Directed percolation with incubation times

We introduce a model for directed percolation with a long-range temporal diffusion, while the spatial diffusion is kept short ranged. In an interpretation of directed percolation as an epidemic process, this non-Markovian modification can be understood as incubation times, which are distributed accordingly to a Levy distribution. We argue that the best approach to find the effective action for this problem is through a generalization of the Cardy-Sugar method, adding the non-Markovian features into the geometrical properties of the lattice. We formulate a field theory for this problem and renormalize it up to one loop in a perturbative expansion. We solve the various technical difficulties that the integrations possess by means of an asymptotic analysis of the divergences. We show the absence of field renormalization at one-loop order, and we argue that this would be the case to all orders in perturbation theory. Consequently, in addition to the characteristic scaling relations of directed percolation, we find a scaling relation valid for the critical exponents of this theory. In this universality class, the critical exponents vary continuously with the Levy parameter.Comment: 17 pages, 7 figures. v.2: minor correction

Transforming Student and Staff Experiences with Active Learning Tutorials in Advanced Chemistry Courses

In order to increase student engagement and provide more opportunities for students to develop their creativity in the context of three large advanced chemistry courses, we have introduced active learning designs in the courses’ tutorial sessions. The tutorial designs focused on collaborative learning, student-generated content and real-world industrial situations. The tutorial activities, carefully scaffolded, focussed on students generating their own problems from scratch, dealing with situations that mimic what might happen on an industrial design team, and writing a short question following the typical format of a final exam question. The tutorial sessions lasted one hour each, and were delivered during the time lapse of three weeks. Most of the students had none or very limited previous experience with active learning instruction. Despite this, students adapted immediately to the active learning format, displaying good collaborative learning skills and a higher level of engagement and attendance to the sessions with respect to traditional taught tutorials. In the post instruction surveys, students reported an increased positive experience, recognising that the sessions allowed them to apply their knowledge to new situations, and stimulated them to learn more on the topics while practising transferable skills in peer discussions. Lecturers who delivered the sessions with active learning for the first time, reported a positive transformation on their own teaching experience. This article discusses the details of the active learning design, the student perceptions and staff teaching experience, highlighting how active learning can be a positive transformative experience not only for the students but also for the academic staff

Effectors of filamentous plant pathogens: Commonalities amid diversity

Fungi and oomycetes are filamentous microorganisms that include a diversity of highly developed pathogens of plants. These are sophisticated modulators of plant processes that secrete an arsenal of effector proteins to target multiple host cell compartments and enable parasitic infection. Genome sequencing revealed complex catalogues of effectors of filamentous pathogens, with some species harboring hundreds of effector genes. Although a large fraction of these effector genes encode secreted proteins with weak or no sequence similarity to known proteins, structural studies have revealed unexpected similarities amid the diversity. This article reviews progress in our understanding of effector structure and function in light of these new insights. We conclude that there is emerging evidence for multiple pathways of evolution of effectors of filamentous plant pathogens but that some families have probably expanded from a common ancestor by duplication and diversification. Conserved folds, such as the oomycete WY and the fungal MAX domains, are not predictive of the precise function of the effectors but serve as a chassis to support protein structural integrity while providing enough plasticity for the effectors to bind different host proteins and evolve unrelated activities inside host cells. Further effector evolution and diversification arise via short linear motifs, domain integration and duplications, and oligomerization

The critical role of toll-like receptors - From microbial recognition to autoimmunity: A comprehensive review

Toll-like receptors (TLRs) constitute an important mechanism in the activation of innate immune cells including monocytes, macrophages and dendritic cells. Macrophage activation by TLRs is pivotal in the initiation of the rapid expression of pro-inflammatory cytokines TNF, IL-1β and IL-6 while promoting Th17 responses, all of which play critical roles in autoimmunity. Surprisingly, in inflammatory arthritis, activation of specific TLRs can not only induce but also inhibit cellular processes associated with bone destruction. The intercellular and intracellular orchestration of signals from different TLRs, their endogenous or microbial ligands and accessory molecules determine the activating or inhibitory responses. Herein, we review the TLR-mediated activation of innate immune cells in their activation and differentiation to osteoclasts and the capacity of these signals to contribute to bone destruction in arthritis. Detailed understanding of the opposing mechanisms of TLRs in the induction and suppression of cellular processes in arthritis may pave the way to develop novel therapies to treat autoimmunity.Instituto de Investigaciones Bioquímicas de La Plat

