Showing papers by "University of Jyväskylä published in 2012"

The gold–sulfur interface at the nanoscale

Abstract: Thiolate-protected gold surfaces and interfaces, relevant for self-assembled monolayers of organic molecules on gold, for passivated gold nanoclusters and for molecule-gold junctions, are archetypal systems in various fields of current nanoscience research, materials science, inorganic chemistry and surface science. Understanding this interface at the nanometre scale is essential for a wide range of potential applications for site-specific bioconjugate labelling and sensing, drug delivery and medical therapy, functionalization of gold surfaces for sensing, molecular recognition and molecular electronics, and gold nanoparticle catalysis. During the past five years, considerable experimental and theoretical advances have furthered our understanding of the molecular structure of the gold-sulfur interface in these systems. This Review discusses the recent progress from the viewpoint of theory and computations, with connections to relevant experiments.

SMATR 3 - an R package for estimation and inference about allometric lines

Abstract: Summary 1. The Standardised Major Axis Tests and Routines (SMATR) software provides tools for estimation and inference about allometric lines, currently widely used in ecology and evolution. 2. This paper describes some significant improvements to the functionality of the package, now available on R in smatr version 3. 3. New inclusions in the package include sma and ma functions that accept formula input and perform the key inference tasks; multiple comparisons; graphical methods for visualising data and checking (S)MA assumptions; robust (S)MA estimation and inference tools.

A Large Hadron Electron Collider at CERN

Abstract: This document provides a brief overview of the recently published report on the design of the Large Hadron Electron Collider (LHeC), which comprises its physics programme, accelerator physics, technology and main detector concepts. The LHeC exploits and develops challenging, though principally existing, accelerator and detector technologies. This summary is complemented by brief illustrations of some of the highlights of the physics programme, which relies on a vastly extended kinematic range, luminosity and unprecedented precision in deep inelastic scattering. Illustrations are provided regarding high precision QCD, new physics (Higgs, SUSY) and electron-ion physics. The LHeC is designed to run synchronously with the LHC in the twenties and to achieve an integrated luminosity of O(100)\,fb$^{-1}$. It will become the cleanest high resolution microscope of mankind and will substantially extend as well as complement the investigation of the physics of the TeV energy scale, which has been enabled by the LHC.

Memetic algorithms and memetic computing optimization: A literature review

Abstract: Memetic computing is a subject in computer science which considers complex structures such as the combination of simple agents and memes, whose evolutionary interactions lead to intelligent complexes capable of problem-solving. The founding cornerstone of this subject has been the concept of memetic algorithms, that is a class of optimization algorithms whose structure is characterized by an evolutionary framework and a list of local search components. This article presents a broad literature review on this subject focused on optimization problems. Several classes of optimization problems, such as discrete, continuous, constrained, multi-objective and characterized by uncertainties, are addressed by indicating the memetic “recipes” proposed in the literature. In addition, this article focuses on implementation aspects and especially the coordination of memes which is the most important and characterizing aspect of a memetic structure. Finally, some considerations about future trends in the subject are given.

Optimal power flow: a bibliographic survey I

Abstract: Over the past half-century, Optimal Power Flow (OPF) has become one of the most important and widely studied nonlinear optimization problems. In general, OPF seeks to optimize the operation of electric power generation, transmission, and distribution networks subject to system constraints and control limits. Within this framework, however, there is an extremely wide variety of OPF formulations and solution methods. Moreover, the nature of OPF continues to evolve due to modern electricity markets and renewable resource integration. In this two-part survey, we survey both the classical and recent OPF literature in order to provide a sound context for the state of the art in OPF formulation and solution methods. The survey contributes a comprehensive discussion of specific optimization techniques that have been applied to OPF, with an emphasis on the advantages, disadvantages, and computational characteristics of each. Part I of the survey (this article) provides an introduction and surveys the deterministic optimization methods that have been applied to OPF. Part II of the survey examines the recent trend towards stochastic, or non-deterministic, search techniques and hybrid methods for OPF.

Derivation of transient relativistic fluid dynamics from the Boltzmann equation

Abstract: In this work we present a general derivation of relativistic fluid dynamics from the Boltzmann equation using the method of moments. The main difference between our approach and the traditional 14-moment approximation is that we will not close the fluid-dynamical equations of motion by truncating the expansion of the distribution function. Instead, we keep all terms in the moment expansion. The reduction of the degrees of freedom is done by identifying the microscopic time scales of the Boltzmann equation and considering only the slowest ones. In addition, the equations of motion for the dissipative quantities are truncated according to a systematic power-counting scheme in Knudsen and inverse Reynolds number. We conclude that the equations of motion can be closed in terms of only 14 dynamical variables, as long as we only keep terms of second order in Knudsen and/or inverse Reynolds number. We show that, even though the equations of motion are closed in terms of these 14 fields, the transport coefficients carry information about all the moments of the distribution function. In this way, we can show that the particle-diffusion and shear-viscosity coefficients agree with the values given by the Chapman-Enskog expansion.

