Force-induced rupture of a DNA duplex

The rupture of double-stranded DNA under stress is a key process in biophysics and nanotechnology. In this article we consider the shear-induced rupture of short DNA duplexes, a system that has been given new importance by recently designed force sensors and nanotechnological devices. We argue that rupture must be understood as an activated process, where the duplex state is metastable and the strands will separate in a finite time that depends on the duplex length and the force applied. Thus, the critical shearing force required to rupture a duplex within a given experiment depends strongly on the time scale of observation. We use simple models of DNA to demonstrate that this approach naturally captures the experimentally observed dependence of the critical force on duplex length for a given observation time. In particular, the critical force is zero for the shortest duplexes, before rising sharply and then plateauing in the long length limit. The prevailing approach, based on identifying when the presence of each additional base pair within the duplex is thermodynamically unfavorable rather than allowing for metastability, does not predict a time-scale-dependent critical force and does not naturally incorporate a critical force of zero for the shortest duplexes. Additionally, motivated by a recently proposed force sensor, we investigate application of stress to a duplex in a mixed mode that interpolates between shearing and unzipping. As with pure shearing, the critical force depends on the time scale of observation; at a fixed time scale and duplex length, the critical force exhibits a sigmoidal dependence on the fraction of the duplex that is subject to shearing.Comment: 10 pages, 6 figure

A dynamic auto-adaptive predictive maintenance policy for degradation with unknown parameters

International audienceWith the development of monitoring equipment, research on condition-based maintenance (CBM) is rapidly growing. CBM optimization aims to find an optimal CBM policy which minimizes the average cost of the system over a specified duration of time. This paper proposes a dynamic auto-adaptive predictive maintenance policy for single-unit systems whose gradual deterioration is governed by an increasing stochastic process. The parameters of the degradation process are assumed to be unknown and Bayes' theorem is used to update the prior information. The time interval between two successive inspections is scheduled based on the remaining useful life (RUL) of the system and is updated along with the degradation parameters. A procedure is proposed to dynamically adapt the maintenance decision variables accordingly. Finally, different possible maintenance policies are considered and compared to illustrate their performance

Competing Active and Passive Interactions Drive Amoeba-like Crystallites and Ordered Bands in Active Colloids

Swimmers and self-propelled particles are physical models for the collective behaviour and motility of a wide variety of living systems, such as bacteria colonies, bird flocks and fish schools. Such artificial active materials are amenable to physical models which reveal the microscopic mechanisms underlying the collective behaviour. Here we study colloids in a DC electric field. Our quasi-two-dimensional system of electrically-driven particles exhibits a rich and exotic phase behaviour. At low field strengths, electrohydrodynamic flows lead to self-organisation into crystallites with hexagonal order. Upon self-propulsion of the particles due to Quincke rotation, we find an ordered phase of active matter in which the motile crystallites constantly change shape and collide with one another. At higher field strengths, this "dissolves" to an active gas. We parameterise a particulate simulation model which reproduces the experimentally observed phases and, at higher field strengths predicts an activity-driven demixing to band-like structures

Directed Assembly of Homopentameric Cholera Toxin B‑Subunit Proteins into Higher-Order Structures Using Coiled-Coil Appendages

The self-assembly of proteins into higher order structures is ubiquitous in living systems. It is also an essential process for the bottom-up creation of novel molecular architectures and devices for synthetic biology. However, the complexity of protein-protein interaction surfaces makes it challenging to mimic natural assembly processes in artificial systems. Indeed, many successful computationally designed protein assemblies are pre-screened for ‘designability’, limiting the choice of components. Here, we report a simple and pragmatic strategy to assemble chosen multi-subunit proteins into more complex structures. A coiled-coil domain appended to one face of the pentameric cholera toxin B-subunit (CTB) enabled the ordered assembly of tubular supra-molecular complexes. X-ray crystallography and analysis of a tubular structure has revealed a hierarchical assembly process that displays features reminiscent of the polymorphic assembly of polyomavirus proteins. The approach provides a simple and straightforward method to direct the assembly of protein building blocks which present either termini on a single face of an oligomer. This scaffolding approach can be used to generate bespoke supramolecular assemblies of functional proteins. Additionally, structural resolution of the scaffolded assemblies highlight ‘native-state’ forced protein-protein interfaces, which may prove useful as starting conformations for future computational design

Introducing improved structural properties and salt dependence into a coarse-grained model of DNA

We introduce an extended version of oxDNA, a coarse-grained model of deoxyribonucleic acid (DNA) designed to capture the thermodynamic, structural, and mechanical properties of single- and double-stranded DNA. By including explicit major and minor grooves and by slightly modifying the coaxial stacking and backbone-backbone interactions, we improve the ability of the model to treat large (kilobase-pair) structures, such as DNA origami, which are sensitive to these geometric features. Further, we extend the model, which was previously parameterised to just one salt concentration ([Na +] = 0.5M), so that it can be used for a range of salt concentrations including those corresponding to physiological conditions. Finally, we use new experimental data to parameterise the oxDNA potential so that consecutive adenine bases stack with a different strength to consecutive thymine bases, a feature which allows a more accurate treatment of systems where the flexibility of single-stranded regions is important. We illustrate the new possibilities opened up by the updated model, oxDNA2, by presenting results from simulations of the structure of large DNA objects and by using the model to investigate some salt-dependent properties of DNA

Replacement and imperfect repair of deteriorating system: Study of a CBM policy and impact of repair efficiency

International audienc

Evaluation of Streptococcal (Type B) rectal colonization incidence in pregnant women at an gestational age greater than 35 weeks and its relationship with infantile premature infection

History and Objectives: Considering the various report on incidence of Streptococcus type-B in rectum and its role in premature infantile infection and lack of information in the region and for determination of its prevalence in pregnant women, this study was carried out in Shabihkhani hospital in Kashan in 2000. Materials and Methods: The descriptive strategy of this study was conducted on 400 pregnant women at a gestational age greater than 35 weeks. For this purpose, a questionnaire was designed for collection of data including age, occupation, academic history, nationality, inhabitation, multiparous state, number of abortion, labor type and antibiotic consumption. Sampling from rectum was done using a sterile swab. Then, it was cultured in special medium and isolated bacteria were identified using biochemical tests. All of the infants up to 48h after labor and those from mothers with signs of positive colonization up to one week were followed up. From the latter group, sampling was done and the related bacteria were identified. For statistical analysis, X² and Fischer tests were used. Results: Out of 400 samples from rectum, 30 cases (7.5) with streptococcus type-B and in 2 cases (6.7) from mothers with positive culture were identified. In addition there was a relationship between streptococcus type-B rectal colonization and premature infantile premature infection (P=0.0055). Conclusion and Recommendations: Considering a 7.5 incidence of this bacterium in rectum and its relationship with type-B streptococcal rectal colonization and premature infections and its complications, it is recommended to conduct more studies in pregnant women