Contact processes with long-range interactions

A class of non-local contact processes is introduced and studied using mean-field approximation and numerical simulations. In these processes particles are created at a rate which decays algebraically with the distance from the nearest particle. It is found that the transition into the absorbing state is continuous and is characterized by continuously varying critical exponents. This model differs from the previously studied non-local directed percolation model, where particles are created by unrestricted Levy flights. It is motivated by recent studies of non-equilibrium wetting indicating that this type of non-local processes play a role in the unbinding transition. Other non-local processes which have been suggested to exist within the context of wetting are considered as well.Comment: Accepted with minor revisions by Journal of Statistical Mechanics: Theory and experiment

Critical dynamics in systems controlled by fractional kinetic equations

The article is devoted to the dynamics of systems with an anomalous scaling near a critical point. The fractional stochastic equation of a Lanvevin type with the $\varphi^3$ nonlinearity is considered. By analogy with the model A the field theoretic model is built, and its propagators are calculated. The nonlocality of the new action functional in the coordinate representation is caused by the involving of the fractional spatial derivative. It is proved that the new model is multiplicatively renormalizable, the Gell-Man-Low function in the one-loop approximation is evaluted. The existence of the scaling behavior in the framework of the $\varepsilon$-expansion for a superdiffusion is established.Comment: 25 pages, 1 figur

Spreading with immunization in high dimensions

We investigate a model of epidemic spreading with partial immunization which is controlled by two probabilities, namely, for first infections, $p_0$, and reinfections, $p$. When the two probabilities are equal, the model reduces to directed percolation, while for perfect immunization one obtains the general epidemic process belonging to the universality class of dynamical percolation. We focus on the critical behavior in the vicinity of the directed percolation point, especially in high dimensions $d>2$. It is argued that the clusters of immune sites are compact for $d\leq 4$. This observation implies that a recently introduced scaling argument, suggesting a stretched exponential decay of the survival probability for $p=p_c$, $p_0\ll p_c$ in one spatial dimension, where $p_c$ denotes the critical threshold for directed percolation, should apply in any dimension $d \leq 3$ and maybe for $d=4$ as well. Moreover, we show that the phase transition line, connecting the critical points of directed percolation and of dynamical percolation, terminates in the critical point of directed percolation with vanishing slope for $d<4$ and with finite slope for $d\geq 4$. Furthermore, an exponent is identified for the temporal correlation length for the case of $p=p_c$ and $p_0=p_c-\epsilon$, $\epsilon\ll 1$, which is different from the exponent $\nu_\parallel$ of directed percolation. We also improve numerical estimates of several critical parameters and exponents, especially for dynamical percolation in $d=4,5$.Comment: LaTeX, IOP-style, 18 pages, 9 eps figures, minor changes, additional reference

Epidemic processes with immunization

We study a model of directed percolation (DP) with immunization, i.e. with different probabilities for the first infection and subsequent infections. The immunization effect leads to an additional non-Markovian term in the corresponding field theoretical action. We consider immunization as a small perturbation around the DP fixed point in d<6, where the non-Markovian term is relevant. The immunization causes the system to be driven away from the neighbourhood of the DP critical point. In order to investigate the dynamical critical behaviour of the model, we consider the limits of low and high first infection rate, while the second infection rate remains constant at the DP critical value. Scaling arguments are applied to obtain an expression for the survival probability in both limits. The corresponding exponents are written in terms of the critical exponents for ordinary DP and DP with a wall. We find that the survival probability does not obey a power law behaviour, decaying instead as a stretched exponential in the low first infection probability limit and to a constant in the high first infection probability limit. The theoretical predictions are confirmed by optimized numerical simulations in 1+1 dimensions.Comment: 12 pages, 11 figures. v.2: minor correction

Novel universality class of absorbing transitions with continuously varying critical exponents

The well-established universality classes of absorbing critical phenomena are directed percolation (DP) and directed Ising (DI) classes. Recently, the pair contact process with diffusion (PCPD) has been investigated extensively and claimed to exhibit a new type of critical phenomena distinct from both DP and DI classes. Noticing that the PCPD possesses a long-term memory effect, we introduce a generalized version of the PCPD (GPCPD) with a parameter controlling the memory effect. The GPCPD connects the DP fixed point to the PCPD point continuously. Monte Carlo simulations show that the GPCPD displays novel type critical phenomena which are characterized by continuously varying critical exponents. The same critical behaviors are also observed in models where two species of particles are coupled cyclically. We suggest that the long-term memory may serve as a marginal perturbation to the ordinary DP fixed point.Comment: 13 pages + 10 figures (Full paper version