Three-Dimensional Trajectories of Spheroidal Particles in Two-Dimensional Flow Fields

We investigate the motion of homogeneous, spheroidal particles immersed in an incompressible, viscous fluid. We assume the particles to be more dense than the surrounding fluid and small enough that inertia is negligible with respect to viscous forces. We give exact solutions for the motion of the particle’s center of mass for steady, linear flows, either irrotational or without strain. For a weakly strained, two-dimensional, rotational flow we give an asymptotic approximation to the solutions, and we compare it with numerical solutions. In the presence of vorticity we find that the spheroid moves along three-dimensional, non-planar paths. With pure strain the three-dimensionality of the paths is transient. If a two-dimensional rotational flow is perturbed by strain, then the generic path of a spheroid is an open curve, even if all the streamlines of the flow are closed. We conclude by speculating about the significance of these findings for the ecology of phytoplankton.     

Environment-mediated control of a quantum system

Recently, a new approach for the controllability of a two-dimensional quantum system S has been proposed, based on its interaction with an initially uncorrelated two-dimensional probe P whose initial state can be arbitrarily modified. Following this scheme and considering a particular model for the environment, we show that, in some specific cases, the environment-induced entanglement is rich enough to completely control the dynamics of S. Under suitable conditions on the interaction of S, P, and the environment, we prove that the state of S can be driven to an arbitrary target state by varying the initial state of P.     

Formamide and the origin of life

The complexity of life boils down to the definition: “self-sustained chemical system capable of undergoing Darwinian evolution” (Joyce, 1994) [1]. The term “self-sustained” implies a set of chemical reactions capable of harnessing energy from the environment, using it to carry out programmed anabolic and catabolic functions. We briefly present our opinion on the general validity of this definition.Running anabolic and catabolic functions entails complex chemical information whose stability, reproducibility and evolution constitute the core of what is dubbed genetics.Life as-we-know-it is made of the intimate interaction of metabolism and genetics, both built around the chemistry of the most common elements of the Universe (hydrogen, oxygen, nitrogen, carbon). Other elements like phosphorus and sulphur play important but ancillary and potentially replaceable roles.The reproducible interaction of metabolic and genetic cycles results in the hypercycles of organization and de-organization of chemical information that we consider living entities. In order to approach the problem of the origin of life it is therefore reasonable to start from the assumption that both metabolism and genetics had a common origin, shared a common chemical frame, were embedded in physical–chemical conditions favourable for the onset of both.The most abundant three-atoms organic compound in interstellar environment is hydrogen cyanide HCN, the most abundant three-atoms inorganic compound is water H₂O. The combination of the two results in the formation of formamide H₂NCOH. We have explored the chemistry of formamide in conditions compatible with the synthesis and the stability of compounds of potential pre-genetic and pre-metabolic interest. We discuss evidence showing (i) that all the compounds necessary for the build-up of nucleic acids are easily obtained abiotically, (ii) that essentially all the steps leading to the spontaneous generation of RNA are abiotically possible, (iii) that the key compounds of extant metabolic cycles are obtained in the same chemical frame, often in the same test tube.How close are these observations to a plausible scenario for the origin of life?     

Structure validation of natural products by quantum-mechanical GIAO calculations of 13C NMR chemical shifts

Geometry optimization and GIAO (gauge including atomic orbitals) (13)C NMR chemical shift calculations at Hartree-Fock level, using the 6-31G(d) basis set, are proposed as a tool to be applied in the structural characterization of new organic compounds, thus providing useful support in the interpretation of experimental NMR data. Parameters related to linear correlation plots of computed versus experimental (13)C NMR chemical shifts for fourteen low-polar natural products, containing 10-20 carbon atoms, were employed to assess the reliability of the proposed structures. A comparison with the hybrid B3LYP method was carried out to evaluate electron correlation contributions to the calculation of (13)C NMR chemical shifts and, eventually, to extend the applicability of such computational methods to the interpretation of NMR spectra in apolar solutions. The method was tested by studying three examples of revised structure assignments, analyzing how the theoretical (13)C chemical shifts of both correct and incorrect structures matched the experimental data.     

Generalized limit analysis in poroplasticity by mathematical programming

Classical limit analysis of structures by the statical approach computationally means maximization of a load multiplier under equilibrium and yield condition constraints, namely convex mathematical programming. In elastoplasticity, generalizations of limit analysis had been proposed in order to achieve, still by load factor constrained optimization, the safety factor with respect to plastic collapse. This paper presents similar generalization in two-phase poroelastoplasticity. A method is here developed (and validated by numerical application to a masonry dam) apt to assess the safety factor of a structure interpretable as a poroplastic system, with respect to both plastic collapse and critical thresholds on deformations, by solving a nonconvex nonsmooth constrained optimization problem usually referred to in the literature as “mathematical program under equilibrium constraints”. Piece-wise linearization of yield surfaces and reduction of yield planes by a “sifting” procedure are adopted to reduce computing efforts.     

