PySP: modeling and solving stochastic programs in Python

Although stochastic programming is a powerful tool for modeling decision-making under uncertainty, various impediments have historically prevented its wide-spread use. One factor involves the ability of non-specialists to easily express stochastic programming problems as extensions of their deterministic counterparts, which are typically formulated first. A second factor relates to the difficulty of solving stochastic programming models, particularly in the mixed-integer, non-linear, and/or multi-stage cases. Intricate, configurable, and parallel decomposition strategies are frequently required to achieve tractable run-times on large-scale problems. We simultaneously address both of these factors in our PySP software package, which is part of the Coopr open-source Python repository for optimization; the latter is distributed as part of IBM’s COIN-OR repository. To formulate a stochastic program in PySP, the user specifies both the deterministic base model (supporting linear, non-linear, and mixed-integer components) and the scenario tree model (defining the problem stages and the nature of uncertain parameters) in the Pyomo open-source algebraic modeling language. Given these two models, PySP provides two paths for solution of the corresponding stochastic program. The first alternative involves passing an extensive form to a standard deterministic solver. For more complex stochastic programs, we provide an implementation of Rockafellar and Wets’ Progressive Hedging algorithm. Our particular focus is on the use of Progressive Hedging as an effective heuristic for obtaining approximate solutions to multi-stage stochastic programs. By leveraging the combination of a high-level programming language (Python) and the embedding of the base deterministic model in that language (Pyomo), we are able to provide completely generic and highly configurable solver implementations. PySP has been used by a number of research groups, including our own, to rapidly prototype and solve difficult stochastic programming problems.     

Halichonadins K and L, new dimeric sesquiterpenoids from a sponge Halichondria sp

Two new structurally unique dimeric sesquiterpenoids, halichonadins K (1) and L (2), were isolated from an Okinawan marine sponge Halichondria sp. The structures of 1 and 2 were elucidated on the basis of spectroscopic analysis including a single crystal X-ray diffraction analysis and chemical conversion. Halichonadins K (1) and L (2) are homodimers of the eudesmane sesquiterpene linked with a piperidine ring through amide bonds. Halichonadin K (1) showed moderate cytotoxicity against KB cells.     

Nature and origin of V-defects present in metalorganic vapor phase epitaxy-grown (InxAl1−x)N layers as a function of InN content,layer thickness and growth parameters

Our study of samples grown in different metalorganic chemical vapor deposition reactors and with different growth conditions reveals that V-pits are always present in (In_xAl_1?x)N films whatever the layer thickness and the InN content. V-pits are empty inverted pyramids terminating threading dislocations. InN-rich triangular regions are present around the threading dislocations terminated by pits with a hexagonal 6-fold symmetry distribution in {11?20} planes. The nature of the facets of the V-pits depends on the growth conditions: pits with either {11?2l}, l being between 1 and 3, or {1?101} facets have been observed. Moreover, the nature of the threading dislocations terminated by pits also depends on the growth conditions. Our observations suggest that with a high V/III ratio only edge a+c-type dislocations are terminated by pits whereas with a low V/III ratio both edge a-type and mixed a+c-type dislocations are terminated by pits.     

Source apportionment of atmospheric particulate carbon in Las Vegas,Nevada,USA

A study was conducted to quantify wintertime contributions of source types to carbonaceous PM_2.5 at four urban sites in the Las Vegas Valley,one of the most rapidly growing urban areas in the southwestern United States.Twenty-four hour average ambient samples were collected for mass,ions,elements,organic carbon（OC）,elemental carbon（EC）,and trace organic markers analysis.Additional measurements were made to determine diurnal patterns in light-absorbing black carbon（BC） as a marker for combustion sources.Carbonaceous PM sources of on-road gasoline vehicles,on-road diesel vehicles,and off-road diesel engines were characterized with their chemical profiles,as well as fuel-based emission factors, using an In-Plume Sampling System.The Effective Variance Chemical Mass Balance（EV-CMB） source apportionment model was applied to the ambient samples collected,using source profiles developed in this study as well as profiles from other relevant studies.Four main sources contributed to PM_2.5 carbon within the Las Vegas Valley:（1） paved road dust,（2） on-road gasoline vehicles,（3） residential wood combustion,and（4） on-road diesel vehicles.CMB estimated that on-road mixed fleet gasoline vehicles are the largest source for OC and EC at all the sites.The contribution of paved road dust to both OC and EC was 5-10%at the four sites.On-road diesel vehicles contribute 22%of the OC and 34%of the EC at a site near the city center,which is located immediately downwind of a major freeway.Residential wood combustion is a more important source than on-road diesel vehicles for two residential neighborhood sites.These results are consistent with our conceptual model,and the research methodology may be applied to studying other urban areas.     

