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At least 109 records · Page 6

The permuted generator hypothesis for the origin of a genetic code

Protocells had no known means of ensuring that their randomly collected proteins would be duplicated. A possible, albeit inexact, mechanism for protein synthesis in a primitive t-RNA is presented, whereby an oligonucleotide (12 units) in a circular configuration is able to align a generator site with amino acid discriminator sites. In this way, unique anticodons could be specified for each site and replication could occur.

Folsome, C.↗

Non-blocking crossbar permutation engine with constant routing latency

The invention is embodied in an N x N crossbar for routing packets from a set of N input ports to a set of N output ports, each packet having a header identifying one of the output ports as its destination, including a plurality of individual links which carry individual packets. Each link has a link input end and a link output end, a plurality of switches. Each of the switches has at least top and bottom switch inputs connected to a corresponding pair of the link output ends and top and bottom switch outputs connected to a corresponding pair of link input ends, whereby each switch is connected to four different links. Each of the switches has an exchange state which routes packets from the top and bottom switch inputs to the bottom and top switch outputs, respectively, and a bypass state which routes packets from the top and bottom switch inputs to the top and bottom switch outputs, respectively. A plurality of individual controller devices governing respective switches for sensing from a header of a packet at each switch input for the identity of the destination output port of the packet and selecting one of the exchange and bypass states in accordance with the identity of the destination output port and with the location of the corresponding switch relative to the destination output port.

Monacos, Steve P.↗

Versatile platform for nanotechnology based on circular permutations of chaperonin protein

The present invention provides chaperonin polypeptides which are modified to include N-terminal and C-terminal ends that are relocated from the central pore region to various different positions in the polypeptide which are located on the exterior of the folded modified chaperonin polypeptide. In the modified chaperonin polypeptide, the naturally-occurring N-terminal and C-terminal ends are joined together directly or with an intervening linker peptide sequence. The relocated N-terminal or C-terminal ends can be covalently joined to, or bound with another molecule such as a nucleic acid molecule, a lipid, a carbohydrate, a second polypeptide, or a nanoparticle. The modified chaperonin polypeptides can assemble into double-ringed chaperonin structures. Further, the chaperonin structures can organize into higher order structures such as nanofilaments or nanoarrays which can be used to produce nanodevices and nanocoatings.

Paavola, Chad D.↗

On the optimum bit orders with respect to the state complexity of trellis diagrams for binary linear codes

It was shown earlier that for a punctured Reed-Muller (RM) code or a primitive BCH code, which contains a punctured RM code of the same minimum distance as a large subcode, the state complexity of the minimal trellis diagram is much greater than that for an equivalent code obtained by a proper permutation on the bit positions. To find a permutation on the bit positions for a given code that minimizes the state complexity of its minimal trellis diagram is an interesting and challenging problem. This permutation problem is related to the generalized Hamming weight hierarchy of a code, and is shown that for RM codes, the standard binary order of bit positions is optimum at every bit position with respect to the state complexity of a minimal trellis diagram by using a theorem due to Wei. The state complexity of trellis diagram for the extended and permuted (64, 24) BCH code is discussed.

Kasami, Tadao↗

Split-helicity tree amplitudes and flag cluster algebras

Recent work has uncovered a connection between the symbol letters of general massless scattering and (permutations of) cluster variables of partial flag varieties. In this paper we explore the cluster adjacency of tree-level gluon amplitudes, specifically focusing on split-helicity amplitudes which can be written in closed form in terms of zigzag diagrams. We check in several cases, and conjecture in general, that the poles in each term satisfy cluster adjacency under a set of permutations that is built from arc permutations of the corresponding zigzag.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Biorefinery upgrading of herbaceous biomass to renewable hydrocarbon fuels, Part 2: Air pollutant emissions and permitting implications

