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

Equilibrium free energies from fast-switching trajectories with large time steps

Jarzynski's identity for the free energy difference between two equilibrium states can be viewed as a special case of a more general procedure based on phase space mappings. Solving a system's equation of motion by approximate means generates a mapping that is perfectly valid for this purpose, regardless of how closely the solution mimics true time evolution. We exploit this fact, using crudely dynamical trajectories to compute free energy differences that are in principle exact. Numerical simulations show that Newton's equation can be discretized to low order over very large time steps (limited only by the computer's ability to represent resulting values of dynamical variables) without sacrificing thermodynamic accuracy. For computing the reversible work required to move a particle through a dense liquid, these calculations are more efficient than conventional fast switching simulations by more than an order of magnitude. We also explore consequences of the phase space mapping perspective for systems at equilibrium, deriving an exact expression for the statistics of energy fluctuations in simulated conservative systems

Interleukin-17A upregulates receptor activator of NF-kappaB on osteoclast precursors.

IntroductionThe interaction between the immune and skeletal systems is evidenced by the bone loss observed in autoimmune diseases such as rheumatoid arthritis. In this paper we describe a new mechanism by which the immune cytokine IL-17A directly affects osteoclastogenesis.MethodsHuman CD14+ cells were isolated from healthy donors, cultured on dentine slices and coverslips and stimulated with IL-17A and/or receptor activator of NF-kappaB ligand (RANKL). Osteoclast differentiation was evaluated by gene expression, flow cytometry, tartrate-resistant acid phosphatase staining, fluorescence and electron microscopy. Physiologic bone remodelling was studied in wild-type (Wt) and IL-17A-/- mice using micro-computer tomography and serum RANKL/osteoprotegerin concentration. Functional osteoclastogenesis assays were performed using bone marrow macrophages isolated from IL-17A-/- and Wt mice.ResultsIL-17A upregulates the receptor activator for NF-kappaB receptor on human osteoclast precursors in vitro, leading to increased sensitivity to RANKL signalling, osteoclast differentiation and bone loss. IL-17A-/- mice have physiological bone homeostasis indistinguishable from Wt mice, and bone marrow macrophages isolated from these mice develop fully functional normal osteoclasts.ConclusionsCollectively our data demonstrate anti-IL-17A treatment as a selective therapeutic target for bone loss associated with autoimmune diseases

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