A Digital Perspective and the Quest for Substrate-Universal Behaviors

Should the Digital Perspective essays collected in these proceedings be viewed more seriously than attempts to play “fundamental theory”—which even in the hands of an Eddington was hard to tell from mythology and numerology? We argue that a nonfrivolous aspect of this Digital Perspective is its heuristic capacity: to help us guess which aspects of our understanding of nature are more “universal,” more robust, more likely to survive theoretical and experimental challenges. Behaviors that are substrate-independent—that can, for instance, thrive well on a digital support, even though they are traditionally imagined as taking place in a continuum—are especially promising candidates.     

Profiling of ornithine lipids in bacterial extracts of Rhodobacter sphaeroides by reversed-phase liquid chromatography with electrospray ionization and multistage mass spectrometry (RPLC-ESI-MS)

Ornithine lipids (OLs), a sub-group of the large (and of emerging interest) family of lipoamino acids of bacterial origin, contain a 3-hydroxy fatty acyl chain linked via an amide bond to the α-amino group of ornithine and via an ester bond to a second fatty acyl chain. OLs in extracts of Rhodobacter sphaeroides (R. sphaeroides) were investigated by high-performance reversed phase liquid chromatography (RPLC) with electrospray ionization mass spectrometry (ESI-MS) in negative ion mode using a linear ion trap (LIT). The presence of OLs bearing both saturated (i.e, 16:0, 17:0, 18:0, 19:0 and 20:0) and unsaturated chains (i.e., 18:1, 19:1, 19:2 and 20:1) was ascertained and their identification, even for isomeric, low abundance and partially co-eluting species, was achieved by low-energy collision induced dissociation (CID) multistage mass spectrometry (MSⁿ, n = 2–4). OLs signatures found in two R. sphaeroides strains, i.e., wild type 2.4.1 and mutant R26, were examined and up to 16 and 17 different OL species were successfully identified, respectively. OLs in both bacterial strains were characterized by several combinations of fatty chains on ester-linked and amide-linked 3-OH fatty acids. Multistage MS spectra of monoenoic amide-linked 3-OH acyl chains, allowed the identification of positional isomer of OL containing 18:1 (i.e. 9-octadecenoic) and 20:1 (i.e. 11-eicosenoic) fatty acids. The most abundant OL ([M−H]⁻ at m/z 717.5) in R. sphaeroides R26 was identified as OL 3-OH 20:1/19:1 (i.e., 3-OH-eicosenoic acid amide-linked to ornithine and esterified to a nonadecenoic chain containing a cyclopropane ring). An unusual OL (m/z 689.5 for the [M−H]⁻ ion), most likely containing a cyclopropene ester-linked acyl chain (i.e., OL 3-OH 18:0/19:2), was retrieved only in the carotenoidless mutant strain R26. Based on the biosynthetic pathways already known for cyclopropa(e)ne ring-including acyl chains, a plausible explanation was invoked for the enzymatic generation of this ester-linked chain in R. sphaeroides.     

Moment equations in the kinetic theory of gases and wave velocities

We consider the evolution system for N-moments of the Boltzmann equation and we require the compatibility with an entropy law. This implies that the distribution function depends only on a single scalar variable which is a polynomial in . It is then possible to construct the generators such that the system assumes a symmetric hyperbolic form in the main field. For an arbitrary we prove that the systems obtained maximise the entropy density. If we require that the entropy coincides with the usual one of non-degenerate gases, we obtain an exponential function for , which was already found by Dreyer. From these results the behaviour of the characteristic wave velocities for an increasing number of moments is studied and we show that in the classical theory the maximum velocity increases and tends to infinity, while in the relativistic case the wave and shock velocities are bounded by the speed of light. Received June 5, 1997     

Diastereo- and enantioseparation of a N-Boc amino acid with a zwitterionic quinine-based stationary phase: Focus on the stereorecognition mechanism

A chiral chromatography method enabling the simultaneous diastereo- and enantioseparation of N^α-Boc-N⁴-(hydroorotyl)-4-aminophenylalanine [Boc-Aph(Hor)-OH, 1] was optimized with a quinine-based zwitterionic stationary phase. The polar-ionic eluent system consisting of ACN:MeOH:water—49.7:49.7:0.6 (v/v/v) with formic acid (4.0 mM) and diethylamine (2.5 mM), allowed the successful separation of the four acid stereoisomers: α_d,d-/d,l-1 = 1.08; α_d,l-/l,d-1 = 1.08; α_l,d-/l,l-1 = 1.40.     

Occurrence of oleic and 18:1 methyl-branched acyl chains in lipids of Rhodobacter sphaeroides 2.4.1

The fatty acids (FAs) composition of lipids extracted from Rhodobacter sphaeroides 2.4.1 was investigated by gas chromatography–mass spectrometry (GC–MS) analysis of the corresponding FA methyl esters (FAMEs), obtained through trans-esterification of the original lipid species. A GC stationary phase based on a highly polar ionic liquid (IL) was selected, aimed to enhance the separation of isomeric FAMEs with particular emphasis on positional and geometrical isomers of monounsaturated 16:1 and 18:1 fatty acyl chains. The occurrence of 18:1 cis-Δ⁹ (oleic) acid, a positional isomer of the well-known and most predominant 18:1 cis-Δ¹¹ (cis-vaccenic) acid, has been demonstrated here for the first time. Furthermore a methyl branched 18:1 FA was also identified and its structure tentatively assigned as 11-methyl-Δ¹²-octadecenoic acid (most likely as trans isomer). The unprecedented observation about 18:1 cis-Δ⁹ FA occurrence in R. sphaeroides 2.4.1 is, even indirectly, supported by a biosynthetic pathway postulated with the aid of the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. The concurrent presence of 16:1 cis-Δ⁷ and 18:1 cis-Δ⁹ FAs suggested the existence of parallel and/or complementary processes to those invoked for the formation of most common 16:1 cis-Δ⁹ and 18:1 cis-Δ¹¹ FAs. A further route was hypothesized for the trans FAs biosynthesis in wild-type cells of R. sphaeroides.     

