Constraint methods for determining pathways and free energy of activated processes

Activated processes from chemical reactions up to conformational transitions of large biomolecules are hampered by barriers which are overcome only by the input of some free energy of activation. Hence, the characteristic and rate-determining barrier regions are not sufficiently sampled by usual simulation techniques. Constraints on a reaction coordinate r have turned out to be a suitable means to explore difficult pathways without changing potential function, energy or temperature. For a dense sequence of values of r, the corresponding sequence of simulations provides a pathway for the process. As only one coordinate among thousands is fixed during each simulation, the pathway essentially reflects the system's internal dynamics. From mean forces the free energy profile can be calculated to obtain reaction rates and insight in the reaction mechanism. In the last decade, theoretical tools and computing capacity have been developed to a degree where simulations give impressive qualitative insight in the processes at quantitative agreement with experiments. Here, we give an introduction to reaction pathways and coordinates, and develop the theory of free energy as the potential of mean force. We clarify the connection between mean force and constraint force which is the central quantity evaluated, and discuss the mass metric tensor correction. Well-behaved coordinates without tensor correction are considered. We discuss the theoretical background and practical implementation on the example of the reaction coordinate of targeted molecular dynamics simulation. Finally, we compare applications of constraint methods and other techniques developed for the same purpose, and discuss the limits of the approach

Physics with the KLOE-2 experiment at the upgraded DAϕ\phiNE

Investigation at a $\phi$--factory can shed light on several debated issues in particle physics. We discuss: i) recent theoretical development and experimental progress in kaon physics relevant for the Standard Model tests in the flavor sector, ii) the sensitivity we can reach in probing CPT and Quantum Mechanics from time evolution of entangled kaon states, iii) the interest for improving on the present measurements of non-leptonic and radiative decays of kaons and eta/eta$^\prime$ mesons, iv) the contribution to understand the nature of light scalar mesons, and v) the opportunity to search for narrow di-lepton resonances suggested by recent models proposing a hidden dark-matter sector. We also report on the $e^+ e^-$ physics in the continuum with the measurements of (multi)hadronic cross sections and the study of gamma gamma processes.Comment: 60 pages, 41 figures; added affiliation for one of the authors; added reference to section

Erratum: "A Gravitational-wave Measurement of the Hubble Constant Following the Second Observing Run of Advanced LIGO and Virgo" (2021, ApJ, 909, 218)

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A Dynamical and Kinematical Model of the Galactic Stellar Halo and Possible Implication for Galaxy Formation Scenarios

We re-analyse the kinematics of the system of blue horizontal branch field (BHBF) stars in the Galactic halo (in particular the outer halo), fitting the kinematics with the model of radial and tangential velocity dispersions in the halo as a function of galactocentric distance r proposed by Sommer-Larsen, Flynn & Christensen (1994), using a much larger sample (almost 700) of BHBF stars. The basic result is that the character of the stellar halo velocity ellipsoid changes markedly from radial anisotropy at the sun to tangential anisotropy in the outer parts of the Galactic halo (r greater than approx 20 kpc). Specifically, the radial component of the stellar halo's velocity ellipsoid decreases fairly rapidly beyond the solar circle, from approx 140 +/- 10 km/s at the sun, to an asymptotic value of 89 +/- 19 km/s at large r. The rapid decrease in the radial velocity dispersion is matched by an increase in the tangential velocity dispersion, with increasing r. Our results may indicate that the Galaxy formed hierarchically (partly or fully) through merging of smaller subsystems - the 'bottom-up' galaxy formation scenario, which for quite a while has been favoured by most theorists and recently also has been given some observational credibility by HST observations of a potential group of small galaxies, at high redshift, possibly in the process of merging to a larger galaxy (Pascarelle et al 1996)

A comparison of Raman, FTIR and ATR-FTIR micro spectroscopy for imaging human skin tissue sections

International audienceRaman and infrared absorption spectroscopies are compared for the analysis of human hand skin tissue sections. The tissue sections have been formalin fixed and paraffin processed, and subsequently dewaxed. Fourier Transform Infrared (FTIR) spectra are preprocessed using the resonant Mie-extended multiplicative scattering algorithm to remove spectral artefacts. FTIR images of resolution 4 cm−1, analysed using K-means cluster analysis, reveal the double layer structure of the dermis and epidermis, but no further layer differentiation is achieved using the higher spatial resolution of the Attenuated Total Reflection imaging or improved spectral resolution of 2 cm−1. At comparable spectral and spatial resolutions and measurement on the same samples, Raman scattering produces spectra of significantly higher spectral detail and can differentiate the stratum corneum from the underlying epithelial layer, and, in the absence of melanin in an artificial skin model, can further differentiate the basal layer from the overlying epithelium. The differences in the performance of the techniques are therefore not instrumentational and are discussed in terms of the technological and fundamental differences between the two complementary techniques