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Nandi S.,Tata Institute of Fundamental Research | Agnihotri A.N.,Tata Institute of Fundamental Research | Kasthurirangan S.,Institute of Chemical Technology | Kumar A.,Bhabha Atomic Research Center | And 5 more authors.
Physical Review A - Atomic, Molecular, and Optical Physics | Year: 2012

We have measured the absolute double-differential cross sections (DDCSs) for electron emission in ionization of O 2 molecules under the impact of 3.5-MeV/u C6 + ions. The data were collected between 10 and 600 eV, in an angular range of 30 - to 150 -. The single-differential cross sections (SDCSs) in emission angle and electron energy are deduced from the electron DDCS spectra. Also, the total cross section has been obtained from the SDCS spectra. The DDCS spectra as well as the SDCS spectra are compared with continuum distorted-wave eikonal initial-state calculations which employ molecular wave functions built as linear combinations of atomic orbitals. The DDCS ratio i.e. σ O 2/ 2σ O, derived by dividing the experimental DDCS for molecular oxygen with the theoretical DDCS for atomic oxygen, does not show any primary or secondary oscillations arising from Young-type interference, which is apparently in contrast to what has been observed earlier for H 2 and in agreement with the model calculation. Similarly, the forward-backward angular asymmetry increases monotonically with the velocity of the emitted electrons. However, the results on the DDCSs, SDCSs, the asymmetry parameter, and the nonexistence of oscillations are in qualitative agreement with the predictions of the model used. © 2012 American Physical Society. Source

Arias-Gonzalez J.R.,Instituto Madrileno Of Estudios Avanzados En Nanociencia | Arias-Gonzalez J.R.,CSIC - National Center for Biotechnology
PLoS ONE | Year: 2012

Information has an entropic character which can be analyzed within the framework of the Statistical Theory in molecular systems. R. Landauer and C.H. Bennett showed that a logical copy can be carried out in the limit of no dissipation if the computation is performed sufficiently slowly. Structural and recent single-molecule assays have provided dynamic details of polymerase machinery with insight into information processing. Here, we introduce a rigorous characterization of Shannon Information in biomolecular systems and apply it to DNA replication in the limit of no dissipation. Specifically, we devise an equilibrium pathway in DNA replication to determine the entropy generated in copying the information from a DNA template in the absence of friction. Both the initial state, the free nucleotides randomly distributed in certain concentrations, and the final state, a polymerized strand, are mesoscopic equilibrium states for the nucleotide distribution. We use empirical stacking free energies to calculate the probabilities of incorporation of the nucleotides. The copied strand is, to first order of approximation, a state of independent and non-indentically distributed random variables for which the nucleotide that is incorporated by the polymerase at each step is dictated by the template strand, and to second order of approximation, a state of non-uniformly distributed random variables with nearest-neighbor interactions for which the recognition of secondary structure by the polymerase in the resultant double-stranded polymer determines the entropy of the replicated strand. Two incorporation mechanisms arise naturally and their biological meanings are explained. It is known that replication occurs far from equilibrium and therefore the Shannon entropy here derived represents an upper bound for replication to take place. Likewise, this entropy sets a universal lower bound for the copying fidelity in replication. © 2012 J. Ricurdo Arias-Gonzalez. Source

Calegari F.,CNR Institute of Neuroscience | Ayuso D.,Autonomous University of Madrid | Trabattoni A.,Polytechnic of Milan | Belshaw L.,Queens University of Belfast | And 11 more authors.
Science | Year: 2014

In the past decade, attosecond technology has opened up the investigation of ultrafast electronic processes in atoms, simple molecules, and solids. Here, we report the application of isolated attosecond pulses to prompt ionization of the amino acid phenylalanine and the subsequent detection of ultrafast dynamics on a sub-4.5-femtosecond temporal scale, which is shorter than the vibrational response of the molecule. The ability to initiate and observe such electronic dynamics in polyatomic molecules represents a crucial step forward in attosecond science, which is progressively moving toward the investigation of more and more complex systems. Source

Catoire F.,University of Bordeaux 1 | Silva R.E.F.,Autonomous University of Madrid | Riviere P.,Autonomous University of Madrid | Bachau H.,University of Bordeaux 1 | And 2 more authors.
Physical Review A - Atomic, Molecular, and Optical Physics | Year: 2014

We present an extension of the resolvent-operator method (ROM), originally designed for atomic systems, to extract differential photoelectron spectra (in photoelectron- and nuclear-kinetic energy) for diatomic molecules interacting with strong, ultrashort laser fields in the single active electron approximation. The method is applied to the study of H2+ photodissociation and photoionization by femtosecond laser pulses in the XUV-IR frequency range. In particular, the method is tested (i) in the perturbative regime, for few-photon absorption and bound-bound electronic transitions, and (ii) in the strong-field regime, in which multiphoton absorption and tunneling are present. In the latter case, we show how the differential ROM allows one to track the transition between both regimes. We also analyze isotopic effects by comparing the dynamics of H2+ and D2+ ionization for different pulses. © 2014 American Physical Society. Source

Yip F.L.,Autonomous University of Madrid | Rescigno T.N.,Lawrence Berkeley National Laboratory | McCurdy C.W.,Lawrence Berkeley National Laboratory | McCurdy C.W.,University of California at Davis | And 2 more authors.
Physical Review Letters | Year: 2013

Triply differential cross sections are calculated for one-photon double ionization of neon and argon at various photon energies and electron energy sharings by using a frozen-core treatment to represent the remaining electrons of the residual ion. Angular distributions agree well with all existing experimental data, showing that in spite of its simplicity the method can treat the double ionization of complex targets reliably. A comparison of the cross sections for helium, neon, and argon into the same final state symmetry at the same relative excess energies reveals a distinctive signature of the role of electron correlation in each target. © 2013 American Physical Society. Source

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