Entropy Production of Run-and-Tumble Particles.

We analyze the entropy production in run-and-tumble models. After presenting the general formalism in the framework of the Fokker-Planck equations in one space dimension, we derive some known exact results in simple physical situations (free run-and-tumble particles and harmonic confinement). We then extend the calculation to the case of anisotropic motion (different speeds and tumbling rates for right- and left-oriented particles), obtaining exact expressions of the entropy production rate. We conclude by discussing the general case of heterogeneous run-and-tumble motion described by space-dependent parameters and extending the analysis to the case of d-dimensional motions.

Entropons as collective excitations in active solids.

The vibrational dynamics of solids is described by phonons constituting basic collective excitations in equilibrium crystals. Here, we consider a non-equilibrium active solid, formed by self-propelled particles, which bring the system into a non-equilibrium steady-state. We identify novel vibrational collective excitations of non-equilibrium (active) origin, which coexist with phonons and dominate over them when the system is far from equilibrium. These vibrational excitations are interpreted in the framework of non-equilibrium physics, in particular, stochastic thermodynamics. We call them "entropons" because they are the modes of spectral entropy production (at a given frequency and wave vector). The existence of entropons could be verified in future experiments on dense self-propelled colloidal Janus particles and granular active matter, as well as in living systems, such as dense cell monolayers.

Trehalose counteracts the dissociation of tetrameric rabbit lactate dehydrogenase induced by acidic pH conditions.

The lactate dehydrogenase from rabbit skeletal muscle (rbLDH) is a tetrameric enzyme, known to undergo dissociation when exposed to acidic pH conditions. Moreover, it should be mentioned that this dissociation translates into a pronounced loss of enzyme activity. Notably, among the compounds able to stabilize proteins and enzymes, the disaccharide trehalose represents an outperformer. In particular, trehalose was shown to efficiently counteract quite a number of physical and chemical agents inducing protein denaturation. However, no information is available on the effect, if any, exerted by trehalose against the dissociation of protein oligomers. Accordingly, we thought it of interest to investigate whether this disaccharide is competent in preventing the dissociation of rbLDH induced by acidic pH conditions. Further, we compared the action of trehalose with the effects triggered by maltose and cellobiose. Surprisingly, both these disaccharides enhanced the dissociation of rbLDH, with maltose being responsible for a major effect when compared to cellobiose. On the contrary, trehalose was effective in preventing enzyme dissociation, as revealed by activity assays and by Dynamic Light Scattering (DLS) experiments. Moreover, we detected a significant decrease of both K0.5 and Vmax when the rbLDH activity was tested (at pH 7.5 and 6.5) as a function of pyruvate concentration in the presence of trehalose. Further, we found that trehalose induces a remarkable increase of Vmax when the enzyme is exposed to pH 5. Overall, our observations suggest that trehalose triggers conformational rearrangements of tetrameric rbLDH mirrored by resistance to dissociation and peculiar catalytic features.

A microfluidic method for passive trapping of sperms in microstructures.

Sperm motility is a prerequisite for male fertility. Enhancing the concentration of motile sperms in assisted reproductive technologies - for human and animal reproduction - is typically achieved through aggressive methods such as centrifugation. Here, we propose a passive technique for the amplification of motile sperm concentration, with no externally imposed forces or flows. The technique is based on the disparity between probability rates, for motile cells, of entering and escaping from complex structures. The effectiveness of the technique is demonstrated in microfluidic experiments with microstructured devices, comparing the trapping power in different geometries. In these micro-traps, we observe an enhancement of cells' concentration close to 10, with a contrast between motile and non-motile cells increased by a similar factor. Simulations of suitable interacting model sperms in realistic geometries reproduce quantitatively the experimental results, extend the range of observations and highlight the components that are key to the optimal trap design.

In vitro evaluation of mutagenic, cytotoxic, genotoxic and oral irritation potential of nicotine pouch products.

Non-clinical in vitro studies were conducted to investigate the characteristics of extracts from tobacco free nicotine pouches alongside a reference snus product and/or 1R6F reference cigarette. In vitro investigations were conducted in the Neutral Red Uptake (NRU) cytotoxicity assay, Bacterial Reverse Mutation (Ames) assay, and in vitro Mammalian Cell Micronucleus (ivMN) assay. These products were also investigated for their oral irritation potential in the EpiGingival™ 3D tissue model. Results from the Ames, in vitro Micronucleus and NRU assays indicated that the tested products were non-mutagenic, non-genotoxic and non-cytotoxic in contrast to results obtained for the 1R6F reference cigarette. Results from Complete Artificial Saliva (CAS) extracts from these products also failed to be classified as irritants (as measured using the MTT assay), in the EpiGingival™ 3D tissue model.

Long range correlations and slow time scales in a boundary driven granular model.