Hyperbolicity and wave propagation in extended thermodynamics

Summary The hyperbolic system of the field equations of the Extended Thermodynamics governing the non-equilibrium thermodynamical processes of gases is studied. First, the extreme cases of strongly degenerate Fermi and Bose gases are discussed so as to complete the previous analysis by Liu and Müller. The physical interpretation of these results appears to be in agreement with quantum and statistical mechanics. Then, the propagation of discontinuity waves and the critical time for classical gases will be dealt with.

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Sommario Si studia il sistema iperbolico delle equazioni di campo della Termodinamica Estesa che governa i processi termodinamici di non equilibrio nei gas. Nella prima parte si discutono i casi limite dei gas di Fermi e Bose fortemente degeneri completando la precedente analisi di Liu e Müller. L'interpretazione fisica di questi risultati appare in accordo con la meccanica quantistica e statistica. Nella seconda parte si studia la propagazione di onde di discontinuitá e il tempo critico per i gas classici.

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Supported by C.N.R., M.P.I. fondi ricerche 40% and 60% and INFN(sez. di Bologna).     

Non-linear stability of doubly curved thin shallow shells on rectangular plan with small geometrical imperfections

Summary This paper deals with some theoretical developments of the problem of stability of doubly curved thin shallow shells on a rectangular plan. After some critical references to results obtained in earlier studies using the linear theory of stability, the problem of elastic equilibrium in the nonlinear range is approached and solved for some types of shells using piecewise linearisation. Load-displacement curves up to post-buckling are obtained. Deflections not conforming to structural symmetry are also considered. The influence of small geometric imperfections deviates the load-displacement curve to other equilibrium positions and hence a shell with imperfections attains its snapping point at a lower load than one without. A comparison with some experimental studies by other authors is given in the appendix.

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Sommario Lo studio tratta di alcuni sviluppi teorici sul problema della stabilità dell'equilibrio delle volte sottili ribassate a doppia curvatura su pianta rettangolare. Nella prima parte vengono esposte alcune considerazioni critiche circa i risultati ottenuti in parte dall'Autore in lavori precedenti con la teoria lineare della stabilità. Il problema dell'equilibrio elastico viene poi affrontato in campo non-lineare e risolto per alcuni tipi di volte mediante una linearizzazione a tratti; le curve carico-spostamento vengono ricavate fino al comportamento post-critico. Vengono altresì ricavate curve carico-spostamento corrispondenti a deformate che non conservano la simmetria di struttura e di carico.La presenza di piccole imperfezioni devia la curva caricospostamento verso altre posizioni di equilibrio e la curva relativa raggiunge il punto di instabilità progressiva per valori del carico notevolmente inferiori di quelli relativi alla stessa volta senza imperfezioni. Infine si riporta in appendice un confronto con risultati sperimentali di altri Autori.

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Study supported by the C.N.R. (Consiglio Nazionale delle Ricerche).     

Traveling waves in a coarse-grained model of volume-filling cell invasion: Simulations and comparisons

Many reaction–diffusion models produce traveling wave solutions that can be interpreted as waves of invasion in biological scenarios such as wound healing or tumor growth. These partial differential equation models have since been adapted to describe the interactions between cells and extracellular matrix (ECM), using a variety of different underlying assumptions. In this work, we derive a system of reaction–diffusion equations, with cross-species density-dependent diffusion, by coarse-graining an agent-based, volume-filling model of cell invasion into ECM. We study the resulting traveling wave solutions both numerically and analytically across various parameter regimes. Subsequently, we perform a systematic comparison between the behaviors observed in this model and those predicted by simpler models in the literature that do not take into account volume-filling effects in the same way. Our study justifies the use of some of these simpler, more analytically tractable models in reproducing the qualitative properties of the solutions in some parameter regimes, but it also reveals some interesting properties arising from the introduction of cell and ECM volume-filling effects, where standard model simplifications might not be appropriate.     

Enhancement of optical luminescence of solids using a capillary lens

The Advanced Photon Source (APS) at Argonne National Laboratory is a 1-km-circumference, 7-GeV, third generation synchrotron light source. It is the largest light source in the Western Hemisphere and attracts about 3,500 users every year from around the globe. The APS is currently preparing for a major upgrade, a goal of which is to focus on high brightness at photon energies of around 20 keV and higher. The APS is particularly well suited for this high photon energy range due to its higher-energy, 7-GeV electron beam, but it also needs new insertion devices with short periods and high fields, i.e., superconducting devices.     

A consistent thermodynamical model of incompressible media as limit case of quasi-thermal-incompressible materials

In this paper we extend the conditions on quasi-thermal-incompressible materials presented in Gouin et al. (2011) [1] so that they satisfy all the principles of thermodynamics, including the stability condition associated with the concavity of the chemical potential. We analyze the approximations under which a quasi-thermal-incompressible medium can be considered as incompressible. We find that the pressure cannot exceed a very large critical value and that the compressibility factor must be greater than a lower limit that is very small. The analysis is first done for the case of fluids and then extended to the case of thermoelastic solids.