichia coli Lac operon by the Lac repressor (LacR) is accompanied by the simultaneous binding of LacR to two operators and the formation of a DNA loop. A recently developed theory of sequence-dependent DNA elasticity enables one to relate the fine structure of the LacR–DNA complex to a wide range of heretofore-unconnected experimental observations. Here, that theory is used to calculate the configuration and free energy of the DNA loop as a function of its length and base-pair sequence, its linking number, and the end conditions imposed by the LacR tetramer. The tetramer can assume two types of conformations. Whereas a rigid V-shaped structure is observed in the crystal, EM images show extended forms in which two dimer subunits are flexibly joined. Upon comparing our computed loop configurations with published experimental observations of permanganate sensitivities, DNase I cutting patterns, and loop stabilities, we conclude that linear DNA segments of short-to-medium chain length (50–180 bp) give rise to loops with the extended form of LacR and that loops formed within negatively supercoiled plasmids induce the V-shaped structure. PMID:16785444

Localization in abelian Chern-Simons theory

NASA Astrophysics Data System (ADS)

McLellan, B. D. K.

2013-02-01

Chern-Simons theory on a closed contact three-manifold is studied when the Lie group for gauge transformations is compact, connected, and abelian. The abelian Chern-Simons partition function is derived using the Faddeev-Popov gauge fixing method. The partition function is then formally computed using the technique of non-abelian localization. This study leads to a natural identification of the abelian Reidemeister-Ray-Singer torsion as a specific multiple of the natural unit symplectic volume form on the moduli space of flat abelian connections for the class of Sasakian three-manifolds. The torsion part of the abelian Chern-Simons partition function is computed explicitly in terms of Seifert data for a given Sasakian three-manifold.

Loop Quantization and Symmetry: Configuration Spaces

NASA Astrophysics Data System (ADS)

Fleischhack, Christian

2018-06-01

Given two sets S 1, S 2 and unital C *-algebras A_1, A_2 of functions thereon, we show that a map {σ : {S}_1 \\longrightarrow {S}_2} can be lifted to a continuous map \\barσ : spec A_1 \\longrightarrow spec A_2 iff σ^\\ast A_2 := σ^\\ast f | f \\in A_2 \\subseteq A_1. Moreover, \\bar σ is unique if existing, and injective iff σ^\\ast A_2 is dense. Then, we apply these results to loop quantum gravity and loop quantum cosmology. For all usual technical conventions, we decide whether the cosmological quantum configuration space is embedded into the gravitational one; indeed, both are spectra of some C *-algebras, say, A_cosm and A_grav, respectively. Typically, there is no embedding, but one can always get an embedding by the defining A_cosm := C^\\ast(σ^\\ast A_grav), where {σ} denotes the embedding between the classical configuration spaces. Finally, we explicitly determine {C^\\ast(σ^\\ast A_grav) in the homogeneous isotropic case for A_grav generated by the matrix functions of parallel transports along analytic paths. The cosmological quantum configuration space so equals the disjoint union of R and the Bohr compactification of R, appropriately glued together.

Loop Quantization and Symmetry: Configuration Spaces

NASA Astrophysics Data System (ADS)

Fleischhack, Christian

2018-04-01

Given two sets S 1, S 2 and unital C *-algebras A_1, A_2 of functions thereon, we show that a map σ : S_1 \\longrightarrow S_2 can be lifted to a continuous map \\barσ : spec A_1 \\longrightarrow spec A_2 iff σ^\\ast A_2 := σ^\\ast f | f \\in A_2 \\subseteq A_1. Moreover, \\bar σ is unique if existing, and injective iff {σ^\\ast A_2 is dense. Then, we apply these results to loop quantum gravity and loop quantum cosmology. For all usual technical conventions, we decide whether the cosmological quantum configuration space is embedded into the gravitational one; indeed, both are spectra of some C *-algebras, say, A_cosm and A_grav, respectively. Typically, there is no embedding, but one can always get an embedding by the defining A_cosm := C^\\ast(σ^\\ast A_grav), where σ denotes the embedding between the classical configuration spaces. Finally, we explicitly determine C^\\ast(σ^\\ast A_grav) in the homogeneous isotropic case for A_grav generated by the matrix functions of parallel transports along analytic paths. The cosmological quantum configuration space so equals the disjoint union of R and the Bohr compactification of R , appropriately glued together.

Formation of chromosomal domains in interphase by loop extrusion

NASA Astrophysics Data System (ADS)

Fudenberg, Geoffrey

While genomes are often considered as one-dimensional sequences, interphase chromosomes are organized in three dimensions with an essential role for regulating gene expression. Recent studies have shown that Topologically Associating Domains (TADs) are fundamental structural and functional building blocks of human interphase chromosomes. Despite observations that architectural proteins, including CTCF, demarcate and maintain the borders of TADs, the mechanisms underlying TAD formation remain unknown. Here we propose that loop extrusion underlies the formation TADs. In this process, cis-acting loop-extruding factors, likely cohesins, form progressively larger loops, but stall at TAD boundaries due to interactions with boundary proteins, including CTCF. This process dynamically forms loops of various sizes within but not between TADs. Using polymer simulations, we find that loop extrusion can produce TADs as determined by our analyses of the highest-resolution experimental data. Moreover, we find that loop extrusion can explain many diverse experimental observations, including: the preferential orientation of CTCF motifs and enrichments of architectural proteins at TAD boundaries; TAD boundary deletion experiments; and experiments with knockdown or depletion of CTCF, cohesin, and cohesin-loading factors. Together, the emerging picture from our work is that TADs are formed by rapidly associating, growing, and dissociating loops, presenting a clear framework for understanding interphase chromosomal organization.

Using the Metropolis Algorithm to Calculate Thermodynamic Quantities: An Undergraduate Computational Experiment

ERIC Educational Resources Information Center

Beddard, Godfrey S.

2011-01-01

Thermodynamic quantities such as the average energy, heat capacity, and entropy are calculated using a Monte Carlo method based on the Metropolis algorithm. This method is illustrated with reference to the harmonic oscillator but is particularly useful when the partition function cannot be evaluated; an example using a one-dimensional spin system…

Morse oscillator propagator in the high temperature limit I: Theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Toutounji, Mohamad, E-mail: Mtoutounji@uaeu.ac.ae

2017-02-15

In an earlier work of the author the time evolution of Morse oscillator was studied analytically and exactly at low temperatures whereupon optical correlation functions were calculated using Morse oscillator coherent states were employed. Morse oscillator propagator in the high temperature limit is derived and a closed form of its corresponding canonical partition function is obtained. Both diagonal and off-diagonal forms of Morse oscillator propagator are derived in the high temperature limit. Partition functions of diatomic molecules are calculated. - Highlights: • Derives the quantum propagator of Morse oscillator in the high temperature limit. • Uses the resulting diagonal propagatormore » to derive a closed form of Morse oscillator partition function. • Provides a more sophisticated formula of the quantum propagator to test the accuracy of the herein results.« less

The complete two-loop integrated jet thrust distribution in soft-collinear effective theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

von Manteuffel, Andreas; Schabinger, Robert M.; Zhu, Hua Xing

2014-03-01

In this work, we complete the calculation of the soft part of the two-loop integrated jet thrust distribution in e+e- annihilation. This jet mass observable is based on the thrust cone jet algorithm, which involves a veto scale for out-of-jet radiation. The previously uncomputed part of our result depends in a complicated way on the jet cone size, r, and at intermediate stages of the calculation we actually encounter a new class of multiple polylogarithms. We employ an extension of the coproduct calculus to systematically exploit functional relations and represent our results concisely. In contrast to the individual contributions, themore » sum of all global terms can be expressed in terms of classical polylogarithms. Our explicit two-loop calculation enables us to clarify the small r picture discussed in earlier work. In particular, we show that the resummation of the logarithms of r that appear in the previously uncomputed part of the two-loop integrated jet thrust distribution is inextricably linked to the resummation of the non-global logarithms. Furthermore, we find that the logarithms of r which cannot be absorbed into the non-global logarithms in the way advocated in earlier work have coefficients fixed by the two-loop cusp anomalous dimension. We also show that in many cases one can straightforwardly predict potentially large logarithmic contributions to the integrated jet thrust distribution at L loops by making use of analogous contributions to the simpler integrated hemisphere soft function.« less

How Incorrect Is the Classical Partition Function for the Ideal Gas?

ERIC Educational Resources Information Center

Kroemer, Herbert

1980-01-01

Discussed is the classical partition function for the ideal gas and how it differs from the exact value for bosons or fermions in the classical regime. The differences in the two values are negligible hence the classical treatment leads in the end to correct answers for all observables. (Author/DS)

Photon-Z mixing the Weinberg-Salam model: Effective charges and the a = -3 gauge

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baulieu, L.; Coquereaux, R.

1982-04-15

We study some properties of the Weinberg-Salam model connected with the photon-Z mixing. We solve the linear Dyson-Schwinger equations between full and 1PI boson propagators. The task is made easier, by the two-point function Ward identities that we derive to all orders and in any gauge. Some aspects of the renormalization of the model are also discussed. We display the exact mass-dependent one-loop two-point functions involving the photon and Z field in any linear xi-gauge. The special gauge a = xi/sup -1/ = -3 is shown to play a peculiar role. In this gauge, the Z field is multiplicatively renormalizablemore » (at the one-loop level), and one can construct both electric and weak effective charges of the theory from the photon and Z propagators, with a very simple expression similar to that of the QED Petermann, Stueckelberg, Gell-Mann and Low charge.« less

Loop Quantum Cosmology.

PubMed

Bojowald, Martin

2008-01-01

Quantum gravity is expected to be necessary in order to understand situations in which classical general relativity breaks down. In particular in cosmology one has to deal with initial singularities, i.e., the fact that the backward evolution of a classical spacetime inevitably comes to an end after a finite amount of proper time. This presents a breakdown of the classical picture and requires an extended theory for a meaningful description. Since small length scales and high curvatures are involved, quantum effects must play a role. Not only the singularity itself but also the surrounding spacetime is then modified. One particular theory is loop quantum cosmology, an application of loop quantum gravity to homogeneous systems, which removes classical singularities. Its implications can be studied at different levels. The main effects are introduced into effective classical equations, which allow one to avoid the interpretational problems of quantum theory. They give rise to new kinds of early-universe phenomenology with applications to inflation and cyclic models. To resolve classical singularities and to understand the structure of geometry around them, the quantum description is necessary. Classical evolution is then replaced by a difference equation for a wave function, which allows an extension of quantum spacetime beyond classical singularities. One main question is how these homogeneous scenarios are related to full loop quantum gravity, which can be dealt with at the level of distributional symmetric states. Finally, the new structure of spacetime arising in loop quantum gravity and its application to cosmology sheds light on more general issues, such as the nature of time. Supplementary material is available for this article at 10.12942/lrr-2008-4.

Finite temperature behavior of the CPT-even and parity-even electrodynamics of the standard model extension

DOE Office of Scientific and Technical Information (OSTI.GOV)

Casana, Rodolfo; Ferreira, Manoel M. Jr; Rodrigues, Josberg S.

2009-10-15

In this work, we examine the finite temperature properties of the CPT-even and Lorentz-invariance-violating (LIV) electrodynamics of the standard model extension, represented by the term W{sub {alpha}}{sub {nu}}{sub {rho}}{sub {phi}}F{sup {alpha}}{sup {nu}}F{sup {rho}}{sup {phi}}. We begin analyzing the Hamiltonian structure following the Dirac's procedure for constrained systems and construct a well-defined and gauge invariant partition function in the functional integral formalism. Next, we specialize for the nonbirefringent coefficients of the tensor W{sub {alpha}}{sub {nu}}{sub {rho}}{sub {phi}}. In the sequel, the partition function is explicitly carried out for the parity-even sector of the tensor W{sub {alpha}}{sub {nu}}{sub {rho}}{sub {phi}}. The modifiedmore » partition function is a power of the Maxwell's partition function. It is observed that the LIV coefficients induce an anisotropy in the black body angular energy density distribution. The Planck's radiation law, however, retains its frequency dependence and the Stefan-Boltzmann law keeps the usual form, except for a change in the Stefan-Boltzmann constant by a factor containing the LIV contributions.« less

Black hole meiosis

NASA Astrophysics Data System (ADS)

van Herck, Walter; Wyder, Thomas

2010-04-01

The enumeration of BPS bound states in string theory needs refinement. Studying partition functions of particles made from D-branes wrapped on algebraic Calabi-Yau 3-folds, and classifying states using split attractor flow trees, we extend the method for computing a refined BPS index, [1]. For certain D-particles, a finite number of microstates, namely polar states, exclusively realized as bound states, determine an entire partition function (elliptic genus). This underlines their crucial importance: one might call them the ‘chromosomes’ of a D-particle or a black hole. As polar states also can be affected by our refinement, previous predictions on elliptic genera are modified. This can be metaphorically interpreted as ‘crossing-over in the meiosis of a D-particle’. Our results improve on [2], provide non-trivial evidence for a strong split attractor flow tree conjecture, and thus suggest that we indeed exhaust the BPS spectrum. In the D-brane description of a bound state, the necessity for refinement results from the fact that tachyonic strings split up constituent states into ‘generic’ and ‘special’ states. These are enumerated separately by topological invariants, which turn out to be partitions of Donaldson-Thomas invariants. As modular predictions provide a check on many of our results, we have compelling evidence that our computations are correct.

Linking nitrogen partitioning and species abundance to invasion resistance in the Great Basin

Treesearch

J. J. James; K. W. Davies; R. L. Sheley; Z. T. Aanderud

2008-01-01

Resource partitioning has been suggested as an important mechanism of invasion resistance. The relative importance of resource partitioning for invasion resistance, however, may depend on how species abundance is distributed in the plant community. This study had two objectives. First, we quantified the degree to which one resource, nitrogen (N), is partitioned by time...

TRL - A FORMAL TEST REPRESENTATION LANGUAGE AND TOOL FOR FUNCTIONAL TEST DESIGNS

NASA Technical Reports Server (NTRS)

Hops, J. M.

1994-01-01

A Formal Test Representation Language and Tool for Functional Test Designs (TRL) is an automatic tool and a formal language that is used to implement the Category-Partition Method and produce the specification of test cases in the testing phase of software development. The Category-Partition Method is particularly useful in defining the inputs, outputs and purpose of the test design phase and combines the benefits of choosing normal cases with error exposing properties. Traceability can be maintained quite easily by creating a test design for each objective in the test plan. The effort to transform the test cases into procedures is simplified by using an automatic tool to create the cases based on the test design. The method allows the rapid elimination of undesired test cases from consideration, and easy review of test designs by peer groups. The first step in the category-partition method is functional decomposition, in which the specification and/or requirements are decomposed into functional units that can be tested independently. A secondary purpose of this step is to identify the parameters that affect the behavior of the system for each functional unit. The second step, category analysis, carries the work done in the previous step further by determining the properties or sub-properties of the parameters that would make the system behave in different ways. The designer should analyze the requirements to determine the features or categories of each parameter and how the system may behave if the category were to vary its value. If the parameter undergoing refinement is a data-item, then categories of this data-item may be any of its attributes, such as type, size, value, units, frequency of change, or source. After all the categories for the parameters of the functional unit have been determined, the next step is to partition each category's range space into mutually exclusive values that the category can assume. In choosing partition values, all possible kinds of values should be included, especially the ones that will maximize error detection. The purpose of the final step, partition constraint analysis, is to refine the test design specification so that only the technically effective and economically feasible test cases are implied. TRL is written in C-language to be machine independent. It has been successfully implemented on an IBM PC compatible running MS DOS, a Sun4 series computer running SunOS, an HP 9000/700 series workstation running HP-UX, a DECstation running DEC RISC ULTRIX, and a DEC VAX series computer running VMS. TRL requires 1Mb of disk space and a minimum of 84K of RAM. The documentation is available in electronic form in Word Perfect format. The standard distribution media for TRL is a 5.25 inch 360K MS-DOS format diskette. Alternate distribution media and formats are available upon request. TRL was developed in 1993 and is a copyrighted work with all copyright vested in NASA.

Determinants of Chromosome Architecture: Insulator Pairing in cis and in trans

PubMed Central

Fujioka, Miki; Mistry, Hemlata; Schedl, Paul; Jaynes, James B.

2016-01-01

The chromosomes of multicellular animals are organized into a series of topologically independent looped domains. This domain organization is critical for the proper utilization and propagation of the genetic information encoded by the chromosome. A special set of architectural elements, called boundaries or insulators, are responsible both for subdividing the chromatin into discrete domains and for determining the topological organization of these domains. Central to the architectural functions of insulators are homologous and heterologous insulator:insulator pairing interactions. The former (pairing between copies of the same insulator) dictates the process of homolog alignment and pairing in trans, while the latter (pairing between different insulators) defines the topology of looped domains in cis. To elucidate the principles governing these architectural functions, we use two insulators, Homie and Nhomie, that flank the Drosophila even skipped locus. We show that homologous insulator interactions in trans, between Homie on one homolog and Homie on the other, or between Nhomie on one homolog and Nhomie on the other, mediate transvection. Critically, these homologous insulator:insulator interactions are orientation-dependent. Consistent with a role in the alignment and pairing of homologs, self-pairing in trans is head-to-head. Head-to-head self-interactions in cis have been reported for other fly insulators, suggesting that this is a general principle of self-pairing. Homie and Nhomie not only pair with themselves, but with each other. Heterologous Homie-Nhomie interactions occur in cis, and we show that they serve to delimit a looped chromosomal domain that contains the even skipped transcription unit and its associated enhancers. The topology of this loop is defined by the heterologous pairing properties of Homie and Nhomie. Instead of being head-to-head, which would generate a circular loop, Homie-Nhomie pairing is head-to-tail. Head-to-tail pairing in cis generates a stem-loop, a configuration much like that observed in classical lampbrush chromosomes. These pairing principles provide a mechanistic underpinning for the observed topologies within and between chromosomes. PMID:26910731

One-loop renormalization of Lee-Wick gauge theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grinstein, Benjamin; O'Connell, Donal

2008-11-15

We examine the renormalization of Lee-Wick gauge theory to one-loop order. We show that only knowledge of the wave function renormalization is necessary to determine the running couplings, anomalous dimensions, and vector boson masses. In particular, the logarithmic running of the Lee-Wick vector boson mass is exactly related to the running of the coupling. In the case of an asymptotically free theory, the vector boson mass runs to infinity in the ultraviolet. Thus, the UV fixed point of the pure gauge theory is an ordinary quantum field theory. We find that the coupling runs more quickly in Lee-Wick gauge theorymore » than in ordinary gauge theory, so the Lee-Wick standard model does not naturally unify at any scale. Finally, we present results on the beta function of more general theories containing dimension six operators which differ from previous results in the literature.« less

Partition functions. I. Improved partition functions and thermodynamic quantities for normal, equilibrium, and ortho and para molecular hydrogen

NASA Astrophysics Data System (ADS)

Popovas, A.; Jørgensen, U. G.

2016-11-01

Context. Hydrogen is the most abundant molecule in the Universe. Its thermodynamic quantities dominate the physical conditions in molecular clouds, protoplanetary disks, etc. It is also of high interest in plasma physics. Therefore thermodynamic data for molecular hydrogen have to be as accurate as possible in a wide temperature range. Aims: We here rigorously show the shortcomings of various simplifications that are used to calculate the total internal partition function. These shortcomings can lead to errors of up to 40 percent or more in the estimated partition function. These errors carry on to calculations of thermodynamic quantities. Therefore a more complicated approach has to be taken. Methods: Seven possible simplifications of various complexity are described, together with advantages and disadvantages of direct summation of experimental values. These were compared to what we consider the most accurate and most complete treatment (case 8). Dunham coefficients were determined from experimental and theoretical energy levels of a number of electronically excited states of H2. Both equilibrium and normal hydrogen was taken into consideration. Results: Various shortcomings in existing calculations are demonstrated, and the reasons for them are explained. New partition functions for equilibrium, normal, and ortho and para hydrogen are calculated and thermodynamic quantities are reported for the temperature range 1-20 000 K. Our results are compared to previous estimates in the literature. The calculations are not limited to the ground electronic state, but include all bound and quasi-bound levels of excited electronic states. Dunham coefficients of these states of H2 are also reported. Conclusions: For most of the relevant astrophysical cases it is strongly advised to avoid using simplifications, such as a harmonic oscillator and rigid rotor or ad hoc summation limits of the eigenstates to estimate accurate partition functions and to be particularly careful when using polynomial fits to the computed values. Reported internal partition functions and thermodynamic quantities in the present work are shown to be more accurate than previously available data. The full datasets in 1 K temperature steps are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/595/A130

Folded Supersymmetry and the LDP Paradox

DOE Office of Scientific and Technical Information (OSTI.GOV)

Burdman, Gustavo; Chacko, Z.; Goh, Hock-Seng

2006-09-21

We present a new class of models that stabilize the weak scale against radiative corrections up to scales of order 5 TeV without large corrections to precision electroweak observables. In these ''folded supersymmetric'' theories the one loop quadratic divergences of the Standard Model Higgs field are canceled by opposite spin partners, but the gauge quantum numbers of these new particles are in general different from those of the conventional superpartners. This class of models is built around the correspondence that exists in the large N limit between the correlation functions of supersymmetric theories and those of their non-supersymmetric orbifold daughters.more » By identifying the mechanism which underlies the cancellation of one loop quadratic divergences in these theories, we are able to construct simple extensions of the Standard Model which are radiatively stable at one loop. Ultraviolet completions of these theories can be obtained by imposing suitable boundary conditions on an appropriate supersymmetric higher dimensional theory compactified down to four dimensions. We construct a specific model based on these ideas which stabilizes the weak scale up to about 20 TeV and where the states which cancel the top loop are scalars not charged under Standard Model color. Its collider signatures are distinct from conventional supersymmetric theories and include characteristic events with hard leptons and missing energy.« less

Postural control model interpretation of stabilogram diffusion analysis

NASA Technical Reports Server (NTRS)

Peterka, R. J.