The development of advanced biofuel production facilities is still at a nascent stage, and the biorefineries could face challenges in obtaining air permits required for their construction and operation because they are novel emission sources. To fill gaps in knowledge regarding potential emissions, we perform a detailed federal regulatory analysis and estimate air pollutant emissions for an advanced biorefinery that produces renewable diesel blendstock (RDB) from lignocellulosic biomass via aerobic respiration documented in Part 1 of the paper. We evaluate 12 design permutations that include two feedstocks, a uniform format blend (UFB) and corn stover; three biorefinery scales, 2,000, 5,200, and 9,100 dry metric tons per day (dmtd) of lignocellulosic biomass feed; and two lignin uses, as either a boiler fuel or for pellet production. We also evaluate 6 additional design permutations by incorporating non-emitting renewable power, which could reduce up to 63% carbon monoxide (CO) and nitrogen oxides (NO x ) each, 21% volatile organic compounds (VOC), and 43% hazardous air pollutants (HAP) as opposed to on-site power production, for biorefineries that produce pellets, using either UFB or corn stover. Our results indicate that all 18 design permutations would be classified as a major source under the Clean Air Act's New Source Review program without additional emission controls. Compared to using lignin as a boiler fuel, diverting lignin for pellet production reduces the emissions of CO up to 88%, NOx up to 73%, sulfur dioxide (SO 2 ) up to 99%, VOCs up to 72%, and HAPs up to 66%. Additionally, we explore control options that could further reduce emissions and assess whether reductions are enough to achieve minor source classification. Insights from our analysis can help biorefinery developers and regulators develop permitting strategies to mitigate investment risks.

09 BIOMASS FUELS↗

Canonical form of three-fermion pure-states with six single particle states

We construct a canonical form for pure states in Λ³(C⁶), the three-fermion system with six single particle states, under local unitary (LU) transformations, i.e., the unitary group U(6). We also construct a minimal set of generators of the algebra of polynomial U(6)-invariants on Λ³(C⁶). It turns out that this algebra is isomorphic to the algebra of polynomial LU-invariants of three-qubits which are additionally invariant under qubit permutations. As a consequence of this surprising fact, we deduce that there is a one-to-one correspondence between the U(6)-orbits of pure three-fermion states in Λ³(C⁶) and the LU orbits of pure three-qubit states when qubit permutations are allowed. As an important byproduct, we obtain a new canonical form for pure three-qubit states under LU transformations U(2) × U(2) × U(2) (no qubit permutations allowed)

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

tSFM 1.0: tRNA Structure–Function Mapper

Structure-conditioned information statistics have proven useful to predict and visualize tRNA Class-Informative Features (CIFs) and their evolutionary divergences. Although permutation P-values can quantify the significance of CIF divergences between two taxa, their naive Monte Carlo approximation is slow and inaccurate. The Peaks-over-Threshold approach of Knijnenburg et al. (2009) promises improvements to both speed and accuracy of permutation P-values, but has no publicly available API. Here, we present tRNA Structure–Function Mapper (tSFM) v1.0, an open-source, multi-threaded application that efficiently computes, visualizes and assesses significance of single- and paired-site CIFs and their evolutionary divergences for any RNA, protein, gene or genomic element sequence family. Multiple estimators of permutation P-values for CIF evolutionary divergences are provided along with confidence intervals. tSFM is implemented in Python 3 with compiled C extensions and is freely available through GitHub (https://github.com/tlawrence3/tSFM) and PyPI.

59 BASIC BIOLOGICAL SCIENCES↗

Finite groups and quantum physics

Concepts of quantum theory are considered from the constructive 'finite' point of view. The introduction of a continuum or other actual infinities in physics destroys constructiveness without any need for them in describing empirical observations. It is shown that quantum behavior is a natural consequence of symmetries of dynamical systems. The underlying reason is that it is impossible in principle to trace the identity of indistinguishable objects in their evolution-only information about invariant statements and values concerning such objects is available. General mathematical arguments indicate that any quantum dynamics is reducible to a sequence of permutations. Quantum phenomena, such as interference, arise in invariant subspaces of permutation representations of the symmetry group of a dynamical system. Observable quantities can be expressed in terms of permutation invariants. It is shown that nonconstructive number systems, such as complex numbers, are not needed for describing quantum phenomena. It is sufficient to employ cyclotomic numbers-a minimal extension of natural numbers that is appropriate for quantum mechanics. The use of finite groups in physics, which underlies the present approach, has an additional motivation. Numerous experiments and observations in the particle physics suggest the importance of finite groups of relatively small orders in some fundamental processes. The origin of these groups is unclear within the currently accepted theories-in particular, within the Standard Model.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

