Interplay between the Gentlest Ascent Dynamics Method and Conjugate Directions to Locate Transition States

An algorithm to locate transition states on a potential energy surface (PES) is proposed and described. The technique is based on the GAD method where the gradient of the PES is projected into a given direction and also perpendicular to it. In the proposed method, named GAD-CD, the projection is not only applied to the gradient but also to the Hessian matrix. Then, the resulting Hessian matrix is block diagonal. The direction is updated according to the GAD method. Furthermore, to ensure stability and to avoid a high computational cost, a trust region technique is incorporated and the Hessian matrix is updated at each iteration. The performance of the algorithm in comparison with the standard ascent dynamics is discussed for a simple two dimensional model PES. Its efficiency for describing the reaction mechanisms involving small and medium size molecular systems is demonstrated for five molecular systems of interest

Quantum Zermelo problem for general energy resource bounds

A solution to the quantum Zermelo problem for control Hamiltonians with general energy resource bounds is provided. Interestingly, the energy resource of the control Hamiltonian and the control time define a pair of conjugate variables that minimize the energy-time uncertainty relation. The resulting control protocol is applied to a single qubit as well as to a two-interacting qubit system represented by a Heisenberg spin dimer. For these low-dimensional systems, it is found that physically realizable control Hamiltonians exist only for certain, quantized, energy resources.Comment: 13 pages, 1 figur

Quantum equilibration of the double-proton transfer in a model system porphine

There is a renewed interest in the derivation of statistical mechanics from the dynamics of closed quantum systems. A central part of this program is to understand how closed quantum systems, i.e., in the absence of a thermal bath, initialized far-from-equilibrium can share a dynamics that is typical to the relaxation towards thermal equilibrium. Equilibration dynamics has been traditionally studied with a focus on the so-called quenches of large-scale many-body systems. We consider here the equilibration of a two-dimensional molecular model system describing the double proton transfer reaction in porphine. Using numerical simulations, we show that equilibration indeed takes place very rapidly (∼200 fs) for initial states induced by pump–dump laser pulse control with energies well above the synchronous barrier. The resulting equilibration state is characterized by a strong delocalization of the probability density of the protons that can be explained, mechanistically, as the result of (i) an initial state consisting of a large superposition of vibrational states, and (ii) the presence of a very effective dephasing mechanism

Congenital Chagas’ disease transmission in the United States: Diagnosis in adulthood

Two brothers with congenitally-acquired Chagas’ disease (CD) diagnosed during adulthood are reported. The patients were born in the USA to a mother from Bolivia who on subsequent assessment was found to be serologically positive for Trypanosoma cruzi. Serologic screening of all pregnant women who migrated from countries with endemic CD is strongly recommended

Optimal Oriented External Electric Fields to Trigger a Barrierless Oxaphosphetane Ring Opening Step of the Wittig Reaction

The Wittig reaction is one of the most important processes in organic chemistry for the asymmetric synthesis of olefinic compounds. In view of the increasingly acknowledged potentiality of the electric fields in promoting reactions, here we will consider the effect of the oriented external electric field (OEEF) on the second step of Wittig reaction (i. e. the ring opening oxaphosphetane) in a model system for non-stabilized ylides. In particular, we have determined the optimal direction and strength of the electric field that should be applied to annihilate the reaction barrier of the ring opening through the polarizable molecular electric dipole (PMED) model that we have recently developed. We conclude that the application of the optimal external electric field for the oxaphosphetane ring opening favours a Bestmann-like mechanism. The perturbed potential energy surface of the oxaphosphetane ring opening due to the optimal electric field demonstrates that the process occurs by first breaking the P-C bond and then breaking the O-C bond. imag

The response of the different soybean metallothionein isoforms to cadmium intoxication

Cadmium is a highly toxic heavy metal for both plants and animals. The presence of Cd in agricultural soils is of major concern regarding its entry into the food chain, since Cd compounds are readily taken up by plants, and accumulated in edible parts due to their high solubility. In this study, we first demonstrate the high capacity for Cd concentration of soybean grains. Consequently, we considered the study and characterization of the molecular determinants of Cd accumulation -such as metallothioneins (MT)- to be of major practical importance. We report here the first characterization of the soybean MT system, with the identification of nine genes (one of which is a truncated pseudogene), belonging to the four plant MT types. The most highly expressed of each type was chosen for further function analysis. All of them are expressed at high levels in soybean tissues: GmMT1, GmMT2 and GmMT3 in roots, shoots and seeds, and GmMT4 only in seeds. The corresponding recombinant soybean MTs, synthesized in Escherichia coli cells cultured in metal supplemented media, exhibit greater cadmium than zinc binding capacity. These results suggest a definite role of GmMTs in Cd(II) accumulation as one of the main responses of soybean to an overload of this metal.Fil: Pagani, María Ayelén. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Centro de Estudios Fotosintéticos y Bioquímicos. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Centro de Estudios Fotosintéticos y Bioquímicos; ArgentinaFil: Tomas, M.. Universidad de Barcelona; España. Universitat Autònoma de Barcelona; EspañaFil: Carrillo, Julieta Beatriz. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Centro de Estudios Fotosintéticos y Bioquímicos. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Centro de Estudios Fotosintéticos y Bioquímicos; ArgentinaFil: Bofill, R.. Universitat Autònoma de Barcelona; EspañaFil: Capdevila, M.. Universitat Autònoma de Barcelona; EspañaFil: Atrian, S. Universidad de Barcelona; EspañaFil: Andreo, Carlos Santiago. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Centro de Estudios Fotosintéticos y Bioquímicos. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Centro de Estudios Fotosintéticos y Bioquímicos; Argentin

