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Peer reviewed: True, Spontaneous material shape changes, such as swelling, growth or thermal expansion, can be used to trigger dramatic elastic instabilities in thin shells. These instabilities originate in geometric incompatibility between the preferred extrinsic and intrinsic curvature of the shell, which may be modified by active deformations through the thickness and in plane, respectively. Here, we solve the simplest possible model of such instabilities, which assumes the shells are shallow, thin enough to bend but not stretch, and subject to homogeneous preferred curvatures. We consider separately the cases of zero, positive and negative Gauss curvature. We identify two types of supercritical symmetry-breaking instability, in which the shell's principal curvature spontaneously breaks discrete up/down symmetry and continuous planar isotropy. These are then augmented by inversion instabilities, in which the shell jumps subcritically between up/down broken symmetry states and rotation instabilities, in which the curvatures rotate by 90° between states of broken isotropy without release of energy. Each instability has a thickness-independent threshold value for the preferred extrinsic curvature proportional to the square root of Gauss curvature. Finally, we show that the threshold for the isotropy-breaking instability is the same for deep spherical caps, in good agreement with recently published data.

There is ongoing and rapid advancement in approaches to modelling the fate of exhaled particles in different environments relevant to disease transmission. It is important that models are verified by comparison with each other using a common set of input parameters to ensure that model differences can be interpreted in terms of model physics rather than unspecified differences in model input parameters. In this paper, we define parameters necessary for such benchmarking of models of airborne particles exhaled by humans and transported in the environment during breathing and speaking.

The bending of epithelial tubes is a fundamental process in organ morphogenesis, driven by various multicellular behaviours. The cochlea in the mammalian inner ear is a representative example of spiral tissue architecture where the continuous bending of the duct is a fundamental component of its morphogenetic process. Although the cochlear duct morphogenesis has been studied by genetic approaches extensively, it is still unclear how the cochlear duct morphology is physically formed. Here, we report that nuclear behaviour changes are associated with the curvature of the pseudostratified epithelium during murine cochlear development. Two-photon live-cell imaging reveals that the nuclei shuttle between the luminal and basal edges of the cell is in phase with cell-cycle progression, known as interkinetic nuclear migration, in the flat region of the pseudostratified epithelium. However, the nuclei become stationary on the luminal side following mitosis in the curved region. Mathematical modelling together with perturbation experiments shows that this nuclear stalling facilitates luminal-basal differential growth within the epithelium, suggesting that the nuclear stalling would contribute to the bending of the pseudostratified epithelium during the cochlear duct development. The findings suggest a possible scenario of differential growth which sculpts the tissue shape, driven by collective nuclear dynamics.

Many small animals, including shrews, most rodents and some marsupials, have fur composed of at least four types of hair, all with distinctive and complex anatomy. A ubiquitous and unexplained feature is periodic, internal banding with spacing in the 6–12 µm range that hints at an underlying infrared function. One bristle-like form, called guard hair, has the correct shape and internal periodic patterns to function as an infrared antenna. Optical analysis of guard hair from a wide range of species shows precise tuning to the optimum wavelength for thermal imaging. For heavily predated, nocturnal animals the ability to sense local infrared sources has a clear survival advantage. The tuned antennae, spectral filters and waveguides present in guard hair, all operating at a scale similar to the infrared wavelength, could be a rich source of bio-inspiration in the field of photonics. The tools developed in this work may enable us to understand the other hair types and their evolution.

Lidar is the optimum technology for measuring bare-Earth elevation beneath, and the structure of, vegetation. Consequently, airborne laser scanning (ALS) is widely employed for use in a range of applications. However, ALS is not available globally nor frequently updated due to its high cost per unit area. Spaceborne lidar can map globally but energy requirements limit existing spaceborne lidars to sparse sampling missions, unsuitable for many common ALS applications. This paper derives the equations to calculate the coverage a lidar satellite could achieve for a given set of characteristics (released open-source), then uses a cloud map to determine the number of satellites needed to achieve continuous, global coverage within a certain time-frame. Using the characteristics of existing in-orbit technology, a single lidar satellite could have a continuous swath width of 300 m when producing a 30 m resolution map. Consequently, 12 satellites would be needed to produce a continuous map every 5 years, increasing to 418 satellites for 5 m resolution. Building 12 of the currently in-orbit lidar systems is likely to be prohibitively expensive and so the potential of technological developments to lower the cost of a global lidar system (GLS) are discussed. Once these technologies achieve a sufficient readiness level, a GLS could be cost-effectively realized.

Haematopoietic lineage commitments are presented by a canonical roadmap in which haematopoietic stem cells or multipotent progenitors (MPPs) bifurcate into progenitors of more restricted lineages and ultimately mature to terminally differentiated cells. Although transcription factors playing significant roles in cell-fate commitments have been extensively studied, integrating such knowledge into the dynamic models to understand the underlying biological mechanism remains challenging. The hypothesis and modelling approach of the endogenous network has been developed previously and tested in various biological processes and is used in the present study of haematopoietic lineage commitments. The endogenous network is constructed based on the key transcription factors and their interactions that determine haematopoietic cell-fate decisions at each lineage branchpoint. We demonstrate that the process of haematopoietic lineage commitments can be reproduced from the landscape which orchestrates robust states of network dynamics and their transitions. Furthermore, some non-trivial characteristics are unveiled in the dynamical model. Our model also predicted previously under-represented regulatory interactions and heterogeneous MPP states by which distinct differentiation routes are intermediated. Moreover, network perturbations resulting in state transitions indicate the effects of ectopic gene expression on cellular reprogrammes. This study provides a predictive model to integrate experimental data and uncover the possible regulatory mechanism of haematopoietic lineage commitments.

