Project description:The past decade witnessed a surge in discoveries where biological systems, such as bacteria or living cells, inherently portray active polar or nematic behavior: they prefer to align with each other and form local order during migration. Although the underlying mechanisms remain unclear, utilizing their physical properties to achieve controllable cell-layer transport will be of fundamental importance. In this study, the ratchet effect is harnessed to control the collective motion of neural progenitor cells (NPCs) in vitro. NPCs travel back-and-forth and do not specify head or tail, and therefore regarded as nematics alike liquid crystals. Ratchet and splay-shaped confinements are crafted to modulate collective cell dynamics in dense environments, while jamming is not explicitly spotted. The adaptation of an agent-based simulation further revealed how the ratchet's asymmetry and active forces from nematic order synergistically reinforce the directional cell flow. These findings provide insights into topotaxis in cell populations when restricted to crowded 2D ratchets and the mechanisms that regulate collective behavior of the cells.
Project description:Activation of eukaryotic transcription is an intricate process that relies on a multitude of regulatory proteins forming complexes on chromatin. Chromatin modifications appear to play a guiding role in protein-complex assembly on chromatin. Together, these processes give rise to stochastic, often bursting, transcriptional activity. Here we present a model of eukaryotic transcription that aims to integrate those mechanisms. We use stochastic and ordinary-differential-equation modeling frameworks to examine various possible mechanisms of gene regulation by multiple transcription factors. We find that the assembly of large transcription factor complexes on chromatin via equilibrium-binding mechanisms is highly inefficient and insensitive to concentration changes of single regulatory proteins. An alternative model that lacks these limitations is a cyclic ratchet mechanism. In this mechanism, small protein complexes assemble sequentially on the promoter. Chromatin modifications mark the completion of a protein complex assembly, and sensitize the local chromatin for the assembly of the next protein complex. In this manner, a strict order of protein complex assemblies is attained. Even though the individual assembly steps are highly stochastic in duration, a sequence of them gives rise to a remarkable precision of the transcription cycle duration. This mechanism explains how transcription activation cycles, lasting for tens of minutes, derive from regulatory proteins residing on chromatin for only tens of seconds. Transcriptional bursts are an inherent feature of such transcription activation cycles. Bursting transcription can cause individual cells to remain in synchrony transiently, offering an explanation of transcriptional cycling as observed in cell populations, both on promoter chromatin status and mRNA levels.
Project description:Self-propelled nanoparticles moving through liquids offer the possibility of creating advanced applications where such nanoswimmers can operate as artificial molecular-sized motors. Achieving control over the motion of nanoswimmers is a crucial aspect for their reliable functioning. While the directionality of micron-sized swimmers can be controlled with great precision, steering nano-sized active particles poses a real challenge. One of the reasons is the existence of large fluctuations of active velocity at the nanoscale. Here, we describe a mechanism that, in the presence of a ratchet potential, transforms these fluctuations into a net current of active nanoparticles. We demonstrate the effect using a generic model of self-propulsion powered by chemical reactions. The net motion along the easy direction of the ratchet potential arises from the coupling of chemical and mechanical processes and is triggered by a constant, transverse to the ratchet, force. The current magnitude sensitively depends on the amplitude and the periodicity of the ratchet potential and the strength of the transverse force. Our results highlight the importance of thermodynamically consistent modeling of chemical reactions in active matter at the nanoscale and suggest new ways of controlling dynamics in such systems.
Project description:As an injury heals, an embryo develops, or a carcinoma spreads, epithelial cells systematically change their shape. In each of these processes cell shape is studied extensively whereas variability of shape from cell-to-cell is regarded most often as biological noise. But where do cell shape and its variability come from? Here we report that cell shape and shape variability are mutually constrained through a relationship that is purely geometrical. That relationship is shown to govern processes as diverse as maturation of the pseudostratified bronchial epithelial layer cultured from non-asthmatic or asthmatic donors, and formation of the ventral furrow in the Drosophila embryo. Across these and other epithelial systems, shape variability collapses to a family of distributions that is common to all. That distribution, in turn, is accounted for by a mechanistic theory of cell-cell interaction showing that cell shape becomes progressively less elongated and less variable as the layer becomes progressively more jammed. These findings suggest a connection between jamming and geometry that spans living organisms and inert jammed systems, and thus transcends system details. Although molecular events are needed for any complete theory of cell shape and cell packing, observations point to the hypothesis that jamming behavior at larger scales of organization sets overriding geometrical constraints.
Project description:As the demand for bandwidth in wireless communication increases, carrier frequencies will reach the terahertz (THz) regime. One of the common preconceived notions is that, at these high frequencies, signals can radiate with high directivity which inherently provides more secure channels. Here, we describe the first study of the vulnerability of these directional links to jamming, in which we identify several features that are distinct from the usual considerations of jamming at low frequencies. We show that the receiver's use of an envelope detector provides the jammer with the ability to thwart active attempts to adapt to their attack. In addition, a jammer can exploit the broadband nature of typical receivers to implement a beat jamming attack, which allows them to optimize the efficacy of the interference even if their broadcast is detuned from the frequency of the intended link. Our work quantifies the increasing susceptibility of broadband receivers to jamming, revealing previously unidentified vulnerabilities which must be considered in the development of future wireless systems operating above 100 GHz.