Speeding up the constraint-based method in difference logic

"The final publication is available at http://link.springer.com/chapter/10.1007%2F978-3-319-40970-2_18"Over the years the constraint-based method has been successfully applied to a wide range of problems in program analysis, from invariant generation to termination and non-termination proving. Quite often the semantics of the program under study as well as the properties to be generated belong to difference logic, i.e., the fragment of linear arithmetic where atoms are inequalities of the form u v = k. However, so far constraint-based techniques have not exploited this fact: in general, Farkas’ Lemma is used to produce the constraints over template unknowns, which leads to non-linear SMT problems. Based on classical results of graph theory, in this paper we propose new encodings for generating these constraints when program semantics and templates belong to difference logic. Thanks to this approach, instead of a heavyweight non-linear arithmetic solver, a much cheaper SMT solver for difference logic or linear integer arithmetic can be employed for solving the resulting constraints. We present encouraging experimental results that show the high impact of the proposed techniques on the performance of the VeryMax verification systemPeer ReviewedPostprint (author's final draft

Detection and quantification of classic and emerging viruses by skimmed-milk flocculation and PCR in river water from two geographical areas

Molecular techniques and virus concentration methods have shown that previously unknown viruses are shed by humans and animals, and may be transmitted by sewage-contaminated water. In the present study, river water from urban areas in Barcelona, Spain and Rio de Janeiro, Brazil, were analyzed to evaluate the dissemination of human viruses, while simultaneously optimizing and validating a low-cost concentration method for virus quantification in fresh water. The following three viral groups were analyzed. (i) Recently described viruses: klassevirus (KV), asfarvirus-like virus (ASFLV), and the polyomaviruses Merkel cell, KI and WU (MCPyV/KIPyV/WUPyV). (ii) Gastroenteritis agents: noroviruses (NoV) and rotaviruses (RV). (iii) Human fecal viral indicators in water: human adenoviruses (HAdV) and JC polyomaviruses (JCPyV). Virus detection was based on nested and quantitative PCR assays. Nested PCR assays were developed for KV and ASFLV. The method applied for virus concentration in water samples was a one-step procedure based on a skimmed milk flocculation procedure described previously for seawater. Using spiked river water samples, inter- and intra-laboratory assays showed a viral recovery rate of about 50% for HAdV, JCPyV, NoV and RV with a coefficient of variation ≤ 50%. HAdV and JCPyV were detected in 100% of the river samples from Barcelona and Rio de Janeiro. Moreover, NoV GGII was detected in 100% and MCPyV in 50% of the samples from Barcelona, whereas none of the other viruses analyzed were detected. NoV GGII was detected in 33%, KV in 33%, ASFLV in 17% and MCPyV in 50% of the samples from Rio de Janeiro, whereas KIPyV and WUPyV were not detected. RV were only tested for in Rio de Janeiro and resulted positive in 67% of the samples. The procedure applied here to river water represents a useful, straightforward and cost-effective method that could be applied in routine water quality testing.  The results of the assays expand our understanding of the global distribution of the viral pathogens studied here and their persistence in the environment. Fil: Calgua, B.. Universidad de Barcelona; España;Fil: Fumian, T.. Ministerio de Salud de Brasil. Fundacion Oswaldo Cruz; Brasil;Fil: Rusinol, M.. Universidad de Barcelona; España;Fil: Rodríguez Manzano, J.. Universidad de Barcelona; España;Fil: Mbayed, Viviana Andrea. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología y Biotecnología. Cátedra de Virología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay; ArgentinaFil: Bofill Mas, S.. Universidad de Barcelona; España;Fil: Miagostovich, M.. Ministerio de Salud de Brasil. Fundacion Oswaldo Cruz; Brasil;Fil: Girones, R.. Universidad de Barcelona; España

A Doubly Nudged Elastic Band Method for Finding Transition States

A modification of the nudged elastic band (NEB) method is presented that enables stable optimisations to be run using both the limited-memory quasi-Newton (L-BFGS) and slow-response quenched velocity Verlet (SQVV) minimisers. The performance of this new `doubly nudged' DNEB method is analysed in conjunction with both minimisers and compared with previous NEB formulations. We find that the fastest DNEB approach (DNEB/L-BFGS) can be quicker by up to two orders of magnitude. Applications to permutational rearrangements of the seven-atom Lennard-Jones cluster (LJ7) and highly cooperative rearrangements of LJ38 and LJ75 are presented. We also outline an updated algorithm for constructing complicated multi-step pathways using successive DNEB runs.Comment: 13 pages, 8 figures, 2 table