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Register a new userSurvival chances of a prey swarm: how the cooperative interaction range affects the outcome
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A swarm of preys when attacked by a predator is known to rely on their cooperative interactions to escape. Understanding such interactions of collectively moving preys and the emerging patterns of their escape trajectories still remain elusive. In this paper, we investigate how the range of cooperative interactions within a prey group affects the survival chances of the group while chased by a predator. As observed in nature, the interaction range of preys may vary due to their vision, age, or even physical structure. Based on a simple theoretical prey-predator model, here, we show that an optimality criterion for the survival can be established on the interaction range of preys. Very short range or long range interactions are shown to be inefficient for the escape mechanism. Interestingly, for an intermediate range of interaction, survival probability of the prey group is found to be maximum. Our analysis also shows that the nature of the escape trajectories strongly depends on the range of interactions between preys and corroborates with the naturally observed escape patterns. Moreover, we find that the optimal survival regime depends on the prey group size and also on the predator strength.
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The Hill coefficient is often used as a direct measure of the cooperativity of binding processes. It is an essential tool for probing properties of reactions in many biochemical systems. Here we analyze existing experimental data and demonstrate that the Hill coefficient characterizing the binding of transcription factors to their cognate sites can in fact be larger than one -- the standard indication of cooperativity -- even in the absence of any standard cooperative binding mechanism. By studying the problem analytically, we demonstrate that this effect occurs due to the disordered binding energy of the transcription factor to the DNA molecule and the steric interactions between the different copies of the transcription factor. We show that the enhanced Hill coefficient implies a significant reduction in the number of copies of the transcription factors which is needed to occupy a cognate site and, in many cases, can explain existing estimates for numbers of the transcription factors in cells. The mechanism is general and should be applicable to other biological recognition processes.
Phase balanced states are a highly under-explored class of solutions of the Kuramoto model and other coupled oscillator models on networks. So far, coupled oscillator research focused on phase synchronized solutions. Yet, global constraints on oscillators may forbid synchronized state, rendering phase balanced states as the relevant stable state. If for example oscillators are driving the contractions of a fluid filled volume, conservation of fluid volume constraints oscillators to balanced states as characterized by a vanishing Kuramoto order parameter. It has previously been shown that stable, balanced patterns in the Kuramoto model exist on circulant graphs. However, which non-circulant graphs first of all allow for balanced states and what characterizes the balanced states is unknown. Here, we derive rules of how to build non-circulant, planar graphs allowing for balanced states from the simple cycle graph by adding loops or edges to it. We thereby identify different classes of small planar networks allowing for balanced states. Investigating the balanced states characteristics, we find that the variance in basin stability scales linearly with the size of the graph for these networks. We introduce the balancing ratio as a new order parameter based on the basin stability approach to classify balanced states on networks and evaluate it analytically for a subset of the network classes. Our results offer an analytical description of non-circulant graphs supporting stable, balanced states and may thereby help to understand the topological requirements on oscillator networks under global constraints.
Several important biological processes are initiated by the binding of a protein to a specific site on the DNA. The strategy adopted by a protein, called transcription factor (TF), for searching its specific binding site on the DNA has been investigated over several decades. In recent times the effects obstacles, like DNA-binding proteins, on the search by TF has begun to receive attention. RNA polymerase (RNAP) motors collectively move along a segment of the DNA during a genomic process called transcription. This RNAP traffic is bound to affect the diffusive scanning of the same segment of the DNA by a TF searching for its binding site. Motivated by this phenomenon, here we develop a kinetic model where a `particle, that represents a TF, searches for a specific site on a one-dimensional lattice. On the same lattice another species of particles, each representing a RNAP, hop from left to right exactly as in a totally asymmetric simple exclusion process (TASEP) which forbids simultaneous occupation of any site by more than one particle, irrespective of their identities. Although the TF is allowed to attach to or detach from any lattice site, the RNAPs can attach only to the first site at the left edge and detach from only the last site on the right edge of the lattice. We formulate the search as a {it first-passage} process; the time taken to reach the target site {it for the first time}, starting from a well defined initial state, is the search time. By approximate analytical calculations and Monte Carlo (MC) computer simulations, we calculate the mean search time. We show that RNAP traffic rectifies the diffusive motion of TF to that of a Brownian ratchet, and the mean time of successful search can be even shorter than that required in the absence of RNAP traffic. Moreover, we show that there is an optimal rate of detachment that corresponds to the shortest mean search time.
We study the survival of a prey that is hunted by N predators. The predators perform independent random walks on a square lattice with V sites and start a direct chase whenever the prey appears within their sighting range. The prey is caught when a predator jumps to the site occupied by the prey. We analyze the efficacy of a lazy, minimal-effort evasion strategy according to which the prey tries to avoid encounters with the predators by making a hop only when any of the predators appears within its sighting range; otherwise the prey stays still. We show that if the sighting range of such a lazy prey is equal to 1 lattice spacing, at least 3 predators are needed in order to catch the prey on a square lattice. In this situation, we establish a simple asymptotic relation ln(Pev)(t) sim (N/V)2ln(Pimm(t)) between the survival probabilities of an evasive and an immobile prey. Hence, when the density of the predators is low N/V<<1, the lazy evasion strategy leads to the spectacular increase of the survival probability. We also argue that a short-sighting prey (its sighting range is smaller than the sighting range of the predators) undergoes an effective superdiffusive motion, as a result of its encounters with the predators, whereas a far-sighting prey performs a diffusive-type motion.
Flagella of eukaryotic cells are transient long cylindrical protrusions. The proteins needed to form and maintain flagella are synthesized in the cell body and transported to the distal tips. What `rulers or `timers a specific type of cells use to strike a balance between the outward and inward transport of materials so as to maintain a particular length of its flagella in the steady state is one of the open questions in cellular self-organization. Even more curious is how the two flagella of biflagellates, like Chlamydomonas Reinhardtii, communicate through their base to coordinate their lengths. In this paper we develop a stochastic model for flagellar length control based on a time-of-flight (ToF) mechanism. This ToF mechanism decides whether or not structural proteins are to be loaded onto an intraflagellar transport (IFT) train just before it begins its motorized journey from the base to the tip of the flagellum. Because of the ongoing turnover, the structural proteins released from the flagellar tip are transported back to the cell body also by IFT trains. We represent the traffic of IFT trains as a totally asymmetric simple exclusion process (TASEP). The ToF mechanism for each flagellum, together with the TASEP-based description of the IFT trains, combined with a scenario of sharing of a common pool of flagellar structural proteins in biflagellates, can account for all key features of experimentally known phenomena. These include ciliogenesis, resorption, deflagellation as well as regeneration after selective amputation of one of the two flagella. We also show that the experimental observations of Ishikawa and Marshall are consistent with the ToF mechanism of length control if the effects of the mutual exclusion of the IFT trains captured by the TASEP are taken into account. Moreover, we make new predictions on the flagellar length fluctuations and the role of the common pool.
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