Vessel wall enhancement (VWE) in contrast-enhanced magnetic resonance imaging (MRI) is a potential biomarker for intracranial aneurysm (IA) risk stratification. In this study, we investigated the relationship between VWE features, risk metrics, morphology and hemodynamics in 41 unruptured aneurysms. We reconstructed the IA geometries from MR angiography and mapped pituitary stalk-normalized MRI intensity on the aneurysm surface using an in-house tool. For each case, we calculated the maximum intensity (CRstalk) and IA risk (via size and the rupture resemblance score (RRS)). We performed correlation analysis to assess relationships between CRstalkand IA risk metrics (size and RRS), as well as each parameter encompassed in RRS, i.e. aneurysmal size ratio (SR), normalized wall shear stress (WSS) and oscillatory shear index. We found that CRstalkhad a strong correlation (Pearson correlation coefficient, PCC = 0.630) with size and a moderate correlation (PCC = 0.472) with RRS, indicating an association between VWE and IA risk. Furthermore, CRstalkhad a weak negative correlation with normalized WSS (PCC = −0.320) and a weak positive correlation with SR (PCC = 0.390). Local voxel-based analysis showed only a weak negative correlation between normalized WSS and contrast-enhanced MRI signal intensity (PCC = −0.240), suggesting that if low-normalized WSS induces enhancement-associated pathobiology, the effect is not localized.

The biological response of organisms exposed to nanoparticles is often studied in vitro using adherent monolayers of cultured cells. In order to derive accurate concentration–response relationships, it is important to determine the local concentration of nanoparticles to which the cells are actually exposed rather than the nominal concentration of nanoparticles in the cell culture medium. In this study, the sedimentation–diffusion process of different sized and charged gold nanoparticles has been investigated in vitro by evaluating their settling dynamics and by developing a theoretical model to predict the concentration depth profile of nanoparticles in solution over time. Experiments were carried out in water and in cell culture media at a range of controlled temperatures. The optical phenomenon of caustics was exploited to track nanoparticles in real time in a conventional optical microscope without any requirement for fluorescent labelling that potentially affects the dynamics of the nanoparticles. The results obtained demonstrate that size, temperature and the stability of the nanoparticles play a pivotal role in regulating the settling dynamics of nanoparticles. For gold nanoparticles larger than 60 nm in diameter, the initial nominal concentration did not accurately represent the concentration of nanoparticles local to the cells. Finally, the theoretical model proposed accurately described the settling dynamics of the nanoparticles and thus represents a promising tool to support the design of in vitro experiments and the study of concentration–response relationships.

Due to the complex permittivity, it is difficult to directly clarify the transient mechanism between electromagnetic waves and Debye media. To overcome the above problem, the temporal relationship between the electromagnetic waves and permittivity is explicitly derived by applying the Fourier inversion and introducing the remnant displacement. With the help of the Poynting theorem and energy conservation equation, the transient power loss density is derived to describe the transient dissipation of electromagnetic field and the mechanism on phase displacement has been explicitly revealed. Besides, the unique solution can be obtained by applying the time-domain analysis method rather than involving the frequency-domain characteristics. The effectiveness of transient analysis is demonstrated by giving a comparison simulation on one-dimensional example.

Dialogues among politicians provide a window into political landscapes and relations among parties and nations. Existing research has focused on the outcomes of such dialogues and on the structure of social networks on which they take place. Little is known, however, about how political discussion networks form and which are the main driving forces behind their formation. We study a collection of ego-networks from 30 randomly sampled Romanian politicians to reveal fundamental processes behind the formation of political discussion networks. We show that ties in such networks tend to be strong and balanced, and that their organization is not affected by sex, age or education homophily. We use the exponential family of random graph models for small networks to assess likely closure mechanisms and possible homophily effects, but we note that further research and additional data are needed to fully understand the impact of context and political affiliations on the generalization of our findings.

Flocking is a fascinating phenomenon observed across a wide range of living organisms. We investigate, based on a simple self-propelled particle model, how the emergence of ordered motion in a collectively moving group is influenced by the local rules of interactions among the individuals, namely, metric versus topological interactions as debated over in the current literature. In the case of the metric ruling, the individuals interact with the neighbours within a certain metric distance; in contrast, in the topological ruling, interaction is confined within a number of fixed nearest neighbours. Here, we explore how the range of interaction versus the number of fixed interacting neighbours affects the dynamics of flocking in an unbounded space, as observed in natural scenarios. Our study reveals the existence of a certain threshold value of the interaction radius in the case of metric ruling and a threshold number of interacting neighbours for the topological ruling to reach an ordered state. Interestingly, our analysis shows that topological interaction is more effective in bringing the order in the group, as observed in field studies. We further compare how the nature of the interactions affects the dynamics for various sizes and speeds of the flock.

The mechanisms inducing unpredictably directional switches in collective and moving biological entities are largely unclear. Deeply understanding such mechanisms is beneficial to delicate design of biologically inspired devices with particular functions. Here, articulating a framework that integrates data-driven, analytical and numerical methods, we investigate the underlying mechanism governing the coordinated rotational flight of pigeon flocks with unpredictably directional switches. Particularly using the sparse Bayesian learning method, we extract the inter-agent interactional dynamics from the high-resolution GPS data of three pigeon flocks, which reveals that the decision-making process in rotational switching flight performs in a more nonlinear manner than in smooth coordinated flight. To elaborate the principle of this nonlinearity of interactions, we establish a data-driven particle model with two potential wells and estimate the mean switching time of rotational direction. Our model with its analytical and numerical results renders the directional switches of moving biological groups more interpretable and predictable. Actually, an appropriate combination of natures, including high density, stronger nonlinearity in interactions, and moderate strength of noise, can enhance such highly ordered, less frequent switches.

Given the ubiquity of bubbles and non-biodegradable wastes in aqueous environments, their transport through bubbles should be widely extant in water bodies. In this study, we investigate the effect of bubble-induced waste transport on microbial growth by using yeasts as model microbes and a silicone rubber object as model waste. Noteworthily, this object repeatedly rises and sinks in fluid through fluctuations in bubble-acquired buoyant forces produced by cyclic nucleation, growth and release of bubbles from object's surface. The rise–sink movement of the object gives rise to a strong bulk mixing and an enhanced resuspension of cells from the floor. Such spatially dynamic contaminant inside a nutrient-rich medium also leads to an increment in the total microbe concentration in the fluid. The enhanced concentration is caused by strong nutrient mixing generated by the object's movement which increases the nutrient supply to growing microbes and thereby, prolonging their growth phases. We confirm these findings through a theoretical model for cell concentration and nutrient distribution in fluid medium. The model is based on the continuum hypothesis and it uses the general conservation law which takes an advection–diffusion growth form. We conclude the study with the demonstration of bubble-induced digging of objects from model sand.

