Modern Approaches to Exact Diagonalization and Selected Configuration Interaction with the Adaptive Sampling CI Method.

Recent advances in selected configuration interaction methods have made them competitive with the most accurate techniques available and, hence, creating an increasingly powerful tool for solving quantum Hamiltonians. In this work, we build on recent advances from the adaptive sampling configuration interaction (ASCI) algorithm. We show that a useful paradigm for generating efficient selected CI/exact diagonalization algorithms is driven by fast sorting algorithms, much in the same way iterative diagonalization is based on the paradigm of matrix vector multiplication. We present several new algorithms for all parts of performing a selected CI, which includes new ASCI search, dynamic bit masking, fast orbital rotations, fast diagonal matrix elements, and residue arrays. The ASCI search algorithm can be used in several different modes, which includes an integral driven search and a coefficient driven search. The algorithms presented here are fast and scalable, and we find that because they are built on fast sorting algorithms they are more efficient than all other approaches we considered. After introducing these techniques, we present ASCI results applied to a large range of systems and basis sets to demonstrate the types of simulations that can be practically treated at the full-CI level with modern methods and hardware, presenting double- and triple-ζ benchmark data for the G1 data set. The largest of these calculations is Si2H6 which is a simulation of 34 electrons in 152 orbitals. We also present some preliminary results for fast deterministic perturbation theory simulations that use hash functions to maintain high efficiency for treating large basis sets

Long-range structural regularities and collectivity of folded proteins

Coarse-grained network models of proteins successfully predict equilibrium properties related to collective modes of motion. In this study, the network construction strategies and their systematic application to proteins are used to explain the role of network models in defining the collective properties of the system. The analysis is based on the radial distribution function, a newly defined angular distribution function and the spectral dimensions of a large set of globular proteins. Our analysis shows that after reaching a certain threshold for cut-off distance, network construction has negligible effect on the collective motions and the fluctuation patterns of the residues

Design and implementation of robust embedded processor for cryptographic applications

Practical implementations of cryptographic algorithms are vulnerable to side-channel analysis and fault attacks. Thus, some masking and fault detection algorithms must be incorporated into these implementations. These additions further increase the complexity of the cryptographic devices which already need to perform computationally-intensive operations. Therefore, the general-purpose processors are usually supported by coprocessors/hardware accelerators to protect as well as to accelerate cryptographic applications. Using a configurable processor is just another solution. This work designs and implements robust execution units as an extension to a configurable processor, which detect the data faults (adversarial or otherwise) while performing the arithmetic operations. Assuming a capable adversary who can injects faults to the cryptographic computation with high precision, a nonlinear error detection code with high error detection capability is used. The designed units are tightly integrated to the datapath of the configurable processor using its tool chain. For different configurations, we report the increase in the space and time complexities of the configurable processor. Also, we present performance evaluations of the software implementations using the robust execution units. Implementation results show that it is feasible to implement robust arithmetic units with relatively low overhead in an embedded processor

Portability of Prolog programs: theory and case-studies

(Non-)portability of Prolog programs is widely considered as an important factor in the lack of acceptance of the language. Since 1995, the core of the language is covered by the ISO standard 13211-1. Since 2007, YAP and SWI-Prolog have established a basic compatibility framework. This article describes and evaluates this framework. The aim of the framework is running the same code on both systems rather than migrating an application. We show that today, the portability within the family of Edinburgh/Quintus derived Prolog implementations is good enough to allow for maintaining portable real-world applications.Comment: Online proceedings of the Joint Workshop on Implementation of Constraint Logic Programming Systems and Logic-based Methods in Programming Environments (CICLOPS-WLPE 2010), Edinburgh, Scotland, U.K., July 15, 201

SWAPHI: Smith-Waterman Protein Database Search on Xeon Phi Coprocessors

The maximal sensitivity of the Smith-Waterman (SW) algorithm has enabled its wide use in biological sequence database search. Unfortunately, the high sensitivity comes at the expense of quadratic time complexity, which makes the algorithm computationally demanding for big databases. In this paper, we present SWAPHI, the first parallelized algorithm employing Xeon Phi coprocessors to accelerate SW protein database search. SWAPHI is designed based on the scale-and-vectorize approach, i.e. it boosts alignment speed by effectively utilizing both the coarse-grained parallelism from the many co-processing cores (scale) and the fine-grained parallelism from the 512-bit wide single instruction, multiple data (SIMD) vectors within each core (vectorize). By searching against the large UniProtKB/TrEMBL protein database, SWAPHI achieves a performance of up to 58.8 billion cell updates per second (GCUPS) on one coprocessor and up to 228.4 GCUPS on four coprocessors. Furthermore, it demonstrates good parallel scalability on varying number of coprocessors, and is also superior to both SWIPE on 16 high-end CPU cores and BLAST+ on 8 cores when using four coprocessors, with the maximum speedup of 1.52 and 1.86, respectively. SWAPHI is written in C++ language (with a set of SIMD intrinsics), and is freely available at http://swaphi.sourceforge.net.Comment: A short version of this paper has been accepted by the IEEE ASAP 2014 conferenc

Exact solution of the Percus-Yevick integral equation for fluid mixtures of hard hyperspheres

Structural and thermodynamic properties of multicomponent hard-sphere fluids at odd dimensions have recently been derived in the framework of the rational function approximation (RFA) [Rohrmann and Santos, Phys. Rev. E \textbf{83}, 011201 (2011)]. It is demonstrated here that the RFA technique yields the exact solution of the Percus-Yevick (PY) closure to the Ornstein-Zernike (OZ) equation for binary mixtures at arbitrary odd dimensions. The proof relies mainly on the Fourier transforms $\hat{c}_{ij}(k)$ of the direct correlation functions defined by the OZ relation. From the analysis of the poles of $\hat{c}_{ij}(k)$ we show that the direct correlation functions evaluated by the RFA method vanish outside the hard core, as required by the PY theory.Comment: 6 page

RPA Green's Functions of the Anisotropic Heisenberg Model

We solve in random-phase approximation the anisotropic Heisenberg model, including nearest and next-nearest neighbour interactions by calculating all Green's functions and pair correlation functions in a cumulant decoupling scheme. The general exposition is pedagogic in tone and is intended to be accessible to any graduate student or physicist who is not an expert in the field.Comment: 26 pages, 4 figure

Range corrections in Proton Halo Nuclei

We analyze the effects of finite-range corrections in halo effective field theory for S-wave proton halo nuclei. We calculate the charge radius to next-to-leading order and the astrophysical S-factor for low-energy proton capture to fifth order in the low-energy expansion. As an application, we confront our results with experimental data for the S-factor for proton capture on Oxygen-16 into the excited $1/2^+$ state of Fluorine-17. Our low-energy theory is characterized by a systematic low-energy expansion, which can be used to quantify an energy-dependent model error to be utilized in data fitting. Finally, we show that the existence of proton halos is suppressed by the need for two fine tunings in the underlying theory.Comment: 30pages, 12 figure