Generalized Fractal Kinetics in Complex Systems (Application to Biophysics and Biothechnology)

We derive a universal function for the kinetics of complex systems. This kinetic function unifies and generalizes previous theoretical attempts to describe what has been called "fractal kinetic".The concentration evolutionary equation is formally similar to the relaxation function obtained in the stochastic theory of relaxation, with two exponents a and n. The first one is due to memory effects and short-range correlations and the second one finds its origin in the long-range correlations and geometrical frustrations which give rise to ageing behavior. These effects can be formally handled by introducing adequate probability distributions for the rate coefficient. We show that the distribution of rate coefficients is the consequence of local variations of the free energy (energy landscape) appearing in the exponent of the Arrhenius formula. We discuss briefly the relation of the (n,a) kinetic formalism with the Tsallis theory of nonextensive systems.Comment: 15 pages, 3 figures, submitted to Physica

Structurally specific thermal fluctuations identify functional sites for DNA transcription

We report results showing that thermally-induced openings of double stranded DNA coincide with the location of functionally relevant sites for transcription. Investigating both viral and bacterial DNA gene promoter segments, we found that the most probable opening occurs at the transcription start site. Minor openings appear to be related to other regulatory sites. Our results suggest that coherent thermal fluctuations play an important role in the initiation of transcription. Essential elements of the dynamics, in addition to sequence specificity, are nonlinearity and entropy, provided by local base-pair constraints

Hydrometeorological threshold conditions for debris flow initiation in Norway

Debris flows, triggered by extreme precipitation events and rapid snow melt, cause considerable damage to the Norwegian infrastructure every year. To define intensity-duration (ID) thresholds for debris flow initiation critical water supply conditions arising from intensive rainfall or snow melt were assessed on the basis of daily hydro-meteorological information for 502 documented debris flow events. Two threshold types were computed: one based on absolute ID relationships and one using ID relationships normalized by the local precipitation day normal (PDN). For each threshold type, minimum, medium and maximum threshold values were defined by fitting power law curves along the 10th, 50th and 90th percentiles of the data population. Depending on the duration of the event, the absolute threshold intensities needed for debris flow initiation vary between 15 and 107 mm day<sup>−1</sup>. Since the PDN changes locally, the normalized thresholds show spatial variations. Depending on location, duration and threshold level, the normalized threshold intensities vary between 6 and 250 mm day<sup>−1</sup>. The thresholds obtained were used for a frequency analysis of over-threshold events giving an estimation of the exceedance probability and thus potential for debris flow events in different parts of Norway. The absolute thresholds are most often exceeded along the west coast, while the normalized thresholds are most frequently exceeded on the west-facing slopes of the Norwegian mountain ranges. The minimum thresholds derived in this study are in the range of other thresholds obtained for regions with a climate comparable to Norway. Statistics reveal that the normalized threshold is more reliable than the absolute threshold as the former shows no spatial clustering of debris flows related to water supply events captured by the threshold

Hysteretic Optimization For Spin Glasses

The recently proposed Hysteretic Optimization (HO) procedure is applied to the 1D Ising spin chain with long range interactions. To study its effectiveness, the quality of ground state energies found as a function of the distance dependence exponent, $\sigma$, is assessed. It is found that the transition from an infinite-range to a long-range interaction at $\sigma=0.5$ is accompanied by a sharp decrease in the performance . The transition is signaled by a change in the scaling behavior of the average avalanche size observed during the hysteresis process. This indicates that HO requires the system to be infinite-range, with a high degree of interconnectivity between variables leading to large avalanches, in order to function properly. An analysis of the way auto-correlations evolve during the optimization procedure confirm that the search of phase space is less efficient, with the system becoming effectively stuck in suboptimal configurations much earlier. These observations explain the poor performance that HO obtained for the Edwards-Anderson spin glass on finite-dimensional lattices, and suggest that its usefulness might be limited in many combinatorial optimization problems.Comment: 6 pages, 9 figures. To appear in JSTAT. Author website: http://www.bgoncalves.co

Structure of Extremely Nanosized and Confined In-O Species in Ordered Porous Materials

Perturbed-angular correlation, x-ray absorption, and small-angle x-ray scattering spectroscopies were suitably combined to elucidate the local structure of highly diluted and dispersed InOx species confined in porous of ZSM5 zeolite. These novel approach allow us to determined the structure of extremely nanosized In-O species exchanged inside the 10-atom-ring channel of the zeolite, and to quantify the amount of In2O3 crystallites deposited onto the external zeolite surface.Comment: 4 pages, 5 postscript figures, REVTEX4, published in Physical Review Letter

On the origin of the Boson peak in globular proteins

We study the Boson Peak phenomenology experimentally observed in globular proteins by means of elastic network models. These models are suitable for an analytic treatment in the framework of Euclidean Random Matrix theory, whose predictions can be numerically tested on real proteins structures. We find that the emergence of the Boson Peak is strictly related to an intrinsic mechanical instability of the protein, in close similarity to what is thought to happen in glasses. The biological implications of this conclusion are also discussed by focusing on a representative case study.Comment: Proceedings of the X International Workshop on Disordered Systems, Molveno (2006

Comparability of Pulmonary Nodule Size Measurements among Different Scanners and Protocols: Should Diameter Be Favorized over Volume?