2000-01-01

Collins and De Luca [Collins JJ. De Luca CJ (1993) Exp Brain Res 95: 308-318] introduced a new method known as stabilogram diffusion analysis that provides a quantitative statistical measure of the apparently random variations of center-of-pressure (COP) trajectories recorded during quiet upright stance in humans. This analysis generates a stabilogram diffusion function (SDF) that summarizes the mean square COP displacement as a function of the time interval between COP comparisons. SDFs have a characteristic two-part form that suggests the presence of two different control regimes: a short-term open-loop control behavior and a longer-term closed-loop behavior. This paper demonstrates that a very simple closed-loop control model of upright stance can generate realistic SDFs. The model consists of an inverted pendulum body with torque applied at the ankle joint. This torque includes a random disturbance torque and a control torque. The control torque is a function of the deviation (error signal) between the desired upright body position and the actual body position, and is generated in proportion to the error signal, the derivative of the error signal, and the integral of the error signal [i.e. a proportional, integral and derivative (PID) neural controller]. The control torque is applied with a time delay representing conduction, processing, and muscle activation delays. Variations in the PID parameters and the time delay generate variations in SDFs that mimic real experimental SDFs. This model analysis allows one to interpret experimentally observed changes in SDFs in terms of variations in neural controller and time delay parameters rather than in terms of open-loop versus closed-loop behavior.

Discovering Link Communities in Complex Networks by an Integer Programming Model and a Genetic Algorithm

PubMed Central

Li, Zhenping; Zhang, Xiang-Sun; Wang, Rui-Sheng; Liu, Hongwei; Zhang, Shihua

2013-01-01

Identification of communities in complex networks is an important topic and issue in many fields such as sociology, biology, and computer science. Communities are often defined as groups of related nodes or links that correspond to functional subunits in the corresponding complex systems. While most conventional approaches have focused on discovering communities of nodes, some recent studies start partitioning links to find overlapping communities straightforwardly. In this paper, we propose a new quantity function for link community identification in complex networks. Based on this quantity function we formulate the link community partition problem into an integer programming model which allows us to partition a complex network into overlapping communities. We further propose a genetic algorithm for link community detection which can partition a network into overlapping communities without knowing the number of communities. We test our model and algorithm on both artificial networks and real-world networks. The results demonstrate that the model and algorithm are efficient in detecting overlapping community structure in complex networks. PMID:24386268

Limit Cycle Bifurcations Near a Piecewise Smooth Generalized Homoclinic Loop with a Saddle-Fold Point

NASA Astrophysics Data System (ADS)

Liang, Feng; Wang, Dechang

In this paper, we suppose that a planar piecewise Hamiltonian system, with a straight line of separation, has a piecewise generalized homoclinic loop passing through a Saddle-Fold point, and assume that there exists a family of piecewise smooth periodic orbits near the loop. By studying the asymptotic expansion of the first order Melnikov function corresponding to the period annulus, we obtain the formulas of the first six coefficients in the expansion, based on which, we provide a lower bound for the maximal number of limit cycles bifurcated from the period annulus. As applications, two concrete systems are considered. Especially, the first one reveals that a quadratic piecewise Hamiltonian system can have five limit cycles near a generalized homoclinic loop under a quadratic piecewise smooth perturbation. Compared with the smooth case [Horozov & Iliev, 1994; Han et al., 1999], three more limit cycles are found.

Probing the Production of Extreme-ultraviolet Late-phase Solar Flares Using the Model Enthalpy-based Thermal Evolution of Loops

NASA Astrophysics Data System (ADS)

Dai, Yu; Ding, Mingde

2018-04-01

Recent observations in extreme-ultraviolet (EUV) wavelengths reveal an EUV late phase in some solar flares that is characterized by a second peak in warm coronal emissions (∼3 MK) several tens of minutes to a few hours after the soft X-ray (SXR) peak. Using the model enthalpy-based thermal evolution of loops (EBTEL), we numerically probe the production of EUV late-phase solar flares. Starting from two main mechanisms of producing the EUV late phase, i.e., long-lasting cooling and secondary heating, we carry out two groups of numerical experiments to study the effects of these two processes on the emission characteristics in late-phase loops. In either of the two processes an EUV late-phase solar flare that conforms to the observational criteria can be numerically synthesized. However, the underlying hydrodynamic and thermodynamic evolutions in late-phase loops are different between the two synthetic flare cases. The late-phase peak due to a long-lasting cooling process always occurs during the radiative cooling phase, while that powered by a secondary heating is more likely to take place in the conductive cooling phase. We then propose a new method for diagnosing the two mechanisms based on the shape of EUV late-phase light curves. Moreover, from the partition of energy input, we discuss why most solar flares are not EUV late flares. Finally, by addressing some other factors that may potentially affect the loop emissions, we also discuss why the EUV late phase is mainly observed in warm coronal emissions.

Genomic analysis of the symbiotic marine crenarchaeon, Cenarchaeumsymbiosum

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hallam, Steven J.; Konstantinidis, Konstantinos T.; Brochier,Celine

2006-06-24

Crenarchaea are ubiquitous and abundant microbial constituents of soils, sediments, lakes and ocean waters, yet relatively little is known about their fundamental evolutionary, ecological, and physiological properties. To better describe the ubiquitous nonthermophilic Crenarchaea, we analyzed the genome sequence of one representative, the uncultivated sponge symbiont, Cenarchaeum symbiosum. C. symbiosum genotypes coinhabiting the same host partitioned into two dominant populations, corresponding to previously described a- and b-type ribosomal RNA variants. Although synthetic, overlapping a- and b-type ribotypes harbored significant genetic variability. A single tiling path comprising the dominant a-type genotype was assembled, and used to explore the biological properties ofmore » C. symbiosum and its planktonic relatives. Out of a total of 2,066 predicted open reading frames, 36% were more highly conserved with other Archaea. The remainder partitioned between bacteria (18%), eukaryotes (1.5%) and viruses (0.1%). A total of 525 open reading frames were more highly conserved with sequences derived from marine environmental genomic surveys, most probably representing orthologous genes found in free-living planktonic Crenarchaea. The remaining genes partitioned between functional RNAs (2.4%), and hypotheticals (42%) with limited homology to known functional genes. The latter category likely contains genes specifically involved in mediated archaeal-sponge symbiosis. Phylogenetic analyses placed C. symbiosum as a basal crenarchaeon, sharing specific genomic features in common with either Crenarchaea, Euryarchaea, or both. The genome sequence of C. symbiosum reflect a unique and unusual evolutionary, physiological, and ecological history, one remarkably distinct from that of any other previously known microbial lineage.« less

Polymer diffusion in quenched disorder: A renormalization group approach

NASA Astrophysics Data System (ADS)

Ebert, Ute

1996-01-01

We study the diffusion of polymers through quenched short-range correlated random media by renormalization group (RG) methods, which allow us to derive universal predictions in the limit of long chains and weak disorder. We take local quenched random potentials with second moment v and the excluded-volume interaction u of the chain segments into account. We show that our model contains the relevant features of polymer diffusion in random media in the RG sense if we focus on the local entropic effects rather than on the topological constraints of a quenched random medium. The dynamic generating functional and the general structure of its perturbation expansion in u and v are derived. The distribution functions for the center-of-mass motion and the internal modes of one chain and for the correlation of the center of mass motions of two chains are calculated to one-loop order. The results allow for sufficient cross-checks to have trust in the one-loop renormalizability of the model. The general structure as well as the one-loop results of the integrated RG flow of the parameters are discussed. Universal results can be found for the effective static interaction w≔u-v≥0 and for small effective disorder couplingbar v(l) on the intermediate length scale l. As a first physical prediction from our analysis, we determine the general nonlinear scaling form of the chain diffusion constant and evaluate it explicitly as[Figure not available: see fulltext.] forbar v(l) ≪ 1.

QSPR modeling of octanol/water partition coefficient of antineoplastic agents by balance of correlations.

PubMed

Toropov, Andrey A; Toropova, Alla P; Raska, Ivan; Benfenati, Emilio

2010-04-01

Three different splits into the subtraining set (n = 22), the set of calibration (n = 21), and the test set (n = 12) of 55 antineoplastic agents have been examined. By the correlation balance of SMILES-based optimal descriptors quite satisfactory models for the octanol/water partition coefficient have been obtained on all three splits. The correlation balance is the optimization of a one-variable model with a target function that provides both the maximal values of the correlation coefficient for the subtraining and calibration set and the minimum of the difference between the above-mentioned correlation coefficients. Thus, the calibration set is a preliminary test set. Copyright (c) 2009 Elsevier Masson SAS. All rights reserved.

Dual little strings and their partition functions

NASA Astrophysics Data System (ADS)

Bastian, Brice; Hohenegger, Stefan; Iqbal, Amer; Rey, Soo-Jong

2018-05-01

We study the topological string partition function of a class of toric, double elliptically fibered Calabi-Yau threefolds XN ,M at a generic point in the Kähler moduli space. These manifolds engineer little string theories in five dimensions or lower and are dual to stacks of M5-branes probing a transverse orbifold singularity. Using the refined topological vertex formalism, we explicitly calculate a generic building block which allows us to compute the topological string partition function of XN ,M as a series expansion in different Kähler parameters. Using this result, we give further explicit proof for a duality found previously in the literature, which relates XN ,M˜XN',M' for N M =N'M' and gcd (N ,M )=gcd (N',M') .

DIVERSITY in binding, regulation, and evolution revealed from high-throughput ChIP.

PubMed

Mitra, Sneha; Biswas, Anushua; Narlikar, Leelavati

2018-04-01

Genome-wide in vivo protein-DNA interactions are routinely mapped using high-throughput chromatin immunoprecipitation (ChIP). ChIP-reported regions are typically investigated for enriched sequence-motifs, which are likely to model the DNA-binding specificity of the profiled protein and/or of co-occurring proteins. However, simple enrichment analyses can miss insights into the binding-activity of the protein. Note that ChIP reports regions making direct contact with the protein as well as those binding through intermediaries. For example, consider a ChIP experiment targeting protein X, which binds DNA at its cognate sites, but simultaneously interacts with four other proteins. Each of these proteins also binds to its own specific cognate sites along distant parts of the genome, a scenario consistent with the current view of transcriptional hubs and chromatin loops. Since ChIP will pull down all X-associated regions, the final reported data will be a union of five distinct sets of regions, each containing binding sites of one of the five proteins, respectively. Characterizing all five different motifs and the corresponding sets is important to interpret the ChIP experiment and ultimately, the role of X in regulation. We present diversity which attempts exactly this: it partitions the data so that each partition can be characterized with its own de novo motif. Diversity uses a Bayesian approach to identify the optimal number of motifs and the associated partitions, which together explain the entire dataset. This is in contrast to standard motif finders, which report motifs individually enriched in the data, but do not necessarily explain all reported regions. We show that the different motifs and associated regions identified by diversity give insights into the various complexes that may be forming along the chromatin, something that has so far not been attempted from ChIP data. Webserver at http://diversity.ncl.res.in/; standalone (Mac OS X/Linux) from https://github.com/NarlikarLab/DIVERSITY/releases/tag/v1.0.0.

Reliable Control Using Disturbance Observer and Equivalent Transfer Function for Position Servo System in Current Feedback Loop Failure

NASA Astrophysics Data System (ADS)

Ishikawa, Kaoru; Nakamura, Taro; Osumi, Hisashi

A reliable control method is proposed for multiple loop control system. After a feedback loop failure, such as case of the sensor break down, the control system becomes unstable and has a big fluctuation even if it has a disturbance observer. To cope with this problem, the proposed method uses an equivalent transfer function (ETF) as active redundancy compensation after the loop failure. The ETF is designed so that it does not change the transfer function of the whole system before and after the loop failure. In this paper, the characteristic of reliable control system that uses an ETF and a disturbance observer is examined by the experiment that uses the DC servo motor for the current feedback loop failure in the position servo system.

Integer Partitions and Convexity

NASA Astrophysics Data System (ADS)

Bouroubi, Sadek

2007-06-01

Let n be an integer >=1, and let p(n,k) and P(n,k) count the number of partitions of n into k parts, and the number of partitions of n into parts less than or equal to k, respectively. In this paper, we show that these functions are convex. The result includes the actual value of the constant of Bateman and Erdos.

State-dependent metabolic partitioning and energy conservation: A theoretical framework for understanding the function of sleep.

PubMed

Schmidt, Markus H; Swang, Theodore W; Hamilton, Ian M; Best, Janet A

2017-01-01

Metabolic rate reduction has been considered the mechanism by which sleep conserves energy, similar to torpor or hibernation. This mechanism of energy savings is in conflict with the known upregulation (compared to wake) of diverse functions during sleep and neglects a potential role in energy conservation for partitioning of biological operations by behavioral state. Indeed, energy savings as derived from state-dependent resource allocations have yet to be examined. A mathematical model is presented based on relative rates of energy deployment for biological processes upregulated during either wake or sleep. Using this model, energy savings from sleep-wake cycling over constant wakefulness is computed by comparing stable limit cycles for systems of differential equations. A primary objective is to compare potential energy savings derived from state-dependent metabolic partitioning versus metabolic rate reduction. Additionally, energy conservation from sleep quota and the circadian system are also quantified in relation to a continuous wake condition. As a function of metabolic partitioning, our calculations show that coupling of metabolic operations with behavioral state may provide comparatively greater energy savings than the measured decrease in metabolic rate, suggesting that actual energy savings derived from sleep may be more than 4-fold greater than previous estimates. A combination of state-dependent metabolic partitioning and modest metabolic rate reduction during sleep may enhance energy savings beyond what is achievable through metabolic partitioning alone; however, the relative contribution from metabolic partitioning diminishes as metabolic rate is decreased during the rest phase. Sleep quota and the circadian system further augment energy savings in the model. Finally, we propose that state-dependent resource allocation underpins both sleep homeostasis and the optimization of daily energy conservation across species. This new paradigm identifies an evolutionary selective advantage for the upregulation of central and peripheral biological processes during sleep, presenting a unifying construct to understand sleep function.

The effect of cholesterol on the partitioning of 1-octanol into POPC vesicles

NASA Astrophysics Data System (ADS)

Zakariaee Kouchaksaraee, Roja

Microcalorimetry has become a method of choice for sensitive characterization of biomolecular interactions. In this study, isothermal titration calorimetry (ITC) was used to measure the partitioning of 1-octanol into lipid bilayers composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), a semi-unsaturated lipid, and cholesterol, a steroid, as a function of cholesterol molar concentration. The ITC instrument measures the heat evolved or absorbed upon titration of a liposome dispersion, at concentrations ranging from 0 to 40% cholesterol, into a suspension of 1-octanol in water. A model function was fit to the data in order to determine the partition coefficient of octanol into POPC bilayers and the enthalpy of interaction. I found that the partition coefficient increases and the heat of interaction becomes less negative with increasing cholesterol content, in contrast to results found by other groups for partitioning of alcohols into lipid-cholesterol bilayers containing saturated lipids. The heat of dilution of vesicles was also measured. Keywords: Partition coefficient; POPC; 1-Octanol; Cholesterol; Isothermal titration calorimetry; Lipid-alcohol interactions. Subject Terms: Calorimetry; Membranes (Biology); Biophysics; Biology -- Technique; Bilayer lipid membranes -- Biotechnology; Lipid membranes -- Biotechnology.

Conformational Sampling in Template-Free Protein Loop Structure Modeling: An Overview

PubMed Central

Li, Yaohang

2013-01-01

Accurately modeling protein loops is an important step to predict three-dimensional structures as well as to understand functions of many proteins. Because of their high flexibility, modeling the three-dimensional structures of loops is difficult and is usually treated as a “mini protein folding problem” under geometric constraints. In the past decade, there has been remarkable progress in template-free loop structure modeling due to advances of computational methods as well as stably increasing number of known structures available in PDB. This mini review provides an overview on the recent computational approaches for loop structure modeling. In particular, we focus on the approaches of sampling loop conformation space, which is a critical step to obtain high resolution models in template-free methods. We review the potential energy functions for loop modeling, loop buildup mechanisms to satisfy geometric constraints, and loop conformation sampling algorithms. The recent loop modeling results are also summarized. PMID:24688696

Conformational sampling in template-free protein loop structure modeling: an overview.

PubMed

Li, Yaohang

2013-01-01

Accurately modeling protein loops is an important step to predict three-dimensional structures as well as to understand functions of many proteins. Because of their high flexibility, modeling the three-dimensional structures of loops is difficult and is usually treated as a "mini protein folding problem" under geometric constraints. In the past decade, there has been remarkable progress in template-free loop structure modeling due to advances of computational methods as well as stably increasing number of known structures available in PDB. This mini review provides an overview on the recent computational approaches for loop structure modeling. In particular, we focus on the approaches of sampling loop conformation space, which is a critical step to obtain high resolution models in template-free methods. We review the potential energy functions for loop modeling, loop buildup mechanisms to satisfy geometric constraints, and loop conformation sampling algorithms. The recent loop modeling results are also summarized.

The AdS/CFT Correspondence: Classical, Quantum, and Thermodynamical Aspects

NASA Astrophysics Data System (ADS)

Young, Donovan

2007-06-01

Certain aspects of the AdS/CFT correspondence are studied in detail. We investigate the one-loop mass shift to certain two-impurity string states in light-cone string field theory on a plane wave background. We find that there exist logarithmic divergences in the sums over intermediate mode numbers which cancel between the cubic Hamiltonian and quartic "contact term". We argue that generically, every order in intermediate state impurities contributes to the mass shift at leading perturbative order. The same mass shift is also computed using an improved 3-string vertex proposed by Dobashi and Yoneya. The result is found to agree with gauge theory at leading order and is close but not quite in agreement at subleading order. We extend the analysis to include discrete light-cone quantization, considering states with up to three units of p+. We study the (apparently) first-order phase transition in the weakly coupled plane-wave matrix model at finite temperature. We analyze the effect of interactions by computing the relevant parts of the effective potential for the Polyakov loop operator to three loop order. We show that the phase transition is indeed of first order. We also compute the 2-loop correction to the Hagedorn temperature. Finally, correlation functions of 1/4 BPS Wilson loops with the infinite family of 1/2 BPS chiral primary operators are computed in N=4 super Yang-Mills theory by summing planar ladder diagrams. The correlation functions are also computed in the strong-coupling limit using string theory; the result is found to agree with the extrapolation of the planar ladders. The result is related to similar correlators of 1/2 BPS loops by a simple re-scaling of the coupling constant, discovered by Drukker for the case of the 1/4 BPS loop VEV.

Autogenous forearm loop arteriovenous fistula creation.

PubMed

Tang, Weng Jun; Mat Saad, Arman Zaharil

2018-03-01

Arteriovenous fistula is a lifeline for end-stage kidney disease patients on dialysis. The quality of the vein and artery to be used plays a crucial role in attaining a functioning, reliable and long-lasting arteriovenous fistula. The aim of the study is to present an alternative for haemodialysis access to preserve the upper arm vasculature for future use - the forearm loop arteriovenous fistula. From October 2015 to September 2016, 202 patients with chronic kidney disease (CKD), stages 4 and 5, underwent arteriovenous fistula creation at the Universiti Sains Malaysia Hospital, Malaysia. Nine patients, with severe atherosclerosis of the distal artery, but with satisfactory veins, underwent forearm loop arteriovenous fistula creation. Maturation of the fistula was based on the classification by the National Kidney Foundation Kidney Disease Outcomes Quality Initiative (NKF KDOQI). All nine patients who underwent forearm loop arteriovenous fistula have had diabetes mellitus for more than 10 years. Only one fistula failed to mature within 6 weeks. Two arteriovenous fistulas thrombosed at 3 and 5 months, respectively, after the commencement of haemodialysis. However, the other six matured fistulas are still functioning well after a year of regular usage. Distal forearm arteries in diabetics may be severely atherosclerotic. Forearm loop arteriovenous fistula can be considered as the primary access for cases decided as inconvenient for fistula creation due to severe occlusive atherosclerotic disease of the forearm arteries; in order to preserve upper arm veins for future access procedures.

Thermodynamic holography.

PubMed

Wei, Bo-Bo; Jiang, Zhan-Feng; Liu, Ren-Bao

2015-10-19

The holographic principle states that the information about a volume of a system is encoded on the boundary surface of the volume. Holography appears in many branches of physics, such as optics, electromagnetism, many-body physics, quantum gravity, and string theory. Here we show that holography is also an underlying principle in thermodynamics, a most important foundation of physics. The thermodynamics of a system is fully determined by its partition function. We prove that the partition function of a finite but arbitrarily large system is an analytic function on the complex plane of physical parameters, and therefore the partition function in a region on the complex plane is uniquely determined by its values along the boundary. The thermodynamic holography has applications in studying thermodynamics of nano-scale systems (such as molecule engines, nano-generators and macromolecules) and provides a new approach to many-body physics.

A massive Feynman integral and some reduction relations for Appell functions

NASA Astrophysics Data System (ADS)

Shpot, M. A.

2007-12-01

New explicit expressions are derived for the one-loop two-point Feynman integral with arbitrary external momentum and masses m12 and m22 in D dimensions. The results are given in terms of Appell functions, manifestly symmetric with respect to the masses mi2. Equating our expressions with previously known results in terms of Gauss hypergeometric functions yields reduction relations for the involved Appell functions that are apparently new mathematical results.

A simplifying feature of the heterotic one loop four graviton amplitude

NASA Astrophysics Data System (ADS)

Basu, Anirban

2018-01-01

We show that the weight four modular graph functions that contribute to the integrand of the t8t8D4R4 term at one loop in heterotic string theory do not require regularization, and hence the integrand is simple. This is unlike the graphs that contribute to the integrands of the other gravitational terms at this order in the low momentum expansion, and these integrands require regularization. This property persists for an infinite number of terms in the effective action, and their integrands do not require regularization. We find non-trivial relations between weight four graphs of distinct topologies that do not require regularization by performing trivial manipulations using auxiliary diagrams.

