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RNA velocity estimation is a potentially powerful tool to reveal the directionality of transcriptional changes in single-cell RNA-sequencing data, but it lacks accuracy, absent advanced metabolic labeling techniques. We developed an approach, TopicVelo, that disentangles simultaneous, yet distinct, dynamics by using a probabilistic topic model, a highly interpretable form of latent space factorization, to infer cells and genes associated with individual processes, thereby capturing cellular pluripotency or multifaceted functionality. Focusing on process-associated cells and genes enables accurate estimation of process-specific velocities via a master equation for a transcriptional burst model accounting for intrinsic stochasticity. The method obtains a global transition matrix by leveraging cell topic weights to integrate process-specific signals. In challenging systems, this method accurately recovers complex transitions and terminal states, while our use of first-passage time analysis provides insights into transient transitions. These results expand the limits of RNA velocity, empowering future studies of cell fate and functional responses. [ABSTRACT FROM AUTHOR]

Biomacromolecular folding kinetics involves fast folding events and broad timescales. Current techniques face limitations in either the required time resolution or the observation window. In this study, we developed the TeZla micromixer, integrating Tesla and Zigzag microstructures with a multistage velocity descending strategy. TeZla achieves a significant short mixing dead time (40 µs) and a wide time window covering four orders of magnitude (up to 300 ms). Using this unique micromixer, we explored the folding landscape of c-Myc G4 and its noncanonical-G4 derivatives with different loop lengths or G-vacancy sites. Our findings revealed that c-Myc can bypass folding intermediates and directly adopt a G4 structure in the cation-deficient buffer. Moreover, we found that the loop length and specific G-vacancy site could affect the folding pathway and significantly slow down the folding rates. These results were also cross-validated with real-time NMR and circular dichroism. In conclusion, TeZla represents a versatile tool for studying biomolecular folding kinetics, and our findings may ultimately contribute to the design of drugs targeting G4 structures. [ABSTRACT FROM AUTHOR]

We investigate signal propagation in a quantum field simulator of the Klein-Gordon model realized by two strongly coupled parallel one-dimensional quasi-condensates. By measuring local phononic fields after a quench, we observe the propagation of correlations along sharp light-cone fronts. If the local atomic density is inhomogeneous, these propagation fronts are curved. For sharp edges, the propagation fronts are reflected at the system's boundaries. By extracting the space-dependent variation of the front velocity from the data, we find agreement with theoretical predictions based on curved geodesics of an inhomogeneous metric. This work extends the range of quantum simulations of nonequilibrium field dynamics in general space-time metrics. [ABSTRACT FROM AUTHOR]

The Earth's climate has been warming rapidly since the beginning of the industrial era, forcing terrestrial organisms to adapt. Migration constitutes one of the most effective processes for surviving and thriving, although the speed at which tree species migrate as a function of climate change is unknown. One way to predict latitudinal movement of trees under the climate of the twenty-first century is to examine past migration since the Last Glacial Maximum. In this study, radiocarbon-dated macrofossils were used to calculate the velocity of past migration of jack pine (Pinus banksiana) and black spruce (Picea mariana), two important fire-adapted conifers of the North American boreal forest. Jack pine migrated at a mean rate of 19 km per century (km-cent) from unglaciated sites in the central and southeastern United States to the northern limit of the species in subarctic Canada. However, the velocity increased between unglaciated and early deglaciated sites in southern Quebec and slowed from early to mid-Holocene in central and eastern Quebec. Migration was at its lowest speed in late-Holocene times, when it stopped about 3,000 y ago. Compared with jack pine, black spruce migrated at a faster mean rate of 25 km-cent from the ice border at the last interstadial (Bølling/Allerød) to the species tree limit. The modern range of both species was nearly occupied about 6,000 y ago. The factors modulating the changing velocity of jack pine migration were closely associated with the warm-dry climate of the late Pleistocene-Holocene transition and the more humid climate of the mid- and late-Holocene. [ABSTRACT FROM AUTHOR]

