Most studies on granular physics have focused dry media, with no liquids between the grains. However, in geology and many real world applications (e.g. food processing, pharmaceuticals, ceramics, civil engineering, construction, industrial applications), liquid is present This produces inter-grain cohesion drastically modifies mechanical properties of media surface angle can be larger than 90 degrees). Here we a review wet particular emphasis effect cohesion. We also list several open...

Many toxin–antitoxin (TA) loci are known to strongly repress their own transcription. This auto-inhibition is often called 'conditional cooperativity' as it relies on cooperative binding of TA complexes operator DNA that occurs only when toxins in a proper stoichiometric relationship with antitoxins. There has recently been an explosion interest systems due role bacterial persistence, however the conditional cooperativity still unclear. We reveal biological function by constructing...

Significance Bacteria are repeatedly exposed to an excess of phages and carry evidence this in terms multiple defense mechanisms encoded their genome. In addition molecular mechanisms, bacteria may exploit the spatial refuges. Here we demonstrate how can limit impact a virulent phage attack by growing as colony which exposes only its surface phages. We identify critical size initial colony, below entirely eliminate above continues grow despite presence Our study suggests that coexistence is...

Transient antibiotic treatment typically eradicates most sensitive bacteria except a few survivors called persisters. The second messenger (p)ppGpp plays key role in persister formation Escherichia coli populations but the underlying mechanisms have remained elusive. In this study we induced synthesis by modulating tRNA charging and then directly observed stochastic appearance, tolerance, resuscitation of cells using live microscopy. Different physiological parameters as well their regularly...

We show that a micropolar fluid model successfully describes collisional granular flows on slope. A is the with internal structures in which coupling between spin of each particle and macroscopic velocity field taken into account. It hydrodynamical framework suitable for systems consists particles size. demonstrate equations can quantitatively reproduce angular profiles obtained from numerical simulation flow slope using simple estimate parameters theory.

Small regulatory RNAs (sRNAs) in eukaryotes and bacteria play an important role the regulation of gene expression either by binding to proteins or directly target mRNAs. Two best-characterized bacterial sRNAs, Spot42 RyhB, form a complementary pair with ribosome region their mRNAs, thereby inhibiting translation promoting mRNA degradation. To investigate steady-state dynamic potential such we examine 2 key parameters characterizing sRNA regulation: capacity overexpress relative its speed at...

We study the effect of precollisional velocity correlations on granular shear flow by molecular dynamics simulations an inelastic hard sphere system. Comparison with kinetic theory reveals that overestimates both energy dissipation rate and normal stress in dense region. find relative colliding particles is smaller than expected from random collisions, discrepancies can be adjusted introducing idea collisional temperature, which we conclude correlation neglected responsible for...

Many toxin-antitoxin operons are regulated by the toxin/antitoxin ratio mechanisms collectively coined "conditional cooperativity". Toxin and antitoxin form heteromers with different stoichiometric ratios, complex intermediate works best as a transcription repressor. This allows at low toxin level, strong repression then again high level. Such regulation has two interesting features; firstly, it provides non-monotonous response to concentration of one proteins, secondly, opens for...

A dense mixture of granules and liquid often shows a severe shear thickening is called dilatant fluid. We construct fluid dynamics model for the by introducing phenomenological state variable local dispersed particles. With simple assumptions an equation variable, we demonstrate that can describe basic features such as stress-shear rate curve represents discontinuous thickening, hysteresis upon changing rate, instantaneous hardening external impact. An analysis reveals instability in flow...

ABSTRACT Bacteria living in physically structured habitats are exposed heterogeneously to both resources and different types of phages. While there have been numerous experimental approaches examine spatially distributed bacteria phages, is little theory guide the design these experiments, interpret their results, or expand inferences drawn a broader ecological evolutionary context. Plaque formation provides window into understanding phage-bacterium interactions populations, including...

We investigate the bulk rheology of dense granular flow down a rough slope, where density profile has been found to show plateau except for boundary layers in simulations [Silbert {\it et al.}, Phys. Rev. E {\bf 64}, 051302 (2001)]. It is demonstrated that both Bagnold scaling and framework kinetic theory are applicable bulk, which allows us extract constitutive relations from simulation data. The detailed comparison our data with shows quantitative agreement normal shear stresses, but there...