Closed-loop carrier phase synchronization techniques motivated by likelihood functions

NASA Technical Reports Server (NTRS)

Tsou, H.; Hinedi, S.; Simon, M.

1994-01-01

This article reexamines the notion of closed-loop carrier phase synchronization motivated by the theory of maximum a posteriori phase estimation with emphasis on the development of new structures based on both maximum-likelihood and average-likelihood functions. The criterion of performance used for comparison of all the closed-loop structures discussed is the mean-squared phase error for a fixed-loop bandwidth.

Ocean surface partitioning strategies using ocean colour remote Sensing: A review

NASA Astrophysics Data System (ADS)

Krug, Lilian Anne; Platt, Trevor; Sathyendranath, Shubha; Barbosa, Ana B.

2017-06-01

The ocean surface is organized into regions with distinct properties reflecting the complexity of interactions between environmental forcing and biological responses. The delineation of these functional units, each with unique, homogeneous properties and underlying ecosystem structure and dynamics, can be defined as ocean surface partitioning. The main purposes and applications of ocean partitioning include the evaluation of particular marine environments; generation of more accurate satellite ocean colour products; assimilation of data into biogeochemical and climate models; and establishment of ecosystem-based management practices. This paper reviews the diverse approaches implemented for ocean surface partition into functional units, using ocean colour remote sensing (OCRS) data, including their purposes, criteria, methods and scales. OCRS offers a synoptic, high spatial-temporal resolution, multi-decadal coverage of bio-optical properties, relevant to the applications and value of ocean surface partitioning. In combination with other biotic and/or abiotic data, OCRS-derived data (e.g., chlorophyll-a, optical properties) provide a broad and varied source of information that can be analysed using different delineation methods derived from subjective, expert-based to unsupervised learning approaches (e.g., cluster, fuzzy and empirical orthogonal function analyses). Partition schemes are applied at global to mesoscale spatial coverage, with static (time-invariant) or dynamic (time-varying) representations. A case study, the highly heterogeneous area off SW Iberian Peninsula (NE Atlantic), illustrates how the selection of spatial coverage and temporal representation affects the discrimination of distinct environmental drivers of phytoplankton variability. Advances in operational oceanography and in the subject area of satellite ocean colour, including development of new sensors, algorithms and products, are among the potential benefits from extended use, scope and applications of ocean surface partitioning using OCRS.

The impact of aerosol composition on the particle to gas partitioning of reactive mercury.

PubMed

Rutter, Andrew P; Schauer, James J

2007-06-01

A laboratory system was developed to study the gas-particle partitioning of reactive mercury (RM) as a function of aerosol composition in synthetic atmospheric particulate matter. The collection of RM was achieved by filter- and sorbent-based methods. Analyses of the RM collected on the filters and sorbents were performed using thermal extraction combined with cold vapor atomic fluorescence spectroscopy (CVAFS), allowing direct measurement of the RM load on the substrates. Laboratory measurements of the gas-particle partitioning coefficients of RM to atmospheric aerosol particles revealed a strong dependence on aerosol composition, with partitioning coefficients that varied by orders of magnitude depending on the composition of the particles. Particles of sodium nitrate and the chlorides of potassium and sodium had high partitioning coefficients, shifting the RM partitioning toward the particle phase, while ammonium sulfate, levoglucosan, and adipic acid caused the RM to partition toward the gas phase and, therefore, had partitioning coefficients that were lower by orders of magnitude.

PERCUTANEOUS RADIOFREQUENCY ASSISTED LIVER PARTITION WITH PORTAL VEIN EMBOLIZATION FOR STAGED HEPATECTOMY (PRALPPS).

PubMed

Giménez, Mariano E; Houghton, Eduardo J; Davrieux, C Federico; Serra, Edgardo; Pessaux, Patrick; Palermo, Mariano; Acquafresca, Pablo A; Finger, Caetano; Dallemagne, Bernard; Marescaux, Jacques

2018-03-01

When a major hepatic resection is necessary, sometimes the future liver remnant is not enough to maintain sufficient liver function and patients are more likely to develop liver failure after surgery. To test the hypothesis that performing a percutaneous radiofrecuency liver partition plus percutaneous portal vein embolization (PRALPPS) for stage hepatectomy in pigs is feasible. Four pigs (Sus scrofa domesticus) both sexes with weights between 25 to 35 kg underwent percutaneous portal vein embolization with coils of the left portal vein. By contrasted CT, the difference between the liver parenchyma corresponding to the embolized zone and the normal one was identified. Immediately, using the fusion of images between ultrasound and CT as a guide, radiofrequency needles were placed percutaneouslyand then ablated until the liver partition was complete. Finally, hepatectomy was completed with a laparoscopic approach. All animals have survived the procedures, with no reported complications. The successful portal embolization process was confirmed both by portography and CT. In the macroscopic analysis of the pieces, the depth of the ablation was analyzed. The hepatic hilum was respected. On the other hand, the correct position of the embolization material on the left portal vein could be also observed. "Percutaneous radiofrequency assisted liver partition with portal vein embolization" (PRALLPS) is a feasible procedure.

Universal dual amplitudes and asymptotic expansions for gg→ H and H→ γ γ in four dimensions

NASA Astrophysics Data System (ADS)

Driencourt-Mangin, Félix; Rodrigo, Germán; Sborlini, Germán F. R.

2018-03-01

Though the one-loop amplitudes of the Higgs boson to massless gauge bosons are finite because there is no direct interaction at tree level in the Standard Model, a well-defined regularization scheme is still required for their correct evaluation. We reanalyze these amplitudes in the framework of the four-dimensional unsubtraction and the loop-tree duality (FDU/LTD), and show how a local renormalization solves potential regularization ambiguities. The Higgs boson interactions are also used to illustrate new additional advantages of this formalism. We show that LTD naturally leads to very compact integrand expressions in four space-time dimensions of the one-loop amplitude with virtual electroweak gauge bosons. They exhibit the same functional form as the amplitudes with top quarks and charged scalars, thus opening further possibilities for simplifications in higher-order computations. Another outstanding application is the straightforward implementation of asymptotic expansions by using dual amplitudes. One of the main benefits of the LTD representation is that it is supported in a Euclidean space. This characteristic feature naturally leads to simpler asymptotic expansions.

Local performance optimization for a class of redundant eight-degree-of-freedom manipulators

NASA Technical Reports Server (NTRS)

Williams, Robert L., II

1994-01-01

Local performance optimization for joint limit avoidance and manipulability maximization (singularity avoidance) is obtained by using the Jacobian matrix pseudoinverse and by projecting the gradient of an objective function into the Jacobian null space. Real-time redundancy optimization control is achieved for an eight-joint redundant manipulator having a three-axis spherical shoulder, a single elbow joint, and a four-axis spherical wrist. Symbolic solutions are used for both full-Jacobian and wrist-partitioned pseudoinverses, partitioned null-space projection matrices, and all objective function gradients. A kinematic limitation of this class of manipulators and the limitation's effect on redundancy resolution are discussed. Results obtained with graphical simulation are presented to demonstrate the effectiveness of local redundant manipulator performance optimization. Actual hardware experiments performed to verify the simulated results are also discussed. A major result is that the partitioned solution is desirable because of low computation requirements. The partitioned solution is suboptimal compared with the full solution because translational and rotational terms are optimized separately; however, the results show that the difference is not significant. Singularity analysis reveals that no algorithmic singularities exist for the partitioned solution. The partitioned and full solutions share the same physical manipulator singular conditions. When compared with the full solution, the partitioned solution is shown to be ill-conditioned in smaller neighborhoods of the shared singularities.

Brain Network Regional Synchrony Analysis in Deafness

PubMed Central

Xu, Lei; Liang, Mao-Jin

2018-01-01

Deafness, the most common auditory disease, has greatly affected people for a long time. The major treatment for deafness is cochlear implantation (CI). However, till today, there is still a lack of objective and precise indicator serving as evaluation of the effectiveness of the cochlear implantation. The goal of this EEG-based study is to effectively distinguish CI children from those prelingual deafened children without cochlear implantation. The proposed method is based on the functional connectivity analysis, which focuses on the brain network regional synchrony. Specifically, we compute the functional connectivity between each channel pair first. Then, we quantify the brain network synchrony among regions of interests (ROIs), where both intraregional synchrony and interregional synchrony are computed. And finally the synchrony values are concatenated to form the feature vector for the SVM classifier. What is more, we develop a new ROI partition method of 128-channel EEG recording system. That is, both the existing ROI partition method and the proposed ROI partition method are used in the experiments. Compared with the existing EEG signal classification methods, our proposed method has achieved significant improvements as large as 87.20% and 86.30% when the existing ROI partition method and the proposed ROI partition method are used, respectively. It further demonstrates that the new ROI partition method is comparable to the existing ROI partition method. PMID:29854776

Confocal Raman Microscopy for in Situ Measurement of Octanol-Water Partitioning within the Pores of Individual C18-Functionalized Chromatographic Particles.

PubMed

Kitt, Jay P; Harris, Joel M

2015-05-19

Octanol-water partitioning is one of the most widely used predictors of hydrophobicity and lipophilicity. Traditional methods for measuring octanol-water partition coefficients (K(ow)), including shake-flasks and generator columns, require hours for equilibration and milliliter quantities of sample solution. These challenges have led to development of smaller-scale methods for measuring K(ow). Recent advances in microfluidics have produced faster and smaller-volume approaches to measuring K(ow). As flowing volumes are reduced, however, separation of water and octanol prior to measurement and detection in small volumes of octanol phase are especially challenging. In this work, we reduce the receiver volume of octanol-water partitioning measurements from current practice by six-orders-of-magnitude, to the femtoliter scale, by using a single octanol-filled reversed-phase, octadecylsilane-modified (C18-silica) chromatographic particle as a collector. The fluid-handling challenges of working in such small volumes are circumvented by eliminating postequilibration phase separation. Partitioning is measured in situ within the pore-confined octanol phase using confocal Raman microscopy, which is capable of detecting and quantifying a wide variety of molecular structures. Equilibration times are fast (less than a minute) because molecular diffusion is efficient over distance scales of micrometers. The demonstrated amount of analyte needed to carry out a measurement is very small, less than 50 fmol, which would be a useful attribute for drug screening applications or testing of small quantities of environmentally sensitive compounds. The method is tested for measurements of pH-dependent octanol-water partitioning of naphthoic acid, and the results are compared to both traditional shake-flask measurements and sorption onto C18-modified silica without octanol present within the pores.

Quantum corrections to the generalized Proca theory via a matter field

NASA Astrophysics Data System (ADS)

Amado, André; Haghani, Zahra; Mohammadi, Azadeh; Shahidi, Shahab

2017-09-01

We study the quantum corrections to the generalized Proca theory via matter loops. We consider two types of interactions, linear and nonlinear in the vector field. Calculating the one-loop correction to the vector field propagator, three- and four-point functions, we show that the non-linear interactions are harmless, although they renormalize the theory. The linear matter-vector field interactions introduce ghost degrees of freedom to the generalized Proca theory. Treating the theory as an effective theory, we calculate the energy scale up to which the theory remains healthy.

Singular Differential Game Numerical Technique and Closed Loop Guidance and Control Strategies,

DTIC Science & Technology

1982-03-01

zero sum games one player tries to minimize and the other player tries to maxwm e payoff functions. In such games a saddle point solu- tion is sought...period- ically in a a-all time interval At tK - ti, i - O,,. e . Whe the game starts running, the pursuer takes a measurement at t 1 t 0 + At and...Loop Solutions to Non-Linear-Zero-Sum Differential Games ," Int. J. Syst., Vol. 7 (5), 1976. 41 . Johnson, D. E ., Convergence Properties of the Method

Thermal stability of static coronal loops: Part 1: Effects of boundary conditions

NASA Technical Reports Server (NTRS)

Antiochos, S. K.; Shoub, E. C.; An, C. H.; Emslie, A. G.

1985-01-01

The linear stability of static coronal-loop models undergoing thermal perturbations was investigated. The effect of conditions at the loop base on the stability properties of the models was considered in detail. The question of appropriate boundary conditions at the loop base was considered and it was concluded that the most physical assumptions are that the temperature and density (or pressure) perturbations vanish there. However, if the base is taken to be sufficiently deep in the chromosphere, either several chromospheric scale heights or several coronal loop lengths in depth, then the effect of the boundary conditions on loop stability becomes negligible so that all physically acceptable conditions are equally appropriate. For example, one could as well assume that the velocity vanishes at the base. The growth rates and eigenmodes of static models in which gravity is neglected and in which the coronal heating is a relatively simple function, either constant per-unit mass or per-unit volume were calculated. It was found that all such models are unstable with a growth rate of the order of the coronal cooling time. The physical implications of these results for the solar corona and transition region are discussed.

Epitopes in α8β1 and other RGD-binding integrins delineate classes of integrin-blocking antibodies and major binding loops in α subunits

PubMed Central

Nishimichi, Norihisa; Kawashima, Nagako; Yokosaki, Yasuyuki

2015-01-01

Identification of epitopes for integrin-blocking monoclonal antibodies (mAbs) has aided our understanding of structure-function relationship of integrins. We mapped epitopes of chicken anti-integrin-α8-subunit-blocking mAbs by mutational analyses, examining regions that harboured all mapped epitopes recognized by mAbs against other α-subunits in the RGD-binding-integrin subfamily. Six mAbs exhibited blocking function, and these mAbs recognized residues on the same W2:41-loop on the top-face of the β-propeller. Loop-tips sufficiently close to W2:41 (<25 Å) contained within a footprint of the mAbs were mutated, and the loop W3:34 on the bottom face was identified as an additional component of the epitope of one antibody, clone YZ5. Binding sequences on the two loops were conserved in virtually all mammals, and that on W3:34 was also conserved in chickens. These indicate 1) YZ5 binds both top and bottom loops, and the binding to W3:34 is by interactions to conserved residues between immunogen and host species, 2) five other blocking mAbs solely bind to W2:41 and 3) the α8 mAbs would cross-react with most mammals. Comparing with the mAbs against the other α-subunits of RGD-integrins, two classes were delineated; those binding to “W3:34 and an top-loop”, and “solely W2:41”, accounting for 82% of published RGD-integrin-mAbs. PMID:26349930

Topological strings on singular elliptic Calabi-Yau 3-folds and minimal 6d SCFTs

NASA Astrophysics Data System (ADS)

Del Zotto, Michele; Gu, Jie; Huang, Min-xin; Kashani-Poor, Amir-Kian; Klemm, Albrecht; Lockhart, Guglielmo

2018-03-01

We apply the modular approach to computing the topological string partition function on non-compact elliptically fibered Calabi-Yau 3-folds with higher Kodaira singularities in the fiber. The approach consists in making an ansatz for the partition function at given base degree, exact in all fiber classes to arbitrary order and to all genus, in terms of a rational function of weak Jacobi forms. Our results yield, at given base degree, the elliptic genus of the corresponding non-critical 6d string, and thus the associated BPS invariants of the 6d theory. The required elliptic indices are determined from the chiral anomaly 4-form of the 2d worldsheet theories, or the 8-form of the corresponding 6d theories, and completely fix the holomorphic anomaly equation constraining the partition function. We introduce subrings of the known rings of Weyl invariant Jacobi forms which are adapted to the additional symmetries of the partition function, making its computation feasible to low base wrapping number. In contradistinction to the case of simpler singularities, generic vanishing conditions on BPS numbers are no longer sufficient to fix the modular ansatz at arbitrary base wrapping degree. We show that to low degree, imposing exact vanishing conditions does suffice, and conjecture this to be the case generally.

Comparison of modeling approaches for carbon partitioning: Impact on estimates of global net primary production and equilibrium biomass of woody vegetation from MODIS GPP

Treesearch

Takeshi Ise; Creighton M. Litton; Christian P. Giardina; Akihiko Ito

2010-01-01

Partitioning of gross primary production (GPP) to aboveground versus belowground, to growth versus respiration, and to short versus long�]lived tissues exerts a strong influence on ecosystem structure and function, with potentially large implications for the global carbon budget. A recent meta-analysis of forest ecosystems suggests that carbon partitioning...

MSTor: A program for calculating partition functions, free energies, enthalpies, entropies, and heat capacities of complex molecules including torsional anharmonicity

NASA Astrophysics Data System (ADS)

Zheng, Jingjing; Mielke, Steven L.; Clarkson, Kenneth L.; Truhlar, Donald G.

2012-08-01

We present a Fortran program package, MSTor, which calculates partition functions and thermodynamic functions of complex molecules involving multiple torsional motions by the recently proposed MS-T method. This method interpolates between the local harmonic approximation in the low-temperature limit, and the limit of free internal rotation of all torsions at high temperature. The program can also carry out calculations in the multiple-structure local harmonic approximation. The program package also includes six utility codes that can be used as stand-alone programs to calculate reduced moment of inertia matrices by the method of Kilpatrick and Pitzer, to generate conformational structures, to calculate, either analytically or by Monte Carlo sampling, volumes for torsional subdomains defined by Voronoi tessellation of the conformational subspace, to generate template input files, and to calculate one-dimensional torsional partition functions using the torsional eigenvalue summation method. Catalogue identifier: AEMF_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEMF_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 77 434 No. of bytes in distributed program, including test data, etc.: 3 264 737 Distribution format: tar.gz Programming language: Fortran 90, C, and Perl Computer: Itasca (HP Linux cluster, each node has two-socket, quad-core 2.8 GHz Intel Xeon X5560 “Nehalem EP” processors), Calhoun (SGI Altix XE 1300 cluster, each node containing two quad-core 2.66 GHz Intel Xeon “Clovertown”-class processors sharing 16 GB of main memory), Koronis (Altix UV 1000 server with 190 6-core Intel Xeon X7542 “Westmere” processors at 2.66 GHz), Elmo (Sun Fire X4600 Linux cluster with AMD Opteron cores), and Mac Pro (two 2.8 GHz Quad-core Intel Xeon processors) Operating system: Linux/Unix/Mac OS RAM: 2 Mbytes Classification: 16.3, 16.12, 23 Nature of problem: Calculation of the partition functions and thermodynamic functions (standard-state energy, enthalpy, entropy, and free energy as functions of temperatures) of complex molecules involving multiple torsional motions. Solution method: The multi-structural approximation with torsional anharmonicity (MS-T). The program also provides results for the multi-structural local harmonic approximation [1]. Restrictions: There is no limit on the number of torsions that can be included in either the Voronoi calculation or the full MS-T calculation. In practice, the range of problems that can be addressed with the present method consists of all multi-torsional problems for which one can afford to calculate all the conformations and their frequencies. Unusual features: The method can be applied to transition states as well as stable molecules. The program package also includes the hull program for the calculation of Voronoi volumes and six utility codes that can be used as stand-alone programs to calculate reduced moment-of-inertia matrices by the method of Kilpatrick and Pitzer, to generate conformational structures, to calculate, either analytically or by Monte Carlo sampling, volumes for torsional subdomain defined by Voronoi tessellation of the conformational subspace, to generate template input files, and to calculate one-dimensional torsional partition functions using the torsional eigenvalue summation method. Additional comments: The program package includes a manual, installation script, and input and output files for a test suite. Running time: There are 24 test runs. The running time of the test runs on a single processor of the Itasca computer is less than 2 seconds. J. Zheng, T. Yu, E. Papajak, I.M. Alecu, S.L. Mielke, D.G. Truhlar, Practical methods for including torsional anharmonicity in thermochemical calculations of complex molecules: The internal-coordinate multi-structural approximation, Phys. Chem. Chem. Phys. 13 (2011) 10885-10907.

Comment on "Troublesome aspects of the Renyi-MaxEnt treatment"

NASA Astrophysics Data System (ADS)

Oikonomou, Thomas; Bagci, G. Baris

2017-11-01

Plastino et al. [Plastino et al., Phys. Rev. E 94, 012145 (2016), 10.1103/PhysRevE.94.012145] recently stated that the Rényi entropy is not suitable for thermodynamics by using functional calculus, since it leads to anomalous results unlike the Tsallis entropy. We first show that the Tsallis entropy also leads to such anomalous behaviors if one adopts the same functional calculus approach. Second, we note that one of the Lagrange multipliers is set in an ad hoc manner in the functional calculus approach of Plastino et al. Finally, the explanation for these anomalous behaviors is provided by observing that the generalized distributions obtained by Plastino et al. do not yield the ordinary canonical partition function in the appropriate limit and therefore cannot be considered as genuine generalized distributions.

A Fabry-Pérot electro-optic sensing system using a drive-current-tuned wavelength laser diode.

PubMed

Kuo, Wen-Kai; Wu, Pei-Yu; Lee, Chang-Ching

2010-05-01

A Fabry-Pérot enhanced electro-optic sensing system that utilizes a drive-current-tuned wavelength laser diode is presented. An electro-optic prober made of LiNbO(3) crystal with an asymmetric Fabry-Pérot cavity is used in this system. To lock the wavelength of the laser diode at resonant condition, a closed-loop power control scheme is proposed. Experiment results show that the system can keep the electro-optic prober at high sensitivity for a long working time when the closed-loop control function is on. If this function is off, the sensitivity may be fluctuated and only one-third of the best level in the worst case.

Distributed numerical controllers

NASA Astrophysics Data System (ADS)

Orban, Peter E.

2001-12-01

While the basic principles of Numerical Controllers (NC) have not changed much during the years, the implementation of NCs' has changed tremendously. NC equipment has evolved from yesterday's hard-wired specialty control apparatus to today's graphics intensive, networked, increasingly PC based open systems, controlling a wide variety of industrial equipment with positioning needs. One of the newest trends in NC technology is the distributed implementation of the controllers. Distributed implementation promises to offer robustness, lower implementation costs, and a scalable architecture. Historically partitioning has been done along the hierarchical levels, moving individual modules into self contained units. The paper discusses various NC architectures, the underlying technology for distributed implementation, and relevant design issues. First the functional requirements of individual NC modules are analyzed. Module functionality, cycle times, and data requirements are examined. Next the infrastructure for distributed node implementation is reviewed. Various communication protocols and distributed real-time operating system issues are investigated and compared. Finally, a different, vertical system partitioning, offering true scalability and reconfigurability is presented.

