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Search Results: 1 - 10 of 394960 matches for " Julien Céré "
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Building an ecological knowledge of virtual worlds
Pierre-Olivier Montiglio,Julien Céré
PeerJ , 2015, DOI: 10.7287/peerj.preprints.473v1
Abstract: Virtual worlds supporting massively multiplayer games have become so complex that they exhibit temporal and spatial dynamics mostly driven by interactions between players. In this respect, virtual worlds resemble closely natural ecosystems. Studying the ecology of virtual worlds is an outstanding opportunity for ecologists as well as the game industry to collaborate in order to test several aspects of ecological theory difficult to study in nature, and build manageable, resilient virtual worlds.
Extended Recursion in Operator Space (EROS), a new impurity solver for the single impurity Anderson model
Jean-Pierre Julien,R. C. Albers
Physics , 2008,
Abstract: We have developed a new efficient and accurate impurity solver for the single impurity Anderson model (SIAM), which is based on a non-perturbative recursion technique in a space of operators and involves expanding the self-energy as a continued fraction. The method has no special occupation number or temperature restrictions; the only approximation is the number of levels of the continued fraction retained in the expansion. We also show how this approach can be used as a new approach to Dynamical Mean Field Theory (DMTF) and illustrate this with the Hubbard model. The three lowest orders of recursion give the Hartree-Fock, Hubbard I, and Hubbard III approximations. A higher level of recursion is able to reproduce the expected 3-peak structure in the spectral function and Fermi liquid behavior.
Compact and Flexible Basis Functions for Quantum Monte Carlo Calculations
F. R. Petruzielo,Julien Toulouse,C. J. Umrigar
Physics , 2009, DOI: 10.1063/1.3342062
Abstract: Molecular calculations in quantum Monte Carlo frequently employ a mixed basis consisting of contracted and primitive Gaussian functions. While standard basis sets of varying size and accuracy are available in the literature, we demonstrate that reoptimizing the primitive function exponents within quantum Monte Carlo yields more compact basis sets for a given accuracy. Particularly large gains are achieved for highly excited states. For calculations requiring non-diverging pseudopotentials, we introduce Gauss-Slater basis functions that behave as Gaussians at short distances and Slaters at long distances. These basis functions further improve the energy and fluctuations of the local energy for a given basis size. Gains achieved by exponent optimization and Gauss-Slater basis use are exemplified by calculations for the ground state of carbon, the lowest lying excited states of carbon with $^5S^o$, $^3P^o$, $^1D^o$, $^3F^o$ symmetries, carbon dimer, and naphthalene. Basis size reduction enables quantum Monte Carlo treatment of larger molecules at high accuracy.
Basis set construction for molecular electronic structure theory: Natural orbital and Gauss-Slater basis for smooth pseudpotentials
F. R. Petruzielo,Julien Toulouse,C. J. Umrigar
Physics , 2010, DOI: 10.1063/1.3551512
Abstract: A simple yet general method for constructing basis sets for molecular electronic structure calculations is presented. These basis sets consist of atomic natural orbitals from a multi-configurational self-consistent field calculation supplemented with primitive functions, chosen such that the asymptotics are appropriate for the potential of the system. Primitives are optimized for the homonuclear diatomic molecule to produce a balanced basis set. Two general features that facilitate this basis construction are demonstrated. First, weak coupling exists between the optimal exponents of primitives with different angular momenta. Second, the optimal primitive exponents for a chosen system depend weakly on the particular level of theory employed for optimization. The explicit case considered here is a basis set appropriate for the Burkatzki-Filippi-Dolg pseudopotentials. Since these pseudopotentials are finite at nuclei and have a Coulomb tail, the recently proposed Gauss-Slater functions are the appropriate primitives. Double- and triple-zeta bases are developed for elements hydrogen through argon. These new bases offer significant gains over the corresponding Burkatzki-Filippi-Dolg bases at various levels of theory. Using a Gaussian expansion of the basis functions, these bases can be employed in any electronic structure method. Quantum Monte Carlo provides an added benefit: expansions are unnecessary since the integrals are evaluated numerically.