What do we need to know about speciation

Abstract: Speciation has been a major focus of evolutionary biology research in recent years, with many important advances. However, some of the traditional organising principles of the subject area no longer provide a satisfactory framework, such as the classification of speciation mechanisms by geographical context into allopatric, parapatric and sympatry classes. Therefore, we have asked where speciation research should be directed in the coming years. Here, we present a distillation of questions about the mechanisms of speciation, the genetic basis of speciation and the relationship between speciation and diversity. Our list of topics is not exhaustive; rather we aim to promote discussion on research priorities and on the common themes that underlie disparate speciation processes.

The limits of the nuclear landscape

Abstract: In 2011, 100 new nuclides were discovered. They joined the approximately 3,000 stable and radioactive nuclides that either occur naturally on Earth or are synthesized in the laboratory. Every atomic nucleus, characterized by a specific number of protons and neutrons, occupies a spot on the chart of nuclides, which is bounded by 'drip lines' indicating the values of neutron and proton number at which nuclear binding ends. The placement of the neutron drip line for the heavier elements is based on theoretical predictions using extreme extrapolations, and so is uncertain. However, it is not known how uncertain it is or how many protons and neutrons can be bound in a nucleus. Here we estimate these limits of the nuclear 'landscape' and provide statistical and systematic uncertainties for our predictions. We use nuclear density functional theory, several Skyrme interactions and high-performance computing, and find that the number of bound nuclides with between 2 and 120 protons is around 7,000. We find that extrapolations for drip-line positions and selected nuclear properties, including neutron separation energies relevant to astrophysical processes, are very consistent between the models used.

AGATA - Advanced GAmma Tracking Array

Abstract: The Advanced GAmma Tracking Array (AGATA) is a European project to develop and operate the next generation gamma-ray spectrometer. AGATA is based on the technique of gamma-ray energy tracking in electrically segmented high-purity germanium crystals. This technique requires the accurate determination of the energy, time and position of every interaction as a gamma ray deposits its energy within the detector volume. Reconstruction of the full interaction path results in a detector with very high efficiency and excellent spectral response. The realisation of gamma-ray tracking and AGATA is a result of many technical advances. These include the development of encapsulated highly segmented germanium detectors assembled in a triple cluster detector cryostat, an electronics system with fast digital sampling and a data acquisition system to process the data at a high rate. The full characterisation of the crystals was measured and compared with detector-response simulations. This enabled pulse-shape analysis algorithms, to extract energy, time and position, to be employed. In addition, tracking algorithms for event reconstruction were developed. The first phase of AGATA is now complete and operational in its first physics campaign. In the future AGATA will be moved between laboratories in Europe and operated in a series of campaigns to take advantage of the different beams and facilities available to maximise its science output. The paper reviews all the achievements made in the AGATA project including all the necessary infrastructure to operate and support the spectrometer.

A synthetic molecular pentafoil knot

Abstract: – hydrogen bonds. The one-pot self-assembly reaction features an exceptional number of different design elements—some well precedented and others less well known within the context of directing the formation of (supra)molecular species. We anticipate that the strategies and tactics used here can be applied to the rational synthesis of other higher-order interlocked molecular architectures.

Adverse metabolic response to regular exercise: Is it a rare or common occurrence?