We build a simple model for feedback systems involving small RNA (sRNA) molecules based on the iron metabolism system in bacterium E. coli, and compare it with corresponding H. pylori which uses purely transcriptional regulation. This reveals several unique features of sRNA-based regulation that could be exploited by cells. Firstly, we show sRNA can maintain smaller turnover target mRNAs than regulation, without sacrificing speed response to external shocks. Secondly, propose single...

Cells can often choose among several stably heritable phenotypes. Examples are the expression of genes in eukaryotic cells where long chromosomal regions adopt persistent and silenced or active states, that may be associated with positive feedback dynamic modification nucleosomes. We generalize this mechanism terms bistability valleys an epigenetic landscape. A transfer matrix method was used to rigorously follow system through disruptive process cell division. This combined treatment noisy...

Ecological systems comprise an astonishing diversity of species that cooperate or compete with each other forming complex mutual dependencies. The minimum requirements to maintain a large on long time scales are in general unknown. Using lichen communities as example, we propose model for the evolution mutually excluding organisms space. We suggest chainlike cyclic invasions open creation spatially separated subpopulations subsequently can lead increased diversity. In contrast its nonspatial...

Abstract Virulent phages can expose their bacterial hosts to devastating epidemics, in principle leading complete elimination of hosts. Although experiments indeed confirm a large reduction susceptible bacteria, there are no reports extinctions. We here address this phenomenon from the perspective spatial organization bacteria and how influence final survival them. By modelling transient dynamics when they introduced into an environment with finite resources, we quantify time delayed lysis,...

Abstract Bacteria have spectacular survival capabilities and can spread in many, vastly different environments. For instance, when pathogenic bacteria infect a host, they expand by proliferation squeezing through narrow pores elastic matrices. However, the exact role of surface structures—important for biofilm formation motility—and matrix density colony expansion morphogenesis is still largely unknown. Using confocal laser-scanning microscopy, we show how satellite colonies emerge around...

Abstract Understanding and facilitating healthy aging has become a major goal in medical research it is becoming increasingly acknowledged that there need for understanding the phenotype as whole rather than focusing on individual factors. Here, we provide universal explanation emergence of Gompertzian mortality patterns using systems approach to describe complex organisms consist many inter-dependent subsystems. Our model relates Sufficient-Component Cause Model, widely used within field...

Bacteria can enter dormancy triggered by stress, such as starvation. When stress is removed, a large part of the population will exhibit some lag time before regrowth. It has been observed that even under stress-free conditions allow for exponential growth, small subpopulation spontaneously temporarily. The dormant often survives antibiotic application because many types antibiotics target cell growth and division process. If bacteria are in an environment where sometimes applied, evolve to...

Phages and bacteria coexist under widely different conditions, ranging from liquid cultures to oceans, soil, the human gut. However, our models are typically limited well-mixed governed by mass-action kinetics. Here, we suggest a modification Lotka-Volterra dynamics including formation of microcolonies. By analyzing model in an open system with steady influx bacteria, predict that colony size distribution is power-low distributed steeper exponents for stronger external influx. In realistic...

The spatiotemporal structure of a traffic flow pattern is investigated under the open boundary condition using optimal velocity model. parameter region where uniform solution convectively unstable determined. It found that localized perturbation triggers linearly oscillatory out state, and it shown also stabilized. demonstrated observed near an on-ramp can be interpreted as noise sustained in system.

Noise in the expression of a gene produces fluctuations concentration product. These can interfere with optimal function or be exploited to generate beneficial diversity between cells; noise is therefore expected subject evolutionary pressure. Shifts modes high and low rates transcription initiation at promoter appear contribute this both eukaryotes prokaryotes. However, models invoked for eukaryotic such as stable activation scaffolds persistent nucleosome alterations seem unlikely apply...

Bacterial populations in natural conditions are expected to experience stochastic environmental fluctuations, and addition, environments affected by bacterial activities since they consume substrates excrete various chemicals. We here study possible outcomes of population dynamics evolution under the repeated cycle substrate-rich starvation, called "feast-famine cycle", a simple model with trade-off relationship between growth rate yield or death rate. In model, feast (substrate-rich) period...