Computer simulations of charged systems in partially periodic geometries

This work presents algorithms for the calculation of the electrostatic interaction in partially periodic systems. The framework for these algorithms is provided by the simulation package ESPResSo, of which the author was one of the main developers. The prominent features of the program are listed and the internal structure is described. In the following, algorithms for the calculation of the Coulomb sum in three dimensionally periodic systems are described. These methods are the foundations for the algorithms for partially periodic systems presented in this work. Starting from the MMM2D method for systems with one non-periodic coordinate, the ELC method for these systems is developed. This method consists of a correction term which allows to use methods for three dimensional periodicity also for the case of two periodic coordinates. The computation time of this correction term is neglible for large numbers of particles. The performance of MMM2D and ELC are demonstrated by results from the implementations contained in ESPResSo. It is also discussed, how different dielectric constants inside and outside of the simulation box can be realized. For systems with one periodic coordinate, the MMM1D method is derived from the MMM2D method. This method is applied to the problem of the attraction of like-charged rods in the presence of counterions, and results of the strong coupling theory for the equilibrium distance of the rods at infinite counterion-coupling are checked against results from computer simulations. The degree of agreement between the simulations at finite coupling and the theory can be characterized by a single parameter gamma_RB. In the special case of T=0, one finds under certain circumstances flat configurations, in which all charges are located in the rod-rod plane. The energetically optimal configuration and its stability are determined analytically, which depends on only one parameter gamma_z, similar to gamma_RB. These findings are in good agreement with results from computer simulations.

Constraint based methods for allocation and scheduling of periodic applications

This work presents exact algorithms for the Resource Allocation and Cyclic Scheduling Problems (RA&CSPs). Cyclic Scheduling Problems arise in a number of application areas, such as in hoist scheduling, mass production, compiler design (implementing scheduling loops on parallel architectures), software pipelining, and in embedded system design. The RA&CS problem concerns time and resource assignment to a set of activities, to be indefinitely repeated, subject to precedence and resource capacity constraints. In this work we present two constraint programming frameworks facing two different types of cyclic problems. In first instance, we consider the disjunctive RA&CSP, where the allocation problem considers unary resources. Instances are described through the Synchronous Data-flow (SDF) Model of Computation. The key problem of finding a maximum-throughput allocation and scheduling of Synchronous Data-Flow graphs onto a multi-core architecture is NP-hard and has been traditionally solved by means of heuristic (incomplete) algorithms. We propose an exact (complete) algorithm for the computation of a maximum-throughput mapping of applications specified as SDFG onto multi-core architectures. Results show that the approach can handle realistic instances in terms of size and complexity. Next, we tackle the Cyclic Resource-Constrained Scheduling Problem (i.e. CRCSP). We propose a Constraint Programming approach based on modular arithmetic: in particular, we introduce a modular precedence constraint and a global cumulative constraint along with their filtering algorithms. Many traditional approaches to cyclic scheduling operate by fixing the period value and then solving a linear problem in a generate-and-test fashion. Conversely, our technique is based on a non-linear model and tackles the problem as a whole: the period value is inferred from the scheduling decisions. The proposed approaches have been tested on a number of non-trivial synthetic instances and on a set of realistic industrial instances achieving good results on practical size problem.

Computer aided design and finite element modeling to predict bulk mechanical properties of bone scaffolds using triply periodic minimal surfaces (progettazione assistita al calcolatore ed analisi con il metodo degli elementi finiti per predire il comportamento meccanico di scaffolds ossei creati con l'uso di superfici minime periodiche in tre direzioni)