Abstract: Background: Individuals differ in the response to regular exercise. Whether there are people who experience adverse changes in cardiovascular and diabetes risk factors has never been addressed. Methodology/Principal Findings: An adverse response is defined as an exercise-induced change that worsens a risk factor beyond measurement error and expected day-to-day variation. Sixty subjects were measured three times over a period of three weeks, and variation in resting systolic blood pressure (SBP) and in fasting plasma HDL-cholesterol (HDL-C), triglycerides (TG), and insulin (FI) was quantified. The technical error (TE) defined as the within-subject standard deviation derived from these measurements was computed. An adverse response for a given risk factor was defined as a change that was at least two TEs away from no change but in an adverse direction. Thus an adverse response was recorded if an increase reached 10 mm Hg or more for SBP, 0.42 mmol/L or more for TG, or 24 pmol/L or more for FI or if a decrease reached 0.12 mmol/L or more for HDL-C. Completers from six exercise studies were used in the present analysis: Whites (N = 473) and Blacks (N = 250) from the HERITAGE Family Study; Whites and Blacks from DREW (N = 326), from INFLAME (N = 70), and from STRRIDE (N = 303); and Whites from a University of Maryland cohort (N = 160) and from a University of Jyvaskyla study (N = 105), for a total of 1,687 men and women. Using the above definitions, 126 subjects (8.4%) had an adverse change in FI. Numbers of adverse responders reached 12.2% for SBP, 10.4% for TG, and 13.3% for HDL-C. About 7% of participants experienced adverse responses in two or more risk factors. Conclusions/Significance: Adverse responses to regular exercise in cardiovascular and diabetes risk factors occur. Identifying the predictors of such unwarranted responses and how to prevent them will provide the foundation for personalized exercise prescription.

Electron Ion Collider: The Next QCD Frontier - Understanding the glue that binds us all

Abstract: This White Paper presents the science case of an Electron-Ion Collider (EIC), focused on the structure and interactions of gluon-dominated matter, with the intent to articulate it to the broader nuclear science community. It was commissioned by the managements of Brookhaven National Laboratory (BNL) and Thomas Jefferson National Accelerator Facility (JLab) with the objective of presenting a summary of scientific opportunities and goals of the EIC as a follow-up to the 2007 NSAC Long Range plan. This document is a culmination of a community-wide effort in nuclear science following a series of workshops on EIC physics and, in particular, the focused ten-week program on "Gluons and quark sea at high energies" at the Institute for Nuclear Theory in Fall 2010. It contains a brief description of a few golden physics measurements along with accelerator and detector concepts required to achieve them, and it benefited from inputs from the users' communities of BNL and JLab. This White Paper offers the promise to propel the QCD science program in the U.S., established with the CEBAF accelerator at JLab and the RHIC collider at BNL, to the next QCD frontier.

Ecosystem restoration with teeth: what role for predators?

Abstract: Recent advances highlight the potential for predators to restore ecosystems and confer resilience against globally threatening processes, including climate change and biological invasions. However, releasing the ecological benefits of predators entails significant challenges. Here, we discuss the economic, environmental and social considerations affecting predator-driven ecological restoration programmes, and suggest approaches for reducing the undesirable impacts of predators. Because the roles of predators are context dependent, we argue for increased emphasis on predator functionality in ecosystems and less on the identities and origins of species and genotypes. We emphasise that insufficient attention is currently given to the importance of variation in the social structures and behaviours of predators in influencing the dynamics of trophic interactions. Lastly, we outline experiments specifically designed to clarify the ecological roles of predators and their potential utility in ecosystem restoration.

Coherent quantum phase slip

Abstract: The magnetic-flux analogue to coherent Josephson tunnelling of electric charge has been observed in a strongly disordered superconducting nanowire. Coherent quantum phase slip (CQPS) has not, until now, been observed experimentally. It is a phenomenon exactly dual to the Josephson effect, but whereas the latter is a coherent transfer of charges between superconducting contacts, CQPS is a coherent transfer of vortices or fluxes across a superconducting wire. This paper reports direct observation of CQPS in a strongly disordered indium oxide superconducting wire inserted in a loop; the effect manifests through the superposition of quantum states with different fluxes. The CQPS may — like the Josephson effect before it — lead to innovative applications in superconducting electronics and quantum metrology. A hundred years after the discovery of superconductivity, one fundamental prediction of the theory, coherent quantum phase slip (CQPS), has not been observed. CQPS is a phenomenon exactly dual1 to the Josephson effect; whereas the latter is a coherent transfer of charges between superconducting leads2,3, the former is a coherent transfer of vortices or fluxes across a superconducting wire. In contrast to previously reported observations4,5,6,7,8 of incoherent phase slip, CQPS has been only a subject of theoretical study9,10,11,12. Its experimental demonstration is made difficult by quasiparticle dissipation due to gapless excitations in nanowires or in vortex cores. This difficulty might be overcome by using certain strongly disordered superconductors near the superconductor–insulator transition. Here we report direct observation of CQPS in a narrow segment of a superconducting loop made of strongly disordered indium oxide; the effect is made manifest through the superposition of quantum states with different numbers of flux quanta13. As with the Josephson effect, our observation should lead to new applications in superconducting electronics and quantum metrology1,10,11.