Approaching Chemical Accuracy with Quantum Monte Carlo
F. R. Petruzielo,Julien Toulouse,C. J. Umrigar
Physics , 2012, DOI: 10.1063/1.3697846
Abstract: A quantum Monte Carlo study of the atomization energies for the G2 set of molecules is presented. Basis size dependence of diffusion Monte Carlo atomization energies is studied with a single determinant Slater-Jastrow trial wavefunction formed from Hartree-Fock orbitals. With the largest basis set, the mean absolute deviation from experimental atomization energies for the G2 set is 3.0 kcal/mol. Optimizing the orbitals within variational Monte Carlo improves the agreement between diffusion Monte Carlo and experiment, reducing the mean absolute deviation to 2.1 kcal/mol. Moving beyond a single determinant Slater-Jastrow trial wavefunction, diffusion Monte Carlo with a small complete active space Slater-Jastrow trial wavefunction results in near chemical accuracy. In this case, the mean absolute deviation from experimental atomization energies is 1.2 kcal/mol. It is shown from calculations on systems containing phosphorus that the accuracy can be further improved by employing a larger active space.
Rationalisation of the Differences between APOBEC3G Structures from Crystallography and NMR Studies by Molecular Dynamics Simulations
Flavia Autore,Julien R. C. Bergeron,Michael H. Malim,Franca Fraternali,Hendrik Huthoff
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0011515
Abstract: The human APOBEC3G (A3G) protein is a cellular polynucleotide cytidine deaminase that acts as a host restriction factor of retroviruses, including HIV-1 and various transposable elements. Recently, three NMR and two crystal structures of the catalytic deaminase domain of A3G have been reported, but these are in disagreement over the conformation of a terminal β-strand, β2, as well as the identification of a putative DNA binding site. We here report molecular dynamics simulations with all of the solved A3G catalytic domain structures, taking into account solubility enhancing mutations that were introduced during derivation of three out of the five structures. In the course of these simulations, we observed a general trend towards increased definition of the β2 strand for those structures that have a distorted starting conformation of β2. Solvent density maps around the protein as calculated from MD simulations indicated that this distortion is dependent on preferential hydration of residues within the β2 strand. We also demonstrate that the identification of a pre-defined DNA binding site is prevented by the inherent flexibility of loops that determine access to the deaminase catalytic core. We discuss the implications of our analyses for the as yet unresolved structure of the full-length A3G protein and its biological functions with regard to hypermutation of DNA.
Electrochemical Investigation of Oligonucleotide-DNA Hybridization on Poly(4-Methoxyphenethylamine)
Francielle B. Silva,Sabrina N. Vieira,Luiz R. Goulart,Julien F. C. Boodts
International Journal of Molecular Sciences , 2008,
Abstract: This work describes the immobilization of purine and pyrimidine bases and immobilization/hybridization of synthetic oligonucleotides on graphite electrodes modified with poly(4-methoxyphenethylamine) produced in acid medium. The immobilization of adenine, guanine, cytosine and thymine on these modified electrodes was efficient, producing characteristic peaks. Another relevant observation is that, according to the literature, pyrimidine bases, cytosine and thymine are more difficult to detect. However, when immobilized onto the poly(4-methoxyphenethylamine), a significant increase in the magnitude of the current was obtained. The observation of the hybridization between the poly(GA) probe and its complementary, poly(CT) target, was possible by monitoring the guanosine and adenosine peaks or through methylene blue indicator, using differential pulse voltammetry. Hybridization results in a decrease of the peak current of guanosine and adenosine or the signal of methylene blue accumulated on the modified electrode surface. The hybridization with the complementary target was also investigated by electrochemical impedance spectroscopy. The results showed a significant modification in the Nyquist plot, after addition of the complementary target, with increase of the charge transference resistance.
Alleviation of the Fermion-sign problem by optimization of many-body wave functions
C. J. Umrigar,Julien Toulouse,Claudia Filippi,S. Sorella,R. G. Hennig
Physics , 2006, DOI: 10.1103/PhysRevLett.99.179902
Abstract: We present a simple, robust and highly efficient method for optimizing all parameters of many-body wave functions in quantum Monte Carlo calculations, applicable to continuum systems and lattice models. Based on a strong zero-variance principle, diagonalization of the Hamiltonian matrix in the space spanned by the wav e function and its derivatives determines the optimal parameters. It systematically reduces the fixed-node error, as demonstrated by the calculation of the binding energy of the small but challenging C$_2$ molecule to the experimental accuracy of 0.02 eV.
