State-Selective Studies of T→R, V Energy Transfer: The H+CO System

Collisional energy transfer from H atoms to CO(v=0, J≈2) has been studied at a collision energy of 1.58±0.07 eV by photolyzing H2S at 222 nm in a nozzle expansion with CO and probing the CO(v , J ) levels using tunable VUV laser-induced fluorescence. The ratio CO(v =1)/CO(v =0) is found to be 0.1±0.008. The rotational distribution of CO(v =0) peaks at J gradually; population is still observed at J \u3e45. The rotational distribution of CO(v =1) is broad and peaks near J =20. The experimental results are compared to quasiclassical trajectory calculations performed both on the H+CO surface of Bowman, Bittman, and Harding (BBH) and on the surface of Murrell and Rodriguez (MR). The experimental rotational distributions, particularly those for CO(v =1), show that the BBH surface is a better model than the MR surface. The most significant difference between the two surfaces appears to be that for energetically accessible regions of configuration space the derivative of the potential with respect to the CO distance is appreciable only in the HCO valley for the BBH surface, but is large for all H atom approaches in the MR potential. Because the H-CO geometry is bent in this valley, vibrational excitation on the BBH surface is accompanied by appreciable rotational excitation, as observed experimentally

Ab-initio study of the relation between electric polarization and electric field gradients in ferroelectrics

The hyperfine interaction between the quadrupole moment of atomic nuclei and the electric field gradient (EFG) provides information on the electronic charge distribution close to a given atomic site. In ferroelectric materials, the loss of inversion symmetry of the electronic charge distribution is necessary for the appearance of the electric polarization. We present first-principles density functional theory calculations of ferroelectrics such as BaTiO3, KNbO3, PbTiO3 and other oxides with perovskite structures, by focusing on both EFG tensors and polarization. We analyze the EFG tensor properties such as orientation and correlation between components and their link with electric polarization. This work supports previous studies of ferroelectric materials where a relation between EFG tensors and polarization was observed, which may be exploited to study ferroelectric order when standard techniques to measure polarization are not easily applied.Comment: 9 pages, 6 figures, 5 tables, corrected typos, as published in Phys. Rev.

Dissociative electron attachment to the H2O molecule. II. Nuclear dynamics on coupled electronic surfaces within the local complex potential model

We report the results of a first-principles study of dissociative electron attachment to H2O. The cross sections are obtained from nuclear dynamics calculations carried out in full dimensionality within the local complex potential model by using the multi-configuration time-dependent Hartree method. The calculations employ our previously obtained global, complex-valued, potential-energy surfaces for the three (doublet B1, doublet A1, and doublet B2) electronic Feshbach resonances involved in this process. These three metastable states of H2O- undergo several degeneracies, and we incorporate both the Renner-Teller coupling between the B1 and A1 states as well as the conical intersection between the A1 and B2 states into our treatment. The nuclear dynamics are inherently multidimensional and involve branching between different final product arrangements as well as extensive excitation of the diatomic fragment. Our results successfully mirror the qualitative features of the major fragment channels observed, but are less successful in reproducing the available results for some of the minor channels. We comment on the applicability of the local complex potential model to such a complicated resonant system.Comment: Corrected version of Phys Rev A 75, 012711 (2007

Statistical inference of the generation probability of T-cell receptors from sequence repertoires

Stochastic rearrangement of germline DNA by VDJ recombination is at the origin of immune system diversity. This process is implemented via a series of stochastic molecular events involving gene choices and random nucleotide insertions between, and deletions from, genes. We use large sequence repertoires of the variable CDR3 region of human CD4+ T-cell receptor beta chains to infer the statistical properties of these basic biochemical events. Since any given CDR3 sequence can be produced in multiple ways, the probability distribution of hidden recombination events cannot be inferred directly from the observed sequences; we therefore develop a maximum likelihood inference method to achieve this end. To separate the properties of the molecular rearrangement mechanism from the effects of selection, we focus on non-productive CDR3 sequences in T-cell DNA. We infer the joint distribution of the various generative events that occur when a new T-cell receptor gene is created. We find a rich picture of correlation (and absence thereof), providing insight into the molecular mechanisms involved. The generative event statistics are consistent between individuals, suggesting a universal biochemical process. Our distribution predicts the generation probability of any specific CDR3 sequence by the primitive recombination process, allowing us to quantify the potential diversity of the T-cell repertoire and to understand why some sequences are shared between individuals. We argue that the use of formal statistical inference methods, of the kind presented in this paper, will be essential for quantitative understanding of the generation and evolution of diversity in the adaptive immune system.Comment: 20 pages, including Appendi