We characterize the dynamics of runners in the famous “Running of the Bulls” Festival by computing the individual and global velocities and densities, as well as the crowd pressure. In contrast with all previously studied pedestrian systems, we unveil a unique regime in which speed increases with density that can be understood in terms of a time-dependent desired velocity of the runners. Also, we discover the existence of an inaccessible region in the speed–density state diagram that is explained by falls of runners. With all these ingredients, we propose a generalization of the pedestrian fundamental diagram for a scenario in which people with different desired speeds coexist. [ABSTRACT FROM AUTHOR]

RNA velocity is a promising technique for quantifying cellular transitions from single-cell transcriptome experiments and revealing transient cellular dynamics among a heterogeneous cell population. However, the cell transitions estimated from highdimensional RNA velocity are often unstable or inaccurate, partly due to the high technical noise and less informative projection. Here, we present Velocity Autoencoder (VeloAE), a tailored representation learning method, to learn a low-dimensional representation of RNA velocity on which cellular transitions can be robustly estimated. On various experimental datasets, we show that VeloAE can both accurately identify stimulation dynamics in time-series designs and effectively capture expected cellular differentiation in different biological systems. VeloAE, therefore, enhances the usefulness of RNA velocity for studying a wide range of biological processes. [ABSTRACT FROM AUTHOR]

Global aridification is projected to intensify. Yet, our knowledge of its potential impacts on species ranges remains limited. Here, we investigate global aridity velocity and its overlap with three sectors (natural protected areas, agricultural areas, and urban areas) and terrestrial biodiversity in historical (1979 through 2016) and future periods (2050 through 2099), with and without considering vegetation physiological response to rising CO2. Both agricultural and urban areas showed a mean drying velocity in history, although the concurrent global aridity velocity was on average +0.05/+0.20 km/yr-1 (no CO2 effects/with CO2 effects; "+" denoting wetting). Moreover, in drylands, the shifts of vegetation greenness isolines were found to be significantly coupled with the tracks of aridity velocity. In the future, the aridity velocity in natural protected areas is projected to change from wetting to drying across RCP (representative concentration pathway) 2.6, RCP6.0, and RCP8.5 scenarios. When accounting for spatial distribution of terrestrial taxa (including plants, mammals, birds, and amphibians), the global aridity velocity would be -0.15/-0.02 km/yr-1 ("-" denoting drying; historical), -0.12/-0.15 km/yr-1 (RCP2.6), -0.36/-0.10 km/yr-1 (RCP6.0), and -0.75/-0.29 km/yr-1 (RCP8.5), with amphibians particularly negatively impacted. Under all scenarios, aridity velocity shows much higher multidirectionality than temperature velocity, which is mainly poleward. These results suggest that aridification risks may significantly influence the distribution of terrestrial species besides warming impacts and further impact the effectiveness of current protected areas in future, especially under RCP8.5, which best matches historical CO2 emissions [C. R. Schwalm et al., Proc. Natl. Acad. Sci. U.S.A. 117, 19656-19657 (2020)]. [ABSTRACT FROM AUTHOR]

Information-driven engines that rectify thermal fluctuations are a modern realization of the Maxwell-demon thought experiment. We introduce a simple design based on a heavy colloidal particle, held by an optical trap and immersed in water. Using a carefully designed feedback loop, our experimental realization of an "information ratchet" takes advantage of favorable "up" fluctuations to lift a weight against gravity, storing potential energy without doing external work. By optimizing the ratchet design for performance via a simple theory, we find that the rate of work storage and velocity of directed motion are limited only by the physical parameters of the engine: the size of the particle, stiffness of the ratchet spring, friction produced by the motion, and temperature of the surrounding medium. Notably, because performance saturates with increasing frequency of observations, the measurement process is not a limiting factor. The extracted power and velocity are at least an order of magnitude higher than in previously reported engines. [ABSTRACT FROM AUTHOR]