Robust adaptive Metropolis algorithm with coerced acceptance rate

Abstract: The adaptive Metropolis (AM) algorithm of Haario, Saksman and Tamminen (Bernoulli 7(2):223---242, 2001) uses the estimated covariance of the target distribution in the proposal distribution. This paper introduces a new robust adaptive Metropolis algorithm estimating the shape of the target distribution and simultaneously coercing the acceptance rate. The adaptation rule is computationally simple adding no extra cost compared with the AM algorithm. The adaptation strategy can be seen as a multidimensional extension of the previously proposed method adapting the scale of the proposal distribution in order to attain a given acceptance rate. The empirical results show promising behaviour of the new algorithm in an example with Student target distribution having no finite second moment, where the AM covariance estimate is unstable. In the examples with finite second moments, the performance of the new approach seems to be competitive with the AM algorithm combined with scale adaptation.

Optimal power flow: A bibliographic survey II non-deterministic and hybrid methods

Abstract: Over the past half-century, Optimal Power Flow (OPF) has become one of the most important and widely studied nonlinear optimization problems. In general, OPF seeks to optimize the operation of electric power generation, transmission, and distribution networks subject to system constraints and control limits. Within this framework, however, there is an extremely wide variety of OPF formulations and solution methods. Moreover, the nature of OPF continues to evolve due to modern electricity markets and renewable resource integration. In this two-part survey, we survey both the classical and recent OPF literature in order to provide a sound context for the state of the art in OPF formulation and solution methods. The survey contributes a comprehensive discussion of specific optimization techniques that have been applied to OPF, with an emphasis on the advantages, disadvantages, and computational characteristics of each. Part I of the survey provides an introduction and surveys the deterministic optimization methods that have been applied to OPF. Part II of the survey (this article) examines the recent trend towards stochastic, or non-deterministic, search techniques and hybrid methods for OPF.

Age-related differences in Achilles tendon properties and triceps surae muscle architecture in vivo.

Abstract: This study examined the concurrent age-related differences in muscle and tendon structure and properties. Achilles tendon morphology and mechanical properties and triceps surae muscle architecture ...

J/psi Suppression at Forward Rapidity in Pb-Pb Collisions at root s(NN)=2.76 TeV

Abstract: The ALICE experiment has measured the inclusive J/psi production in Pb-Pb collisions at root s(NN) = 2.76 TeV down to zero transverse momentum in the rapidity range 2.5 < y < 4. A suppression of the inclusive J/psi yield in Pb-Pb is observed with respect to the one measured in pp collisions scaled by the number of binary nucleon-nucleon collisions. The nuclear modification factor, integrated over the 0%-80% most central collisions, is 0.545 +/- 0.032(stat) +/- 0.083dsyst_ and does not exhibit a significant dependence on the collision centrality. These features appear significantly different from measurements at lower collision energies. Models including J/psi production from charm quarks in a deconfined partonic phase can describe our data.

Who enjoys listening to sad music and why

Abstract: although people generally avoid negative emotional experiences in general, they often enjoy sadness portrayed in music and other arts. The present study investigated what kinds of subjective emotional experiences are induced in listeners by sad music, and whether the tendency to enjoy sad music is associated with particular personality traits. One hundred forty-eight participants listened to 16 music excerpts and rated their emotional responses. As expected, sadness was the most salient emotion experienced in response to sad excerpts. However, other more positive and complex emotions such as nostalgia, peacefulness, and wonder were also evident. Furthermore, two personality traits – Openness to Experience and Empathy – were associated with liking for sad music and with the intensity of emotional responses induced by sad music, suggesting that aesthetic appreciation and empathetic engagement play a role in the enjoyment of sad music.

Cross-lagged associations between perceived external employability, job insecurity, and exhaustion: Testing gain and loss spirals according to the Conservation of Resources Theory

Abstract: Summary This study investigates perceived external employability (PEE) as a personal resource in relation to job insecurity and exhaustion. We advance the idea that PEE may reduce feelings of job insecurity and, through felt job insecurity, also exhaustion. That is, we probe the paths from PEE to job insecurity and from job insecurity to exhaustion. We furthermore account for possible reversed causality, so that exhaustion felt job insecurity and felt job insecurity PEE. This aligns with insights from the Conservation of Resources Theory, which is built on the assumption of resource caravans passageways and associated gain and loss spirals. We based the results on a sample of 1314 workers from two Finnish universities. Respondents participated twice in the study with a time lag of one year. We found that PEE related negatively to felt job insecurity and vice versa. Similarly, there was a reciprocal positive relationship between felt job insecurity and exhaustion. We conclude that PEE may prevent feelings of insecurity and, through reduced job insecurity, also exhaustion. Copyright © 2012 John Wiley & Sons, Ltd.