Whole-genome in-silico subtractive hybridization (WISH) - using massive sequencing for the identification of unique and repetitive sex-specific sequences: the example of Schistosoma mansoni
Julien Portela, Christoph Grunau, Céline Cosseau, Sophie Beltran, Christelle Dantec, Hugues Parrinello,r?me Boissier
BMC Genomics , 2010, DOI: 10.1186/1471-2164-11-387
Abstract: Genomic DNA was extracted from male and female (heterogametic) S. mansoni adults and sequenced with a Genome Analyzer (Illumina). Sequences are available at the NCBI sequence read archive http://www.ncbi.nlm.nih.gov/Traces/sra/ webcite under study accession number SRA012151.6. Sequencing reads were aligned to the genome, and a pseudogenome composed of known repeats. Straightforward comparative bioinformatics analysis was performed to compare male and female schistosome genomes and identify female-specific sequences. We found that the S. mansoni female W chromosome contains only few specific unique sequences (950 Kb i.e. about 0.2% of the genome). The majority of W-specific sequences are repeats (10.5 Mb i.e. about 2.5% of the genome). Arbitrarily selected W-specific sequences were confirmed by PCR. Primers designed for unique and repetitive sequences allowed to reliably identify the sex of both larval and adult stages of the parasite.Our genome-to-genome comparison method that we call "whole-genome in-silico subtractive hybridization" (WISH) allows for rapid identification of sequences that are specific for a certain genotype (e.g. the heterogametic sex). It can in principle be used for the detection of any sequence differences between isolates (e.g. strains, pathovars) or even closely related species.Massive sequencing, or next-generation sequencing (NGS), has remarkably reduced the cost, time and amount of biological material required for (re-)sequencing of entire genomes. Recently, for instance, whole-genome wide sequence variation in Caenorhabditis elegans was assessed comparing Solexa Sequence Analyser reads to a reference genome (strain-to-reference comparison) [1]. In principle, it is possible with this method to identify differences between genomes without a priori knowledge of their location in the genome. This is a fundamental question in many ecological or medical important species. Here, we describe how to identify differences in the DNA sequence of two
The SOCS-Box of HIV-1 Vif Interacts with ElonginBC by Induced-Folding to Recruit Its Cul5-Containing Ubiquitin Ligase Complex
Julien R. C. Bergeron,Hendrik Huthoff,Dennis A. Veselkov,Rebecca L. Beavil,Peter J. Simpson,Stephen J. Matthews,Michael H. Malim ,Mark R. Sanderson
PLOS Pathogens , 2010, DOI: 10.1371/journal.ppat.1000925
Abstract: The HIV-1 viral infectivity factor (Vif) protein recruits an E3 ubiquitin ligase complex, comprising the cellular proteins elongin B and C (EloBC), cullin 5 (Cul5) and RING-box 2 (Rbx2), to the anti-viral proteins APOBEC3G (A3G) and APOBEC3F (A3F) and induces their polyubiquitination and proteasomal degradation. In this study, we used purified proteins and direct in vitro binding assays, isothermal titration calorimetry and NMR spectroscopy to describe the molecular mechanism for assembly of the Vif-EloBC ternary complex. We demonstrate that Vif binds to EloBC in two locations, and that both interactions induce structural changes in the SOCS box of Vif as well as EloBC. In particular, in addition to the previously established binding of Vif's BC box to EloC, we report a novel interaction between the conserved Pro-Pro-Leu-Pro motif of Vif and the C-terminal domain of EloB. Using cell-based assays, we further show that this interaction is necessary for the formation of a functional ligase complex, thus establishing a role of this motif. We conclude that HIV-1 Vif engages EloBC via an induced-folding mechanism that does not require additional co-factors, and speculate that these features distinguish Vif from other EloBC specificity factors such as cellular SOCS proteins, and may enhance the prospects of obtaining therapeutic inhibitors of Vif function.
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