Item-focussed Trees for the Identification of Items in Differential Item Functioning.

PubMed

Tutz, Gerhard; Berger, Moritz

2016-09-01

A novel method for the identification of differential item functioning (DIF) by means of recursive partitioning techniques is proposed. We assume an extension of the Rasch model that allows for DIF being induced by an arbitrary number of covariates for each item. Recursive partitioning on the item level results in one tree for each item and leads to simultaneous selection of items and variables that induce DIF. For each item, it is possible to detect groups of subjects with different item difficulties, defined by combinations of characteristics that are not pre-specified. The way a DIF item is determined by covariates is visualized in a small tree and therefore easily accessible. An algorithm is proposed that is based on permutation tests. Various simulation studies, including the comparison with traditional approaches to identify items with DIF, show the applicability and the competitive performance of the method. Two applications illustrate the usefulness and the advantages of the new method.

2D CFT partition functions at late times

NASA Astrophysics Data System (ADS)

Dyer, Ethan; Gur-Ari, Guy

2017-08-01

We consider the late time behavior of the analytically continued partition function Z( β + it) Z( β - it) in holographic 2 d CFTs. This is a probe of information loss in such theories and in their holographic duals. We show that each Virasoro character decays in time, and so information is not restored at the level of individual characters. We identify a universal decaying contribution at late times, and conjecture that it describes the behavior of generic chaotic 2 d CFTs out to times that are exponentially large in the central charge. It was recently suggested that at sufficiently late times one expects a crossover to random matrix behavior. We estimate an upper bound on the crossover time, which suggests that the decay is followed by a parametrically long period of late time growth. Finally, we discuss gravitationally-motivated integrable theories and show how information is restored at late times by a series of characters. This hints at a possible bulk mechanism, where information is restored by an infinite sum over non-perturbative saddles.

Multi-petascale highly efficient parallel supercomputer

DOEpatents

Asaad, Sameh; Bellofatto, Ralph E.; Blocksome, Michael A.; Blumrich, Matthias A.; Boyle, Peter; Brunheroto, Jose R.; Chen, Dong; Cher, Chen -Yong; Chiu, George L.; Christ, Norman; Coteus, Paul W.; Davis, Kristan D.; Dozsa, Gabor J.; Eichenberger, Alexandre E.; Eisley, Noel A.; Ellavsky, Matthew R.; Evans, Kahn C.; Fleischer, Bruce M.; Fox, Thomas W.; Gara, Alan; Giampapa, Mark E.; Gooding, Thomas M.; Gschwind, Michael K.; Gunnels, John A.; Hall, Shawn A.; Haring, Rudolf A.; Heidelberger, Philip; Inglett, Todd A.; Knudson, Brant L.; Kopcsay, Gerard V.; Kumar, Sameer; Mamidala, Amith R.; Marcella, James A.; Megerian, Mark G.; Miller, Douglas R.; Miller, Samuel J.; Muff, Adam J.; Mundy, Michael B.; O'Brien, John K.; O'Brien, Kathryn M.; Ohmacht, Martin; Parker, Jeffrey J.; Poole, Ruth J.; Ratterman, Joseph D.; Salapura, Valentina; Satterfield, David L.; Senger, Robert M.; Smith, Brian; Steinmacher-Burow, Burkhard; Stockdell, William M.; Stunkel, Craig B.; Sugavanam, Krishnan; Sugawara, Yutaka; Takken, Todd E.; Trager, Barry M.; Van Oosten, James L.; Wait, Charles D.; Walkup, Robert E.; Watson, Alfred T.; Wisniewski, Robert W.; Wu, Peng

2015-07-14

A Multi-Petascale Highly Efficient Parallel Supercomputer of 100 petaOPS-scale computing, at decreased cost, power and footprint, and that allows for a maximum packaging density of processing nodes from an interconnect point of view. The Supercomputer exploits technological advances in VLSI that enables a computing model where many processors can be integrated into a single Application Specific Integrated Circuit (ASIC). Each ASIC computing node comprises a system-on-chip ASIC utilizing four or more processors integrated into one die, with each having full access to all system resources and enabling adaptive partitioning of the processors to functions such as compute or messaging I/O on an application by application basis, and preferably, enable adaptive partitioning of functions in accordance with various algorithmic phases within an application, or if I/O or other processors are underutilized, then can participate in computation or communication nodes are interconnected by a five dimensional torus network with DMA that optimally maximize the throughput of packet communications between nodes and minimize latency.

First cytoplasmic loop of glucagon-like peptide-1 receptor can function at the third cytoplasmic loop position of rhodopsin.

PubMed

Yamashita, Takahiro; Tose, Koji; Shichida, Yoshinori

2008-01-01

G protein-coupled receptors (GPCRs) are classified into several families based on their amino acid sequences. In family 1, GPCRs such as rhodopsin and adrenergic receptor, the structure-function relationship has been extensively investigated to demonstrate that exposure of the third cytoplasmic loop is essential for selective G protein activation. In contrast, much less is known about other families. Here we prepared chimeric mutants between Gt-coupled rhodopsin and Gi/Go- and Gs-coupled glucagon-like peptide-1 (GLP-1) receptor of family 2 and tried to identify the loop region that functions at the third cytoplasmic loop position of rhodopsin. We succeeded in expressing a mutant having the first cytoplasmic loop of GLP-1 receptor and found that this mutant activated Gi and Go efficiently but did not activate Gt. Moreover, the rhodopsin mutant having the first loop of Gs-coupled secretin receptor of family 2 decreased the Gi and Go activation efficiencies. Therefore, the first loop of GLP-1 receptor would share a similar role to the third loop of rhodopsin in G protein activation. This result strongly suggested that different families of GPCRs have maintained molecular architectures of their ancestral types to generate a common mechanism, namely exposure of the cytoplasmic loop, to activate peripheral G protein.

Dissecting protein loops with a statistical scalpel suggests a functional implication of some structural motifs.

PubMed

Regad, Leslie; Martin, Juliette; Camproux, Anne-Claude

2011-06-20

One of the strategies for protein function annotation is to search particular structural motifs that are known to be shared by proteins with a given function. Here, we present a systematic extraction of structural motifs of seven residues from protein loops and we explore their correspondence with functional sites. Our approach is based on the structural alphabet HMM-SA (Hidden Markov Model - Structural Alphabet), which allows simplification of protein structures into uni-dimensional sequences, and advanced pattern statistics adapted to short sequences. Structural motifs of interest are selected by looking for structural motifs significantly over-represented in SCOP superfamilies in protein loops. We discovered two types of structural motifs significantly over-represented in SCOP superfamilies: (i) ubiquitous motifs, shared by several superfamilies and (ii) superfamily-specific motifs, over-represented in few superfamilies. A comparison of ubiquitous words with known small structural motifs shows that they contain well-described motifs as turn, niche or nest motifs. A comparison between superfamily-specific motifs and biological annotations of Swiss-Prot reveals that some of them actually correspond to functional sites involved in the binding sites of small ligands, such as ATP/GTP, NAD(P) and SAH/SAM. Our findings show that statistical over-representation in SCOP superfamilies is linked to functional features. The detection of over-represented motifs within structures simplified by HMM-SA is therefore a promising approach for prediction of functional sites and annotation of uncharacterized proteins.

Dissecting protein loops with a statistical scalpel suggests a functional implication of some structural motifs

PubMed Central

2011-01-01

Background One of the strategies for protein function annotation is to search particular structural motifs that are known to be shared by proteins with a given function. Results Here, we present a systematic extraction of structural motifs of seven residues from protein loops and we explore their correspondence with functional sites. Our approach is based on the structural alphabet HMM-SA (Hidden Markov Model - Structural Alphabet), which allows simplification of protein structures into uni-dimensional sequences, and advanced pattern statistics adapted to short sequences. Structural motifs of interest are selected by looking for structural motifs significantly over-represented in SCOP superfamilies in protein loops. We discovered two types of structural motifs significantly over-represented in SCOP superfamilies: (i) ubiquitous motifs, shared by several superfamilies and (ii) superfamily-specific motifs, over-represented in few superfamilies. A comparison of ubiquitous words with known small structural motifs shows that they contain well-described motifs as turn, niche or nest motifs. A comparison between superfamily-specific motifs and biological annotations of Swiss-Prot reveals that some of them actually correspond to functional sites involved in the binding sites of small ligands, such as ATP/GTP, NAD(P) and SAH/SAM. Conclusions Our findings show that statistical over-representation in SCOP superfamilies is linked to functional features. The detection of over-represented motifs within structures simplified by HMM-SA is therefore a promising approach for prediction of functional sites and annotation of uncharacterized proteins. PMID:21689388

Exact deconstruction of the 6D (2,0) theory

NASA Astrophysics Data System (ADS)

Hayling, J.; Papageorgakis, C.; Pomoni, E.; Rodríguez-Gómez, D.

2017-06-01

The dimensional-deconstruction prescription of Arkani-Hamed, Cohen, Kaplan, Karch and Motl provides a mechanism for recovering the A-type (2,0) theories on T 2, starting from a four-dimensional N=2 circular-quiver theory. We put this conjecture to the test using two exact-counting arguments: in the decompactification limit, we compare the Higgs-branch Hilbert series of the 4D N=2 quiver to the "half-BPS" limit of the (2,0) superconformal index. We also compare the full partition function for the 4D quiver on S 4 to the (2,0) partition function on S 4 × T 2. In both cases we find exact agreement. The partition function calculation sets up a dictionary between exact results in 4D and 6D.

Spatial assignment of symmetry adapted perturbation theory interaction energy components: The atomic SAPT partition

NASA Astrophysics Data System (ADS)

Parrish, Robert M.; Sherrill, C. David

2014-07-01

We develop a physically-motivated assignment of symmetry adapted perturbation theory for intermolecular interactions (SAPT) into atom-pairwise contributions (the A-SAPT partition). The basic precept of A-SAPT is that the many-body interaction energy components are computed normally under the formalism of SAPT, following which a spatially-localized two-body quasiparticle interaction is extracted from the many-body interaction terms. For electrostatics and induction source terms, the relevant quasiparticles are atoms, which are obtained in this work through the iterative stockholder analysis (ISA) procedure. For the exchange, induction response, and dispersion terms, the relevant quasiparticles are local occupied orbitals, which are obtained in this work through the Pipek-Mezey procedure. The local orbital atomic charges obtained from ISA additionally allow the terms involving local orbitals to be assigned in an atom-pairwise manner. Further summation over the atoms of one or the other monomer allows for a chemically intuitive visualization of the contribution of each atom and interaction component to the overall noncovalent interaction strength. Herein, we present the intuitive development and mathematical form for A-SAPT applied in the SAPT0 approximation (the A-SAPT0 partition). We also provide an efficient series of algorithms for the computation of the A-SAPT0 partition with essentially the same computational cost as the corresponding SAPT0 decomposition. We probe the sensitivity of the A-SAPT0 partition to the ISA grid and convergence parameter, orbital localization metric, and induction coupling treatment, and recommend a set of practical choices which closes the definition of the A-SAPT0 partition. We demonstrate the utility and computational tractability of the A-SAPT0 partition in the context of side-on cation-π interactions and the intercalation of DNA by proflavine. A-SAPT0 clearly shows the key processes in these complicated noncovalent interactions, in systems with up to 220 atoms and 2845 basis functions.

Spatial assignment of symmetry adapted perturbation theory interaction energy components: The atomic SAPT partition

DOE Office of Scientific and Technical Information (OSTI.GOV)

Parrish, Robert M.; Sherrill, C. David, E-mail: sherrill@gatech.edu

2014-07-28

We develop a physically-motivated assignment of symmetry adapted perturbation theory for intermolecular interactions (SAPT) into atom-pairwise contributions (the A-SAPT partition). The basic precept of A-SAPT is that the many-body interaction energy components are computed normally under the formalism of SAPT, following which a spatially-localized two-body quasiparticle interaction is extracted from the many-body interaction terms. For electrostatics and induction source terms, the relevant quasiparticles are atoms, which are obtained in this work through the iterative stockholder analysis (ISA) procedure. For the exchange, induction response, and dispersion terms, the relevant quasiparticles are local occupied orbitals, which are obtained in this work throughmore » the Pipek-Mezey procedure. The local orbital atomic charges obtained from ISA additionally allow the terms involving local orbitals to be assigned in an atom-pairwise manner. Further summation over the atoms of one or the other monomer allows for a chemically intuitive visualization of the contribution of each atom and interaction component to the overall noncovalent interaction strength. Herein, we present the intuitive development and mathematical form for A-SAPT applied in the SAPT0 approximation (the A-SAPT0 partition). We also provide an efficient series of algorithms for the computation of the A-SAPT0 partition with essentially the same computational cost as the corresponding SAPT0 decomposition. We probe the sensitivity of the A-SAPT0 partition to the ISA grid and convergence parameter, orbital localization metric, and induction coupling treatment, and recommend a set of practical choices which closes the definition of the A-SAPT0 partition. We demonstrate the utility and computational tractability of the A-SAPT0 partition in the context of side-on cation-π interactions and the intercalation of DNA by proflavine. A-SAPT0 clearly shows the key processes in these complicated noncovalent interactions, in systems with up to 220 atoms and 2845 basis functions.« less

The interdigitating loop of the enolase superfamily as a specificity binding determinant or 'flying buttress'.

PubMed

Bearne, Stephen L

2017-05-01

Enzymes of the enolase superfamily (ENS) are mechanistically diverse, yet share a common partial reaction (abstraction of the α-proton from a carboxylate substrate). While the catalytic machinery responsible for the deprotonation reaction has been conserved, divergent evolution has led to numerous ENS members that catalyze different overall reactions. This rich functional diversity has made the ENS an excellent model system for developing the approaches necessary to validate enzyme function. However, enzymes of the ENS also share a common bidomain structure ((β/α) 7 β-barrel domain and α+β capping domain) which makes validation of function from structural information challenging. This review presents a comparative survey of the structural data obtained over the past decade for enzymes from all seven subgroups that comprise the ENS. Of the seven ENS subgroups (enolase, mandelate racemase (MR), muconate lactonizing enzyme, β-methylaspartate ammonia lyase, d-glucarate dehydratase, d-mannonate dehydratase (ManD), and galactarate dehydratase 2), only enzymes of the MR and ManD subgroups exhibit an additional feature of structural complexity-an interdigitating loop. This loop emanates from one protomer of a homodimeric pair and penetrates into the adjacent, symmetry-related protomer to either contribute a binding determinant to the active site of the adjacent protomer, or act as a 'flying buttress' to support residues of the active site. The analysis presented in this review suggests that the interdigitating loop is the only gross structural element that permits functional distinction between ENS subgroups at the tertiary level of protein structure. Copyright © 2017 Elsevier B.V. All rights reserved.

Functional characteristics of a double positive feedback loop coupled with autorepression

NASA Astrophysics Data System (ADS)

Banerjee, Subhasis; Bose, Indrani

2008-12-01

We study the functional characteristics of a two-gene motif consisting of a double positive feedback loop and an autoregulatory negative feedback loop. The motif appears in the gene regulatory network controlling the functional activity of pancreatic β-cells. The model exhibits bistability and hysteresis in appropriate parameter regions. The two stable steady states correspond to low (OFF state) and high (ON state) protein levels, respectively. Using a deterministic approach, we show that the region of bistability increases in extent when the copy number of one of the genes is reduced from 2 to 1. The negative feedback loop has the effect of reducing the size of the bistable region. Loss of a gene copy, brought about by mutations, hampers the normal functioning of the β-cells giving rise to the genetic disorder, maturity-onset diabetes of the young (MODY). The diabetic phenotype makes its appearance when a sizable fraction of the β-cells is in the OFF state. Using stochastic simulation techniques we show that, on reduction of the gene copy number, there is a transition from the monostable ON to the ON state in the bistable region of the parameter space. Fluctuations in the protein levels, arising due to the stochastic nature of gene expression, can give rise to transitions between the ON and OFF states. We show that as the strength of autorepression increases, the ON → OFF state transitions become less probable whereas the reverse transitions are more probable. The implications of the results in the context of the occurrence of MODY are pointed out.

Explaining observed red and blue-shifts using multi-stranded coronal loops

NASA Astrophysics Data System (ADS)

Regnier, S.; Walsh, R. W.; Pearson, J.

2012-03-01

Magnetic plasma loops have been termed the building blocks of the solar atmosphere. However, it must be recognised that if the range of loop structures we can observe do consist of many ''sub-resolution'' elements, then current one-dimensional hydrodynamic models are really only applicable to an individual plasma element or strand. Thus a loop should be viewed is an amalgamation of these strands. They could operate in thermal isolation from one another with a wide range of temperatures occurring across the structural elements. This scenario could occur when the energy release mechanism consists of localised, discrete bursts of energy that are due to small scale reconnection sites within the coronal magnetic field- the nanoflare coronal heating mechanism. These energy bursts occur in a time-dependent manner, distributed along the loop/strand length, giving a heating function that depends on space and time. An important observational discovery with the Hinode/EIS spectrometer is the existence of red and blue-shifts in coronal loops depending on the location of the footpoints (inner or outer parts of the active region), and the temperature of the emission line in which the Doppler shifts are measured. Based on the multi-stranded model developed by Sarkar and Walsh (2008, ApJ, 683, 516), we show that red and blue-shifts exist in different simulated Hinode/EIS passbands: cooler lines (OV-SiVII) being dominated by red-shifts, whilst hotter lines (FeXV-CaXVII) are a combination of both. The distribution of blue-shifts depends on the energy input and not so much on the heating location. Characteristic Doppler shifts generated fit well with observed values. We also simulate the Hinode/EIS rasters to closely compare our simulation with the observations. Even if not statistically significant, loops can have footpoints with opposite Doppler shifts.

Two-loop beam and soft functions for rapidity-dependent jet vetoes

NASA Astrophysics Data System (ADS)

Gangal, Shireen; Gaunt, Jonathan R.; Stahlhofen, Maximilian; Tackmann, Frank J.

2017-02-01

Jet vetoes play an important role in many analyses at the LHC. Traditionally, jet vetoes have been imposed using a restriction on the transverse momentum p Tj of jets. Alternatively, one can also consider jet observables for which p Tj is weighted by a smooth function of the jet rapidity y j that vanishes as | y j | → ∞. Such observables are useful as they provide a natural way to impose a tight veto on central jets but a looser one at forward rapidities. We consider two such rapidity-dependent jet veto observables, T_{Bj} and {T_{Cj} , and compute the required beam and dijet soft functions for the jet-vetoed color-singlet production cross section at two loops. At this order, clustering effects from the jet algorithm become important. The dominant contributions are computed fully analytically while corrections that are subleading in the limit of small jet radii are expressed in terms of finite numerical integrals. Our results enable the full NNLL' resummation and are an important step towards N3LL resummation for cross sections with a T_{Bj} or T_{Cj} jet veto.

Design and Test of a Closed-Loop FES System for Supporting Function of the Hemiparetic Hand Based on Automatic Detection using the Microsoft Kinect sensor.

PubMed

Simonsen, Daniel; Spaich, Erika G; Hansen, John; Andersen, Ole K

2016-10-26

This paper describes the design of a FES system automatically controlled in a closed loop using a Microsoft Kinect sensor, for assisting both cylindrical grasping and hand opening. The feasibility of the system was evaluated in real-time in stroke patients with hand function deficits. A hand function exercise was designed in which the subjects performed an arm and hand exercise in sitting position. The subject had to grasp one of two differently sized cylindrical objects and move it forward or backwards in the sagittal plane. This exercise was performed with each cylinder with and without FES support. Results showed that the stroke patients were able to perform up to 29% more successful grasps when they were assisted by FES. Moreover, the hand grasp-and-hold and hold-and-release durations were shorter for the smaller of the two cylinders. FES was appropriately timed in more than 95% of all trials indicating successful closed loop FES control. Future studies should incorporate options for assisting forward reaching in order to target a larger group of stroke patients.

Principles for computational design of binding antibodies

PubMed Central

Pszolla, M. Gabriele; Lapidoth, Gideon D.; Norn, Christoffer; Dym, Orly; Unger, Tamar; Albeck, Shira; Tyka, Michael D.; Fleishman, Sarel J.

2017-01-01

Natural proteins must both fold into a stable conformation and exert their molecular function. To date, computational design has successfully produced stable and atomically accurate proteins by using so-called “ideal” folds rich in regular secondary structures and almost devoid of loops and destabilizing elements, such as cavities. Molecular function, such as binding and catalysis, however, often demands nonideal features, including large and irregular loops and buried polar interaction networks, which have remained challenging for fold design. Through five design/experiment cycles, we learned principles for designing stable and functional antibody variable fragments (Fvs). Specifically, we (i) used sequence-design constraints derived from antibody multiple-sequence alignments, and (ii) during backbone design, maintained stabilizing interactions observed in natural antibodies between the framework and loops of complementarity-determining regions (CDRs) 1 and 2. Designed Fvs bound their ligands with midnanomolar affinities and were as stable as natural antibodies, despite having >30 mutations from mammalian antibody germlines. Furthermore, crystallographic analysis demonstrated atomic accuracy throughout the framework and in four of six CDRs in one design and atomic accuracy in the entire Fv in another. The principles we learned are general, and can be implemented to design other nonideal folds, generating stable, specific, and precise antibodies and enzymes. PMID:28973872

A microprocessor application to a strapdown laser gyro navigator

NASA Technical Reports Server (NTRS)

Giardina, C.; Luxford, E.