Project description:The sonar systems of bats and dolphins are in many ways superior to man-made sonar and radar systems, and considerable effort has been devoted to understanding the signal-processing strategies underlying these capabilities. A major feature determining the efficiency of sonar systems is the sensitivity to noise and jamming signals. Previous studies indicated that echolocating bats may adjust their signal structure to avoid jamming ('jamming avoidance response'; JAR). However, these studies relied on behavioural correlations and not controlled experiments. Here, we provide the first experimental evidence for JAR in bats. We presented bats (Tadarida brasiliensis) with 'playback stimuli' consisting of recorded echolocation calls at one of six frequencies. The bats exhibited a JAR by shifting their call frequency away from the presented playback frequency. When the approaching bats were challenged by an abrupt change in the playback stimulus, they responded by shifting their call frequencies upwards, away from the playback. Interestingly, even bats initially calling below the playback's frequency shifted their frequencies upwards, 'jumping' over the playback frequency. These spectral shifts in the bats' calls occurred often within less than 200 ms, in the first echolocation call emitted after the stimulus switch-suggesting that rapid jamming avoidance is important for the bat.
Project description:Liquids in the Leidenfrost state were shown by Linke to self-propel if placed on ratchets. The vapour flow below the liquid rectified by the asymmetric teeth entrains levitating drops by viscosity. This effect is observed above the Leidenfrost temperature of the substrate, typically 200°C for water. Here we show that coating ratchets with super-hydrophobic microtextures extends quick self-propulsion down to a substrate temperature of 100°C, which exploits the persistence of Leidenfrost state with such coatings. Surprisingly, propulsion is even observed below 100°C, implying that levitation is not necessary to induce the motion. Finally, we model the drop velocity in this novel "cold regime" of self-propulsion.
Project description:Cryptococcus neoformans is a pathogenic basidiomycetous fungus that engages in outcrossing, inbreeding, and selfing forms of unisexual reproduction as well as canonical sexual reproduction between opposite mating types. Long thought to be clonal, >99% of sampled environmental and clinical isolates of C. neoformans are MATα, limiting the frequency of opposite mating-type sexual reproduction. Sexual reproduction allows eukaryotic organisms to exchange genetic information and shuffle their genomes to avoid the irreversible accumulation of deleterious changes that occur in asexual populations, known as Muller's ratchet. We tested whether unisexual reproduction, which dispenses with the requirement for an opposite mating-type partner, is able to purge the genome of deleterious mutations. We report that the unisexual cycle can restore mutant strains of C. neoformans to wild-type genotype and phenotype, including prototrophy and growth rate. Furthermore, the unisexual cycle allows attenuated strains to purge deleterious mutations and produce progeny that are returned to wild-type virulence. Our results show that unisexual populations of C. neoformans are able to avoid Muller's ratchet and loss of fitness through a unisexual reproduction cycle involving α-α cell fusion, nuclear fusion, and meiosis. Similar types of unisexual reproduction may operate in other pathogenic and saprobic eukaryotic taxa.
Project description:For decades, researchers have speculated how echolocating bats deal with masking by conspecific calls when flying in aggregations. To date, only a few attempts have been made to mathematically quantify the probability of jamming, or its effects. We developed a comprehensive sensorimotor predator-prey simulation, modeling numerous bats foraging in proximity. We used this model to examine the effectiveness of a spectral Jamming Avoidance Response (JAR) as a solution for the masking problem. We found that foraging performance deteriorates when bats forage near conspecifics, however, applying a JAR does not improve insect sensing or capture. Because bats constantly adjust their echolocation to the performed task (even when flying alone), further shifting the signals' frequencies does not mitigate jamming. Our simulations explain how bats can hunt successfully in a group despite competition and despite potential masking. This research demonstrates the advantages of a modeling approach when examining a complex biological system.
Project description:The concept of jamming has attracted great research interest due to its broad relevance in soft-matter, such as liquids, glasses, colloids, foams, and granular materials, and its deep connection to sphere packing and optimization problems. Here, we show that the domain of amorphous jammed states of frictionless spheres can be significantly extended, from the well-known jamming-point at a fixed density, to a jamming-plane that spans the density and shear strain axes. We explore the jamming-plane, via athermal and thermal simulations of compression and shear jamming, with initial equilibrium configurations prepared by an efficient swap algorithm. The jamming-plane can be divided into reversible-jamming and irreversible-jamming regimes, based on the reversibility of the route from the initial configuration to jamming. Our results suggest that the irreversible-jamming behavior reflects an escape from the metastable glass basin to which the initial configuration belongs to or the absence of such basins. All jammed states, either compression- or shear-jammed, are isostatic and exhibit jamming criticality of the same universality class. However, the anisotropy of contact networks nontrivially depends on the jamming density and strain. Among all state points on the jamming-plane, the jamming-point is a unique one with the minimum jamming density and the maximum randomness. For crystalline packings, the jamming-plane shrinks into a single shear jamming-line that is independent of initial configurations. Our study paves the way for solving the long-standing random close-packing problem and provides a more complete framework to understand jamming.