Cyclic RGD peptidomimetics containing bifunctional diketopiperazine scaffolds as new potent integrin ligands

The synthesis of eight bifunctional diketopiperazine (DKP) scaffolds is described; these were formally derived from 2,3-diaminopropionic acid and aspartic acid (DKP-1-DKP-7) or glutamic acid (DKP-8) and feature an amine and a carboxylic acid functional group. The scaffolds differ in the configuration at the two stereocenters and the substitution at the diketopiperazinic nitrogen atoms. The bifunctional diketopiperazines were introduced into eight cyclic peptidomimetics containing the Arg-Gly-Asp (RGD) sequence. The resulting RGD peptidomimetics were screened for their ability to inhibit biotinylated vitronectin binding to the purified integrins α(v)β(3) and α(v)β(5), which are involved in tumor angiogenesis. Nanomolar IC(50) values were obtained for the RGD peptidomimetics derived from trans DKP scaffolds (DKP-2-DKP-8). Conformational studies of the cyclic RGD peptidomimetics by (1)H?NMR spectroscopy experiments (VT-NMR and NOESY spectroscopy) in aqueous solution and Monte Carlo/Stochastic Dynamics (MC/SD) simulations revealed that the highest affinity ligands display well-defined preferred conformations featuring intramolecular hydrogen-bonded turn motifs and an extended arrangement of the RGD sequence [Cβ(Arg)-Cβ(Asp) average distance ≥8.8??]. Docking studies were performed, starting from the representative conformations obtained from the MC/SD simulations and taking as a reference model the crystal structure of the extracellular segment of integrin α(v)β(3) complexed with the cyclic pentapeptide, Cilengitide. The highest affinity ligands produced top-ranked poses conserving all the important interactions of the X-ray complex.     

New insights into urea action on proteins: a SANS study of the lysozyme case

We present a study on lysozyme dissolved in mixtures of water and urea, which is ubiquitously used as a protein denaturant. Despite the wide use of urea, the basic molecular mechanisms inducing protein unfolding are not still clarified. Small-angle neutron scattering (SANS) experiments have been performed using little amounts of denaturant in solutions in order to investigate the urea effect on lysozyme preceding the unfolding process. A global fit strategy, applied to analyze SANS experiments, provides an estimation of the average composition of the solvent in the close vicinity of the protein surface and the change of the protein-protein interactions due to the presence of urea. In particular, the thermodynamic equilibrium constant responsible for cosolvent balancing between the bulk and solvation layer has been determined. It turns out that urea is preferentially driven to the protein surface, confirming literature results at infinite dilute conditions. SANS data also reveal a possible variation of the protein net charge as a function of urea concentration, opening new perspectives and questions about the protein surface architecture at the first stages of unfolding processes.     

Low temperature kinetics, crossed beam dynamics and theoretical studies of the reaction S((1)D) + CH4 and low temperature kinetics of S((1)D) + C2H2

The reaction between sulfur atoms in the first electronically excited state, S((1)D), and methane (CH(4)), has been investigated in a complementary fashion in (a) crossed-beam dynamics experiments with mass spectrometric detection and time-of-flight (TOF) analysis at two collision energies (30.4 and 33.6 kJ mol(-1)), (b) low temperature kinetics experiments ranging from 298 K down to 23 K, and (c) electronic structure calculations of stationary points and product energetics on the CH(4)S singlet potential energy surface. The rate coefficients for total loss of S((1)D) are found to be very large (ca. 2 × 10(-10) cm(3) molec(-1) s(-1)) down to very low temperatures indicating that the overall reaction is barrier-less. Similar measurements are also performed for S((1)D) + C(2)H(2), and also for this system the rate coefficients are found to be very large (ca. 3 × 10(-10) cm(3) molec(-1) s(-1)) down to very low temperatures. From laboratory angular and TOF distributions at different product masses for the reaction S((1)D) + CH(4), it is found that the only open reaction channel at the investigated collision energies is that leading to SH + CH(3). The product angular, T(θ), and translational energy, P(E'(T)), distributions in the center-of-mass frame are derived. The reaction dynamics are discussed in terms of two different micromechanisms: a dominant long-lived complex mechanism at small and intermediate impact parameters with a strongly polarized T(θ), and a direct pickup-type (stripping) mechanism occurring at large impact parameters with a strongly forward peaked T(θ). Interpretation of the experimental results on the S((1)D) + CH(4) reaction kinetics and dynamics is assisted by high-level theoretical calculations on the CH(4)S singlet potential energy surface. The dynamics of the SH + CH(3) forming channel are compared with those of the corresponding channel (leading to OH + CH(3)) in the related O((1)D) + CH(4) reaction, previously investigated in crossed-beams in other laboratories at comparable collision energies. The possible astrophysical relevance of S((1)D) reactions with hydrocarbons, especially in the chemistry of cometary comae, is discussed.