1980-01-01

The replacement of analog circuit control loops for laser gyros (path length control, cross axis temperature compensation loops, dither servo and current regulators) with digital filters residing in microcomputers is addressed. In addition to the control loops, a discussion is given on applying the microprocessor hardware to compensation for coning and skulling motion where simple algorithms are processed at high speeds to compensate component output data (digital pulses) for linear and angular vibration motions. Highlights are given on the methodology and system approaches used in replacing differential equations describing the analog system in terms of the mechanized difference equations of the microprocessor. Standard one for one frequency domain techniques are employed in replacing analog transfer functions by their transform counterparts. Direct digital design techniques are also discussed along with their associated benefits. Time and memory loading analyses are also summarized, as well as signal and microprocessor architecture. Trade offs in algorithm, mechanization, time/memory loading, accuracy, and microprocessor architecture are also given.

Partitioning of Alkali Metal Salts and Boric Acid from Aqueous Phase into the Polyamide Active Layers of Reverse Osmosis Membranes.

PubMed

Wang, Jingbo; Kingsbury, Ryan S; Perry, Lamar A; Coronell, Orlando

2017-02-21

The partition coefficient of solutes into the polyamide active layer of reverse osmosis (RO) membranes is one of the three membrane properties (together with solute diffusion coefficient and active layer thickness) that determine solute permeation. However, no well-established method exists to measure solute partition coefficients into polyamide active layers. Further, the few studies that measured partition coefficients for inorganic salts report values significantly higher than one (∼3-8), which is contrary to expectations from Donnan theory and the observed high rejection of salts. As such, we developed a benchtop method to determine solute partition coefficients into the polyamide active layers of RO membranes. The method uses a quartz crystal microbalance (QCM) to measure the change in the mass of the active layer caused by the uptake of the partitioned solutes. The method was evaluated using several inorganic salts (alkali metal salts of chloride) and a weak acid of common concern in water desalination (boric acid). All partition coefficients were found to be lower than 1, in general agreement with expectations from Donnan theory. Results reported in this study advance the fundamental understanding of contaminant transport through RO membranes, and can be used in future studies to decouple the contributions of contaminant partitioning and diffusion to contaminant permeation.

Reduced functional connectivity within the limbic cortico-striato-thalamo-cortical loop in unmedicated adults with obsessive-compulsive disorder.

PubMed

Posner, Jonathan; Marsh, Rachel; Maia, Tiago V; Peterson, Bradley S; Gruber, Allison; Simpson, H Blair

2014-06-01

Cortico-striato-thalamo-cortical (CSTC) loops project from the cortex to the striatum, then from the striatum to the thalamus via the globus pallidus, and finally from the thalamus back to the cortex again. These loops have been implicated in Obsessive-Compulsive Disorder (OCD) with particular focus on the limbic CSTC loop, which encompasses the orbitofrontal and anterior cingulate cortices, as well as the ventral striatum. Resting state functional-connectivity MRI (rs-fcMRI) studies, which examine temporal correlations in neural activity across brain regions at rest, have examined CSTC loop connectivity in patients with OCD and suggest hyperconnectivity within these loops in medicated adults with OCD. We used rs-fcMRI to examine functional connectivity within CSTC loops in unmedicated adults with OCD (n = 23) versus healthy controls (HCs) (n = 20). Contrary to prior rs-fcMRI studies in OCD patients on medications that report hyperconnectivity in the limbic CSTC loop, we found that compared with HCs, unmedicated OCD participants had reduced connectivity within the limbic CSTC loop. Exploratory analyses revealed that reduced connectivity within the limbic CSTC loop correlated with OCD symptom severity in the OCD group. Our finding of limbic loop hypoconnectivity in unmedicted OCD patients highlights the potential confounding effects of antidepressants on connectivity measures and the value of future examinations of the effects of pharmacological and/or behavioral treatments on limbic CSTC loop connectivity. Copyright © 2013 Wiley Periodicals, Inc.

Faces of matrix models

NASA Astrophysics Data System (ADS)

Morozov, A.

2012-08-01

Partition functions of eigenvalue matrix models possess a number of very different descriptions: as matrix integrals, as solutions to linear and nonlinear equations, as τ-functions of integrable hierarchies and as special-geometry prepotentials, as result of the action of W-operators and of various recursions on elementary input data, as gluing of certain elementary building blocks. All this explains the central role of such matrix models in modern mathematical physics: they provide the basic "special functions" to express the answers and relations between them, and they serve as a dream model of what one should try to achieve in any other field.

Quantum canonical ensemble: A projection operator approach

NASA Astrophysics Data System (ADS)

Magnus, Wim; Lemmens, Lucien; Brosens, Fons

2017-09-01

Knowing the exact number of particles N, and taking this knowledge into account, the quantum canonical ensemble imposes a constraint on the occupation number operators. The constraint particularly hampers the systematic calculation of the partition function and any relevant thermodynamic expectation value for arbitrary but fixed N. On the other hand, fixing only the average number of particles, one may remove the above constraint and simply factorize the traces in Fock space into traces over single-particle states. As is well known, that would be the strategy of the grand-canonical ensemble which, however, comes with an additional Lagrange multiplier to impose the average number of particles. The appearance of this multiplier can be avoided by invoking a projection operator that enables a constraint-free computation of the partition function and its derived quantities in the canonical ensemble, at the price of an angular or contour integration. Introduced in the recent past to handle various issues related to particle-number projected statistics, the projection operator approach proves beneficial to a wide variety of problems in condensed matter physics for which the canonical ensemble offers a natural and appropriate environment. In this light, we present a systematic treatment of the canonical ensemble that embeds the projection operator into the formalism of second quantization while explicitly fixing N, the very number of particles rather than the average. Being applicable to both bosonic and fermionic systems in arbitrary dimensions, transparent integral representations are provided for the partition function ZN and the Helmholtz free energy FN as well as for two- and four-point correlation functions. The chemical potential is not a Lagrange multiplier regulating the average particle number but can be extracted from FN+1 -FN, as illustrated for a two-dimensional fermion gas.

Conformal correlation functions in the Brownian loop soup

NASA Astrophysics Data System (ADS)

Camia, Federico; Gandolfi, Alberto; Kleban, Matthew

2016-01-01

We define and study a set of operators that compute statistical properties of the Brownian loop soup, a conformally invariant gas of random Brownian loops (Brownian paths constrained to begin and end at the same point) in two dimensions. We prove that the correlation functions of these operators have many of the properties of conformal primaries in a conformal field theory, and compute their conformal dimension. The dimensions are real and positive, but have the novel feature that they vary continuously as a periodic function of a real parameter. We comment on the relation of the Brownian loop soup to the free field, and use this relation to establish that the central charge of the loop soup is twice its intensity.

Neuroelectric Tuning of Cortical Oscillations by Apical Dendrites in Loop Circuits

PubMed Central

LaBerge, David; Kasevich, Ray S.

2017-01-01

Bundles of relatively long apical dendrites dominate the neurons that make up the thickness of the cerebral cortex. It is proposed that a major function of the apical dendrite is to produce sustained oscillations at a specific frequency that can serve as a common timing unit for the processing of information in circuits connected to that apical dendrite. Many layer 5 and 6 pyramidal neurons are connected to thalamic neurons in loop circuits. A model of the apical dendrites of these pyramidal neurons has been used to simulate the electric activity of the apical dendrite. The results of that simulation demonstrated that subthreshold electric pulses in these apical dendrites can be tuned to specific frequencies and also can be fine-tuned to narrow bandwidths of less than one Hertz (1 Hz). Synchronous pulse outputs from the circuit loops containing apical dendrites can tune subthreshold membrane oscillations of neurons they contact. When the pulse outputs are finely tuned, they function as a local “clock,” which enables the contacted neurons to synchronously communicate with each other. Thus, a shared tuning frequency can select neurons for membership in a circuit. Unlike layer 6 apical dendrites, layer 5 apical dendrites can produce burst firing in many of their neurons, which increases the amplitude of signals in the neurons they contact. This difference in amplitude of signals serves as basis of selecting a sub-circuit for specialized processing (e.g., sustained attention) within the typically larger layer 6-based circuit. After examining the sustaining of oscillations in loop circuits and the processing of spikes in network circuits, we propose that cortical functioning can be globally viewed as two systems: a loop system and a network system. The loop system oscillations influence the network system’s timing and amplitude of pulse signals, both of which can select circuits that are momentarily dominant in cortical activity. PMID:28659768

Neuroelectric Tuning of Cortical Oscillations by Apical Dendrites in Loop Circuits.

PubMed

LaBerge, David; Kasevich, Ray S

2017-01-01

Bundles of relatively long apical dendrites dominate the neurons that make up the thickness of the cerebral cortex. It is proposed that a major function of the apical dendrite is to produce sustained oscillations at a specific frequency that can serve as a common timing unit for the processing of information in circuits connected to that apical dendrite. Many layer 5 and 6 pyramidal neurons are connected to thalamic neurons in loop circuits. A model of the apical dendrites of these pyramidal neurons has been used to simulate the electric activity of the apical dendrite. The results of that simulation demonstrated that subthreshold electric pulses in these apical dendrites can be tuned to specific frequencies and also can be fine-tuned to narrow bandwidths of less than one Hertz (1 Hz). Synchronous pulse outputs from the circuit loops containing apical dendrites can tune subthreshold membrane oscillations of neurons they contact. When the pulse outputs are finely tuned, they function as a local "clock," which enables the contacted neurons to synchronously communicate with each other. Thus, a shared tuning frequency can select neurons for membership in a circuit. Unlike layer 6 apical dendrites, layer 5 apical dendrites can produce burst firing in many of their neurons, which increases the amplitude of signals in the neurons they contact. This difference in amplitude of signals serves as basis of selecting a sub-circuit for specialized processing (e.g., sustained attention) within the typically larger layer 6-based circuit. After examining the sustaining of oscillations in loop circuits and the processing of spikes in network circuits, we propose that cortical functioning can be globally viewed as two systems: a loop system and a network system. The loop system oscillations influence the network system's timing and amplitude of pulse signals, both of which can select circuits that are momentarily dominant in cortical activity.

Practical deviations from Henry`s law for water/air partitioning of volatile organic compounds

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schabron, J.F.; Rovani, J.F. Jr.

A study was conducted to define parameters relating to the use of a down hole submersible photoionization detector (PID) probe to measure volatile organic compounds (VOCs) in an artificial headspace. The partitioning of toluene and trichloroethylene between water and air was studied as a function of analyte concentration and water temperature. The Henry`s law constant governing this partitioning represents an ideal condition at infinite dilution for a particular temperature. The results show that in practice. this partitioning is far from ideal. Conditions resulting in apparent, practical deviations from Henry`s law include temperature and VOC concentration. Thus, a single value ofmore » Henry`s law constant for a particular VOC such as toluene can provide only an approximation of concentration in the field. Detector response in saturated humidity environments as a function of water temperature and analyte concentration was studied also.« less

Dimerization controls the lipid raft partitioning of uPAR/CD87 and regulates its biological functions

PubMed Central

Cunningham, Orla; Andolfo, Annapaola; Santovito, Maria Lisa; Iuzzolino, Lucia; Blasi, Francesco; Sidenius, Nicolai

2003-01-01

The urokinase-type plasminogen activator receptor (uPAR/CD87) is a glycosylphosphatidylinositol-anchored membrane protein with multiple functions in extracellular proteolysis, cell adhesion, cell migration and proliferation. We now report that cell surface uPAR dimerizes and that dimeric uPAR partitions preferentially to detergent-resistant lipid rafts. Dimerization of uPAR did not require raft partitioning as the lowering of membrane cholesterol failed to reduce dimerization and as a transmembrane uPAR chimera, which does not partition to lipid rafts, also dimerized efficiently. While uPA bound to uPAR independently of its membrane localization and dimerization status, uPA-induced uPAR cleavage was strongly accelerated in lipid rafts. In contrast to uPA, the binding of Vn occurred preferentially to raft- associated dimeric uPAR and was completely blocked by cholesterol depletion. PMID:14609946

Thermodynamic limit of random partitions and dispersionless Toda hierarchy

NASA Astrophysics Data System (ADS)

Takasaki, Kanehisa; Nakatsu, Toshio

2012-01-01

We study the thermodynamic limit of random partition models for the instanton sum of 4D and 5D supersymmetric U(1) gauge theories deformed by some physical observables. The physical observables correspond to external potentials in the statistical model. The partition function is reformulated in terms of the density function of Maya diagrams. The thermodynamic limit is governed by a limit shape of Young diagrams associated with dominant terms in the partition function. The limit shape is characterized by a variational problem, which is further converted to a scalar-valued Riemann-Hilbert problem. This Riemann-Hilbert problem is solved with the aid of a complex curve, which may be thought of as the Seiberg-Witten curve of the deformed U(1) gauge theory. This solution of the Riemann-Hilbert problem is identified with a special solution of the dispersionless Toda hierarchy that satisfies a pair of generalized string equations. The generalized string equations for the 5D gauge theory are shown to be related to hidden symmetries of the statistical model. The prepotential and the Seiberg-Witten differential are also considered.

Invariant measure of the one-loop quantum gravitational backreaction on inflation

NASA Astrophysics Data System (ADS)

Miao, S. P.; Tsamis, N. C.; Woodard, R. P.

2017-06-01

We use dimensional regularization in pure quantum gravity on a de Sitter background to evaluate the one-loop expectation value of an invariant operator which gives the local expansion rate. We show that the renormalization of this nonlocal composite operator can be accomplished using the counterterms of a simple local theory of gravity plus matter, at least at one-loop order. This renormalization completely absorbs the one-loop correction, which accords with the prediction that the lowest secular backreaction should be a two-loop effect.

New epitopes and function of anti-M3 muscarinic acetylcholine receptor antibodies in patients with Sjögren's syndrome

PubMed Central

Tsuboi, H; Matsumoto, I; Wakamatsu, E; Nakamura, Y; Iizuka, M; Hayashi, T; Goto, D; Ito, S; Sumida, T

2010-01-01

M3 muscarinic acetylcholine receptor (M3R) plays a crucial role in the secretion of saliva from salivary glands. It is reported that some patients with Sjögren's syndrome (SS) carried inhibitory autoantibodies against M3R. The purpose of this study is to clarify the epitopes and function of anti-M3R antibodies in SS. We synthesized peptides encoding the extracellular domains of human-M3R including the N-terminal region and the first, second and third extracellular loops. Antibodies against these regions were examined by enzyme-linked immunosorbent assay in sera from 42 SS and 42 healthy controls. For functional analysis, human salivary gland (HSG) cells were preincubated with immunoglobulin G (IgG) separated from sera of anti-M3R antibody-positive SS, -negative SS and controls for 12 h. After loading with Fluo-3, HSG cells were stimulated with cevimeline hydrochloride, and intracellular Ca2+ concentrations [(Ca2+)i] were measured. Antibodies to the N-terminal, first, second and third loops were detected in 42·9% (18 of 42), 47·6% (20 of 42), 54·8% (23 of 42) and 45·2% (19 of 42) of SS, while in 4·8% (two of 42), 7·1% (three of 42), 2·4% (one of 42) and 2·4% (one of 42) of controls, respectively. Antibodies to the second loop positive SS-IgG inhibited the increase of (Ca2+)i induced by cevimeline hydrochloride. Antibodies to the N-terminal positive SS-IgG and antibodies to the first loop positive SS-IgG enhanced it, while antibodies to the third loop positive SS-IgG showed no effect on (Ca2+)i as well as anti-M3R antibody-negative SS-IgG. Our results indicated the presence of several B cell epitopes on M3R in SS. The influence of anti-M3R antibodies on salivary secretion might differ based on these epitopes. PMID:20731676

New epitopes and function of anti-M3 muscarinic acetylcholine receptor antibodies in patients with Sjögren's syndrome.

PubMed

Tsuboi, H; Matsumoto, I; Wakamatsu, E; Nakamura, Y; Iizuka, M; Hayashi, T; Goto, D; Ito, S; Sumida, T

2010-10-01

M3 muscarinic acetylcholine receptor (M3R) plays a crucial role in the secretion of saliva from salivary glands. It is reported that some patients with Sjögren's syndrome (SS) carried inhibitory autoantibodies against M3R. The purpose of this study is to clarify the epitopes and function of anti-M3R antibodies in SS. We synthesized peptides encoding the extracellular domains of human-M3R including the N-terminal region and the first, second and third extracellular loops. Antibodies against these regions were examined by enzyme-linked immunosorbent assay in sera from 42 SS and 42 healthy controls. For functional analysis, human salivary gland (HSG) cells were preincubated with immunoglobulin G (IgG) separated from sera of anti-M3R antibody-positive SS, -negative SS and controls for 12 h. After loading with Fluo-3, HSG cells were stimulated with cevimeline hydrochloride, and intracellular Ca(2+) concentrations [(Ca(2+) )i] were measured. Antibodies to the N-terminal, first, second and third loops were detected in 42·9% (18 of 42), 47·6% (20 of 42), 54·8% (23 of 42) and 45·2% (19 of 42) of SS, while in 4·8% (two of 42), 7·1% (three of 42), 2·4% (one of 42) and 2·4% (one of 42) of controls, respectively. Antibodies to the second loop positive SS-IgG inhibited the increase of (Ca(2+) )i induced by cevimeline hydrochloride. Antibodies to the N-terminal positive SS-IgG and antibodies to the first loop positive SS-IgG enhanced it, while antibodies to the third loop positive SS-IgG showed no effect on (Ca(2+) )i as well as anti-M3R antibody-negative SS-IgG. Our results indicated the presence of several B cell epitopes on M3R in SS. The influence of anti-M3R antibodies on salivary secretion might differ based on these epitopes. © 2010 The Authors. Clinical and Experimental Immunology © 2010 British Society for Immunology.

Solution nuclear magnetic resonance analyses of the anticodon arms of proteinogenic and nonproteinogenic tRNA(Gly).

PubMed

Chang, Andrew T; Nikonowicz, Edward P

2012-05-01

Although the fate of most tRNA molecules in the cell is aminoacylation and delivery to the ribosome, some tRNAs are destined to fulfill other functional roles. In addition to their central role in translation, tRNA molecules participate in processes such as regulation of gene expression, bacterial cell wall biosynthesis, viral replication, antibiotic biosynthesis, and suppression of alternative splicing. In bacteria, glycyl-tRNA molecules with anticodon sequences GCC and UCC exhibit multiple extratranslational functions, including transcriptional regulation and cell wall biosynthesis. We have determined the high-resolution structures of three glycyl-tRNA anticodon arms with anticodon sequences GCC and UCC. Two of the tRNA molecules are proteinogenic (tRNA(Gly,GCC) and tRNA(Gly,UCC)), and the third is nonproteinogenic (np-tRNA(Gly,UCC)) and participates in cell wall biosynthesis. The UV-monitored thermal melting curves show that the anticodon arm of tRNA(Gly,UCC) with a loop-closing C-A(+) base pair melts at a temperature 10 °C lower than those of tRNA(Gly,GCC) and np-tRNA(Gly,UCC). U-A and C-G pairs close the loops of the latter two molecules and enhance stem stability. Mg(2+) stabilizes the tRNA(Gly,UCC) anticodon arm and reduces the T(m) differential. The structures of the three tRNA(Gly) anticodon arms exhibit small differences among one another, but none of them form the classical U-turn motif. The anticodon loop of tRNA(Gly,GCC) becomes more dynamic and disordered in the presence of multivalent cations, whereas metal ion coordination in the anticodon loops of tRNA(Gly,UCC) and np-tRNA(Gly,UCC) establishes conformational homogeneity. The conformational similarity of the molecules is greater than their functional differences might suggest. Because aminoacylation of full-length tRNA molecules is accomplished by one tRNA synthetase, the similar structural context of the loop may facilitate efficient recognition of each of the anticodon sequences.

Modeling Cooperative Threads to Project GPU Performance for Adaptive Parallelism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meng, Jiayuan; Uram, Thomas; Morozov, Vitali A.

Most accelerators, such as graphics processing units (GPUs) and vector processors, are particularly suitable for accelerating massively parallel workloads. On the other hand, conventional workloads are developed for multi-core parallelism, which often scale to only a few dozen OpenMP threads. When hardware threads significantly outnumber the degree of parallelism in the outer loop, programmers are challenged with efficient hardware utilization. A common solution is to further exploit the parallelism hidden deep in the code structure. Such parallelism is less structured: parallel and sequential loops may be imperfectly nested within each other, neigh boring inner loops may exhibit different concurrency patternsmore » (e.g. Reduction vs. Forall), yet have to be parallelized in the same parallel section. Many input-dependent transformations have to be explored. A programmer often employs a larger group of hardware threads to cooperatively walk through a smaller outer loop partition and adaptively exploit any encountered parallelism. This process is time-consuming and error-prone, yet the risk of gaining little or no performance remains high for such workloads. To reduce risk and guide implementation, we propose a technique to model workloads with limited parallelism that can automatically explore and evaluate transformations involving cooperative threads. Eventually, our framework projects the best achievable performance and the most promising transformations without implementing GPU code or using physical hardware. We envision our technique to be integrated into future compilers or optimization frameworks for autotuning.« less

Monochromatic Transmittance/Radiance Computations

DTIC Science & Technology

1974-12-31

In the infrared region, these tran- sitions are normally between various vibration -rotation states. There are usually a large number of possible...energy level of the transition, and Q (e,m.) and Q (0,m.) are respectively the ratio of the vibrational and rotational partition function at...values used are listed in Table 2 (Ref. 2). For source conditions, the vibrational partition function cannot be ignored and has been calculated 4

Phase diagram of q-deformed Yang-Mills theory on S 2 at non-zero θ-angle

NASA Astrophysics Data System (ADS)

Okuyama, Kazumi

2018-04-01

We study the phase diagram of q-deformed Yang-Mills theory on S 2 at non-zero θ-angle using the exact partition function at finite N . By evaluating the exact partition function numerically, we find evidence for the existence of a series of phase transitions at non-zero θ-angle as conjectured in [hep-th/0509004

GPS/INS integration by functional partitioning

NASA Astrophysics Data System (ADS)

Diesel, John W.