We built a flexible platform to study the mechanical operation of the organ of Corti (OoC) in the transduction of basilar membrane (BM) vibrations to oscillations of an inner hair cell bundle (IHB). The anatomical components that we consider are the outer hair cells (OHCs), the outer hair cell bundles, Deiters cells, Hensen cells, the IHB and various sections of the reticular lamina. In each of the components we apply Newton's equations of motion. The components are coupled to each other and are further coupled to the endolymph fluid motion in the subtectorial gap. This allows us to obtain the forces acting on the IHB, and thus study its motion as a function of the parameters of the different components. Some of the components include a nonlinear mechanical response. We found that slight bending of the apical ends of the OHCs can have a significant impact on the passage of motion from the BM to the IHB, including critical oscillator behaviour. In particular, our model implies that the components of the OoC could cooperate to enhance frequency selectivity, amplitude compression and signal to noise ratio in the passage from the BM to the IHB. Since the model is modular, it is easy to modify the assumptions and parameters for each component., Comment: A similar version was posted in bioRxiv

Cooperation is one of the key collective behaviours of human society. Despite discoveries of several social mechanisms underpinning cooperation, relatively little is known about how our neural functions affect cooperative behaviours. Here, we study the effect of a main neural function, working-memory capacity, on cooperation in repeated Prisoner's Dilemma experiments. Our experimental paradigm overcomes the obstacles in measuring and changing subjects' working-memory capacity. We find that the optimal cooperation level occurs when subjects remember two previous rounds of information, and cooperation increases abruptly from no memory capacity to minimal memory capacity. The results can be explained by memory-based conditional cooperation of subjects. We propose evolutionary models based on replicator dynamics and Markov processes, respectively, which are in good agreement with experimental results of different memory capacities. Our experimental findings differ from previous hypotheses and predictions of existent models and theories, and suggest a neural basis and evolutionary roots of cooperation beyond cultural influences.

In this paper, the thermoelectric properties of p-type and n-type GeSe are studied systematically by using first principles and Boltzmann transport theory. The calculation includes electronic structure, electron relaxation time, lattice thermal conductivity and thermoelectric transport properties. The results show that GeSe is an indirect band gap semiconductor with band gap 1.34 eV. Though p-type GeSe has a high density of states near Fermi level, the electronic conductivity is relative low because there is no carrier transport pathway along the a -axis direction. For n-type GeSe, a charge density channel is formed near conduction band minimum, which improves the electrical conductivity of n-type GeSe along the a -axis direction. At 700 K, the optimal ZT value reaches 2.5 at 4 × 10 19 cm −3 for n-type GeSe, while that is 0.6 at 1 × 10 20 cm −3 for p-type GeSe. The results show n-type GeSe has better thermoelectric properties than p-type GeSe, indicating that n-type GeSe is a promising thermoelectric material in middle temperature.

Baleen whales reliably produce stereotyped vocalizations, enabling their spatio-temporal distributions to be inferred from acoustic detections. Soundscape analysis provides an integrated approach whereby vocal species, such as baleen whales, are sampled holistically with other acoustic contributors to their environment. Acoustic elements that occur concurrently in space, time and/or frequency can indicate overlaps between free-ranging species and potential stressors. Such information can inform risk assessment framework models. Here, we demonstrate the utility of soundscape monitoring in central New Zealand, an area of high cetacean diversity where potential threats are poorly understood. Pygmy blue whale calls were abundant in the South Taranaki Bight (STB) throughout recording periods and were also detected near Kaikōura during autumn. Humpback, Antarctic blue and Antarctic minke whales were detected in winter and spring, during migration. Wind, rain, tidal and wave activity increased ambient sound levels in both deep- and shallow-water environments across a broad range of frequencies, including those used by baleen whales, and sound from shipping, seismic surveys and earthquakes overlapped in time, space and frequency with whale calls. The results highlight the feasibility of soundscape analysis to quantify and understand potential stressors to free-ranging species, which is essential for conservation and management decisions.

We investigate theoretically the ballistic motion of small legged insects and legless larvae after a jump. Notwithstanding their completely different morphologies and jumping strategies, some legged and legless animals have convergently evolved to jump with a take-off angle of 60°, which differs significantly from the leap angle of 45° that allows reaching maximum range. We show that in the presence of uniformly distributed random obstacles the probability of a successful jump is directly proportional to the area under the trajectory. In the presence of negligible air drag, the probability is maximized by a take-off angle of 60°. The numerical calculation of the trajectories shows that they are significantly affected by air drag, but the maximum probability of a successful jump still occurs for a take-off angle of 59–60° in a wide range of the dimensionless Reynolds and Froude numbers that control the process. We discuss the implications of our results for the exploration of unknown environments such as planets and disaster scenarios by using jumping robots.

The development of cooperation in human societies is a major unsolved problem in biological and social sciences. Extensive studies in game theory have shown that cooperative behaviour can evolve only under very limited conditions or with additional complexities, such as spatial structure. Non-trivial two-person games are categorized into three types of games, namely, the prisoner's dilemma game, the chicken game and the stag hunt game. Recently, the weight-lifting game has been shown to cover all five games depending on the success probability of weight lifting, which include the above three games and two trivial cases (all cooperation and all defection; conventionally not distinguished as separate classes). Here, we introduce the concept of the environmental value of a society. Cultural development and deterioration are represented by changes in this probability. We discuss cultural evolution in human societies and the biological communities of living systems.

Because the local concentration of vacancies in any material is bounded, their motion must be accompanied by nonlinear effects. Here we look for such effects in a simple model for electric field driven vacancy motion in memristors, solving the corresponding nonlinear Burgers' equation with impermeable nonlinear boundary conditions analytically. We find non-monotonous relaxation of the resistance while switching between the stable (``on''/``off'') states of the memristor; and qualitatively different film thickness dependencies of switching time (under applied current) and relaxation time (under no current). Our exact solution can serve as a useful benchmark for simulations of more complex memristor models., Comment: 5 pages, 3 figures (v2: clarifications/improvements as per referee comments and other minor changes)

A large number of living creatures are able to use ambient light effectively in biological signalling. Atherinomorus lacunosus , a teleost fish has alignments of circular spots on its dorsal trunk. The spot consists of iridophores, whose diameters are approximately 7–10 µm. The iridophore contains guanine crystals with diameters of 1–3 µm. Here, it is found that more than one spot with a diameter of approximately 0.1 mm causes a rhythmic flashing of light when viewed under white light. The typical light flash has a pulse width of approximately one second. When a pulsed train of flashes appears, the flash repeats at a typical frequency of 0.5–1 Hz. The observed phenomenon is one example of the evidence for the existence of rapid colour changing teleost fish.