Quantitative knowledge about which natural and anthropogenic factors influence the global spread of plague remains sparse. We estimated the worldwide spreading velocity of plague during the Third Pandemic, using more than 200 years of extensive human plague case records and genomic data, and analyzed the association of spatiotemporal environmental factors with spreading velocity. Here, we show that two lineages, 2.MED and 1.ORI3, spread significantly faster than others, possibly reflecting differences among strains in transmission mechanisms and virulence. Plague spread fastest in regions with low population density and high proportion of pasture- or forestland, findings that should be taken into account for effective plague monitoring and control. Temperature exhibited a nonlinear, U-shaped association with spread speed, with a minimum around 20 °C, while precipitation showed a positive association. Our results suggest that global warming may accelerate plague spread in warm, tropical regions and that the projected increased precipitation in the Northern Hemisphere may increase plague spread in relevant regions. [ABSTRACT FROM AUTHOR]

Contrasting with its sluggish behavior on standard solids, water is extremely mobile on superhydrophobic materials, as shown, for instance, by the continuous acceleration of drops on tilted waterrepellent leaves. For much longer substrates, however, drops reach a terminal velocity that results from a balance between weight and friction, allowing us to question the nature of this friction. We report that the relationship between force and terminal velocity is nonlinear. This is interpreted by showing that classical sources of friction are minimized, so that the aerodynamical resistance to motion becomes dominant, which eventually explains the matchless mobility of water. Our results are finally extended to viscous liquids, also known to be unusually quick on these materials. [ABSTRACT FROM AUTHOR]

Active matter comprises individual units that convert energy into mechanical motion. In many examples, such as bacterial systems and biofilament assays, constituent units are elongated and can give rise to local nematic orientational order. Such "active nematics"systems have attracted much attention from both theorists and experimentalists. However, despite intense research efforts, data-driven quantitative modeling has not been achieved, a situation mainly due to the lack of systematic experimental data and to the large number of parameters of current models. Here, we introduce an active nematics system made of swarming filamentous bacteria. We simultaneously measure orientation and velocity fields and show that the complex spatiotemporal dynamics of our system can be quantitatively reproduced by a type of microscopic model for active suspensions whose important parameters are all estimated from comprehensive experimental data. This provides unprecedented access to key effective parameters and mechanisms governing active nematics. Our approach is applicable to different types of dense suspensions and shows a path toward more quantitative active matter research. [ABSTRACT FROM AUTHOR]

The formation of a fracture network is a key process for many geophysical and industrial practices from energy resource recovery to induced seismic management. We focus on the initial stage of a fracture network formation using experiments on the symmetric coalescence of two equal coplanar, fluid-driven, penny-shaped fractures in a brittle elastic medium. Initially, the fractures propagate independently of each other. The fractures then begin to interact and coalesce, forming a bridge between them. Within an intermediate period after the initial contact, most of the fracture growth is localized along this bridge, perpendicular to the line connecting the injection sources. Using light attenuation and particle image velocimetry to measure both the fracture aperture and velocity field, we characterize the growth of this bridge. We model this behavior using a geometric volume conservation argument dependent on the symmetry of the interaction, with a 2D approximation for the bridge. We also verify experimentally the scaling for the bridge growth and the shape of the thickness profile along the bridge. The influence of elasticity and toughness of the solid, injection rate of the fluid, and initial location of the fractures are captured by our scaling. [ABSTRACT FROM AUTHOR]

Epidemics, flame propagation, and cardiac rhythms are classic examples of reaction-diffusion waves that describe a switch from one alternative state to another. Only two types of waves are known: pulled, driven by the leading edge, and pushed, driven by the bulk of the wave. Here, we report a distinct class of semipushed waves for which both the bulk and the leading edge contribute to the dynamics. These hybrid waves have the kinetics of pushed waves, but exhibit giant fluctuations similar to pulled waves. The transitions between pulled, semipushed, and fully pushed waves occur at universal ratios of the wave velocity to the Fisher velocity. We derive these results in the context of a species invading a new habitat by examining front diffusion, rate of diversity loss, and fluctuation-induced corrections to the expansion velocity. All three quantities decrease as a power law of the population density with the same exponent. We analytically calculate this exponent, taking into account the fluctuations in the shape of the wave front. For fully pushed waves, the exponent is -1, consistent with the central limit theorem. In semipushed waves, however, the fluctuations average out much more slowly, and the exponent approaches 0 toward the transition to pulled waves. As a result, a rapid loss of genetic diversity and large fluctuations in the position of the front occur, even for populations with cooperative growth and other forms of an Allee effect. The evolutionary outcome of spatial spreading in such populations could therefore be less predictable than previously thought. [ABSTRACT FROM AUTHOR]