It is shown that a GPS/INS system integrated by functional partitioning can satisfy all of the RTCA navigation requirements and goals. This is accomplished by accurately calibrating the INS using GPS after the inertial instruments are thermally stabilized and by exploiting the very slow subsequent error growth in the INS information. In this way, autonomous integrity monitoring can be achieved using only existing or presently planned systems.

Companion Chip: Building a Segregated Hardware Architecture

NASA Astrophysics Data System (ADS)

Pareaud, Thomas; Houelle, Alain; Vaucher, Niolas; Albinet, Mathieu; Honvault, Christophe

2011-08-01

Partitioning is a more and more mature concept in Space industry. It aims at assuring that some error propagation modes are not possible. This paper gives an overview of an analysis conducted in the frame of a research and technology study performed in 2010/2011. The "Java Companion Chip" study addresses an interesting approach to partitioning using hardware concepts: a SoC architecture integrates a master processor, a companion chip and additional hardware functions aiming at enforcing the time and space segregation between the master processor and the slave one.This paper discusses the benefits and the main challenges of the proposed approach. In addition, it presents an application of these concepts to a case study: a Leon/Java processor architecture able to concurrently execute native and Java applications.

Experimental study of histological changes in vascular loops according to the duration of the postoperative period: Application in reconstructive microsurgery

PubMed Central

Paulos, Renata Gregorio; Rudelli, Bruno Alves; Filippe, Renee Zon; dos Santos, Gustavo Bispo; Herrera, Ana Abarca; Ribeiro, Andre Araujo; de Rezende, Marcelo Rosa; Hsiang-Wei, Teng; Mattar-Jr, Rames

2017-01-01

OBJECTIVES: To analyze the histological changes observed in venous grafts subjected to arterial blood flow as a function of the duration of the postoperative period to optimize their use in free flap reconstructions. METHOD: Twenty-five rats (7 females and 18 males) underwent surgery. Surgeries were performed on one animal per week. Five weeks after the first surgery, the same five animals were subjected to an additional surgery to assess the presence or absence of blood flow through the vascular loop, and samples were collected for histological analysis. This cycle was performed five times. RESULTS: Of the rats euthanized four to five weeks after the first surgery, no blood flow was observed through the graft in 80% of the cases. In the group euthanized three weeks after the first surgery, no blood flow was observed in 20% of the cases. In the groups euthanized one to two weeks after the first surgery, blood flow through the vascular loop was observed in all animals. Moreover, intimal proliferation tended to increase with the duration of the postoperative period. Two weeks after surgery, intimal proliferation increased slightly, whereas strong intimal proliferation was observed in all rats evaluated five weeks after surgery. CONCLUSION: Intimal proliferation was the most significant change noted in venous grafts as a function of the duration of the postoperative period and was directly correlated with graft occlusion. In cases in which vascular loops are required during free flap reconstruction, both procedures should preferably be performed during the same surgery. PMID:29069256

Experimental study of histological changes in vascular loops according to the duration of the postoperative period: Application in reconstructive microsurgery.

PubMed

Paulos, Renata Gregorio; Rudelli, Bruno Alves; Filippe, Renee Zon; Dos Santos, Gustavo Bispo; Herrera, Ana Abarca; Ribeiro, Andre Araujo; de Rezende, Marcelo Rosa; Hsiang-Wei, Teng; Mattar, Rames

2017-10-01

To analyze the histological changes observed in venous grafts subjected to arterial blood flow as a function of the duration of the postoperative period to optimize their use in free flap reconstructions. Twenty-five rats (7 females and 18 males) underwent surgery. Surgeries were performed on one animal per week. Five weeks after the first surgery, the same five animals were subjected to an additional surgery to assess the presence or absence of blood flow through the vascular loop, and samples were collected for histological analysis. This cycle was performed five times. Of the rats euthanized four to five weeks after the first surgery, no blood flow was observed through the graft in 80% of the cases. In the group euthanized three weeks after the first surgery, no blood flow was observed in 20% of the cases. In the groups euthanized one to two weeks after the first surgery, blood flow through the vascular loop was observed in all animals. Moreover, intimal proliferation tended to increase with the duration of the postoperative period. Two weeks after surgery, intimal proliferation increased slightly, whereas strong intimal proliferation was observed in all rats evaluated five weeks after surgery. Intimal proliferation was the most significant change noted in venous grafts as a function of the duration of the postoperative period and was directly correlated with graft occlusion. In cases in which vascular loops are required during free flap reconstruction, both procedures should preferably be performed during the same surgery.

Endogenous fatty acids in olfactory hairs influence pheromone binding protein structure and function in Lymantria dispar.

PubMed

Nardella, Jason; Terrado, Mailyn; Honson, Nicolette S; Plettner, Erika

2015-08-01

The gypsy moth utilizes a pheromone, (7R,8S)-2-methyl-7,8-epoxyoctadecane, for mate location. The pheromone is detected by sensory hairs (sensilla) on the antennae of adult males. Sensilla contain the dendrites of olfactory neurons bathed in lymph, which contains pheromone binding proteins (PBPs). We have extracted and identified free fatty acids from lymph of sensory hairs, and we demonstrate that these function as endogenous ligands for gypsy moth PBP1 and PBP2. Homology modeling of both PBPs, and docking of fatty acids reveal multiple binding sites: one internal, the others external. Pheromone binding assays suggest that these fatty acids increase PBP-pheromone binding affinity. We show that fatty acid binding causes an increase in α-helix content in the N-terminal domain, but not in the C-terminal peptide of both proteins. The C-terminal peptide was shown to form a α-helix in a hydrophobic, homogeneous environment, but not in the presence of fatty acid micelles. Through partition assays we show that the fatty acids prevent adsorption of the pheromone on hydrophobic surfaces and facilitate pheromone partition into an aqueous phase. We propose that lymph is an emulsion of fatty acids and PBP that influence each other and thereby control the partition equilibria of hydrophobic odorants. Copyright © 2015 Elsevier Inc. All rights reserved.

Resolving anatomical and functional structure in human brain organization: identifying mesoscale organization in weighted network representations.

PubMed

Lohse, Christian; Bassett, Danielle S; Lim, Kelvin O; Carlson, Jean M

2014-10-01

Human brain anatomy and function display a combination of modular and hierarchical organization, suggesting the importance of both cohesive structures and variable resolutions in the facilitation of healthy cognitive processes. However, tools to simultaneously probe these features of brain architecture require further development. We propose and apply a set of methods to extract cohesive structures in network representations of brain connectivity using multi-resolution techniques. We employ a combination of soft thresholding, windowed thresholding, and resolution in community detection, that enable us to identify and isolate structures associated with different weights. One such mesoscale structure is bipartivity, which quantifies the extent to which the brain is divided into two partitions with high connectivity between partitions and low connectivity within partitions. A second, complementary mesoscale structure is modularity, which quantifies the extent to which the brain is divided into multiple communities with strong connectivity within each community and weak connectivity between communities. Our methods lead to multi-resolution curves of these network diagnostics over a range of spatial, geometric, and structural scales. For statistical comparison, we contrast our results with those obtained for several benchmark null models. Our work demonstrates that multi-resolution diagnostic curves capture complex organizational profiles in weighted graphs. We apply these methods to the identification of resolution-specific characteristics of healthy weighted graph architecture and altered connectivity profiles in psychiatric disease.

Development of a floating photobioreactor with internal partitions for efficient utilization of ocean wave into improved mass transfer and algal culture mixing.

PubMed

Kim, Z-Hun; Park, Hanwool; Hong, Seong-Joo; Lim, Sang-Min; Lee, Choul-Gyun

2016-05-01

Culturing microalgae in the ocean has potentials that may reduce the production cost and provide an option for an economic biofuel production from microalgae. The ocean holds great potentials for mass microalgal cultivation with its high specific heat, mixing energy from waves, and large cultivable area. Suitable photobioreactors (PBRs) that are capable of integrating marine energy into the culture systems need to be developed for the successful ocean cultivation. In this study, prototype floating PBRs were designed and constructed using transparent low-density polyethylene film for microalgal culture in the ocean. To improve the mixing efficiency, various types of internal partitions were introduced within PBRs. Three different types of internal partitions were evaluated for their effects on the mixing efficiency in terms of mass transfer (k(L)a) and mixing time in the PBRs. The partition type with the best mixing efficiency was selected, and the number of partitions was varied from one to three for investigation of its effect on mixing efficiency. When the number of partitions is increased, mass transfer increased in proportion to the number of partitions. However, mixing time was not directly related to the number of partitions. When a green microalga, Tetraselmis sp. was cultivated using PBRs with the selected partition under semi-continuous mode in the ocean, biomass and fatty acid productivities in the PBRs were increased by up to 50 % and 44% at high initial cell density, respectively, compared to non-partitioned ones. The results of internally partitioned PBRs demonstrated potentials for culturing microalgae by efficiently utilizing ocean wave energy into culture mixing in the ocean.

Intelligent robust tracking control for a class of uncertain strict-feedback nonlinear systems.

PubMed

Chang, Yeong-Chan

2009-02-01

This paper addresses the problem of designing robust tracking controls for a large class of strict-feedback nonlinear systems involving plant uncertainties and external disturbances. The input and virtual input weighting matrices are perturbed by bounded time-varying uncertainties. An adaptive fuzzy-based (or neural-network-based) dynamic feedback tracking controller will be developed such that all the states and signals of the closed-loop system are bounded and the trajectory tracking error should be as small as possible. First, the adaptive approximators with linearly parameterized models are designed, and a partitioned procedure with respect to the developed adaptive approximators is proposed such that the implementation of the fuzzy (or neural network) basis functions depends only on the state variables but does not depend on the tuning approximation parameters. Furthermore, we extend to design the nonlinearly parameterized adaptive approximators. Consequently, the intelligent robust tracking control schemes developed in this paper possess the properties of computational simplicity and easy implementation. Finally, simulation examples are presented to demonstrate the effectiveness of the proposed control algorithms.

A fast object-oriented Matlab implementation of the Reproducing Kernel Particle Method

NASA Astrophysics Data System (ADS)

Barbieri, Ettore; Meo, Michele

2012-05-01

Novel numerical methods, known as Meshless Methods or Meshfree Methods and, in a wider perspective, Partition of Unity Methods, promise to overcome most of disadvantages of the traditional finite element techniques. The absence of a mesh makes meshfree methods very attractive for those problems involving large deformations, moving boundaries and crack propagation. However, meshfree methods still have significant limitations that prevent their acceptance among researchers and engineers, namely the computational costs. This paper presents an in-depth analysis of computational techniques to speed-up the computation of the shape functions in the Reproducing Kernel Particle Method and Moving Least Squares, with particular focus on their bottlenecks, like the neighbour search, the inversion of the moment matrix and the assembly of the stiffness matrix. The paper presents numerous computational solutions aimed at a considerable reduction of the computational times: the use of kd-trees for the neighbour search, sparse indexing of the nodes-points connectivity and, most importantly, the explicit and vectorized inversion of the moment matrix without using loops and numerical routines.

Evolution and Design Governing Signal Precision and Amplification in a Bacterial Chemosensory Pathway

PubMed Central

Espinosa, Leon; Baronian, Grégory; Molle, Virginie; Mauriello, Emilia M. F.; Brochier-Armanet, Céline; Mignot, Tâm

2015-01-01

Understanding the principles underlying the plasticity of signal transduction networks is fundamental to decipher the functioning of living cells. In Myxococcus xanthus, a particular chemosensory system (Frz) coordinates the activity of two separate motility systems (the A- and S-motility systems), promoting multicellular development. This unusual structure asks how signal is transduced in a branched signal transduction pathway. Using combined evolution-guided and single cell approaches, we successfully uncoupled the regulations and showed that the A-motility regulation system branched-off an existing signaling system that initially only controlled S-motility. Pathway branching emerged in part following a gene duplication event and changes in the circuit structure increasing the signaling efficiency. In the evolved pathway, the Frz histidine kinase generates a steep biphasic response to increasing external stimulations, which is essential for signal partitioning to the motility systems. We further show that this behavior results from the action of two accessory response regulator proteins that act independently to filter and amplify signals from the upstream kinase. Thus, signal amplification loops may underlie the emergence of new connectivity in signal transduction pathways. PMID:26291327

THE CORONAL LOOP INVENTORY PROJECT: EXPANDED ANALYSIS AND RESULTS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schmelz, J. T.; Christian, G. M.; Chastain, R. A., E-mail: jschmelz@usra.edu

We have expanded upon earlier work that investigates the relative importance of coronal loops with isothermal versus multithermal cross-field temperature distributions. These results are important for determining if loops have substructure in the form of unresolved magnetic strands. We have increased the number of loops targeted for temperature analysis from 19 to 207 with the addition of 188 new loops from multiple regions. We selected all loop segments visible in the 171 Å images of the Atmospheric Imaging Assembly (AIA) that had a clean background. Eighty-six of the new loops were rejected because they could not be reliably separated frommore » the background in other AIA filters. Sixty-one loops required multithermal models to reproduce the observations. Twenty-eight loops were effectively isothermal, that is, the plasma emission to which AIA is sensitive could not be distinguished from isothermal emission, within uncertainties. Ten loops were isothermal. Also, part of our inventory was one small flaring loop, one very cool loop whose temperature distribution could not be constrained by the AIA data, and one loop with inconclusive results. Our survey can confirm an unexpected result from the pilot study: we found no isothermal loop segments where we could properly use the 171-to-193 ratio method, which would be similar to the analysis done for many loops observed with TRACE and EIT. We recommend caution to observers who assume the loop plasma is isothermal, and hope that these results will influence the direction of coronal heating models and the effort modelers spend on various heating scenarios.« less

The haloarchaeal MCM proteins: bioinformatic analysis and targeted mutagenesis of the β7-β8 and β9-β10 hairpin loops and conserved zinc binding domain cysteines.

PubMed

Kristensen, Tatjana P; Maria Cherian, Reeja; Gray, Fiona C; MacNeill, Stuart A

2014-01-01

The hexameric MCM complex is the catalytic core of the replicative helicase in eukaryotic and archaeal cells. Here we describe the first in vivo analysis of archaeal MCM protein structure and function relationships using the genetically tractable haloarchaeon Haloferax volcanii as a model system. Hfx. volcanii encodes a single MCM protein that is part of the previously identified core group of haloarchaeal MCM proteins. Three structural features of the N-terminal domain of the Hfx. volcanii MCM protein were targeted for mutagenesis: the β7-β8 and β9-β10 β-hairpin loops and putative zinc binding domain. Five strains carrying single point mutations in the β7-β8 β-hairpin loop were constructed, none of which displayed impaired cell growth under normal conditions or when treated with the DNA damaging agent mitomycin C. However, short sequence deletions within the β7-β8 β-hairpin were not tolerated and neither was replacement of the highly conserved residue glutamate 187 with alanine. Six strains carrying paired alanine substitutions within the β9-β10 β-hairpin loop were constructed, leading to the conclusion that no individual amino acid within that hairpin loop is absolutely required for MCM function, although one of the mutant strains displays greatly enhanced sensitivity to mitomycin C. Deletions of two or four amino acids from the β9-β10 β-hairpin were tolerated but mutants carrying larger deletions were inviable. Similarly, it was not possible to construct mutants in which any of the conserved zinc binding cysteines was replaced with alanine, underlining the likely importance of zinc binding for MCM function. The results of these studies demonstrate the feasibility of using Hfx. volcanii as a model system for reverse genetic analysis of archaeal MCM protein function and provide important confirmation of the in vivo importance of conserved structural features identified by previous bioinformatic, biochemical and structural studies.

River rating complexity

USGS Publications Warehouse

Holmes, Robert R.

2016-01-01

Accuracy of streamflow data depends on the veracity of the rating model used to derive a continuous time series of discharge from the surrogate variables that can readily be collected autonomously at a streamgage. Ratings are typically represented as a simple monotonic increasing function (simple rating), meaning the discharge is a function of stage alone, however this is never truly the case unless the flow is completely uniform at all stages and in transitions from one stage to the next. For example, at some streamflow-monitoring sites the discharge on the rising limb of the hydrograph is discernably larger than the discharge at the same stage on the falling limb of the hydrograph. This is the so-called “loop rating curve” (loop rating). In many cases, these loops are quite small and variation between rising- and falling-limb discharge measurements made at the same stage are well within the accuracy of the measurements. However, certain hydraulic conditions can produce a loop that is large enough to preclude use of a monotonic rating. A detailed data campaign for the Mississippi River at St. Louis, Missouri during a multi-peaked flood over a 56-day period in 2015 demonstrates the rating complexity at this location. The shifting-control method used to deal with complexity at this site matched all measurements within 8%.

STRUCTURAL DYNAMICS OF METAL PARTITIONING TO MINERAL SURFACES

EPA Science Inventory

The conceptual understanding of surface complexation reactions that control trace element partitioning to mineral surfaces is limited by the assumption that the solid reactant possesses a finite, time-invariant population of surface functional groups. This assumption has limited...

Systems and methods to control multiple peripherals with a single-peripheral application code

DOEpatents

Ransom, Ray M.

2013-06-11

Methods and apparatus are provided for enhancing the BIOS of a hardware peripheral device to manage multiple peripheral devices simultaneously without modifying the application software of the peripheral device. The apparatus comprises a logic control unit and a memory in communication with the logic control unit. The memory is partitioned into a plurality of ranges, each range comprising one or more blocks of memory, one range being associated with each instance of the peripheral application and one range being reserved for storage of a data pointer related to each peripheral application of the plurality. The logic control unit is configured to operate multiple instances of the control application by duplicating one instance of the peripheral application for each peripheral device of the plurality and partitioning a memory device into partitions comprising one or more blocks of memory, one partition being associated with each instance of the peripheral application. The method then reserves a range of memory addresses for storage of a data pointer related to each peripheral device of the plurality, and initializes each of the plurality of peripheral devices.

Protein Phosphatase 1 inactivates Mps1 to ensure efficient Spindle Assembly Checkpoint silencing.

PubMed

Moura, Margarida; Osswald, Mariana; Leça, Nelson; Barbosa, João; Pereira, António J; Maiato, Helder; Sunkel, Claudio E; Conde, Carlos

2017-05-02

Faithfull genome partitioning during cell division relies on the Spindle Assembly Checkpoint (SAC), a conserved signaling pathway that delays anaphase onset until all chromosomes are attached to spindle microtubules. Mps1 kinase is an upstream SAC regulator that promotes the assembly of an anaphase inhibitor through a sequential multi-target phosphorylation cascade. Thus, the SAC is highly responsive to Mps1, whose activity peaks in early mitosis as a result of its T-loop autophosphorylation. However, the mechanism controlling Mps1 inactivation once kinetochores attach to microtubules and the SAC is satisfied remains unknown. Here we show in vitro and in Drosophila that Protein Phosphatase 1 (PP1) inactivates Mps1 by dephosphorylating its T-loop. PP1-mediated dephosphorylation of Mps1 occurs at kinetochores and in the cytosol, and inactivation of both pools of Mps1 during metaphase is essential to ensure prompt and efficient SAC silencing. Overall, our findings uncover a mechanism of SAC inactivation required for timely mitotic exit.

Loop-loop interactions govern multiple steps in indole-3-glycerol phosphate synthase catalysis

PubMed Central

Zaccardi, Margot J; O'Rourke, Kathleen F; Yezdimer, Eric M; Loggia, Laura J; Woldt, Svenja; Boehr, David D

2014-01-01

Substrate binding, product release, and likely chemical catalysis in the tryptophan biosynthetic enzyme indole-3-glycerol phosphate synthase (IGPS) are dependent on the structural dynamics of the β1α1 active-site loop. Statistical coupling analysis and molecular dynamic simulations had previously indicated that covarying residues in the β1α1 and β2α2 loops, corresponding to Arg54 and Asn90, respectively, in the Sulfolobus sulfataricus enzyme (ssIGPS), are likely important for coordinating functional motions of these loops. To test this hypothesis, we characterized site mutants at these positions for changes in catalytic function, protein stability and structural dynamics for the thermophilic ssIGPS enzyme. Although there were only modest changes in the overall steady-state kinetic parameters, solvent viscosity and solvent deuterium kinetic isotope effects indicated that these amino acid substitutions change the identity of the rate-determining step across multiple temperatures. Surprisingly, the N90A substitution had a dramatic effect on the general acid/base catalysis of the dehydration step, as indicated by the loss of the descending limb in the pH rate profile, which we had previously assigned to Lys53 on the β1α1 loop. These changes in enzyme function are accompanied with a quenching of ps-ns and µs-ms timescale motions in the β1α1 loop as measured by nuclear magnetic resonance studies. Altogether, our studies provide structural, dynamic and functional rationales for the coevolution of residues on the β1α1 and β2α2 loops, and highlight the multiple roles that the β1α1 loop plays in IGPS catalysis. Thus, substitution of covarying residues in the active-site β1α1 and β2α2 loops of indole-3-glycerol phosphate synthase results in functional, structural, and dynamic changes, highlighting the multiple roles that the β1α1 loop plays in enzyme catalysis and the importance of regulating the structural dynamics of this loop through noncovalent interactions with nearby structural elements. PMID:24403092

Viable inflationary evolution from Einstein frame loop quantum cosmology

NASA Astrophysics Data System (ADS)

de Haro, Jaume; Odintsov, S. D.; Oikonomou, V. K.

2018-04-01

In this work we construct a bottom-up reconstruction technique for loop quantum cosmology scalar-tensor theories, from the observational indices. Particularly, the reconstruction technique is based on fixing the functional form of the scalar-to-tensor ratio as a function of the e -foldings number. The aim of the technique is to realize viable inflationary scenarios, and the only assumption that must hold true in order for the reconstruction technique to work is that the dynamical evolution of the scalar field obeys the slow-roll conditions. We use two functional forms for the scalar-to-tensor ratio, one of which corresponds to a popular inflationary class of models, the α attractors. For the latter, we calculate the leading order behavior of the spectral index and we demonstrate that the resulting inflationary theory is viable and compatible with the latest Planck and BICEP2/Keck-Array data. In addition, we find the classical limit of the theory, and as we demonstrate, the loop quantum cosmology corrected theory and the classical theory are identical at leading order in the perturbative expansion quantified by the parameter ρc, which is the critical density of the quantum theory. Finally, by using the formalism of slow-roll scalar-tensor loop quantum cosmology, we investigate how several inflationary potentials can be realized by the quantum theory, and we calculate directly the slow-roll indices and the corresponding observational indices. In addition, the f (R ) gravity frame picture is presented.