Recent advances in steroidal supramolecular gels

Abstract: During the last decade or two the interest towards small molecules capable of self-assembly leading to gelation has increased intensively The investigation of these supramolecular gels aims not only at understanding the fundamental processes underlying gel formation but also at development of new materials with a myriad of applications Steroids are widely-spread natural products with a large and rigid steroidal nucleus combined with derivatizable functional groups leading to an adjustable polarity profile, which makes them attractive building blocks when designing novel low molecular weight gelators Due to their unique properties, steroid-based supramolecular gels may find use in applications ranging from materials science and nanoelectronics to their application as reaction media or as sensing and responsive materials Moreover, biomaterials based on steroidal gels may find use in biomedicine, drug delivery, regenerative medicine, and tissue engineering This article summarizes the most recent advances in the field of steroidal supramolecular gels in terms of steroid-derived hydro- and organogels, metallogels, two-component gels, and stimuli-responsive gels Furthermore, the potential applications of the systems are discussed

Observation of Direct-Photon Collective Flow in Au plus Au Collisions at root s(NN)=200 GeV

Abstract: The second Fourier component v(2) of the azimuthal anisotropy with respect to the reaction plane is measured for direct photons at midrapidity and transverse momentum (p(T)) of 1-12 GeV/c in Au + Au collisions at root s(NN) = 200 GeV. Previous measurements of this quantity for hadrons with p(T) 6 GeV/c a reduced anisotropy is interpreted in terms of a path-length dependence for parton energy loss. In this measurement with the PHENIX detector at the Relativistic Heavy Ion Collider we find that for p(T) > 4 GeV/c the anisotropy for direct photons is consistent with zero, which is as expected if the dominant source of direct photons is initial hard scattering. However, in the p(T) < 4 GeV/c region dominated by thermal photons, we find a substantial direct-photon v(2) comparable to that of hadrons, whereas model calculations for thermal photons in this kinematic region underpredict the observed v(2).

Structural and theoretical basis for ligand exchange on thiolate monolayer protected gold nanoclusters.

Abstract: Ligand exchange reactions are widely used for imparting new functionality on or integrating nanoparticles into devices. Thiolate-for-thiolate ligand exchange in monolayer protected gold nanoclusters has been used for over a decade; however, a firm structural basis of this reaction has been lacking. Herein, we present the first single-crystal X-ray structure of a partially exchanged Au102(p-MBA)40(p-BBT)4 (p-MBA = para-mercaptobenzoic acid, p-BBT = para-bromobenzene thiol) with p-BBT as the incoming ligand. The crystal structure shows that 2 of the 22 symmetry-unique p-MBA ligand sites are partially exchanged to p-BBT under the initial fast kinetics in a 5 min timescale exchange reaction. Each of these ligand-binding sites is bonded to a different solvent-exposed Au atom, suggesting an associative mechanism for the initial ligand exchange. Density functional theory calculations modeling both thiol and thiolate incoming ligands postulate a mechanistic pathway for thiol-based ligand exchange. The discrete mo...

BioImageXD: an open, general-purpose and high-throughput image-processing platform

Abstract: BioImageXD puts open-source computer science tools for three-dimensional visualization and analysis into the hands of all researchers, through a user-friendly graphical interface tuned to the needs of biologists. BioImageXD has no restrictive licenses or undisclosed algorithms and enables publication of precise, reproducible and modifiable workflows. It allows simple construction of processing pipelines and should enable biologists to perform challenging analyses of complex processes. We demonstrate its performance in a study of integrin clustering in response to selected inhibitors.

Health literacy as a learning outcome in schools

Abstract: Purpose – The aim of this paper is to define health literacy as a learning outcome in schools, and to describe the learning conditions that are relevant for targeting health literacy.Design/methodology/approach – The paper draws on theoretical and empirical educational literature, and also the experiences of the authors.Findings – Health literacy is defined as consisting of five core components: theoretical knowledge, practical knowledge, critical thinking, self‐awareness, and citizenship. The first three components are rather similar to the commonly‐accepted health literacy concept, but the definition given in this paper expands the concept via two additional – but essential – components. It is emphasized that when one is aiming to develop students' internal capacity to construct their own meanings regarding health topics, these two additional components are called for. The paper argues that one of the main aims of health teaching in schools should be to foster students' ability to define their own belie...