Due to the foveal organization of our visual system we have to constantly move our eyes to gain precise information about our environment. Doing so massively alters the retinal input. This is problematic for the perception of moving objects, because physical motion and retinal motion become decoupled and the brain has to discount the eye movements to recover the speed of moving objects. Two different types of eye movements, pursuit and saccades, are combined for tracking. We investigated how the way we track moving targets can affect the perceived target speed. We found that the execution of corrective saccades during pursuit initiation modifies how fast the target is perceived compared with pure pursuit. When participants executed a forward (catch-up) saccade they perceived the target to be moving faster. When they executed a backward saccade they perceived the target to be moving more slowly. Variations in pursuit velocity without corrective saccades did not affect perceptual judgments. We present a model for these effects, assuming that the eye velocity signal for small corrective saccades gets integrated with the retinal velocity signal during pursuit. In our model, the execution of corrective saccades modulates the integration of these two signals by giving less weight to the retinal information around the time of corrective saccades. [ABSTRACT FROM AUTHOR]

Homodimeric KIF17 and heterotrimeric KIF3AB are processive, kinesin-2 family motors that act jointly to carry out anterograde intraflagellar transport (IFT), ferrying cargo along microtubules (MTs) toward the tips of cilia. How IFT trains attain speeds that exceed the unloaded rate of the slower, KIF3AB motor remains unknown. By characterizing the motility properties of kinesin-2 motors as a function of load we find that the increase in KIF3AB velocity, elicited by forward loads from KIF17 motors, cannot alone account for the speed of IFT trains in vivo. Instead, higher IFT velocities arise from an increased likelihood that KIF3AB motors dissociate from the MT, resulting in transport by KIF17 motors alone, unencumbered by opposition from KIF3AB. The rate of transport is therefore set by an equilibrium between a faster state, where only KIF17 motors move the train, and a slower state, where at least one KIF3AB motor on the train remains active in transport. The more frequently the faster state is accessed, the higher the overall velocity of the IFT train. We conclude that IFT velocity is governed by (i) the absolute numbers of each motor type on a given train, (ii) how prone KIF3AB is to dissociation from MTs relative to KIF17, and (iii) how prone both motors are to dissociation relative to binding MTs. [ABSTRACT FROM AUTHOR]

We use an accurate coarse-grained model for DNA and stochastic molecular dynamics simulations to study the pore translocation of 10-kbp-long DNA rings that are knotted. By monitoring various topological and physical observables we find that there is not one, as previously assumed, but rather two qualitatively different modes of knot translocation. For both modes the pore obstruction caused by knot passage has a brief duration and typically occurs at a late translocation stage. Both effects are well in agreement with experiments and can be rationalized with a transparent model based on the concurrent tensioning and sliding of the translocating knotted chains. We also observed that the duration of the pore obstruction event is more controlled by the knot translocation velocity than the knot size. These features should advance the interpretation and design of future experiments aimed at probing the spontaneous knotting of biopolymers. [ABSTRACT FROM AUTHOR]

We compute parameters characterizing many-body quantum chaos for a critical Fermi surface without quasiparticle excitations. We examine a theory of N species of fermions at nonzero density coupled to a U(1) gauge field in two spatial dimensions and determine the Lyapunov rate and the butterfly velocity in an extended random-phase approximation. The thermal diffusivity is found to be universally related to these chaos parameters; i.e., the relationship is independent of N, the gauge-coupling constant, the Fermi velocity, the Fermi surface curvature, and high-energy details. [ABSTRACT FROM AUTHOR]