Disturbed neuronal ER-Golgi sorting of unassembled glycine receptors suggests altered subcellular processing is a cause of human hyperekplexia.

PubMed

Schaefer, Natascha; Kluck, Christoph J; Price, Kerry L; Meiselbach, Heike; Vornberger, Nadine; Schwarzinger, Stephan; Hartmann, Stephanie; Langlhofer, Georg; Schulz, Solveig; Schlegel, Nadja; Brockmann, Knut; Lynch, Bryan; Becker, Cord-Michael; Lummis, Sarah C R; Villmann, Carmen

2015-01-07

Recent studies on the pathogenic mechanisms of recessive hyperekplexia indicate disturbances in glycine receptor (GlyR) α1 biogenesis. Here, we examine the properties of a range of novel glycine receptor mutants identified in human hyperekplexia patients using expression in transfected cell lines and primary neurons. All of the novel mutants localized in the large extracellular domain of the GlyR α1 have reduced cell surface expression with a high proportion of receptors being retained in the ER, although there is forward trafficking of glycosylated subpopulations into the ER-Golgi intermediate compartment and cis-Golgi compartment. CD spectroscopy revealed that the mutant receptors have proportions of secondary structural elements similar to wild-type receptors. Two mutants in loop B (G160R, T162M) were functional, but none of those in loop D/β2-3 were. One nonfunctional truncated mutant (R316X) could be rescued by coexpression with the lacking C-terminal domain. We conclude that a proportion of GlyR α1 mutants can be transported to the plasma membrane but do not necessarily form functional ion channels. We suggest that loop D/β2-3 is an important determinant for GlyR trafficking and functionality, whereas alterations to loop B alter agonist potencies, indicating that residues here are critical elements in ligand binding. Copyright © 2015 the authors 0270-6474/15/350422-16$15.00/0.

Possibility-based robust design optimization for the structural-acoustic system with fuzzy parameters

NASA Astrophysics Data System (ADS)

Yin, Hui; Yu, Dejie; Yin, Shengwen; Xia, Baizhan

2018-03-01

The conventional engineering optimization problems considering uncertainties are based on the probabilistic model. However, the probabilistic model may be unavailable because of the lack of sufficient objective information to construct the precise probability distribution of uncertainties. This paper proposes a possibility-based robust design optimization (PBRDO) framework for the uncertain structural-acoustic system based on the fuzzy set model, which can be constructed by expert opinions. The objective of robust design is to optimize the expectation and variability of system performance with respect to uncertainties simultaneously. In the proposed PBRDO, the entropy of the fuzzy system response is used as the variability index; the weighted sum of the entropy and expectation of the fuzzy response is used as the objective function, and the constraints are established in the possibility context. The computations for the constraints and objective function of PBRDO are a triple-loop and a double-loop nested problem, respectively, whose computational costs are considerable. To improve the computational efficiency, the target performance approach is introduced to transform the calculation of the constraints into a double-loop nested problem. To further improve the computational efficiency, a Chebyshev fuzzy method (CFM) based on the Chebyshev polynomials is proposed to estimate the objective function, and the Chebyshev interval method (CIM) is introduced to estimate the constraints, thereby the optimization problem is transformed into a single-loop one. Numerical results on a shell structural-acoustic system verify the effectiveness and feasibility of the proposed methods.

Evidence for equivalence of diffusion processes of passive scalar and magnetic fields in anisotropic Navier-Stokes turbulence.

PubMed

Jurčišinová, E; Jurčišin, M

2017-05-01

The influence of the uniaxial small-scale anisotropy on the kinematic magnetohydrodynamic turbulence is investigated by using the field theoretic renormalization group technique in the one-loop approximation of a perturbation theory. The infrared stable fixed point of the renormalization group equations, which drives the scaling properties of the model in the inertial range, is investigated as the function of the anisotropy parameters and it is shown that, at least at the one-loop level of approximation, the diffusion processes of the weak passive magnetic field in the anisotropically driven kinematic magnetohydrodynamic turbulence are completely equivalent to the corresponding diffusion processes of passively advected scalar fields in the anisotropic Navier-Stokes turbulent environments.

Filter for third order phase locked loops

NASA Technical Reports Server (NTRS)

Crow, R. B.; Tausworthe, R. C. (Inventor)

1973-01-01

Filters for third-order phase-locked loops are used in receivers to acquire and track carrier signals, particularly signals subject to high doppler-rate changes in frequency. A loop filter with an open-loop transfer function and set of loop constants, setting the damping factor equal to unity are provided.

High-temperature asymptotics of supersymmetric partition functions

DOE PAGES

Ardehali, Arash Arabi

2016-07-05

We study the supersymmetric partition function of 4d supersymmetric gauge theories with a U(1) R-symmetry on Euclidean S 3 × S β 1, with S 3 the unit-radius squashed three-sphere, and β the circumference of the circle. For superconformal theories, this partition function coincides (up to a Casimir energy factor) with the 4d superconformal index. The partition function can be computed exactly using the supersymmetric localization of the gauge theory path-integral. It takes the form of an elliptic hypergeometric integral, which may be viewed as a matrix-integral over the moduli space of the holonomies of the gauge fields around Smore » β 1. At high temperatures (β → 0, corresponding to the hyperbolic limit of the elliptic hypergeometric integral) we obtain from the matrix-integral a quantum effective potential for the holonomies. The effective potential is proportional to the temperature. Therefore the high-temperature limit further localizes the matrix-integral to the locus of the minima of the potential. If the effective potential is positive semi-definite, the leading high-temperature asymptotics of the partition function is given by the formula of Di Pietro and Komargodski, and the subleading asymptotics is connected to the Coulomb branch dynamics on R 3 × S 1. In theories where the effective potential is not positive semi-definite, the Di Pietro-Komargodski formula needs to be modified. In particular, this modification occurs in the SU(2) theory of Intriligator-Seiberg-Shenker, and the SO(N) theory of Brodie-Cho-Intriligator, both believed to exhibit “misleading” anomaly matchings, and both believed to yield interacting superconformal field theories with c < a. Lastly, two new simple tests for dualities between 4d supersymmetric gauge theories emerge as byproducts of our analysis.« less

LoopX: A Graphical User Interface-Based Database for Comprehensive Analysis and Comparative Evaluation of Loops from Protein Structures.

PubMed

Kadumuri, Rajashekar Varma; Vadrevu, Ramakrishna

2017-10-01

Due to their crucial role in function, folding, and stability, protein loops are being targeted for grafting/designing to create novel or alter existing functionality and improve stability and foldability. With a view to facilitate a thorough analysis and effectual search options for extracting and comparing loops for sequence and structural compatibility, we developed, LoopX a comprehensively compiled library of sequence and conformational features of ∼700,000 loops from protein structures. The database equipped with a graphical user interface is empowered with diverse query tools and search algorithms, with various rendering options to visualize the sequence- and structural-level information along with hydrogen bonding patterns, backbone φ, ψ dihedral angles of both the target and candidate loops. Two new features (i) conservation of the polar/nonpolar environment and (ii) conservation of sequence and conformation of specific residues within the loops have also been incorporated in the search and retrieval of compatible loops for a chosen target loop. Thus, the LoopX server not only serves as a database and visualization tool for sequence and structural analysis of protein loops but also aids in extracting and comparing candidate loops for a given target loop based on user-defined search options.

SA-Mot: a web server for the identification of motifs of interest extracted from protein loops

PubMed Central

Regad, Leslie; Saladin, Adrien; Maupetit, Julien; Geneix, Colette; Camproux, Anne-Claude

2011-01-01

The detection of functional motifs is an important step for the determination of protein functions. We present here a new web server SA-Mot (Structural Alphabet Motif) for the extraction and location of structural motifs of interest from protein loops. Contrary to other methods, SA-Mot does not focus only on functional motifs, but it extracts recurrent and conserved structural motifs involved in structural redundancy of loops. SA-Mot uses the structural word notion to extract all structural motifs from uni-dimensional sequences corresponding to loop structures. Then, SA-Mot provides a description of these structural motifs using statistics computed in the loop data set and in SCOP superfamily, sequence and structural parameters. SA-Mot results correspond to an interactive table listing all structural motifs extracted from a target structure and their associated descriptors. Using this information, the users can easily locate loop regions that are important for the protein folding and function. The SA-Mot web server is available at http://sa-mot.mti.univ-paris-diderot.fr. PMID:21665924

SA-Mot: a web server for the identification of motifs of interest extracted from protein loops.

PubMed

Regad, Leslie; Saladin, Adrien; Maupetit, Julien; Geneix, Colette; Camproux, Anne-Claude

2011-07-01

The detection of functional motifs is an important step for the determination of protein functions. We present here a new web server SA-Mot (Structural Alphabet Motif) for the extraction and location of structural motifs of interest from protein loops. Contrary to other methods, SA-Mot does not focus only on functional motifs, but it extracts recurrent and conserved structural motifs involved in structural redundancy of loops. SA-Mot uses the structural word notion to extract all structural motifs from uni-dimensional sequences corresponding to loop structures. Then, SA-Mot provides a description of these structural motifs using statistics computed in the loop data set and in SCOP superfamily, sequence and structural parameters. SA-Mot results correspond to an interactive table listing all structural motifs extracted from a target structure and their associated descriptors. Using this information, the users can easily locate loop regions that are important for the protein folding and function. The SA-Mot web server is available at http://sa-mot.mti.univ-paris-diderot.fr.

The photochemical formation and gas-particle partitioning of oxidation products of decamethyl cyclopentasiloxane and decamethyl tetrasiloxane in the atmosphere

NASA Astrophysics Data System (ADS)

Chandramouli, Bharadwaj; Kamens, Richard M.

Decamethyl cyclopentasiloxane (D 5) and decamethyl tetrasiloxane (MD 2M) were injected into a smog chamber containing fine Arizona road dust particles (95% surface area <2.6 μM) and an urban smog atmosphere in the daytime. A photochemical reaction - gas-particle partitioning reaction scheme, was implemented to simulate the formation and gas-particle partitioning of hydroxyl oxidation products of D 5 and MD 2M. This scheme incorporated the reactions of D 5 and MD 2M into an existing urban smog chemical mechanism carbon bond IV and partitioned the products between gas and particle phase by treating gas-particle partitioning as a kinetic process and specifying an uptake and off-gassing rate. A photochemical model PKSS was used to simulate this set of reactions. A Langmuirian partitioning model was used to convert the measured and estimated mass-based partitioning coefficients ( KP) to a molar or volume-based form. The model simulations indicated that >99% of all product silanol formed in the gas-phase partition immediately to particle phase and the experimental data agreed with model predictions. One product, D 4TOH was observed and confirmed for the D 5 reaction and this system was modeled successfully. Experimental data was inadequate for MD 2M reaction products and it is likely that more than one product formed. The model set up a framework into which more reaction and partitioning steps can be easily added.

AGT/ℤ2

NASA Astrophysics Data System (ADS)

Le Floch, Bruno; Turiaci, Gustavo J.

2017-12-01

We relate Liouville/Toda CFT correlators on Riemann surfaces with boundaries and cross-cap states to supersymmetric observables in four-dimensional N=2 gauge theories. Our construction naturally involves four-dimensional theories with fields defined on different ℤ2 quotients of the sphere (hemisphere and projective space) but nevertheless interacting with each other. The six-dimensional origin is a ℤ2 quotient of the setup giving rise to the usual AGT correspondence. To test the correspondence, we work out the ℝℙ4 partition function of four-dimensional N=2 theories by combining a 3d lens space and a 4d hemisphere partition functions. The same technique reproduces known ℝℙ2 partition functions in a form that lets us easily check two-dimensional Seiberg-like dualities on this nonorientable space. As a bonus we work out boundary and cross-cap wavefunctions in Toda CFT.

Polynomial solution of quantum Grassmann matrices

NASA Astrophysics Data System (ADS)

Tierz, Miguel

2017-05-01

We study a model of quantum mechanical fermions with matrix-like index structure (with indices N and L) and quartic interactions, recently introduced by Anninos and Silva. We compute the partition function exactly with q-deformed orthogonal polynomials (Stieltjes-Wigert polynomials), for different values of L and arbitrary N. From the explicit evaluation of the thermal partition function, the energy levels and degeneracies are determined. For a given L, the number of states of different energy is quadratic in N, which implies an exponential degeneracy of the energy levels. We also show that at high-temperature we have a Gaussian matrix model, which implies a symmetry that swaps N and L, together with a Wick rotation of the spectral parameter. In this limit, we also write the partition function, for generic L and N, in terms of a single generalized Hermite polynomial.

ParABS Systems of the Four Replicons of Burkholderia cenocepacia: New Chromosome Centromeres Confer Partition Specificity†

PubMed Central

Dubarry, Nelly; Pasta, Franck; Lane, David

2006-01-01

Most bacterial chromosomes carry an analogue of the parABS systems that govern plasmid partition, but their role in chromosome partition is ambiguous. parABS systems might be particularly important for orderly segregation of multipartite genomes, where their role may thus be easier to evaluate. We have characterized parABS systems in Burkholderia cenocepacia, whose genome comprises three chromosomes and one low-copy-number plasmid. A single parAB locus and a set of ParB-binding (parS) centromere sites are located near the origin of each replicon. ParA and ParB of the longest chromosome are phylogenetically similar to analogues in other multichromosome and monochromosome bacteria but are distinct from those of smaller chromosomes. The latter form subgroups that correspond to the taxa of their hosts, indicating evolution from plasmids. The parS sites on the smaller chromosomes and the plasmid are similar to the “universal” parS of the main chromosome but with a sequence specific to their replicon. In an Escherichia coli plasmid stabilization test, each parAB exhibits partition activity only with the parS of its own replicon. Hence, parABS function is based on the independent partition of individual chromosomes rather than on a single communal system or network of interacting systems. Stabilization by the smaller chromosome and plasmid systems was enhanced by mutation of parS sites and a promoter internal to their parAB operons, suggesting autoregulatory mechanisms. The small chromosome ParBs were found to silence transcription, a property relevant to autoregulation. PMID:16452432

Super energy saver heat pump with dynamic hybrid phase change material

DOEpatents

Ally, Moonis Raza [Oak Ridge, TN; Tomlinson, John Jager [Knoxville, TN; Rice, Clifford Keith [Clinton, TN

2010-07-20

A heat pump has a refrigerant loop, a compressor in fluid communication with the refrigerant loop, at least one indoor heat exchanger in fluid communication with the refrigerant loop, and at least one outdoor heat exchanger in fluid communication with the refrigerant loop. The at least one outdoor heat exchanger has a phase change material in thermal communication with the refrigerant loop and in fluid communication with an outdoor environment. Other systems, devices, and methods are described.

Inflationary magnetogenesis and non-local actions: the conformal anomaly

DOE Office of Scientific and Technical Information (OSTI.GOV)

El-Menoufi, Basem Kamal, E-mail: bmahmoud@physics.umass.edu

2016-02-01

We discuss the possibility of successful magnetogenesis during inflation by employing the one-loop effective action of massless QED. The action is strictly non-local and results from the long distance fluctuations of massless charged particles present at the inflationary scale. Most importantly, it encodes the conformal anomaly of QED which is crucial to avoid the vacuum preservation in classical electromagnetism. In particular, we find a blue spectrum for the magnetic field with spectral index n{sub B} ≅ 2 − α{sub e} where α{sub e} depends on both the number of e-folds during inflation as well as the coefficient of the one-loop beta function. In particular,more » the sign of the beta function has important bearing on the final result. A low reheating temperature is required for the present day magnetic field to be consistent with the lower bound inferred on the field in the intergalactic medium.« less

The effect of jitter on the performance of space coherent optical communication system with Costas loop

NASA Astrophysics Data System (ADS)

Li, Xin; Hong, Yifeng; Wang, Jinfang; Liu, Yang; Sun, Xun; Li, Mi

2018-01-01

Numerous communication techniques and optical devices successfully applied in space optical communication system indicates a good portability of it. With this good portability, typical coherent demodulation technique of Costas loop can be easily adopted in space optical communication system. As one of the components of pointing error, the effect of jitter plays an important role in the communication quality of such system. Here, we obtain the probability density functions (PDF) of different jitter degrees and explain their essential effect on the bit error rate (BER) space optical communication system. Also, under the effect of jitter, we research the bit error rate of space coherent optical communication system using Costas loop with different system parameters of transmission power, divergence angle, receiving diameter, avalanche photodiode (APD) gain, and phase deviation caused by Costas loop. Through a numerical simulation of this kind of communication system, we demonstrate the relationship between the BER and these system parameters, and some corresponding methods of system optimization are presented to enhance the communication quality.

Partitioning Strategy Using Static Analysis Techniques

NASA Astrophysics Data System (ADS)

Seo, Yongjin; Soo Kim, Hyeon

2016-08-01

Flight software is software used in satellites' on-board computers. It has requirements such as real time and reliability. The IMA architecture is used to satisfy these requirements. The IMA architecture has the concept of partitions and this affected the configuration of flight software. That is, situations occurred in which software that had been loaded on one system was divided into many partitions when being loaded. For new issues, existing studies use experience based partitioning methods. However, these methods have a problem that they cannot be reused. In this respect, this paper proposes a partitioning method that is reusable and consistent.

Package-X 2.0: A Mathematica package for the analytic calculation of one-loop integrals

NASA Astrophysics Data System (ADS)

Patel, Hiren H.

2017-09-01

This article summarizes new features and enhancements of the first major update of Package-X. Package-X 2.0 can now generate analytic expressions for arbitrarily high rank dimensionally regulated tensor integrals with up to four distinct propagators, each with arbitrary integer weight, near an arbitrary even number of spacetime dimensions, giving UV divergent, IR divergent, and finite parts at (almost) any real-valued kinematic point. Additionally, it can generate multivariable Taylor series expansions of these integrals around any non-singular kinematic point to arbitrary order. All special functions and abbreviations output by Package-X 2.0 support Mathematica's arbitrary precision evaluation capabilities to deal with issues of numerical stability. Finally, tensor algebraic routines of Package-X have been polished and extended to support open fermion chains both on and off shell. The documentation (equivalent to over 100 printed pages) is accessed through Mathematica's Wolfram Documentation Center and contains information on all Package-X symbols, with over 300 basic usage examples, 3 project-scale tutorials, and instructions on linking to FEYNCALC and LOOPTOOLS. Program files doi:http://dx.doi.org/10.17632/yfkwrd4d5t.1 Licensing provisions: CC by 4.0 Programming language: Mathematica (Wolfram Language) Journal reference of previous version: H. H. Patel, Comput. Phys. Commun 197, 276 (2015) Does the new version supersede the previous version?: Yes Summary of revisions: Extension to four point one-loop integrals with higher powers of denominator factors, separate extraction of UV and IR divergent parts, testing for power IR divergences, construction of Taylor series expansions of one-loop integrals, numerical evaluation with arbitrary precision arithmetic, manipulation of fermion chains, improved tensor algebraic routines, and much expanded documentation. Nature of problem: Analytic calculation of one-loop integrals in relativistic quantum field theory. Solution method: Passarino-Veltman reduction formula, Denner-Dittmaier reduction formulae, and additional algorithms described in the manuscript. Restrictions: One-loop integrals are limited to those involving no more than four denominator factors.

Computer program for calculating and fitting thermodynamic functions

NASA Technical Reports Server (NTRS)

Mcbride, Bonnie J.; Gordon, Sanford

1992-01-01

A computer program is described which (1) calculates thermodynamic functions (heat capacity, enthalpy, entropy, and free energy) for several optional forms of the partition function, (2) fits these functions to empirical equations by means of a least-squares fit, and (3) calculates, as a function of temperture, heats of formation and equilibrium constants. The program provides several methods for calculating ideal gas properties. For monatomic gases, three methods are given which differ in the technique used for truncating the partition function. For diatomic and polyatomic molecules, five methods are given which differ in the corrections to the rigid-rotator harmonic-oscillator approximation. A method for estimating thermodynamic functions for some species is also given.

Autopilot for frequency-modulation atomic force microscopy.

PubMed

Kuchuk, Kfir; Schlesinger, Itai; Sivan, Uri

2015-10-01

One of the most challenging aspects of operating an atomic force microscope (AFM) is finding optimal feedback parameters. This statement applies particularly to frequency-modulation AFM (FM-AFM), which utilizes three feedback loops to control the cantilever excitation amplitude, cantilever excitation frequency, and z-piezo extension. These loops are regulated by a set of feedback parameters, tuned by the user to optimize stability, sensitivity, and noise in the imaging process. Optimization of these parameters is difficult due to the coupling between the frequency and z-piezo feedback loops by the non-linear tip-sample interaction. Four proportional-integral (PI) parameters and two lock-in parameters regulating these loops require simultaneous optimization in the presence of a varying unknown tip-sample coupling. Presently, this optimization is done manually in a tedious process of trial and error. Here, we report on the development and implementation of an algorithm that computes the control parameters automatically. The algorithm reads the unperturbed cantilever resonance frequency, its quality factor, and the z-piezo driving signal power spectral density. It analyzes the poles and zeros of the total closed loop transfer function, extracts the unknown tip-sample transfer function, and finds four PI parameters and two lock-in parameters for the frequency and z-piezo control loops that optimize the bandwidth and step response of the total system. Implementation of the algorithm in a home-built AFM shows that the calculated parameters are consistently excellent and rarely require further tweaking by the user. The new algorithm saves the precious time of experienced users, facilitates utilization of FM-AFM by casual users, and removes the main hurdle on the way to fully automated FM-AFM.

