Monte Carlo simulations of the HP model (the "Ising model" of protein folding)

Using Wang–Landau sampling with suitable Monte Carlo trial moves (pull moves and bond-rebridging moves combined) we have determined the density of states and thermodynamic properties for a short sequence of the HP protein model. For free chains these proteins are known to first undergo a collapse “transition” to a globule state followed by a second “transition” into a native state. When placed in the proximity of an attractive surface, there is a competition between surface adsorption and folding that leads to an intriguing sequence of “transitions”. These transitions depend upon the relative interaction strengths and are largely inaccessible to “standard” Monte Carlo methods.     

Algorithms to Compute Minimum Cycle Basis in Directed Graphs

We consider the problem of computing a minimum cycle basis in a directed graph G with m arcs and n vertices. The arcs of G have non-negative weights assigned to them. In this problem a {-1,0,1} incidence vector is associated with each cycle and the vector space over generated by these vectors is the cycle space of G. A set of cycles is called a cycle basis of G if it forms a basis for its cycle space. A cycle basis where the sum of weights of the cycles is minimum is called a minimum cycle basis of G. This paper presents an algorithm, which is the first polynomial-time algorithm for computing a minimum cycle basis in G. We then improve it to an algorithm. The problem of computing a minimum cycle basis in an undirected graph has been well studied. In this problem a {0,1} incidence vector is associated with each cycle and the vector space over generated by these vectors is the cycle space of the graph. There are directed graphs in which the minimum cycle basis has lower weight than any cycle basis of the underlying undirected graph. Hence algorithms for computing a minimum cycle basis in an undirected graph cannot be used as black boxes to solve the problem in directed graphs.     

Bias in bacteriophage morphological classification by transmission electron microscopy due to breakage or loss of tail structures

Virtually every study that has used transmission electron microscopy (TEM) to estimate viral diversity has acknowledged that loss of phage tails during sample preparation may have biased the results. However, the magnitude of this potential bias has yet to be constrained. To characterize biases in virus morphological diversity due to tail loss, six phage strains representing the order Caudovirales were inoculated into sterile sediments and soils. Phage particles were then extracted using standard methods. Morphologies of extracted phage particles were compared to those of unmanipulated control samples to determine the extent of tail breakage incurred by extraction procedures. Podoviruses exhibited the smallest frequency of tail loss during extraction (1.2-14%), myoviruses were moderately susceptible to tail breakage (15-40%), and siphoviruses were highly susceptible (32-76%). Thus, TEM assessments of viral diversity in soils or sediments by distribution of tail morphologies may be biased toward podoviruses and virions lacking tails, while simultaneously underestimating the abundance of siphoviruses. However, since the majority of viral capsids observed under TEM were intact, estimates of viral diversity based on the distribution of capsid diameters may provide a more reliable basis for morphological comparisons within and across ecosystems.     

Consumers' Creative Talent: Which Characteristics Qualify Consumers for Open Innovation Projects? An Exploration of Asymmetrical Effects

Virtual customer integration and open innovation are considered as appropriate means to improve the success of new product development. However, only when consumers are qualified and motivated to contribute promising ideas and relevant know‐how they are able to add value to a producer's innovation process. In this study, we explore the symmetric and asymmetric impact of various creativity components on consumers' idea generation, concept development, or prototype building abilities as well as interest in co‐creation projects. Our results show that creativity components are of different importance. While some characteristics are needed above certain thresholds to successfully accomplish a certain development task, exceeding those does not necessarily lead to better outputs. Other characteristics improve the creative output only if they exceed specific levels.     

Interplay Between Wetting and Phase Behavior in Binary Polymer Films and Wedges: Monte Carlo Simulations and Mean Field Calculations

