Precision shooting: Sampling long transition pathways

The kinetics of collective rearrangements in solution, such as protein folding and nanocrystal phase transitions, often involve free energy barriers that are both long and rough. Applying methods of transition path sampling to harvest simulated trajectories that exemplify such processes is typically made difficult by a very low acceptance rate for newly generated trajectories. We address this problem by introducing a new generation algorithm based on the linear short-time behavior of small disturbances in phase space. Using this ``precision shooting'' technique, arbitrarily small disturbances can be propagated in time, and any desired acceptance ratio of shooting moves can be obtained. We demonstrate the method for a simple but computationally problematic isomerization process in a dense liquid of soft spheres. We also discuss its applicability to barrier crossing events involving metastable intermediate states.Comment: 9 pages, 12 figures, submitted to J. Chem. Phy

'Transport to Where?': Reflections on the problem of value and time à propos an awkward practice in medical research.

Based upon Kenyan ethnography, this article examines the gap between the bioethics aversion to value transfers in clinical trials, and research participants' and researchers' expectations of these. This article focuses upon so-called 'transport reimbursement' (TR): monetary payments to participants that are framed as mere refund of transport expenses, but which are of considerable value to recipients. The interest in this case lies not so much in the unsurprising gap between regulatory norms and poor study subjects' lives, but in the way in which this discrepancy between bioethical discourse and materialities of survival is silenced. In spite of the general awareness that TR indeed is about the material value of research, about value calculation, and expectations of return, it is not publicly discussed as such - unless ironically, in jest, or in private. This double-blindness around 'reimbursement' has provoked discussions among ethicists and anthropologists, some of which propose that the work that generates scientific value should be recognised as labour and participants, accordingly, paid. Here, this paper argues that such a re-vision of trial participation as work rather than as a gift for the public good, risks abrogating the possibility of 'the public' that is not only a precondition of public medical science, but also its potential product. The supposedly radical solution of tearing away the veils of misrecognition that 'free' gifting ideology lays upon the realities of free labour, though analytically plausible, fails to recognise the utopian openings within clinical trial transactions that point beyond the present - towards larger forms of social association, and towards future alignments of scientific possibilities and human lives

Force-induced unfolding of a homopolymer on fractal lattice: exact results vs. mean field predictions

We study the force-induced unfolding of a homopolymer on the three dimensional Sierpinski gasket. The polymer is subject to a contact energy between nearest neighbour sites not consecutive along the chain and to a stretching force. The hierarchical nature of the lattice we consider allows for an exact treatment which yields the phase diagram and the critical behaviour. We show that for this model mean field predictions are not correct, in particular in the exact phase diagram there is {\em not} a low temperature reentrance and we find that the force induced unfolding transition below the theta temperature is second order.Comment: 15 pages, 5 eps figure

Two-stage coarsening mechanism in a kinetically constrained model of an attractive colloid

We study an attractive version of the East model using the real-space renormalization group (RG) introduced by Stella et al. The former is a kinetically constrained model with an Ising-like interaction between excitations, and shows striking agreement with the phenomonology of attractive colloidal systems. We find that the RG predicts two nonuniversal dynamic exponents, which suggests that in the out-of-equilibrium regime the model coarsens via a two-stage mechanism. We explain this mechanism physically, and verify this prediction numerically. In addition, we find that the characteristic relaxation time of the model is a non-monotonic function of attraction strength, again in agreement with numerical results.Comment: 10 page

T-SP1: a novel serine protease-like protein predominantly expressed in testis

Here, we describe a novel member in the group of membrane-anchored chymotrypsin (S1)-like serine proteases, namely testis serine protease 1 (T-SP1), as it is principally expressed in testis tissue. The human T-SP1 gene encompasses 28.7 kb on the short arm of chromosome 8 and consists of seven exons. Rapid amplification of cDNA ends ( RACE) experiments revealed that due to alternative splicing three different variants (T-SP1/1, -2, -3) are detectable in testis tissue displaying pronounced heterogeneity at their 3'-end. T-SP1/1 consists of an 18 amino acid signal peptide and of a 49 amino acid propeptide. The following domain with the catalytic triad of His(108), Asp(156), and Ser(250) shares sequence identities of 42% and 40% with the blood coagulation factor XI and plasma kallikrein, respectively. Only T-SP1/1 contains a hydrophobic part at the C-terminus, which provides the basis for cell membrane anchoring. Using a newly generated polyclonal anti-T-SP1 antibody, expression of the T-SP1 protein was found in the Leydig and Sertoli cells of the testis and in the epithelial cells of the ductuli efferentes. Notably, T-SP1 protein was also detectable in prostate cancer and in some ovarian cancer tissues, indicating tumor-related synthesis of T-SP1 beyond testis tissue

