New lower bounds on the size of (n,r)‐arcs in PG(2,q)

An $\left(n,r\right)$‐arc in $\text{PG}\left(2,q\right)$ is a set of $n$ points such that each line contains at most $r$ of the selected points. It is well known that $\left(n,r\right)$‐arcs in $\text{PG}\left(2,q\right)$ correspond to projective linear codes. Let $m_r\left(2,q\right)$ denote the maximal number $n$ of points for which an $\left(n,r\right)$‐arc in $\text{PG}\left(2,q\right)$ exists. In this paper we obtain improved lower bounds on $m_r\left(2,q\right)$ by explicitly constructing $\left(n,r\right)$‐arcs. Some of the constructed $\left(n,r\right)$‐arcs correspond to linear codes meeting the Griesmer bound. All results are obtained by integer linear programming.     

Optimising the Termofluids CFD code for petascale simulations

ABSTRACT

This paper presents some recent efforts carried out on the expansion of the scalability of TermoFluids multi-physics Computational Fluid Dynamics (CFD) code, aiming to achieve petascale capacity for a single simulation. We describe different aspects that we have improved in our code in order to efficiently run it on 131,072 CPU-cores. This work has been developed using the BlueGene/Q Mira supercomputer of the Argonne Leadership Computing Facility, where we have obtained feedback at the targeted scale. In summary, this is a practical paper showing our experience at reaching the petascale paradigm for a single simulation with TermoFluids.     

Efficient implementation of restricted active space configuration interaction with the hole and particle approximation

The restricted active space configuration interaction (RASCI) formalism with the hole and particle truncation of the wavefunction, that is, RASCI(h,p), holds very nice properties such as balanced treatment of ground and low‐lying excited states, spin‐completeness, large flexibility of the wavefunction, and moderate computational cost. In this article, I present a new implementation of the RASCI(h,p) method using a general algorithm based on the integral‐driven approach. The new implementation allows to choose any electronic configuration as the single reference in combination with an excitation operator with any number of ionization, electron attachment, or spin‐flip (SF) excitations. The applicability and good performance of the new computational code is tested in the ground state calculation of water molecule with increasingly large active spaces and up to the full‐CI limit, the calculation of all‐trans linear polyenes with variable number of SF excitations, and the low‐lying states of fluorine molecule with a double‐ionization potential operator. © 2012 Wiley Periodicals, Inc.     

Flexizyme‐Mediated Genetic Reprogramming As a Tool for Noncanonical Peptide Synthesis and Drug Discovery

Noncanonical peptides occur frequently in Nature, and often display high bioactivity. However, the lack of tractable systems for the synthesis of diverse libraries of such peptides has thus far hampered their development as drugs. Genetic reprogramming techniques, in which noncanonical amino acids may be incorporated into peptides, have largely removed this limitation. This Concept article outlines the development of these techniques with an emphasis on drug discovery.     

The depth spectrums of constacyclic codes over finite chain rings

In light of the generator polynomials of constacyclic codes over finite chain rings, the depth spectrum of constacyclic codes can be determined if (n,p)=1$(n,p)=1$.     

Classification of Graeco‐Latin Cubes

A q‐ary code of length n, size M, and minimum distance d is called an code. An code with is said to be maximum distance separable (MDS). Here one‐error‐correcting () MDS codes are classified for small alphabets. In particular, it is shown that there are unique (5, 5³, 3)₅ and (5, 7³, 3)₇ codes and equivalence classes of (5, 8³, 3)₈ codes. The codes are equivalent to certain pairs of mutually orthogonal Latin cubes of order q, called Graeco‐Latin cubes.     

Uniform stable conformal convolutional perfectly matched layer for enlarged cell technique conformal finite-difference time-domain method

Based on conformal construction of physical model in a three-dimensional Cartesian grid,an integral-based conformal convolutional perfectly matched layer(CPML) is given for solving the truncation problem of the open port when the enlarged cell technique conformal finite-difference time-domain(ECT-CFDTD) method is used to simulate the wave propagation inside a perfect electric conductor(PEC) waveguide.The algorithm has the same numerical stability as the ECT-CFDTD method.For the long-time propagation problems of an evanescent wave in a waveguide,several numerical simulations are performed to analyze the reflection error by sweeping the constitutive parameters of the integral-based conformal CPML.Our numerical results show that the integral-based conformal CPML can be used to efficiently truncate the open port of the waveguide.     

Construction of a Live‐Attenuated HIV‐1 Vaccine through Genetic Code Expansion

A safe and effective vaccine against human immunodeficiency virus type 1 (HIV‐1) is urgently needed to combat the worldwide AIDS pandemic, but still remains elusive. The fact that uncontrolled replication of an attenuated vaccine can lead to regaining of its virulence creates safety concerns precluding many vaccines from clinical application. We introduce a novel approach to control HIV‐1 replication, which entails the manipulation of essential HIV‐1 protein biosynthesis through unnatural amino acid (UAA*)‐mediated suppression of genome‐encoded blank codon. We successfully demonstrate that HIV‐1 replication can be precisely turned on and off in vitro.