Understanding the ultralow velocity zones (ULVZs) places constraints on the chemical composition and thermal structure of deep Earth and provides critical information on the dynamics of largescale mantle convection, but their origin has remained enigmatic for decades. Recent studies suggest that metallic iron and carbon are produced in subducted slabs when they sink beyond a depth of 250 km. Here we show that the eutectic melting curve of the iron-carbon system crosses the current geotherm near Earth's core-mantle boundary, suggesting that dense metallic melt may form in the lowermost mantle. If concentrated into isolated patches, such melt could produce the seismically observed density and velocity features of ULVZs. Depending on the wetting behavior of the metallic melt, the resultant ULVZs may be short-lived domains that are replenished or regenerated through subduction, or long-lasting regions containing both metallic and silicate melts. Slab-derived metallic melt may produce another type of ULVZ that escapes core sequestration by reacting with the mantle to form iron-rich postbridgmanite or ferropericlase. The hypotheses connect peculiar features near Earth's core-mantle boundary to subduction of the oceanic lithosphere through the deep carbon cycle. [ABSTRACT FROM AUTHOR]

We report on the nucleation of bubbles on solids that are gently rubbed against each other in a liquid. The phenomenon is found to depend strongly on the material and roughness of the solid surfaces. For a given surface, temperature, and gas content, a trail of growing bubbles is observed if the rubbing force and velocity exceed a certain threshold. Direct observation through a transparent solid shows that each bubble in the trail results from the early coalescence of several microscopic bubbles, themselves detaching from microscopic gas pockets forming between the solids. From a detailed study of the wear tracks, with atomic force and scanning electron microscopy imaging, we conclude that these microscopic gas pockets originate from a local fracturing of the surface asperities, possibly enhanced by chemical reactions at the freshly created surfaces. Our findings will be useful either for preventing undesired bubble formation or, on the contrary, for "writing with bubbles," i.e., creating controlled patterns of microscopic bubbles. [ABSTRACT FROM AUTHOR]

Flocks of birds exhibit a remarkable degree of coordination and collective response. It is not just that thousands of individuals fly, on average, in the same direction and at the same speed, but that even the fluctuations around the mean velocity are correlated over long distances. Quantitative measurements on flocks of starlings, in particular, show that these fluctuations are scale-free, with effective correlation lengths proportional to the linear size of the flock. Here we construct models for the joint distribution of velocities in the flock that reproduce the observed local correlations between individuals and their neighbors, as well as the variance of flight speeds across individuals, but otherwise have as little structure as possible. These minimally structured or maximum entropy models provide quantitative, parameter-free predictions for the spread of correlations throughout the flock, and these are in excellent agreement with the data. These models are mathematically equivalent to statistical physics models for ordering in magnets, and the correct prediction of scale-free correlations arises because the parameters- completely determined by the data-are in the critical regime. In biological terms, criticality allows the flock to achieve maximal correlation across long distances with limited speed fluctuations. [ABSTRACT FROM AUTHOR]

The role of protein flexibility in molecular motor function has previously been studied by considering a Brownian ratchet motor that is connected to its cargo by an elastic spring, with the result that the average velocity of the motor/cargo system is increased by reducing the stiffness of the linkage. Here, we extend this investigation to the case of chromosome transport during anaphase A, in which the relevant flexibility is not primarily in the motor/cargo linkage but rather in the cargo itself, i.e., in the chromosome. We model the motor mechanism as an imperfect Brownian ratchet with a built-in opposing load and the chromosome as a collection of discrete segments linked by an elastic energy function that discretizes the potential energy of an elastic rod. Thermal fluctuations are produced in the model by random forces, as in Brownian dynamics. All of the parameters that characterize the chromosome are known or can be estimated from experimental data, as can all but one of the motor parameters, which is adjusted to give the correct transport velocity of normal-length chromosomes. With the parameters so determined, we then reproduce the experimental finding of Nicklas [Nicklas, R. B. (1965) J. Cell Biol. 25, 119-135] that chromosome speed is essentially independent of chromosome length, even though our model contains no "velocity governor." We find instead that this effect is a consequence of chromosome flexibility, as it disappears when stiffer than normal chromosomes are considered. [ABSTRACT FROM AUTHOR]