In scanning field emission microscopy (SFEM), a tip (the source) is approached to few (or a few tens of) nanometres distance from a surface (the collector) and biased to field-emit electrons. In a previous study (Zanin et al. 2016 Proc. R. Soc. A472, 20160475. (doi:10.1098/rspa.2016.0475)), the field-emitted current was found to change by approximately 1% at a monatomic surface step (approx. 200 pm thick). Here we prepare surface domains of adjacent different materials that, in some instances, have a topographic contrast smaller than 15 pm. Nevertheless, we observe a contrast in the field-emitted current as high as 10%. This non-topographic collector material dependence is a yet unexplored degree of freedom calling for a new understanding of the quantum mechanical tunnelling barrier at the source site that takes into account the properties of the material at the collector site., Royal Society Open Science, 8 (7), ISSN:2054-5703

The collective motion of animal groups often exhibits velocity–velocity correlations between nearest neighbours, with the strongest velocity correlations observed at the shortest inter-animal spacings. This may have been a motivational factor in the development of models based primarily on short-ranged interactions. Here we ask whether such observations necessarily mean that the interactions are short-ranged. We develop a minimal model of collective motion capable of supporting interactions of arbitrary range and show that it represents a counterexample: the strongest velocity correlations emerge at the shortest distances, even when the interactions are explicitly non-local.

For field electron emission (FE), an empirical equation for measured current I_m as a function of measured voltage V_m has the form I_m = C*(V_m)^k*exp[-B/(V_m)], where B is a constant and C and k are constants or vary weakly with V_m. Values for k can be extracted (a) from simulations based on some specific FE theory, and in principle (b) from current-voltage measurements of sufficiently high quality. This paper shows that comparison of theoretically derived and experimentally derived k-values could provide a sensitive and useful tool for comparing FE theory and experiment, and for choosing between alternative theories. Existing methods of extracting k-values from experimental or simulated current-voltage data are discussed, including a modernised "least residual" method, and existing knowledge concerning k-values is summarised. Exploratory simulations are reported. Where an analytical result for k is independently known, this value is reliably extracted. More generally, extracted k-values are sensitive to details of the emission theory used, but also depend on assumed emitter shape; these two influences will need to be disentangled by future research, and a range of emitter shapes will need examination. Other procedural conclusions are reported. Some scientific issues that this new tool may be able to help investigate are indicated., 29 submitted pages, 3 figures, + intended Electronic Supplementary Material; modified version as submitted after review and accepted for publication

Active goal-directed motion requires real-time adjustment of control signals depending on the system’s status, also known as control. The amount of information that needs to be processed depends on the desired motion and control, and on the system’s morphology. The morphology of the system may directly effectuate or support the desired motion. This morphology-based reduction to the neuronal ‘control effort’ can be quantified by a novel information-entropy-based approach. Here, we apply this novel measure of ‘control effort’ to active microswimmers of different morphology. Their motion is a combination of directed deterministic and stochastic motion. In spherical microswimmers, the active propulsion leads to linear velocities. Active propulsion of asymmetric L-shaped particles leads to circular or—on tilted substrates—directed motion. Thus, the difference in shape, i.e. the morphology of the particles, directly influence the motion. Here, we quantify how this morphology can be exploited by control schemes for the purpose of steering the particles towards targets. Using computer simulations, we found in both cases a significantly lower control effort for L-shaped particles. However, certain movements can only be achieved by spherical particles. This demonstrates that a suitably designed microswimmer’s morphology might be exploited to perform specific tasks.

The vast amount of research devoted to public goods games has shown that contributions may be dramatically affected by varying framing conditions. This is particularly relevant in the context of donations to charities and non-governmental organizations. Here, we design a multiple public goods experiment by introducing five types of funds, each differing in the fraction of the contribution that is donated to a charity. We found that people contribute more to public goods when the associated social donations are presented as indirect rather than as direct donations. At the same time, the fraction of the donations devoted to charity is not affected by the framing. We have also found that, on average, women contribute to public goods and donate to charity significantly more than men. These findings are of potential interest to the design of social investment tools, in particular for charities to ask for better institutional designs from policy makers., This work was partially supported by MINECO (Spain) and FEDER funds through grant no. FIS2017-87519-P (Y.M.) and FJCI-2016-28276 (A.A.); by Ministerio de Ciencia, Innovación y Universidades/FEDER (Spain/UE) through grant no. PGC2018-098186-B-I00 (BASIC) (A.S. and J.C.); by Comunidad de Madrid under grant no. PRACTICO-CM and by Comunidad de Madrid/Universidad Carlos III de Madrid under grant no. CAVTIONS-CM-UC3M (A.S.); by Comunidad de Aragón (Spain) through grant no. E36-20R to FENOL (C.G.L. and Y.M.); by the EU through FET-Proactive Project MULTIPLEX (contract no. 317532, Y.M.) and FET-Proactive Project DOLFINS (contract no. 640772, C.G.L., Y.M. and A.S.), and by the Spanish State Research Agency and FEDER funds, through the María de Maeztu Program for Units of Excellence in R&D (MDM-2017-0711, S.M.) and under the PACSS grant no. (RTI2018-093732-B-C22, S.M.).

The study and the investigation of structural and dynamical properties of complex systems have attracted considerable interest among scientists in general and physicists and biologists in particular. The present review paper represents a broad overview of the research performed over the nonlinear dynamics of DNA, devoted to some different aspects of DNA physics and including analytical, quantum and computational tools to understand nonlinear DNA physics. We review in detail the semi-discrete approximation within helicoidal Peyrard–Bishop model and show that localized modulated solitary waves, usually called breathers, can emerge and move along the DNA. Since living processes occur at submolecular level, we then discuss a quantum treatment to address the problem of how charge and energy are transported on DNA and how they may play an important role for the functioning of living cells. While this problem has attracted the attention of researchers for a long time, it is still poorly understood how charge and energy transport can occur at distances comparable to the size of macromolecules. Here, we review a theory based on the mechanism of ‘self-trapping’ of electrons due to their interaction with mechanical (thermal) oscillation of the DNA structure. We also describe recent computational models that have been developed to capture nonlinear mechanics of DNA in vitro and in vivo , possibly under topological constraints. Finally, we provide some conjectures on potential future directions for this field.