Global Health Research in an Unequal World

This book is a collection of fictionalised case studies of everyday ethical dilemmas and challenges, encountered in the process of conducting global health research in places where the effects of global, political and economic inequality are particularly evident. It is a training tool to fill the gap between research ethics guidelines, and their implementation 'on the ground'. The case studies, therefore, focus on 'relational' ethics: ethical actions and ideas that emerge through relations with others, rather than in regulations

A mineralized zone in Western Candor Chasma, Mars

Spectral evidence from Viking and Phobos orbiting spacecraft suggests the local development of crystalline ferric oxides in a small region within Mars' equatorial Valles Marineris canyon system. This is the same area noted for its anomalous coloration in Viking Orbiter image 583 A by McEwen. The unique hue of the region in Viking color data is due to a reduced green filter reflectance, relative to violet and red, in comparison to surrounding materials of similar albedo or average reflectance. For this reason, the region does not appear spectrally distinctive in later Survey Mission images which were acquired without the green filter. In high resolution, the spectral unit can be seen to correspond to two 20 km long depressions on the margins of Candor Mensa, a heavily eroded plateau-forming deposit on the canyon floor. Laminae are conspicuous in several places on the plateau, particularly where 15 to 20 cycles of alternating bright and dark laminae are exposed at approximately 200 meter vertical intervals. Laminae are also visible on the steep, vertically fluted cliffs to the south of this depression. Concentric laminae indicate a basis in the depression on the southeastern margin of Candor Mensa at the location of the less pronounced hue anomaly. A distinct lineation at the base of the scarp at the western end of the canyon transects mottled canyon floor deposits believed to be among the youngest in the Valles marineris. Water is implicated in the formation of the iron oxides, since the steep surfaces of layered sediments elsewhere on Candor Mensa show no evidence of unusual coloration despite the fact that these materials were deposited concurrently with the strata exposed in the depressions. This suggests that the mineralization is secondary in nature and developed locally in association with the depressions, which could have ponded surface runoff or groundwater seepage

Transferable Pair Potentials for CdS and ZnS Crystals

A set of interatomic pair potentials is developed for CdS and ZnS crystals. We show that a simple energy function, which has been used to describe the properties of CdSe [J. Chem. Phys. 116, 258 (2002)], can be parametrized to accurately describe the lattice and elastic constants, and phonon dispersion relations of bulk CdS and ZnS in the wurtzite and rocksalt crystal structures. The predicted coexistence pressure of the wurtzite and rocksalt structures, as well as the equation of state are in good agreement with experimental observations. These new pair potentials enable the study of a wide range of processes in bulk and nanocrystalline II-VI semiconductor materials

INTRODUCTION: SUSTAINING THE LIFE OF THE POLIS.

How are publics of protection and care defined in African cities today? The effects of globalization and neo-liberal policies on urban space are well documented. From London to São Paulo, denationalization, privatization, offshoring and cuts in state expenditure are creating enclaves and exclusions, resulting in fragmented, stratified social geographies (see Caldeira 2000; Ong 2006; Harvey 2006; Murray 2011). 'Networked archipelagoes', islands connected by transnational circulations of capital, displace other spatial relations and imaginaries. Spaces of encompassment, especially, such as 'the nation' or simply 'society' as defined by inclusion within a whole, lose practical value and intellectual purchase as referents of citizenship (Gupta and Ferguson 2002; Ferguson 2005). In African cities, where humanitarian, experimental or market logics dominate the distribution of sanitation and healthcare, this fragmentation is particularly stark (see, for example, Redfield 2006, 2012; Fassin 2007; Bredeloup et al. 2008; Nguyen 2012). Privilege and crisis interrupt older contiguities, delineating spaces and times of exception. The 'public' of health is defined by survival or consumption, obscuring the human as bearer of civic rights and responsibilities, as inhabitants of 'objective' material worlds 'common to all of us' (Arendt 1958: 52). Is it possible, under these conditions, to enact and imagine public health as a project of citizens, animated in civic space