Confining a binary mixture, one can profoundly alter its miscibility behavior. The qualitative features of miscibility in confined geometry are ratheruniversal and shared by polymer mixtures as well as small molecules, but the unmixing transition in the bulk and the wetting transition are typically well separated in polymer blends. The interplay between wetting and miscibility of a symmetric polymer mixture via large-scale Monte Carlo simulations in the framework of the bond fluctuation model and via numerical self–consistent field calculations is studied. The film surfaces interact with the monomers via short ranged potentials, and the wetting transition of the semi–infinite system is of first order. It can be accurately located in the simulations by measuring the surface and interface tensions and using Young’s equation. If both surfaces in a film attract the same component, capillary condensation occurs and the critical point is close to the critical point of the bulk. If surfaces attract different components, an interface localization/delocalization occurs which gives rise to phase diagrams with two critical points in the vicinity of the pre-wetting critical point of the semi–infinite system. The crossover between these two types of phase diagrams as a function of the surface field asymmetry is studied. The dependence of the phase diagram on the film thickness Δ for antisymmetric surface fields is investigated. Upon decreasing the film thickness, the two critical points approach the symmetry axis of the phase diagram, and below a certain thickness Δ_tri, there remains only a single critical point at the symmetric composition. This corresponds to a second-order interface localization/delocalization transition even though the wetting transition is of first order. At a specific film thickness, Δ_tri, tricritical behavior is found. The behavior of antisymmetric films is compared with the phase behavior in an antisymmetric double wedge. While the former is the analog of the wetting transition of a planar surface, the latter is related to the filling behavior of a single wedge. Evidence for a second-order interface localization/delocalization transition in an antisymmetric double wedge is presented, and its unconventional critical behavior is related to the predictions of Parry et al. (Phys. Rev. Lett. 83:5535 (1999)) for wedge filling. The critical behavior differs from the Ising universality class and is characterized by strong anisotropic fluctuations.Invited paper presented at the Fifteenth Symposium on Thermophysical Properties, June 022–27, 2003, Boulder, Colorado, U.S.A.     

Pole placement with sensitivity function shaping using 2nd order digital notch filters

This technical note deals with the design of robust digital controllers using pole placement with sensitivity shaping by means of the use of digital notch (band-stop) filters. The use of this type of filters drastically simplifies the effective shaping of the sensitivity functions and the resulting procedure competes with the procedure based on the use of Q-parameterization combined with convex optimization (Automatica 35 (1999) 1111). The feasibility of the technique is illustrated by its application to the control of a very flexible arm.     

A Simulation Framework for Heterogeneous Agents

We introduce a generic simulation framework suitable for agent-based simulations featuring the support of heterogeneous agents, hierarchical scheduling, and flexible specification of design parameters. One key aspect of this framework is the design specification: we use a format based on the Extendible Markup Language (XML) that is simple-structured yet still enables the design of flexible models. Another issue in agent-based simulations, especially when ready-made components are used, is the heterogeneity arising from both the agents' implementations and the underlying platforms. To tackle such obstacles, we introduce a wrapper technique for mapping the functionality of agents living in an interpreter-based environment to a standardized JAVA interface, thus facilitating the task for any control mechanism (like a simulation manager) because it has to handle only one set of commands for all agents involved. Again, this mapping is made by an XML-based definition format. We demonstrate the technique by applying it to a simple sample simulation of two mass marketing firms operating in an artificial consumer environment.     

Simulation of thermally induced package effects with regard to piezoresistive pressure sensors

Microsystems are on their way out of laboratories into production. One of these microsystems, a piezoresistive pressure sensor developed by Robert Bosch GmbH, is examined within this paper. Obviously, one can detect undesirable temperature effects resulting from the sensor package, which influence the electrical characteristics of the sensor. By means of finite-element modelling (FEM), a simulation of the temperature effects can be managed. It is also possible to search for alternative designs of the sensor package.     

Gadolinium-enhanced magnetic resonance angiography of the pelvis in patients with erectile impotence

This study evaluted the potential of contrast-enhanced digital-subtraction magnetic resonance angiography (CE-DS-MRA) for noninvasive angiographic delineation of the arterial supply of the penis in patients with erectile dysfunction. After induction of an erection with prostaglandin E, a three-dimensional fast imaging with steady-state precision (FISP) sequence with TE of 1.8–2 milliseconds, TR of 4.4–5 milliseconds, and flip angle of 40°–60° was used to obtain high-resolution angiograms of the pelvis and penis during the injection of gadolinium diethylenetriaminepentaacetic acid (Gd-DTPA) 0.3 mmol/kg body weight, within 30–50 seconds. DS maximum intensity projections (MIPs) and multiplanar reconstructions (MPRs) were compared with clinical work-up and directional Doppler ultrasound in 11 patients. In all 11 patients (100%), the arterial supply of the penis could be delineated from the aortic bifurcation via the iliac and internal pudendal arteries to the dorsal and deep penile arteries. Of the 22 internal pudendal arteries, 6 (27%) were occluded on CE-DS-MRA and 5 (23%) had stenoses, of which 4 (18%) were greater than 50%. In 7 patients (64%) good correlation between CE-DS-MRA and clinical findings and/or Doppler ultrasound was found; in 2 patients (18%), the correlation was moderate, and in 2 patients (18%) results were discrepant. In 6 patients (55%), MRA provided additional information to the clinical and Doppler ultrasound work-up. CE-DS-MRA can delineate small sessels such as the internal pudendal and penile arteries and thus has the potential to become a noninvasive angiography method in the work-up of erectile impotence. Supported by Siemens Medical Systems, Erlangen; Schering AG, Berlin; and Agfa-Gevaert AG, Leverkusen.