The aim of Tissue Engineering is to develop biological substitutes that will restore lost morphological and functional features of diseased or damaged portions of organs. Recently computer-aided technology has received considerable attention in the area of tissue engineering and the advance of additive manufacture (AM) techniques has significantly improved control over the pore network architecture of tissue engineering scaffolds. To regenerate tissues more efficiently, an ideal scaffold should have appropriate porosity and pore structure. More sophisticated porous configurations with higher architectures of the pore network and scaffolding structures that mimic the intricate architecture and complexity of native organs and tissues are then required. This study adopts a macro-structural shape design approach to the production of open porous materials (Titanium foams), which utilizes spatial periodicity as a simple way to generate the models. From among various pore architectures which have been studied, this work simulated pore structure by triply-periodic minimal surfaces (TPMS) for the construction of tissue engineering scaffolds. TPMS are shown to be a versatile source of biomorphic scaffold design. A set of tissue scaffolds using the TPMS-based unit cell libraries was designed. TPMS-based Titanium foams were meant to be printed three dimensional with the relative predicted geometry, microstructure and consequently mechanical properties. Trough a finite element analysis (FEA) the mechanical properties of the designed scaffolds were determined in compression and analyzed in terms of their porosity and assemblies of unit cells. The purpose of this work was to investigate the mechanical performance of TPMS models trying to understand the best compromise between mechanical and geometrical requirements of the scaffolds. The intention was to predict the structural modulus in open porous materials via structural design of interconnected three-dimensional lattices, hence optimising geometrical properties. With the aid of FEA results, it is expected that the effective mechanical properties for the TPMS-based scaffold units can be used to design optimized scaffolds for tissue engineering applications. Regardless of the influence of fabrication method, it is desirable to calculate scaffold properties so that the effect of these properties on tissue regeneration may be better understood.

Periodic Higgs-de Rham flows and representations of algebraic fundamental groups

Let k := bar{F}_p for p > 2, W_n(k) := W(k)/p^n and X_n be a projective smooth W_n(k)-scheme which is W_{n+1}(k)-liftable. For all n > 1, we construct explicitly a functor, which we call the inverse Cartier functor, from a subcategory of Higgs bundles over X_n to a subcategory of flat Bundles over X_n. Then we introduce the notion of periodic Higgs-de Rham flows and show that a periodic Higgs-de Rham flow is equivalent to a Fontaine-Faltings module. Together with a p-adic analogue of Riemann-Hilbert correspondence established by Faltings, we obtain a coarse p-adic Simpson correspondence.

Nocturnal periodic breathing during acclimatization at very high altitude at Mount Muztagh Ata (7,546 m)

Quantitative data on ventilation during acclimatization at very high altitude are scant. Therefore, we monitored nocturnal ventilation and oxygen saturation in mountaineers ascending Mt. Muztagh Ata (7,546 m).

Assessing periodicity of periodic leg movements during sleep

Periodic leg movements (PLM) during sleep consist of involuntary periodic movements of the lower extremities. The debated functional relevance of PLM during sleep is based on correlation of clinical parameters with the PLM index (PLMI). However, periodicity in movements may not be reflected best by the PLMI. Here, an approach novel to the field of sleep research is used to reveal intrinsic periodicity in inter movement intervals (IMI) in patients with PLM.

Characterisation of extreme winter precipitation in Mediterranean coastal sites and associated anomalous atmospheric circulation patterns

We present an analysis of daily extreme precipitation events for the extended winter season (October–March) at 20 Mediterranean coastal sites covering the period 1950–2006. The heavy tailed behaviour of precipitation extremes and estimated return levels, including associated uncertainties, are derived applying a procedure based on the Generalized Pareto Distribution, in combination with recently developed methods. Precipitation extremes have an important contribution to make seasonal totals (approximately 60% for all series). Three stations (one in the western Mediterranean and the others in the eastern basin) have a 5-year return level above 100 mm, while the lowest value (estimated for two Italian series) is equal to 58 mm. As for the 50-year return level, an Italian station (Genoa) has the highest value of 264 mm, while the other values range from 82 to 200 mm. Furthermore, six series (from stations located in France, Italy, Greece, and Cyprus) show a significant negative tendency in the probability of observing an extreme event. The relationship between extreme precipitation events and the large scale atmospheric circulation at the upper, mid and low troposphere is investigated by using NCEP/NCAR reanalysis data. A 2-step classification procedure identifies three significant anomaly patterns both for the western-central and eastern part of the Mediterranean basin. In the western Mediterranean, the anomalous southwesterly surface to mid-tropospheric flow is connected with enhanced moisture transport from the Atlantic. During ≥5-year return level events, the subtropical jet stream axis is aligned with the African coastline and interacts with the eddy-driven jet stream. This is connected with enhanced large scale ascending motions, instability and leads to the development of severe precipitation events. For the eastern Mediterranean extreme precipitation events, the identified anomaly patterns suggest warm air advection connected with anomalous ascent motions and an increase of the low- to mid-tropospheric moisture. Furthermore, the jet stream position (during ≥5-year return level events) supports the eastern basin being in a divergence area, where ascent motions are favoured. Our results contribute to an improved understanding of daily precipitation extremes in the cold season and associated large scale atmospheric features.