Acoustic Analysis in Asthmatics and the Influence of Inhaled Corticosteroid Therapy

The impact of sustained inhaled corticosteroid (ICS) therapy on the larynx and pharynx was assessed using a prospective, cross-sectional, and investigator-blinded study conducted at the University Hospital Aintree, Liverpool, UK. Forty-six adults recruited from two local general practices and from general ENT clinics at our University hospital were investigated for the study. Patients were allocated to three groups according to ICS use. Laryngeal effects were measured by correlating the results of a vocal performance questionnaire, a respiratory symptom questionnaire, and measurements obtained by computerized speech analysis. Sustained vowels and connected speech were analyzed in normal and asthmatic subjects. Acoustic analysis was correlated with cellular markers of inflammation after biopsy. Regular ICS users had significantly more pharyngeal inflammation and throat discomfort (P < 0.0001). Vocal performance was also worse in this group (P < 0.0001). They were more likely to have hoarseness, weakness of voice, aphonia, sore throat, throat irritation, and cough (P < 0.0001). All these variables were directly related to one another (P < 0.0001). Multiple linear regression analysis showed that jitter was a good objective measure of hoarseness (P < 0.05). Regular ICS users were significantly more likely to have abnormal jitter, shimmer, and closed-phase quotient scores (P < 0.0001). There was no difference between the groups in the observed parameters of inflammation (P > 0.01). A higher pharyngitis score did not correlate with any of the histological markers of inflammation (P > 0.01). Local side effects are more common in asthmatics that use ICS regularly. Measures of laryngeal function are significantly worse in regular ICS users. However, histological markers and oropharyngeal redness are not reliable measures of inflammation.     

Resolving 3D magnetism in nanoparticles using polarization analyzed SANS

Utilizing a polarized ³He cell as an analyzer we were able to perform a full polarization analysis on small-angle neutron scattering (SANS) data from an ensemble of 7 nm magnetite nanoparticles. The results led to clear separation of magnetic and nuclear scattering plus a 3D vectorial decomposition of the magnetism observed. At remanence variation in long-range magnetic correlation length was found to be highly dependent on temperature from 50 to 300 K. Additionally, we were able to compare the magnetic scattering from moments along and perpendicular to an applied field at saturation and in remanence.     

Ohmic contact formation to bulk and heterostructure gallium nitride family semiconductors

We describe experiments investigating the quality of ohmic contacts to both bulk GaN and to III-nitride heterostructures. Titanium-based contacts were investigated to assess the role of intermixing and surface impurities for contact formation to n-type GaN. Direct contact to the two-dimensional electron gas in GaN/AlGaN heterostructures was also studied. These contacts were made by photochemical etching of the samples to expose the heterointerface. It was observed that even in the latter case contact annealing leads to a lower contact resistance by consuming surface contaminants and promoting beneficial interfacial reactions. Various passivation techniques were tried to reduce surface leakage current between contact pads and PECVD-deposited silicon nitride was found to be the best material for this application.     

Practical sequential bounds for approximating two-terminal reliability

With increasing emphases on better and more reliable services, network systems have incorporated reliability analysis as an integral part in their planning, design and operation. This article first presents a simple exact decomposition algorithm for computing the NP-hard two-terminal reliability, which measures the probability of successful communication from specified source node to sink node in the network. Then a practical bounding algorithm, which is indispensable for large networks, is presented by modifying the exact algorithm for obtaining sequential lower and upper bounds on two-terminal reliability. Based on randomly generated large networks, computational experiments are conducted to compare the proposed algorithm to the well-known and widely used edge-packing approximation model and to explore the performance of the proposed bounding algorithm. Computational results reveal that the proposed bounding algorithm is superior to the edge-packing model, and the trade-off of accuracy for execution time ensures that an exact difference between upper and lower bounds on two-terminal reliability can be obtained within an acceptable time.