Autopilot for frequency-modulation atomic force microscopy

NASA Astrophysics Data System (ADS)

Kuchuk, Kfir; Schlesinger, Itai; Sivan, Uri

2015-10-01

One of the most challenging aspects of operating an atomic force microscope (AFM) is finding optimal feedback parameters. This statement applies particularly to frequency-modulation AFM (FM-AFM), which utilizes three feedback loops to control the cantilever excitation amplitude, cantilever excitation frequency, and z-piezo extension. These loops are regulated by a set of feedback parameters, tuned by the user to optimize stability, sensitivity, and noise in the imaging process. Optimization of these parameters is difficult due to the coupling between the frequency and z-piezo feedback loops by the non-linear tip-sample interaction. Four proportional-integral (PI) parameters and two lock-in parameters regulating these loops require simultaneous optimization in the presence of a varying unknown tip-sample coupling. Presently, this optimization is done manually in a tedious process of trial and error. Here, we report on the development and implementation of an algorithm that computes the control parameters automatically. The algorithm reads the unperturbed cantilever resonance frequency, its quality factor, and the z-piezo driving signal power spectral density. It analyzes the poles and zeros of the total closed loop transfer function, extracts the unknown tip-sample transfer function, and finds four PI parameters and two lock-in parameters for the frequency and z-piezo control loops that optimize the bandwidth and step response of the total system. Implementation of the algorithm in a home-built AFM shows that the calculated parameters are consistently excellent and rarely require further tweaking by the user. The new algorithm saves the precious time of experienced users, facilitates utilization of FM-AFM by casual users, and removes the main hurdle on the way to fully automated FM-AFM.

Evaluation of Hierarchical Clustering Algorithms for Document Datasets

DTIC Science & Technology

2002-06-03

link, complete-link, and group average ( UPGMA )) and a new set of merging criteria derived from the six partitional criterion functions. Overall, we...used the single-link, complete-link, and UPGMA schemes, as well as, the various partitional criterion functions described in Section 3.1. The single-link...other (complete-link approach). The UPGMA scheme [16] (also known as group average) overcomes these problems by measuring the similarity of two clusters

A partition function-based weighting scheme in force field parameter development using ab initio calculation results in global configurational space.

PubMed

Wu, Yao; Dai, Xiaodong; Huang, Niu; Zhao, Lifeng

2013-06-05

In force field parameter development using ab initio potential energy surfaces (PES) as target data, an important but often neglected matter is the lack of a weighting scheme with optimal discrimination power to fit the target data. Here, we developed a novel partition function-based weighting scheme, which not only fits the target potential energies exponentially like the general Boltzmann weighting method, but also reduces the effect of fitting errors leading to overfitting. The van der Waals (vdW) parameters of benzene and propane were reparameterized by using the new weighting scheme to fit the high-level ab initio PESs probed by a water molecule in global configurational space. The molecular simulation results indicate that the newly derived parameters are capable of reproducing experimental properties in a broader range of temperatures, which supports the partition function-based weighting scheme. Our simulation results also suggest that structural properties are more sensitive to vdW parameters than partial atomic charge parameters in these systems although the electrostatic interactions are still important in energetic properties. As no prerequisite conditions are required, the partition function-based weighting method may be applied in developing any types of force field parameters. Copyright © 2013 Wiley Periodicals, Inc.

Statistical Systems with Z

NASA Astrophysics Data System (ADS)

William, Peter

In this dissertation several two dimensional statistical systems exhibiting discrete Z(n) symmetries are studied. For this purpose a newly developed algorithm to compute the partition function of these models exactly is utilized. The zeros of the partition function are examined in order to obtain information about the observable quantities at the critical point. This occurs in the form of critical exponents of the order parameters which characterize phenomena at the critical point. The correlation length exponent is found to agree very well with those computed from strong coupling expansions for the mass gap and with Monte Carlo results. In Feynman's path integral formalism the partition function of a statistical system can be related to the vacuum expectation value of the time ordered product of the observable quantities of the corresponding field theoretic model. Hence a generalization of ordinary scale invariance in the form of conformal invariance is focussed upon. This principle is very suitably applicable, in the case of two dimensional statistical models undergoing second order phase transitions at criticality. The conformal anomaly specifies the universality class to which these models belong. From an evaluation of the partition function, the free energy at criticality is computed, to determine the conformal anomaly of these models. The conformal anomaly for all the models considered here are in good agreement with the predicted values.

Comment on "Troublesome aspects of the Renyi-MaxEnt treatment".

PubMed

Oikonomou, Thomas; Bagci, G Baris

2017-11-01

Plastino et al. [Plastino et al., Phys. Rev. E 94, 012145 (2016)1539-375510.1103/PhysRevE.94.012145] recently stated that the Rényi entropy is not suitable for thermodynamics by using functional calculus, since it leads to anomalous results unlike the Tsallis entropy. We first show that the Tsallis entropy also leads to such anomalous behaviors if one adopts the same functional calculus approach. Second, we note that one of the Lagrange multipliers is set in an ad hoc manner in the functional calculus approach of Plastino et al. Finally, the explanation for these anomalous behaviors is provided by observing that the generalized distributions obtained by Plastino et al. do not yield the ordinary canonical partition function in the appropriate limit and therefore cannot be considered as genuine generalized distributions.

Control and optimization system and method for chemical looping processes

DOEpatents

Lou, Xinsheng; Joshi, Abhinaya; Lei, Hao

2014-06-24

A control system for optimizing a chemical loop system includes one or more sensors for measuring one or more parameters in a chemical loop. The sensors are disposed on or in a conduit positioned in the chemical loop. The sensors generate one or more data signals representative of an amount of solids in the conduit. The control system includes a data acquisition system in communication with the sensors and a controller in communication with the data acquisition system. The data acquisition system receives the data signals and the controller generates the control signals. The controller is in communication with one or more valves positioned in the chemical loop. The valves are configured to regulate a flow of the solids through the chemical loop.

Control and optimization system and method for chemical looping processes

DOEpatents

Lou, Xinsheng; Joshi, Abhinaya; Lei, Hao

2015-02-17

A control system for optimizing a chemical loop system includes one or more sensors for measuring one or more parameters in a chemical loop. The sensors are disposed on or in a conduit positioned in the chemical loop. The sensors generate one or more data signals representative of an amount of solids in the conduit. The control system includes a data acquisition system in communication with the sensors and a controller in communication with the data acquisition system. The data acquisition system receives the data signals and the controller generates the control signals. The controller is in communication with one or more valves positioned in the chemical loop. The valves are configured to regulate a flow of the solids through the chemical loop.

RNAdualPF: software to compute the dual partition function with sample applications in molecular evolution theory.

PubMed

Garcia-Martin, Juan Antonio; Bayegan, Amir H; Dotu, Ivan; Clote, Peter

2016-10-19

RNA inverse folding is the problem of finding one or more sequences that fold into a user-specified target structure s 0 , i.e. whose minimum free energy secondary structure is identical to the target s 0 . Here we consider the ensemble of all RNA sequences that have low free energy with respect to a given target s 0 . We introduce the program RNAdualPF, which computes the dual partition function Z ∗ , defined as the sum of Boltzmann factors exp(-E(a,s 0 )/RT) of all RNA nucleotide sequences a compatible with target structure s 0 . Using RNAdualPF, we efficiently sample RNA sequences that approximately fold into s 0 , where additionally the user can specify IUPAC sequence constraints at certain positions, and whether to include dangles (energy terms for stacked, single-stranded nucleotides). Moreover, since we also compute the dual partition function Z ∗ (k) over all sequences having GC-content k, the user can require that all sampled sequences have a precise, specified GC-content. Using Z ∗ , we compute the dual expected energy 〈E ∗ 〉, and use it to show that natural RNAs from the Rfam 12.0 database have higher minimum free energy than expected, thus suggesting that functional RNAs are under evolutionary pressure to be only marginally thermodynamically stable. We show that C. elegans precursor microRNA (pre-miRNA) is significantly non-robust with respect to mutations, by comparing the robustness of each wild type pre-miRNA sequence with 2000 [resp. 500] sequences of the same GC-content generated by RNAdualPF, which approximately [resp. exactly] fold into the wild type target structure. We confirm and strengthen earlier findings that precursor microRNAs and bacterial small noncoding RNAs display plasticity, a measure of structural diversity. We describe RNAdualPF, which rapidly computes the dual partition function Z ∗ and samples sequences having low energy with respect to a target structure, allowing sequence constraints and specified GC-content. Using different inverse folding software, another group had earlier shown that pre-miRNA is mutationally robust, even controlling for compositional bias. Our opposite conclusion suggests a cautionary note that computationally based insights into molecular evolution may heavily depend on the software used. C/C++-software for RNAdualPF is available at http://bioinformatics.bc.edu/clotelab/RNAdualPF .

Sequence-structure relationships in RNA loops: establishing the basis for loop homology modeling.

PubMed

Schudoma, Christian; May, Patrick; Nikiforova, Viktoria; Walther, Dirk

2010-01-01

The specific function of RNA molecules frequently resides in their seemingly unstructured loop regions. We performed a systematic analysis of RNA loops extracted from experimentally determined three-dimensional structures of RNA molecules. A comprehensive loop-structure data set was created and organized into distinct clusters based on structural and sequence similarity. We detected clear evidence of the hallmark of homology present in the sequence-structure relationships in loops. Loops differing by <25% in sequence identity fold into very similar structures. Thus, our results support the application of homology modeling for RNA loop model building. We established a threshold that may guide the sequence divergence-based selection of template structures for RNA loop homology modeling. Of all possible sequences that are, under the assumption of isosteric relationships, theoretically compatible with actual sequences observed in RNA structures, only a small fraction is contained in the Rfam database of RNA sequences and classes implying that the actual RNA loop space may consist of a limited number of unique loop structures and conserved sequences. The loop-structure data sets are made available via an online database, RLooM. RLooM also offers functionalities for the modeling of RNA loop structures in support of RNA engineering and design efforts.

Closed-loop control of cellular functions using combinatory drugs guided by a stochastic search algorithm

PubMed Central

Wong, Pak Kin; Yu, Fuqu; Shahangian, Arash; Cheng, Genhong; Sun, Ren; Ho, Chih-Ming

2008-01-01

A mixture of drugs is often more effective than using a single effector. However, it is extremely challenging to identify potent drug combinations by trial and error because of the large number of possible combinations and the inherent complexity of the underlying biological network. With a closed-loop optimization modality, we experimentally demonstrate effective searching for potent drug combinations for controlling cellular functions through a large parametric space. Only tens of iterations out of one hundred thousand possible trials were needed to determine a potent combination of drugs for inhibiting vesicular stomatitis virus infection of NIH 3T3 fibroblasts. In addition, the drug combination reduced the required dosage by ≈10-fold compared with individual drugs. In another example, a potent mixture was identified in thirty iterations out of a possible million combinations of six cytokines that regulate the activity of nuclear factor kappa B in 293T cells. The closed-loop optimization approach possesses the potential of being an effective approach for manipulating a wide class of biological systems. PMID:18356295

Pilot Subjective Assessments During an Investigation of Separation Function Allocation Using a Human-In-The-Loop Simulation

NASA Technical Reports Server (NTRS)

Burke, Kelly A.; Wing, David J.; Lewis, Timothy

2013-01-01

Two human-in-the-loop simulation experiments were conducted to investigate allocation of separation assurance functions between ground and air and between humans and automation. The experiments modeled a mixed-operations concept in which aircraft receiving ground-based separation services shared the airspace with aircraft providing their own separation service (i.e., self-separation). The two experiments, one pilot-focused and the other controller-focused, addressed selected key issues of mixed operations and modeling an emergence of NextGen technologies and procedures. This paper focuses on the results of the subjective assessments of pilots collected during the pilot-focused human-in-the-loop simulation, specifically workload and situation awareness. Generally the results revealed that across all conditions, pilots' perceived workload was low to medium, with the highest reported levels of workload occurring when the pilots experienced a loss of separation during the scenario. Furthermore, the results from the workload data and situation awareness data were complimentary such that when pilots reported lower levels of workload they also experienced higher levels of situation awareness.

Sphinx: merging knowledge-based and ab initio approaches to improve protein loop prediction

PubMed Central

Marks, Claire; Nowak, Jaroslaw; Klostermann, Stefan; Georges, Guy; Dunbar, James; Shi, Jiye; Kelm, Sebastian

2017-01-01

Abstract Motivation: Loops are often vital for protein function, however, their irregular structures make them difficult to model accurately. Current loop modelling algorithms can mostly be divided into two categories: knowledge-based, where databases of fragments are searched to find suitable conformations and ab initio, where conformations are generated computationally. Existing knowledge-based methods only use fragments that are the same length as the target, even though loops of slightly different lengths may adopt similar conformations. Here, we present a novel method, Sphinx, which combines ab initio techniques with the potential extra structural information contained within loops of a different length to improve structure prediction. Results: We show that Sphinx is able to generate high-accuracy predictions and decoy sets enriched with near-native loop conformations, performing better than the ab initio algorithm on which it is based. In addition, it is able to provide predictions for every target, unlike some knowledge-based methods. Sphinx can be used successfully for the difficult problem of antibody H3 prediction, outperforming RosettaAntibody, one of the leading H3-specific ab initio methods, both in accuracy and speed. Availability and Implementation: Sphinx is available at http://opig.stats.ox.ac.uk/webapps/sphinx. Contact: deane@stats.ox.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:28453681

Sphinx: merging knowledge-based and ab initio approaches to improve protein loop prediction.

PubMed

Marks, Claire; Nowak, Jaroslaw; Klostermann, Stefan; Georges, Guy; Dunbar, James; Shi, Jiye; Kelm, Sebastian; Deane, Charlotte M

2017-05-01

Loops are often vital for protein function, however, their irregular structures make them difficult to model accurately. Current loop modelling algorithms can mostly be divided into two categories: knowledge-based, where databases of fragments are searched to find suitable conformations and ab initio, where conformations are generated computationally. Existing knowledge-based methods only use fragments that are the same length as the target, even though loops of slightly different lengths may adopt similar conformations. Here, we present a novel method, Sphinx, which combines ab initio techniques with the potential extra structural information contained within loops of a different length to improve structure prediction. We show that Sphinx is able to generate high-accuracy predictions and decoy sets enriched with near-native loop conformations, performing better than the ab initio algorithm on which it is based. In addition, it is able to provide predictions for every target, unlike some knowledge-based methods. Sphinx can be used successfully for the difficult problem of antibody H3 prediction, outperforming RosettaAntibody, one of the leading H3-specific ab initio methods, both in accuracy and speed. Sphinx is available at http://opig.stats.ox.ac.uk/webapps/sphinx. deane@stats.ox.ac.uk. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

Damage structures in fission-neutron irradiated Ni-based alloys at high temperatures

NASA Astrophysics Data System (ADS)

Yamakawa, K.; Shimomura, Y.

1999-01-01

The defects formed in Ni based (Ni-Si, Ni-Cu and Ni-Fe) alloys which were irradiated with fission-neutrons were examined by electron microscopy. Irradiations were carried out at 473 K and 573 K. In the 473 K irradiated specimens, a high density of large interstitial loops and small vacancy clusters with stacking fault tetrahedra (SFT) were observed. The number densities of these two types of defects did not strongly depend on the amount of solute atoms in each alloy. The density of the loops in Ni-Si alloys was much higher than those in Ni-Cu and Ni-Fe alloys, while the density of SFT only slightly depended on the kind of solute. Also, the size of the loops depended on the kinds and amounts of solute. In 573 K irradiated Ni-Cu specimens, a high density of dislocation lines developed during the growth of interstitial loops. In Ni-Si alloys, the number density and size of the interstitial loops changed as a function of the amount of solute. Voids were formed in Ni-Cu alloys but scarcely formed in Ni-Si alloys. The number density of voids was one hundredth of that of SFT observed in 473 K irradiated Ni-Cu alloys. Possible formation processes of interstitial loops, SFT dislocation lines and voids are discussed.

All orders results for self-crossing Wilson loops mimicking double parton scattering

DOE PAGES

Dixon, Lance J.; Esterlis, Ilya

2016-07-21

Loop-level scattering amplitudes for massless particles have singularities in regions where tree amplitudes are perfectly smooth. For example, a 2 → 4 gluon scattering process has a singularity in which each incoming gluon splits into a pair of gluons, followed by a pair of 2 → 2 collisions between the gluon pairs. This singularity mimics double parton scattering because it occurs when the transverse momentum of a pair of outgoing gluons vanishes. The singularity is logarithmic at fixed order in perturbation theory. We exploit the duality between scattering amplitudes and polygonal Wilson loops to study six-point amplitudes in this limitmore » to high loop order in planar N = 4 super-Yang-Mills theory. The singular configuration corresponds to the limit in which a hexagonal Wilson loop develops a self-crossing. The singular terms are governed by an evolution equation, in which the hexagon mixes into a pair of boxes; the mixing back is suppressed in the planar (large N c) limit. Because the kinematic dependence of the box Wilson loops is dictated by (dual) conformal invariance, the complete kinematic dependence of the singular terms for the self-crossing hexagon on the one nonsingular variable is determined to all loop orders. The complete logarithmic dependence on the singular variable can be obtained through nine loops, up to a couple of constants, using a correspondence with the multi-Regge limit. As a byproduct, we obtain a simple formula for the leading logs to all loop orders. Furthermore, we also show that, although the MHV six-gluon amplitude is singular, remarkably, the transcendental functions entering the non-MHV amplitude are finite in the same limit, at least through four loops.« less

All orders results for self-crossing Wilson loops mimicking double parton scattering

NASA Astrophysics Data System (ADS)

Dixon, Lance J.; Esterlis, Ilya

2016-07-01

Loop-level scattering amplitudes for massless particles have singularities in regions where tree amplitudes are perfectly smooth. For example, a 2 → 4 gluon scattering process has a singularity in which each incoming gluon splits into a pair of gluons, followed by a pair of 2 → 2 collisions between the gluon pairs. This singularity mimics double parton scattering because it occurs when the transverse momentum of a pair of outgoing gluons vanishes. The singularity is logarithmic at fixed order in perturbation theory. We exploit the duality between scattering amplitudes and polygonal Wilson loops to study six-point amplitudes in this limit to high loop order in planar {N} = 4 super-Yang-Mills theory. The singular configuration corresponds to the limit in which a hexagonal Wilson loop develops a self-crossing. The singular terms are governed by an evolution equation, in which the hexagon mixes into a pair of boxes; the mixing back is suppressed in the planar (large N c) limit. Because the kinematic dependence of the box Wilson loops is dictated by (dual) conformal invariance, the complete kinematic dependence of the singular terms for the self-crossing hexagon on the one nonsingular variable is determined to all loop orders. The complete logarithmic dependence on the singular variable can be obtained through nine loops, up to a couple of constants, using a correspondence with the multi-Regge limit. As a byproduct, we obtain a simple formula for the leading logs to all loop orders. We also show that, although the MHV six-gluon amplitude is singular, remarkably, the transcendental functions entering the non-MHV amplitude are finite in the same limit, at least through four loops.

Simple way to calculate a UV-finite one-loop quantum energy in the Randall-Sundrum model

NASA Astrophysics Data System (ADS)

Altshuler, Boris L.

2017-04-01

The surprising simplicity of Barvinsky-Nesterov or equivalently Gelfand-Yaglom methods of calculation of quantum determinants permits us to obtain compact expressions for a UV-finite difference of one-loop quantum energies for two arbitrary values of the parameter of the double-trace asymptotic boundary conditions. This result generalizes the Gubser and Mitra calculation for the particular case of difference of "regular" and "irregular" one-loop energies in the one-brane Randall-Sundrum model. The approach developed in the paper also allows us to get "in one line" the one-loop quantum energies in the two-brane Randall-Sundrum model. The relationship between "one-loop" expressions corresponding to the mixed Robin and to double-trace asymptotic boundary conditions is traced.

Scheduling applications for execution on a plurality of compute nodes of a parallel computer to manage temperature of the nodes during execution

DOEpatents

Archer, Charles J; Blocksome, Michael A; Peters, Amanda E; Ratterman, Joseph D; Smith, Brian E

2012-10-16

Methods, apparatus, and products are disclosed for scheduling applications for execution on a plurality of compute nodes of a parallel computer to manage temperature of the plurality of compute nodes during execution that include: identifying one or more applications for execution on the plurality of compute nodes; creating a plurality of physically discontiguous node partitions in dependence upon temperature characteristics for the compute nodes and a physical topology for the compute nodes, each discontiguous node partition specifying a collection of physically adjacent compute nodes; and assigning, for each application, that application to one or more of the discontiguous node partitions for execution on the compute nodes specified by the assigned discontiguous node partitions.

Fault Gauge Numerical Simulation : Dynamic Rupture Propagation and Local Energy Partitioning

NASA Astrophysics Data System (ADS)

Mollon, G.

2017-12-01

In this communication, we present dynamic simulations of the local (centimetric) behaviour of a fault filled with a granular gauge submitted to dynamic rupture. The numerical tool (Fig. 1) combines classical Discrete Element Modelling (albeit with the ability to deal with arbitrary grain shapes) for the simualtion of the gauge, and continuous modelling for the simulation of the acoustic waves emission and propagation. In a first part, the model is applied to the simulation of steady-state shearing of the fault under remote displacement boudary conditions, in order to observe the shear accomodation at the interface (R1 cracks, localization, wear, etc.). It also makes it possible to fit to desired values the Rate and State Friction properties of the granular gauge by adapting the contact laws between grains. Such simulations provide quantitative insight in the steady-state energy partitionning between fracture, friction and acoustic emissions as a function of the shear rate. In a second part, the model is submitted to dynamic rupture. For that purpose, the fault is elastically preloaded just below rupture, and a displacement pulse is applied at one end of the sample (and on only one side of the fault). This allows to observe the propagation of the instability along the fault and the interplay between this propagation and the local granular phenomena. Energy partitionning is then observed both in space and time.