Dissociation of periodic leg movements from arousals in restless legs syndrome

The purpose of this study was to characterize the nature of the relation between periodic leg movements during sleep (PLMS) and cortical arousals to contribute to the debate on the clinical significance and treatment of PLMS.

Seasonal variation and sources of low molecular weight organic acids in precipitation in the rural area of Anshun

Low mol. wt. (LMW) org. acids are important and ubiquitous chem. constituents in the atm. A comprehensive study of the chem. compn. of pptn. was carried out from June 2007 to June 2008 at a rural site in Anshun, in the west of Guizhou Province, China. During this period, 118 rainwater samples were collected and the main LMW carboxylic acids were detd. using ion chromatog. The av. pH of rainwater was 4.89 which is a typical acidic value. The most abundant carboxylic acids were formic acid (vol. wt. mean concn.: 8.77 μmol L-1) and acetic acid (6.90 μmol L-1), followed by oxalic acid (2.05 μmol L-1). The seasonal variation of concns. and wet deposition fluxes of org. acids indicated that direct vegetation emissions were the main sources of the org. acids. Highest concns. were obsd. in winter and were ascribed to the low winter rainfall and the contribution of other air pollution sources northeast of the study area. The ratio of formic and acetic acids in the pptn. ([F/A]T) was proposed as an indicator of pollution source. This suggested that the pollution resulted from direct emissions from natural or anthropogenic sources. Comparison with acid pptn. in other urban and rural areas in Guizhou showed that there was a decreasing contribution of LMW org. acids to free acidity and all anions in rainwater from urban to remote rural areas. Consequently, it is necessary to control emissions of org. acids to reduce the frequency of acid rain, esp. in rural and remote areas. [on SciFinder(R)]

Anisotropically oriented electrospun matrices with an imprinted periodic micropattern: a new scaffold for engineered muscle constructs

Engineered muscle constructs provide a promising perspective on the regeneration or substitution of irreversibly damaged skeletal muscle. However, the highly ordered structure of native muscle tissue necessitates special consideration during scaffold development. Multiple approaches to the design of anisotropically structured substrates with grooved micropatterns or parallel-aligned fibres have previously been undertaken. In this study we report the guidance effect of a scaffold that combines both approaches, oriented fibres and a grooved topography. By electrospinning onto a topographically structured collector, matrices of parallel-oriented poly(ε-caprolactone) fibres with an imprinted wavy topography of 90 µm periodicity were produced. Matrices of randomly oriented fibres or parallel-oriented fibres without micropatterns served as controls. As previously shown, un-patterned, parallel-oriented substrates induced myotube orientation that is parallel to fibre direction. Interestingly, pattern addition induced an orientation of myotubes at an angle of 24° (statistical median) relative to fibre orientation. Myotube length was significantly increased on aligned micropatterned substrates in comparison to that on aligned substrates without pattern (436 ± 245 µm versus 365 ± 212 µm; p < 0.05). We report an innovative, yet simple, design to produce micropatterned electrospun scaffolds that induce an unexpected myotube orientation and an increase in myotube length.