IAEA CRP on HTGR Uncertainties in Modeling: Assessment of Phase I Lattice to Core Model Uncertainties

Best-estimate plus uncertainty analysis of reactors is replacing the traditional conservative (stacked uncertainty) method for safety and licensing analysis. To facilitate uncertainty analysis applications, a comprehensive approach and methodology must be developed and applied. High temperature gas cooled reactors (HTGRs) have several features that require techniques not used in light-water reactor analysis (e.g., coated-particle design and large graphite quantities at high temperatures). The International Atomic Energy Agency has therefore launched the Coordinated Research Project on HTGR Uncertainty Analysis in Modeling to study uncertainty propagation in the HTGR analysis chain. The benchmark problem defined for the prismatic design is represented by the General Atomics Modular HTGR 350. The main focus of this report is the compilation and discussion of the results obtained for various permutations of Exercise I 2c and the use of the cross section data in Exercise II 1a of the prismatic benchmark, which is defined as the last and first steps of the lattice and core simulation phases, respectively. The report summarizes the Idaho National Laboratory (INL) best estimate results obtained for Exercise I 2a (fresh single-fuel block), Exercise I 2b (depleted single-fuel block), and Exercise I 2c (super cell) in addition to the first results of an investigation into the cross section generation effects for the super-cell problem. The two dimensional deterministic code known as the New ESC based Weighting Transport (NEWT) included in the Standardized Computer Analyses for Licensing Evaluation (SCALE) 6.1.2 package was used for the cross section evaluation, and the results obtained were compared to the three dimensional stochastic SCALE module KENO VI. The NEWT cross section libraries were generated for several permutations of the current benchmark super-cell geometry and were then provided as input to the Phase II core calculation of the stand alone neutronics Exercise II 1a. The steady state core calculations were simulated with the INL coupled-code system known as the Parallel and Highly Innovative Simulation for INL Code System (PHISICS) and the system thermal-hydraulics code known as the Reactor Excursion and Leak Analysis Program (RELAP) 5 3D using the nuclear data libraries previously generated with NEWT. It was observed that significant differences in terms of multiplication factor and neutron flux exist between the various permutations of the Phase I super-cell lattice calculations. The use of these cross section libraries only leads to minor changes in the Phase II core simulation results for fresh fuel but shows significantly larger discrepancies for spent fuel cores. Furthermore, large incongruities were found between the SCALE NEWT and KENO VI results for the super cells, and while some trends could be identified, a final conclusion on this issue could not yet be reached. This report will be revised in mid 2016 with more detailed analyses of the super-cell problems and their effects on the core models, using the latest version of SCALE (6.2). The super-cell models seem to show substantial improvements in terms of neutron flux as compared to single-block models, particularly at thermal energies.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Parallel solution of closely coupled systems

An odd-even permutation and a nested dissection technique were used to circumvent the strong seriality of a system of closely coupled equations. The effect of transforming the n x n Hermitian definite positive matrix coefficient on the topology of Cholesky factors is discussed. A series of directed graphs is constructed in order to show the computational steps required for the odd-even permutation. Numerical expressions for the speed-up and efficiency of parallel N-processing techniques and sequential processing by a single computer are derived. Similar expressions are derived for the case of insufficient processing capacity. The application of the odd-even permutation to the ensemble class of computer architectures is demonstrated.

Utku, S.↗

Engineering calculations for solving the orbital allotment problem

Four approaches for calculating downlink interferences for shaped-beam antennas are described. An investigation of alternative mixed-integer programming models for satellite synthesis is summarized. Plans for coordinating the various programs developed under this grant are outlined. Two procedures for ordering satellites to initialize the k-permutation algorithm are proposed. Results are presented for the k-permutation algorithms. Feasible solutions are found for 5 of the 6 problems considered. Finally, it is demonstrated that the k-permutation algorithm can be used to solve arc allotment problems.

Reilly, C.↗