The electrostatics arising in ferroelectric/dielectric two-dimensional heterostructures and superlatitices is revisited here within a simplest Kittel model, in order to define a clear paradigmatic reference for domain formation. The screening of the depolarizing field in isolated ferroelectric or polar thin films via the formation of 180$^{\circ}$ domains is well understood, whereby the width of the domains $w$ grows as the square-root of the film thickness $d$, following Kittel's law, for thick enough films ($w\ll d$). This behavior is qualitatively unaltered when the film is deposited on a dielectric substrate, sandwiched between dielectrics, and even in a superlattice setting, with just a suitable renormalisation of Kittel's length. As $d$ decreases, $w(d)$ deviates from Kittel's law, reaching a minimum and then diverging onto the mono-domain limit for thin enough films, always assuming a given spontaneous polarization $P$ of the ferrolectric, only modified by linear response to the depolarizing field. In most cases of experimental relevance $P$ would vanish before reaching that thin-film regime. This is not the case for superlattices. Unlike single films, for which the increase of the dielectric constant of the surrounding medium pushes the deviation from the Kittel's regime to lower values of $d$, there is a critical value of the relative thickness of ferroelectric/dielectric films in superlattices beyond which that behavior is reversed, and which defines the separation between strong and weak ferroelectric coupling in superlattices., 11 pages, 11 figures

Molecular motors are responsible for intracellular transport of a variety of biological cargo. We consider the collective behaviour of a finite number of motors attached on a cargo. We extend previous analytical work on processive motors to the case of non-processive motors, which stochastically bind on and off cytoskeletal filaments with a limited number of binding sites available. Physically, motors attached to a cargo cannot bind anywhere along the filaments, so the number of accessible binding sites on the filament should be limited. Thus, we analytically study the distribution and the velocity of a cluster of non-processive motors with limited number of binding sites. To validate our analytical results and to go beyond the level of detail possible analytically, we perform Monte Carlo latticed based stochastic simulations. In particular, in our simulations, we include sequence preservation of motors performing stepping and binding obeying a simple exclusion process. We find that limiting the number of binding sites reduces the probability of non-processive motors binding but has a relatively small effect on force–velocity relations. Our analytical and stochastic simulation results compare well to published data from in vitro and in vivo experiments.

Multicellular aggregate growth is regulated by nutrient availability and removal of metabolites, but the specifics of growth dynamics are dependent on cell type and environment. Classical models of growth are based on differential equations. While in some cases these classical models match experimental observations, they can only predict growth of a limited number of cell types and so can only be selectively applied. Currently, no classical model provides a general mathematical representation of growth for any cell type and environment. This discrepancy limits their range of applications, which a general modelling framework can enhance. In this work, a hybrid cellular Potts model is used to explain the discrepancy between classical models as emergent behaviours from the same mathematical system. Intracellular processes are described using probability distributions of local chemical conditions for proliferation and death and simulated. By fitting simulation results to a generalization of the classical models, their emergence is demonstrated. Parameter variations elucidate how aggregate growth may behave like one classical growth model or another. Three classical growth model fits were tested, and emergence of the Gompertz equation was demonstrated. Effects of shape changes are demonstrated, which are significant for final aggregate size and growth rate, and occur stochastically.

Este artículo contiene 16 páginas, 9 figuras., Emergence of collective, as well as superorganism-like, behaviour in biological populations requires the existence of rules of communication, either direct or indirect, between organisms. Because reaching an understanding of such rules at the individual level can be often difficult, approaches carried out at higher, or effective, levels of description can represent a useful alternative. In the present work, we show how a spinglass approach characteristic of statistical physics can be used as a tool to characterize the properties of the spatial occupancy patterns of a biological population. We exploit the presence of pairwise interactions in spin-glass models for detecting correlations between occupancies at different sites in the media. Such correlations, we claim, represent a proxy to the existence of planned and/or social strategies in the spatial organization of the population. Our spin-glass approach does not only identify those correlations but produces a statistical replica of the system (at the level of occupancy patterns) that can be subsequently used for testing alternative conditions/ hypothesis. Here, this methodology is presented and illustrated for a particular case of study: we analyse occupancy patterns of Aphaenogaster senilis ants during foraging through a simplified environment consisting of a discrete (tree-like) artificial lattice. Our spin-glass approach consistently reproduces the experimental occupancy patterns across time, and besides, an intuitive biological interpretation of the parameters is attainable. Likewise, we prove that pairwise correlations are important for reproducing these dynamics by showing how a null model, where such correlations are neglected, would perform much worse; this provides a solid evidence to the existence of superorganism-like strategies in the colony., This research has been supported by the Spanish government through grants no. CGL2016-78156-C2-2-R ( J.C, D.C and V.M), FIS2015-72434-EXP ( J.C, D.C and V.M) and CGL2016-78156-C2-1-R (F.B.)

Ocular surface health, the cognitive status, psychological health or human neurological disorders, among others, can be assessed by studying eye blinking, which can be differentiated in spontaneous, reflex and voluntary. Its diagnostic potential has provided a great number of works that evaluate their characteristics and variations depending on the subject's condition (sex, tiredness, health, …). The objective of this study was to analyse the differences in blinking kinematics of spontaneous and reflex blinks, distinguishing between direct and consensual reflexes, using a self-developed, non-invasive and image processing-based method. A video-oculography system is proposed using an air jet driven by a syringe to induce reflex and a high-speed camera to record the blinking of both eyes. The light intensity diffused by the eye changes during blinking and peaks when the eyelid closes. Sixty-second sequences were recorded of 25 subjects blinking. Intensity curves were off-line fitted to an exponentially modified Gaussian (EMG) function, whose σ , μ and τ parameters were analysed. A two-way analysis of variance (ANOVA) of these parameters was conducted to test the influence of the subject, the eye and blink type. In the closing phase, direct and consensual corneal reflexes are faster than spontaneous blinking, but there was no significant difference between them, nor between right and left eyes. In the opening phase, the direct corneal reflex was the slowest and significant differences appeared between right and left eyes.