BACKGROUND: To assess the impact of the lung cancer screening protocol recommended by the European Society of Thoracic Imaging (ESTI) on nodule diameter, volume, and density throughout different computed tomography (CT) scanners. METHODS: An anthropomorphic chest phantom containing fourteen different-sized (range 3-12 mm) and CT-attenuated (100 HU, -630 HU and -800 HU, termed as solid, GG1 and GG2) pulmonary nodules was imaged on five CT scanners with institute-specific standard protocols (P$_{S}$) and the lung cancer screening protocol recommended by ESTI (ESTI protocol, P$_{E}$). Images were reconstructed with filtered back projection (FBP) and iterative reconstruction (REC). Image noise, nodule density and size (diameter/volume) were measured. Absolute percentage errors (APEs) of measurements were calculated. RESULTS: Using P$_{E}$, dosage variance between different scanners tended to decrease compared to P$_{S}$, and the mean differences were statistically insignificant (p = 0.48). P$_{S}$ and P$_{E(REC)}$ showed significantly less image noise than P$_{E(FBP)}$ (p < 0.001). The smallest size measurement errors were noted with volumetric measurements in P$_{E(REC)}$ and highest with diametric measurements in P$_{E(FBP)}$. Volume performed better than diameter measurements in solid and GG1 nodules (p < 0.001). However, in GG2 nodules, this could not be observed (p = 0.20). Regarding nodule density, REC values were more consistent throughout different scanners and protocols. CONCLUSION: Considering radiation dose, image noise, nodule size, and density measurements, we fully endorse the ESTI screening protocol including the use of REC. For size measurements, volume should be preferred over diameter

Thermodynamics of protein folding: a random matrix formulation

The process of protein folding from an unfolded state to a biologically active, folded conformation is governed by many parameters e.g the sequence of amino acids, intermolecular interactions, the solvent, temperature and chaperon molecules. Our study, based on random matrix modeling of the interactions, shows however that the evolution of the statistical measures e.g Gibbs free energy, heat capacity, entropy is single parametric. The information can explain the selection of specific folding pathways from an infinite number of possible ways as well as other folding characteristics observed in computer simulation studies.Comment: 21 Pages, no figure

Periskop-, Kamin- und Sandwichtechnik sowie VORTEC zur Vereinfachung der Behandlung von Aneurysmen der Aorta abdominalis und thoracoabdominalis

Zusammenfassung: VORTEC (Viabahn Open Revascularisation TEChnique) und die Kaminprothesentechnik sind Verfahren zur Erhaltung oder Wiederherstellung des Blutflusses von Aortenästen, die geplant oder als Notlösung bei offener Operation oder endovaskulärem Vorgehen eingesetzt werden können. VORTEC ist eine stentbasierte vaskuläre Verbindungstechnik zur Herstellung einer End-zu-End-Anastomose, die insbesondere geeignet ist, wenn die herkömmliche Nahttechnik schwierig ist (sein könnte). Es handelt sich um ein schnelles Verfahren, das praktisch ohne Blutflussunterbrechung und ohne Anastomosenblutung ist, die Durchgängigkeitsraten sind ähnlich gut wie bei Nahtanastomosen. Die Kamin-Periskop-Sandwich-Prothesentechnik ("chimney/periscope and sandwich graft technique”, CHIMPES) ist ein endovaskuläres Verfahren, bei dem parallele Endoprothesen zur Erhaltung oder Wiederherstellung des Blutflusses von Aortenästen verwendet werden, während ein herkömmlicher Aortenstent oberhalb ihres Ursprungs platziert wird. Es ist ein relativ schnelles Verfahren mit der Möglichkeit, selbst in Notfällen handelsübliche Produkte zu verwenden. Bei der Sandwichtechnik verlaufen parallele Prothesen zwischen 2Aortenstents. Publizierten Erfahrungen zufolge scheinen diese beiden Techniken besonders für die Behandlung von Aneurysmen der Aortenäste und der Aorta thoracoabdominalis geeignet zu sein, vor allem in Hochrisiko- oder Akutfällen. Die englische Volltextversion dieses Beitrags ist über SpringerLink (unter "Supplemental") verfügba