Understanding chemical reactions within a generalized Hamilton-Jacobi framework

Reaction paths and classical and quantum trajectories are studied within a generalized Hamilton-Jacobi framework, which allows to put on equal footing topology and dynamics in chemical reactivity problems. In doing so, we show how high-dimensional problems could be dealt with by means of Caratheodory plots or how trajectory-based quantum-classical analyses reveal unexpected discrepancies. As a working model, we consider the reaction dynamics associated with a Mueller-Brown potential energy surface, where we focus on the relationship between reaction paths and trajectories as well as on reaction probability calculations from classical and quantum trajectories.Comment: 22 pages, 5 figures, 1 tabl

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

MPI+OpenMP tasking scalability for the simulation of the human brain

The simulation of the behavior of the Human Brain is one of the most ambitious challenges today with a non-end of important applications. We can find many different initiatives in the USA, Europe and Japan which attempt to achieve such a challenging target. In this work we focus on the most important European initiative (Human Brain Project) and on one of the tools (Arbor). This tool simulates the spikes triggered in a neuronal network by computing the voltage capacitance on the neurons' morphology, being one of the most precise simulators today. In the present work, we have evaluated the use of MPI+OpenMP tasking on top of the Arbor simulator. In this paper, we present the main characteristics of the Arbor tool and how these can be efficiently managed by using MPI+OpenMP tasking. We prove that this approach is able to achieve a good scaling even when computing a relatively low workload (number of neurons) per node using up to 32 nodes. Our target consists of achieving not only a highly scalable implementation based on MPI, but also to develop a tool with a high degree of abstraction without losing control and performance by using MPI+OpenMP tasking.We would like to apreciate the valuable feedback and help provided by Benjamin Cumming and Alexander Peyser. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 720270 (HBP SGA1 and HBP SGA2), from the Spanish Ministry of Economy and Competitiveness under the project Computacion de Altas Prestaciones VII (TIN2015- ´ 65316-P) and the Departament d’Innovacio, Universitats i ´ Empresa de la Generalitat de Catalunya, under project MPEXPAR: Models de Programacio i Entorns d’Execuci ´ o Paral ´ ·lels (2014-SGR-1051). This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska Curie grand agreement No.749516Peer ReviewedPostprint (author version

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

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

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

Equity, barriers and cancer disparities: study of the Spanish Society of Medical Oncology on the access to oncologic drugs in the Spanish Regions

[Purpose] The Spanish Society of Medical Oncology (SEOM) has conducted a study on the access to oncologic drugs across the 17 Spanish Regions with the aim of identifying potential heterogeneities and making proposals for eliminating the barriers identified at the different levels.[Methods] An Expert Panel made up of medical oncologists designed a survey on certain indications approved for 11 drugs in the approach of breast cancer, melanoma, lung cancer, prostate cancer and support treatment. This survey was sent to 144 National Health System (NHS) hospitals. [Results] 77 hospitals answered the survey. The information modules analysed were: scope of the Commission that establishes binding decisions related to drug access; conditions, stages and periods of drug application, approval and administration processes; barriers to accessing drugs. [Conclusions] The study shows variability in drug access. The SEOM makes proposals addressed to reducing the differences identified and homogenizing drug access conditions.This study was funded by SEOM