Computer-aided design software and additive manufacturing provide flexibility for the direct fabrication of multi-material devices. This design and fabrication versatility has been investigated for the manufacture of dielectric spiral phase plates (SPP) that generate electromagnetic waves with helical wavefronts. Three types of SPPs designed to produce an orbital angular momentum (OAM) mode number l = |1| were additively manufactured using material extrusion and polyjet fabrication methods. The OAM mode characteristics of the transformed helical microwaves as a function of the SPP geometrical features were investigated experimentally in the 12–18 GHz frequency range. The SPPs were further combined with an additively manufactured dielectric lens that provided a marked improvement in OAM mode purity. Finally, multiplexing and de-multiplexing of two OAM modes were demonstrated successfully using an optimum SPP geometry and arrangement.

Interactions along the neuro-cardiac axis are being explored with regard to their involvement in cardiac diseases, including catecholaminergic polymorphic ventricular tachycardia, hypertension, atrial fibrillation, long QT syndrome and sudden death in epilepsy. Interrogation of the pathophysiology and pathogenesis of neuro-cardiac diseases in animal models present challenges resulting from species differences, phenotypic variation, developmental effects and limited availability of data relevant at both the tissue and cellular level. By contrast, tissue-engineered models containing cardiomyocytes and peripheral sympathetic and parasympathetic neurons afford characterization of cellular- and tissue-level behaviours while maintaining precise control over developmental conditions, cellular genotype and phenotype. Such approaches are uniquely suited to long-term, high-throughput characterization using optical recording techniques with the potential for increased translational benefit compared to more established techniques. Furthermore, tissue-engineered constructs provide an intermediary between whole animal/tissue experiments and in silico models. This paper reviews the advantages of tissue engineering methods of multiple cell types and optical imaging techniques for the characterization of neuro-cardiac diseases.

Using an immunoassay in combination with surface plasmon fluorescence spectroscopy (SPFS), we report the rapid detection of troponin I, a valuable biomarker for diagnosis of myocardial infarction. We discuss the implementation of (i) direct, (ii) sandwich, and (iii) competitive assay formats, based on surface plasmon resonance and SPFS. To elucidate the results, we relate the experiments to orientation-dependent interaction of troponin I epitopes with respective immunoglobulin G antibodies. A limit of detection (LoD) of 19 pM, with 45 min readout time, was achieved using single monoclonal antibody that is specific for one epitope. The borderline between normal people and patients is 20 pM to 83 pM cTnI concentration, and upon the outbreak of acute myocardial infraction it can raise to 2 nM and levels at 20 nM for 6–8 days, therefore the achieved LoD covers most of the clinically relevant range. In addition, this system allows for the detection of troponin I using a single specific monoclonal antibody, which is highly beneficial in case of detection in real samples, where the protein has a complex form leading to hidden epitopes, thus paving the way towards a system that can improve early-stage screening of heart attacks.

We introduce interference-contrast optical activity (ICOA) as a new technique for probing the chirality of anisotropic samples and more. ICOA could underpin a new class of ‘chiral microscopes’, with potential applications spanning the range of chirality and beyond. Two possible versions of ICOA are described explicitly; one designed to probe the optical rotation of a transparent sample regardless of the sample’s linear birefringence (ICOA-OR) and another designed to probe gradients in the optical rotation of a transparent sample (ICOA-GOR). Simulated results for α -quartz lead us to suggest that ICOA-GOR might be applied to help monitor the growth of chiral crystals in the pharmaceutical industry. Possible directions for future research are highlighted.

We report all-atom molecular dynamics simulations of asymmetric bilayers containing phosphoinositides in the presence of monovalent and divalent cations. We have characterized the molecular mechanism by which these divalent cations interact with phosphoinositides. Ca 2+ desolvates more readily, consistent with single-molecule calculations, and forms a network of ionic-like bonds that serve as a ‘molecular glue’ that allows a single ion to coordinate with up to three phosphatidylinositol-(4,5)-bisphosphate (PI(4, 5)P 2 ) lipids. The phosphatidylinositol-(3,5)-bisphosphate isomer shows no such effect and neither does PI(4, 5)P 2 in the presence of Mg 2+ . The resulting network of Ca 2+ -mediated lipid-lipid bonds grows to span the entire simulation space and therefore has implications for the lateral distribution of phosophoinositides in the bilayer. We observe context-specific differences in lipid diffusion rates, lipid surface densities and bilayer structure. The molecular-scale delineation of ion-lipid arrangements reported here provides insight into similar nanocluster formation induced by peripheral proteins to regulate the formation of functional signalling complexes on the membrane.

Postural stability is one of the most crucial elements in bipedal locomotion. Bipeds are dynamically unstable and need to maintain their trunk upright against the rotations induced by the ground reaction forces (GRFs), especially when running. Gait studies report that the GRF vectors focus around a virtual point above the center of mass (VPA), while the trunk moves forward in pitch axis during the stance phase of human running. However, a recent simulation study suggests that a virtual point below the center of mass (VPB) might be present in human running, since a VPA yields backward trunk rotation during the stance phase. In this work, we perform a gait analysis to investigate the existence and location of the VP in human running at 5 ms-1, and support our findings numerically using the spring-loaded inverted pendulum model with a trunk (TSLIP). We extend our analysis to include perturbations in terrain height (visible and camouflaged), and investigate the response of the VP mechanism to step-down perturbations both experimentally and numerically. Our experimental results show that the human running gait displays a VPB of ~-30cm and a forward trunk motion during the stance phase. The camouflaged step-down perturbations affect the location of the VPB. Our simulation results suggest that the VPB is able to encounter the step-down perturbations and bring the system back to its initial equilibrium state., 18 pages, 18 figures, submitted to the journal Royal Society Open Science

