Search results for "REDUCE"
showing 10 items of 233 documents
The CCSD(T) model with Cholesky decomposition of orbital energy denominators
2010
A new implementation of the coupled cluster singles and doubles with approximate triples correction method [CCSD(T)] using Cholesky decomposition of the orbital energy denominators is described. The new algorithm reduces the scaling of CCSD(T) from N-7 to N-6, where N is the number of orbitals. The Cholesky decomposition is carried out using simple analytical expressions that allow us to evaluate a priori the order in which the decomposition should be carried out and to obtain the relevant parts of the vectors whenever needed in the calculation. Several benchmarks have been carried out comparing the performance of the conventional and Cholesky CCSD(T) implementations. The Cholesky implement…
Meaning and magnitude of the reduced density matrix cumulants
2012
Abstract Within the framework of a generalized normal ordering (GNO), invented by Mukherjee [1] , the reduced density matrix cumulants of the (multiconfigurational) reference wave function play a central role, as they arise directly from the contraction rules. The extended Wick theorem allows contractions of an arbitrary number of active annihilators and creators through a cumulant of corresponding rank. Because the cumulant rank truncates naturally only at the number of active spin orbitals, practical applications of the GNO concept seem to rely on a fast convergence of the cumulant series, allowing one to neglect cumulants with high rank. By computing cumulant norms for selected systems (…
The influence of the cycloid disc bearing type on the cycloidal speed reducer efficiency
2021
The robotics industry has experienced a rapid expansion in the last decade. As a result, the market of speed reducers with high gear ratios, high precision and a compact design is growing rapidly. In addition to these characteristics, it is very important for gear trains to have high efficiency. Because of their compact design, cycloidal speed reducers are not exposed to axial forces, which is their important characteristic. This means that radial bearings can be used in their supports. The bearing type has significant effects not only on the design and dimensions of the cycloid speed reducer but also on its efficiency. In this paper, an analysis of power losses for different types of rolli…
FASTA/Q data compressors for MapReduce-Hadoop genomics: space and time savings made easy
2021
Abstract Background Storage of genomic data is a major cost for the Life Sciences, effectively addressed via specialized data compression methods. For the same reasons of abundance in data production, the use of Big Data technologies is seen as the future for genomic data storage and processing, with MapReduce-Hadoop as leaders. Somewhat surprisingly, none of the specialized FASTA/Q compressors is available within Hadoop. Indeed, their deployment there is not exactly immediate. Such a State of the Art is problematic. Results We provide major advances in two different directions. Methodologically, we propose two general methods, with the corresponding software, that make very easy to deploy …
Efficient prediction of thermodynamic properties of quadrupolar fluids from simulation of a coarse-grained model: the case of carbon dioxide.
2008
Monte Carlo simulations are presented for a coarse-grained model of real quadrupolar fluids. Molecules are represented by particles interacting with Lennard-Jones forces plus the thermally averaged quadrupole-quadrupole interaction. The properties discussed include the vapor-liquid coexistence curve, the vapor pressure along coexistence, and the surface tension. The full isotherms are also accessible over a wide range of temperatures and densities. It is shown that the critical parameters (critical temperature, density, and pressure) depend almost linearly on a quadrupolar parameter q=Q(*4)T*, where Q* is the reduced quadrupole moment of the molecule and T* the reduced temperature. The mode…
Mapreduce in computational biology - A synopsis
2017
In the past 20 years, the Life Sciences have witnessed a paradigm shift in the way research is performed. Indeed, the computational part of biological and clinical studies has become central or is becoming so. Correspondingly, the amount of data that one needs to process, compare and analyze, has experienced an exponential growth. As a consequence, High Performance Computing (HPC, for short) is being used intensively, in particular in terms of multi-core architectures. However, recently and thanks to the advances in the processing of other scientific and commercial data, Distributed Computing is also being considered for Bioinformatics applications. In particular, the MapReduce paradigm, to…
Mapreduce in computational biology via hadoop and spark
2017
Bioinformatics has a long history of software solutions developed on multi-core computing systems for solving computational intensive problems. This option suffer from some issues solvable by shifting to Distributed Systems. In particular, the MapReduce computing paradigm, and its implementations, Hadoop and Spark, is becoming increasingly popular in the Bioinformatics field because it allows for virtual-unlimited horizontal scalability while being easy-to-use. Here we provide a qualitative evaluation of some of the most significant MapReduce bioinformatics applications. We also focus on one of these applications to show the importance of correctly engineering an application to fully exploi…
Tumor and its microenvironment: a synergistic interplay.
2013
The mutual and interdependent interaction between tumor and its microenvironment is a crucial topic in cancer research. Recently, it was reported that targeting stromal events could improve efficacies of current therapeutics and prevent metastatic spreading. Tumor microenvironment is a "complex network" of different cell types, soluble factors, signaling molecules and extracellular matrix components, which orchestrate the fate of tumor progression. As by definition, cancer stem cells (CSCs) are proposed to be the unique cell type able to maintain tumor mass and survive outside the primary tumor at metastatic sites. Being exposed to environmental stressors, including reactive oxygen species …
Feasibility of thiotepa addition to the fludarabine-busulfan conditioning with tacrolimus/sirolimus as graft vs host disease prophylaxis.
2020
In classical reduced-intensity conditioning (RIC) regimens, including the fludarabine and busulphan (BF) combination, sirolimus and tacrolimus (SIR-TAC) as graft vs host disease (GVHD) prophylaxis has shown acceptable results. The outcomes of SIR-TAC in a more intense RIC regimen as Thiotepa-fludarabine-busulfan (TBF) have been hardly investigated. This retrospective study included all consecutive patients receiving an allogeneic hematopoietic stem cell transplantation for myeloid malignancies (January 2009-2017) conditioned with either TBF or BF and receiving SIR-TAC. Patients receiving TBF presented higher non-relapse mortality (31.6 vs 12.3%,p = .01), along with shorter overall survival …
Carbapenem-Susceptible OXA-23-Producing Proteus mirabilis in the French Community
2019
International audience; Nineteen Proteus mirabilis isolates producing the carbapenemase OXA-23 were recovered over a 2-year period in 19 French hospitalized patients, of whom 12 had community onset infections. The isolates exhibited a slightly reduced susceptibility to carbapenems. Whole-genome analysis revealed that all 19 isolates formed a cluster compared to 149 other P. mirabilis isolates. Because of its susceptibility to carbapenems, this clone may be misidentified as a penicillinase producer while it constitutes a reservoir of the OXA-23-encoding gene in the community.