Active Brownian Particles. From Individual to Collective Stochastic Dynamics

We review theoretical models of individual motility as well as collective dynamics and pattern formation of active particles. We focus on simple models of active dynamics with a particular emphasis on nonlinear and stochastic dynamics of such self-propelled entities in the framework of statistical mechanics. Examples of such active units in complex physico-chemical and biological systems are chemically powered nano-rods, localized patterns in reaction-diffusion system, motile cells or macroscopic animals. Based on the description of individual motion of point-like active particles by stochastic differential equations, we discuss different velocity-dependent friction functions, the impact of various types of fluctuations and calculate characteristic observables such as stationary velocity distributions or diffusion coefficients. Finally, we consider not only the free and confined individual active dynamics but also different types of interaction between active particles. The resulting collective dynamical behavior of large assemblies and aggregates of active units is discussed and an overview over some recent results on spatiotemporal pattern formation in such systems is given.Comment: 161 pages, Review, Eur Phys J Special-Topics, accepte

Why Does the Giant Panda Eat Bamboo? A Comparative Analysis of Appetite-Reward-Related Genes among Mammals

Background: The giant panda has an interesting bamboo diet unlike the other species in the order of Carnivora. The umami taste receptor gene T1R1 has been identified as a pseudogene during its genome sequencing project and confirmed using a different giant panda sample. The estimated mutation time for this gene is about 4.2 Myr. Such mutation coincided with the giant panda’s dietary change and also reinforced its herbivorous life style. However, as this gene is preserved in herbivores such as cow and horse, we need to look for other reasons behind the giant panda’s diet switch. Methodology/Principal Findings: Since taste is part of the reward properties of food related to its energy and nutrition contents, we did a systematic analysis on those genes involved in the appetite-reward system for the giant panda. We extracted the giant panda sequence information for those genes and compared with the human sequence first and then with seven other species including chimpanzee, mouse, rat, dog, cat, horse, and cow. Orthologs in panda were further analyzed based on the coding region, Kozak consensus sequence, and potential microRNA binding of those genes. Conclusions/Significance: Our results revealed an interesting dopamine metabolic involvement in the panda’s food choice

Mobility justice in low carbon energy transitions

Mobility systems raise multiple questions of justice. Work on mobility justice and policy often treats different elements of the debate separately, for example focussing on environmental justice or accessibility. This is problematic as it can privilege policy solutions without a full view of the winners and losers and the values implicit in that. Using analysis of current policy, we investigate how mobility justice can reconcile its different components, and find two major consequences. First, is doubt about the justice of the existing policy approach which tries to tackle transport pollution primarily through a shift to low emission vehicles. This approach privileges those with access to private vehicles and further privileges certain sets of activities. Second is a need to reassess which basic normative ideas should be applied in mobility justice. Work on mobility justice has tended to appeal to conceptions of justice concerned with access to resources including resources enabling mobility. These conceptions say little about how resources should be used. We show that avoiding stark inequalities means collectively thinking about how resources are used, about how we value activities involving mobility, and about what sorts of goods and services we create

Requirements Capture in Natural Language Problem Statements

Requirements elicitation and analysis remains a stubbornly intractable problem to automate. This paper looks at the use of natural language analysis techniques in the requirements capture process. It begins with a review of past work and then develops an algorithmic approach to analysing and restructuring natural language text. We begin by marking the text up as parts of speech, before we restructure this mark-up into subject-verb-object clauses. After a user-assisted pronoun replacement step, a relatively comprehensive UML class diagram can be generated. Further analysis then allows us to generate use cases. To illustrate the algorithm in practice we use a case study

Object-Oriented Analysis Using Natural Language Processing

There is often a wealth of extant domain-specific, natural-language data available to help guide developers of object-oriented systems. This data is generally amenable to natural language processing in order to derive valuable design information. However, from a review of the field, we contend that current approaches have not been able to extract all the semantic and design detail that is present in such data. For instance: we see a lack of dynamic system representations; we detect reluctance for researchers to adopt hybrid solutions - where users confirm and elaborate automated analyses; and we suggest there is work needed to determine a comprehensive repertoire of potential relationships between system components. In partial pursuit of such a manifesto, this paper mentions briefly our algorithmic proposal for processing natural language into UML with supplemental user involvement

Evaluation of variation in the phosphoinositide-3-kinase catalytic subunit alpha oncogene and breast cancer risk.

BACKGROUND: Somatic mutations in phosphoinositide-3-kinase catalytic subunit alpha (PIK3CA) are frequent in breast tumours and have been associated with oestrogen receptor (ER) expression, human epidermal growth factor receptor-2 overexpression, lymph node metastasis and poor survival. The goal of this study was to evaluate the association between inherited variation in this oncogene and risk of breast cancer. METHODS: A single-nucleotide polymorphism from the PIK3CA locus that was associated with breast cancer in a study of Caucasian breast cancer cases and controls from the Mayo Clinic (MCBCS) was genotyped in 5436 cases and 5280 controls from the Cancer Genetic Markers of Susceptibility (CGEMS) study and in 30 949 cases and 29 788 controls from the Breast Cancer Association Consortium (BCAC). RESULTS: Rs1607237 was significantly associated with a decreased risk of breast cancer in MCBCS, CGEMS and all studies of white Europeans combined (odds ratio (OR)=0.97, 95% confidence interval (CI) 0.95-0.99, P=4.6 × 10(-3)), but did not reach significance in the BCAC replication study alone (OR=0.98, 95% CI 0.96-1.01, P=0.139). CONCLUSION: Common germline variation in PIK3CA does not have a strong influence on the risk of breast cancer

Indistinguishability and correlations of photons generated by quantum emitters undergoing spectral diffusion

Photon-based quantum information processing is based on manipulating multi photon interference. We focus on the Hong-Ou-Mandel (HOM) dip in the photon coincidence rate which provides a direct measure of interference of indistinguishable photons linked to their Bose statistics. The effect has been first observed with entangled photons generated by parametric down conversion and then extended to independent emitters. Fluctuations caused by coupling between emitters and a bath can erode the interference which causes the dip. Here we show how the magnitude and shape of the HOM dip is affected by spectral diffusion induced by coupling to a brownian oscillator bath. Conditions for maintaining and controlling the interference are specified