The type 1 pilus is a bacterial filament consisting of a long coiled proteic chain of subunits joined together by non-covalent bonding between complementing $\beta$-strands. Its strength and structural stability are critical for its anchoring function in uropathogenic Escherichia coli bacteria. The pulling and unravelling of the FimG subunit of the pilus was recently studied by atomic force microscopy (AFM) experiments and steered molecular dynamics (SMD) simulations [A. Alonso-Caballero et al., Nature Commun. 9, 2758 (2018)]. In this work we perform a quantitative comparison between experiment and simulation, showing a good agreement in the underlying work values for the unfolding. The simulation results are then used to estimate the free energy difference for the detachment of FimG from the complementing strand of the neighbouring subunit in the chain, FimF. Finally, we show that the large free energy difference for the unravelling and detachment of the subunits which leads to the high stability of the chain is entirely entropic in nature., Comment: 9 pages, 5 figures

The silks of certain orb weaving spiders are emerging as high-quality optical materials. This motivates study of the optical properties of such silk and particularly the comparative optical properties of the silks of different species. Any differences in optical properties may impart biological advantage for a spider species and make the silks interesting for biomimetic prospecting as optical materials. A prior study of the reflectance of spider silks from 18 species reported results for three species of modern orb weaving spiders ( Nephila clavipes, Argiope argentata and Micrathena Schreibersi ) as having reduced reflectance in the UV range. (Modern in the context used here means more recently derived.) The reduced UV reflectance was interpreted as an adaptive advantage in making the silks less visible to insects. Herein, a standard, experimental technique for measuring the reflectance spectrum of diffuse surfaces, using commercially available equipment, has been applied to samples of the silks of four modern species of orb weaving spiders: Phonognatha graeffei , Eriophora transmarina , Nephila plumipes and Argiope keyserlingi . This is a different technique than used in the previous study. Three of the four silks measured have a reduced signal in the UV. By taking the form of the silks as optical elements into account, it is shown that this is attributable to a combination of wavelength-dependent absorption and scattering by the silks rather than differences in reflectance for the different silks. Phonognatha graeffei dragline silk emerges as a very interesting spider silk with a flat ‘reflectance'/scattering spectrum which may indicate it is a low UV absorbing dielectric micro-fibre. Overall the measurement emerges as having the potential to compare the large numbers of silks from different species to prospect for those which have desirable optical properties.

Understanding the failure modes of curved hollow tree trunks is essential from both safety and conservation perspectives. Despite extensive research, the underlying mechanism that determines the cracking failure of curved hollow tree trunks remains unclear due to the lack of theoretical analysis that considers both the initial curvature and orthotropic material properties. Here we derive new mathematical expressions for predicting the bending moment, M crack , at which the cracking failure occurs. The failure mode of a tree species is then determined, as a function of t / R and cR , by comparing M crack with M bend , where t , R and c are, respectively, the trunk wall thickness, outer radius and initial curvature; M bend is the bending moment for conventional bending failure. Our equation shows that M crack is proportional to the tangential tensile strength of wood σ T , increases with t / R , and decreases with the final cR . We analyse 11 tree species and find that hardwoods are more likely to fail in conventional bending, whereas softwoods tend to break due to cracking. This is due to the softwoods' much smaller tangential tensile strength, as observed from the data of 66 hardwoods and 43 softwoods. For larger cR , cracking failure is easier to occur in curvature-decreasing bending than curvature-increasing due to additional normal tensile force F acting on the neutral cross-section; on the other hand, for smaller cR , bending failure is easier to occur due to decreased final curvature. Our formulae are applicable to other natural and man-made curved hollow beams with orthotropic material properties. Our findings provide insights for those managing trees in urban situations and those managing for conservation of hollow-dependent fauna in both urban and rural settings.

We present KITE, a general purpose open-source tight-binding software for accurate real-space simulations of electronic structure and quantum transport properties of large-scale molecular and condensed systems with tens of billions of atomic orbitals (N~10^10). KITE's core is written in C++, with a versatile Python-based interface, and is fully optimised for shared memory multi-node CPU architectures, thus scalable, efficient and fast. At the core of KITE is a seamless spectral expansion of lattice Green's functions, which enables large-scale calculations of generic target functions with uniform convergence and fine control over energy resolution. Several functionalities are demonstrated, ranging from simulations of local density of states and photo-emission spectroscopy of disordered materials to large-scale computations of optical conductivity tensors and real-space wave-packet propagation in the presence of magneto-static fields and spin-orbit coupling. On-the-fly calculations of real-space Green's functions are carried out with an efficient domain decomposition technique, allowing KITE to achieve nearly ideal linear scaling in its multi-threading performance. Crystalline defects and disorder, including vacancies, adsorbates and charged impurity centers, can be easily set up with KITE's intuitive interface, paving the way to user-friendly large-scale quantum simulations of equilibrium and non-equilibrium properties of molecules, disordered crystals and heterostructures subject to a variety of perturbations and external conditions., Comment: 38 pages, 13 figures, 3 tables. Published version

Royal Society Open Science 7(10), 201507 (2020). doi:10.1098/rsos.201507, Published by Royal Soc. Publ., London

Type 2 diabetes mellitus (T2DM) has been associated with insulin resistance and the failure of β-cells to produce and secrete enough insulin as the disease progresses. However, clinical treatments based solely on insulin secretion and action have had limited success. The focus is therefore shifting towards α-cells, in particular to the dysregulated secretion of glucagon. Our qualitative electron-microscopy-based observations gave an indication that mitochondria in α-cells are altered in Western-diet-induced T2DM. In particular, α-cells extracted from mouse pancreatic tissue showed a lower density of mitochondria, a less expressed matrix and a lower number of cristae. These deformities in mitochondrial ultrastructure imply a decreased efficiency in mitochondrial ATP production, which prompted us to theoretically explore and clarify one of the most challenging problems associated with T2DM, namely the lack of glucagon secretion in hypoglycaemia and its oversecretion at high blood glucose concentrations. To this purpose, we constructed a novel computational model that links α-cell metabolism with their electrical activity and glucagon secretion. Our results show that defective mitochondrial metabolism in α-cells can account for dysregulated glucagon secretion in T2DM, thus improving our understanding of T2DM pathophysiology and indicating possibilities for new clinical treatments.