Single-molecule analysis of RAG-mediated V(D)J DNA cleavage

The recombination-activating gene products, RAG1 and RAG2, initiate V(D)J recombination during lymphocyte development by cleaving DNA adjacent to conserved recombination signal sequences (RSSs). The reaction involves DNA binding, synapsis, and cleavage at two RSSs located on the same DNA molecule and results in the assembly of antigen receptor genes. We have developed single-molecule assays to examine RSS binding by RAG1/2 and their cofactor high-mobility group-box protein 1 (HMGB1) as they proceed through the steps of this reaction. These assays allowed us to observe in real time the individual molecular events of RAG-mediated cleavage. As a result, we are able to measure the binding statistics (dwell times) and binding energies of the initial RAG binding events and characterize synapse formation at the single-molecule level, yielding insights into the distribution of dwell times in the paired complex and the propensity for cleavage on forming the synapse. Interestingly, we find that the synaptic complex has a mean lifetime of roughly 400 s and that its formation is readily reversible, with only ∼40% of observed synapses resulting in cleavage at consensus RSS binding sites

Surface plasmons at single nanoholes in Au-films

The generation of surface plasmon polaritons (SPP's) at isolated nanoholes in 100 nm thick Au films is studied using near-field scanning optical microscopy (NSOM). Finite-difference time-domain calculations, some explicitly including a model of the NSOM tip, are used to interpret the results. We find the holes act as point-like sources of SPP's and demonstrate that interference between SPP's and a directly transmitted wave allows for determination of the wavelength, phase, and decay length of the SPP. The near-field intensity patterns can be manipulated by varying the angle and polarization of the incident beam.Comment: 12 pages, 3 figure

An Approximation for the rp-Process

Hot (explosive) hydrogen burning or the Rapid Proton Capture Process (rp-process) occurs in a number of astrophysical environments. Novae and X-ray bursts are the most prominent ones, but accretion disks around black holes and other sites are candidates as well. The expensive and often multidimensional hydro calculations for such events require an accurate prediction of the thermonuclear energy generation, while avoiding full nucleosynthesis network calculations. In the present investigation we present an approximation scheme applicable in a temperature range which covers the whole range of all presently known astrophysical sites. It is based on the concept of slowly varying hydrogen and helium abundances and assumes a kind of local steady flow by requiring that all reactions entering and leaving a nucleus add up to a zero flux. This scheme can adapt itself automatically and covers situations at low temperatures, characterized by a steady flow of reactions, as well as high temperature regimes where a $(p,\gamma)-(\gamma,p)$-equilibrium is established. In addition to a gain of a factor of 15 in computational speed over a full network calculation, and an energy generation accurate to more than 15 %, this scheme also allows to predict correctly individual isotopic abundances. Thus, it delivers all features of a full network at a highly reduced cost and can easily be implemented in hydro calculations.Comment: 18 pages, LaTeX using astrobib and aas2pp4, includes PostScript figures; Astrophysical Journal, in press. PostScript source also available at http://quasar.physik.unibas.ch/preps.htm

Thermal neutron induced (n,p) and (n,alpha) reactions on 37Ar

The 37Ar(n_th,alpha)34S and 37Ar(n_th,p)37Cl reactions were studied at the high flux reactor of the ILL in Grenoble. For the 37Ar(n_th,alpha_0) and 37Ar(n_th,p) reaction cross sections, values of (1070+/-80)b and (37+/-4)b, respectively, were obtained. Both values are about a factor 2 smaller than results of older measurements. The observed suppression of the 37(n_th,alpha_1) transition could be verified from theoretical considerations. Finally, evidence was found for the two-step 37Ar(n_th,gamma-alpha) process.Comment: 11 pages, 5 figures, accepted for publication in Nuclear Physics

Critical Point For The Blue-Phase-III-Isotropic Phase Transition In Chiral Liquid Crystals

The highly chiral compound S,S-4 \u27\u27-(methylbutyl)phenyl-4\u27-(methylbutyl) biphenyl carboxylate (S,S-MBBPC) undergoes a continuous supercritical evolution from the isotropic (I) phase to the third blue phase (BPI III). Mixtures of S,S-MBBPC and its racemate have been studied with high-resolution calorimetry capable of quantitative latent heat determinations and with optical activity measurements. Both experiments indicate that the first-order BP III-I transition line ends at a critical point when the chiral mole fraction X(c) similar or equal to 0.45. Analysis of C-p and optical activity data for the near-critical mixture with X = 0.45 indicates mean-field behavior instead of the theoretically predicted Ising fluctuation behavior, which would be analogous to that at the liquid-gas critical point of a simple fluid. It is speculated that the Ginzburg criterion can explain this mean-field behavior since the critical regime may be too small for experimental observation, as is the case for almost all Smectic-A -Smectic-C transitions