Inferring the processes underlying the emergence of observed patterns is a key challenge in theoretical ecology. Much effort has been made in the past decades to collect extensive and detailed information about the spatial distribution of tropical rainforests, as demonstrated, e.g., in the 50 ha tropical forest plot on Barro Colorado Island, Panama. These kind of plots have been crucial to shed light on diverse qualitative features, emerging both at the single-species or the community level, like the spatial aggregation or clustering at short scales. Here, we build on the progress made in the study of the density correlation functions applied to biological systems, focusing on the importance of accurately defining the borders of the set of trees, and removing the induced biases. We also pinpoint the importance of combining the study of correlations with the scale dependence of fluctuations in density, which are linked to the well known empirical Taylor's power law. Density correlations and fluctuations, in conjunction, provide an unique opportunity to interpret the behaviors and possibly to allow comparisons between data and models. We also study such quantities in models of spatial patterns and, in particular, we find that a spatially explicit neutral model generates patterns with many qualitative features in common with the empirical ones., Comment: 19 pages, 7 figures and Supp. Inf

Convection is a fundamental fluid transport phenomenon, where the large-scale motion of a fluid is driven, for example, by a thermal gradient or an electric potential. Modeling convection has given rise to the development of chaos theory and the reduced-order modeling of multiphysics systems; however, these models have been limited to relatively simple thermal convection phenomena. In this work, we develop a reduced-order model for chaotic electroconvection at high electric Rayleigh number. The chaos in this system is related to the standard Lorenz model obtained from Rayleigh-Benard convection, although our system is driven by a more complex three-way coupling between the fluid, the charge density, and the electric field. Coherent structures are extracted from temporally and spatially resolved charge density fields via proper orthogonal decomposition (POD). A nonlinear model is then developed for the chaotic time evolution of these coherent structures using the sparse identification of nonlinear dynamics (SINDy) algorithm, constrained to preserve the symmetries observed in the original system. The resulting model exhibits the dominant chaotic dynamics of the original high-dimensional system, capturing the essential nonlinear interactions with a simple reduced-order model., Comment: 14 pages, 4 figures

Exact mathematical identities are presented between the relevant parameters of droplets displaying circular contact boundary based on flat tilted surfaces. Two of the identities are derived from the force balance, and one from the torque balance. The tilt surfaces cover the full range of inclinations for sessile or pendant drops, including the intermediate case of droplets on a wall (vertical surface). The identities are put under test both by the available solutions of a linear response approximation at small Bond numbers as well as the ones obtained from numerical solutions, making use of the Surface Evolver software. The subtleties to obtain certain angle-averages appearing in identities by the numerical solutions are discussed in detail. It is argued how the identities are useful in two respects. First is to replace some unknown values in the Young-Laplace equation by their expressions obtained from the identities. Second is to use the identities to estimate the error for approximate analytical or numerical solutions without any reference to an exact solution., Comment: v1: 22 pages, 10 figures. v2: Typos fixed

Nutshells achieve remarkable properties by optimizing structure and chemistry at different hierarchical levels. Probing nutshells from the cellular down to the nano- and molecular level by microchemical and nanomechanical imaging techniques reveals insights into nature's packing concepts. In walnut and pistachio shells, carbohydrate and lignin polymers assemble to form thick-walled puzzle cells, which interlock three-dimensionally and show high tissue strength. Pistachio additionally achieves high-energy absorption by numerous lobes interconnected via ball-joint-like structures. By contrast, the three times more lignified walnut shells show brittle LEGO-brick failure, often along the numerous pit channels. In both species, cell walls (CWs) show distinct lamellar structures. These lamellae involve a helicoidal arrangement of cellulose macrofibrils as a recurring motif. Between the two nutshell species, these lamellae show differences in thickness and pitch angle, which can explain the different mechanical properties on the nanolevel. Our in-depth study of the two nutshell tissues highlights the role of cell form and their interlocking as well as plant CW composition and structure for mechanical protection. Understanding these plant shell concepts might inspire biomimetic material developments as well as using walnut and pistachio shell waste as sustainable raw material in future applications.

Detailed examinations of both the movement and muscle activation patterns used by animals and humans to complete complex tasks are difficult to obtain in many environments. Therefore, the ability to infer movement and muscle activation patterns after capture of a single set of easily obtained data is highly sought after. One possible solution to this problem is to capture force-time data through the use of appropriate transducers, then interrogate the signal's derivative, the yank-time signal, which amplifies, and thus highlights, temporal force-time changes. Because the countermovement vertical jump (CMJ) is a complex movement that has been well studied in humans, it provides an excellent preliminary model to test the validity of this solution. The aim of the present study was therefore to explore the use of yank-time signal, derived from vertical ground reaction force-time data, to identify and describe important kinematic (captured using three-dimensional motion analysis) and kinetic events in the CMJ, and to relate these to possible muscle activation (electromyography) events that underpin them. It was found that the yank-time signal could be used to accurately identify several key events during the CMJ that are likely to be missed or misidentified when only force-time data are inspected, including the first instances of joint flexion and centre of mass movement. Four different jump profiles (i.e. kinematic patterns) were inferred from the yank-time data, which were linked to different patterns of muscle activation. Therefore, yank-time signal interrogation provides a viable method of estimating kinematic patterns and muscle activation strategies in complex human movements.

With technologies rapidly evolving, many research institutions are now opting to invest in costly, high-quality, specialized microscopes which are shared by many researchers. As a consequence, the user may not have the ability to adapt a microscope to their specific needs and limitations in experimental design are introduced. A flexible work-horse microscopy system is a valuable tool in any laboratory to meet the diverse needs of a research team and promote innovation in experimental design. We have developed the Flexiscope; a multi-functional, adaptable, efficient and high-performance microscopy/electrophysiology system for everyday applications in a neurobiology laboratory. The core optical components are relatively constant in the three configurations described here: an upright configuration, an inverted configuration and an upright/electrophysiology configuration. We have provided a comprehensive description of the Flexiscope. We show that this method is capable of oblique infrared illumination imaging, multi-channel fluorescent imaging and automated three-dimensional scanning of larger specimens. Image quality is conserved across the three configurations of the microscope, and conversion between configurations is possible quickly and easily, while the motion control system can be repurposed to allow sub-micrometre computer-controlled micromanipulation. The Flexiscope provides similar performance and usability to commercially available systems. However, as it can be easily reconfigured for multiple roles, it can remove the need to purchase multiple microscopes, giving significant cost savings. The modular reconfigurable nature allows the user to customize the system to their specific needs and adapt/upgrade the system as challenges arise, without requiring specialized technical skills.