We consider a velocity field with linear viscous interactions defined on a one dimensional lattice. Brownian baths with different parameters can be coupled to the boundary sites and to the bulk sites, determining different kinds of non-equilibrium steady states or free-cooling dynamics. Analytical results for spatial and temporal correlations are provided by analytical diagonalisation of the system's equations in the infinite size limit. We demonstrate that spatial correlations are scale-free and time-scales become exceedingly long when the system is driven only at the boundaries. On the contrary, in the case a bath is coupled to the bulk sites too, an exponential correlation decay is found with a finite characteristic length. This is also true in the free cooling regime, but in this case the correlation length grows diffusively in time. We discuss the crucial role of boundary driving for long-range correlations and slow time-scales, proposing an analogy between this simplified dynamical model and dense vibro-fluidized granular materials. Several generalizations and connections with the statistical physics of active matter are also suggested.

Optimization of an active heat engine.

Optimization of heat engines at the microscale has applications in biological and artificial nanotechnology and stimulates theoretical research in nonequilibrium statistical physics. Here we consider noninteracting overdamped particles confined by an external harmonic potential, in contact with either a thermal reservoir or a stochastic self-propulsion force (active Ornstein-Uhlenbeck model). A cyclical machine is produced by periodic variation of the parameters of the potential and of the noise. An exact mapping between the passive and the active model allows us to define the effective temperature T_{eff}(t), which is meaningful for the thermodynamic performance of the engine. We show that T_{eff}(t) is different from all other known active temperatures, typically used in static situations. The mapping allows us to optimize the active engine, regardless of the values of the persistence time or self-propulsion velocity. In particular, through linear irreversible thermodynamics (small amplitude of the cycle), we give an explicit formula for the optimal cycle period and phase delay (between the two modulated parameters, stiffness and temperature) achieving maximum power with Curzon-Ahlborn efficiency. In the quasistatic limit, the formula for T_{eff}(t) simplifies and coincides with a recently proposed temperature for stochastic thermodynamics, bearing a compact expression for the maximum efficiency. A point, which has been overlooked in recent literature, is made about the difficulty in defining efficiency without a consistent definition of effective temperature.

Production in Escherichia coli of recombinant COVID-19 spike protein fragments fused to CRM197.

During 2020, the COVID-19 pandemic affected almost 108 individuals. Quite a number of vaccines against COVID-19 were therefore developed, and a few recently received authorization for emergency use. Overall, these vaccines target specific viral proteins by antibodies whose synthesis is directly elicited or indirectly triggered by nucleic acids coding for the desired targets. Among these targets, the receptor binding domain (RBD) of COVID-19 spike protein (SP) does frequently occur in the repertoire of candidate vaccines. However, the immunogenicity of RBD per se is limited by its low molecular mass, and by a structural rearrangement of full-length SP accompanied by the detachment of RBD. Here we show that the RBD of COVID-19 SP can be conveniently produced in Escherichia coli when fused to a fragment of CRM197, a variant of diphtheria toxin currently used for a number of conjugated vaccines. In particular, we show that the CRM197-RBD chimera solubilized from inclusion bodies can be refolded and purified to a state featuring the 5 native disulphide bonds of the parental proteins, the competence in binding angiotensin-converting enzyme 2, and a satisfactory stability at room temperature. Accordingly, our observations provide compulsory information for the development of a candidate vaccine directed against COVID-19.

Narrow-escape time and sorting of active particles in circular domains.

It is now well established that microswimmers can be sorted or segregated fabricating suitable microfluidic devices or using external fields. A natural question is how these techniques can be employed for dividing swimmers of different motility. In this paper, using numerical simulations in the dilute limit, we investigate how motility parameters (time of persistence and velocity) impact the narrow-escape time of active particles from circular domains. We show that the escape time undergoes a crossover between two asymptotic regimes. The control parameters of the crossover is the ratio between the persistence length of the active motion and the typical length scale of the circular domain. We explore the possibility of taking advantage of this finding for sorting active particles by motility parameters.

Slow time scales in a dense vibrofluidized granular material.

Modeling collective motion in nonconservative systems, such as granular materials, is difficult since a general microscopic-to-macroscopic approach is not available: there is no Hamiltonian, no known stationary densities in phase space, and not a known small set of relevant variables. Phenomenological coarse-grained models are a good alternative, provided that one has identified a few slow observables and collected a sufficient amount of data for their dynamics. Here we study the case of a vibrofluidized dense granular material. The experimental study of a tracer, dispersed into the media, showed evidence of many time scales: Fast ballistic, intermediate caged, slow superdiffusive, and very slow diffusive. A numerical investigation has demonstrated that a tracer's superdiffusion is related to slow rotating drifts of the granular medium. Here we offer a deeper insight into the slow scales of the granular medium, and we propose a phenomenological model for such a "secular" dynamics. Based upon the model for the granular medium, we also introduce a model for the tracer (fast and slow) dynamics, which consists in a stochastic system of equations for three coupled variables, and is therefore more refined and successful than previous models.

Diffusion properties of self-propelled particles in cellular flows.

We study the dynamics of a self-propelled particle advected by a steady laminar flow. The persistent motion of the self-propelled particle is described by an active Ornstein-Uhlenbeck process. We focus on the diffusivity properties of the particle as a function of persistence time and free-diffusion coefficient, revealing non-monotonic behaviors, with the occurrence of a minimum and a steep growth in the regime of large persistence time. In the latter limit, we obtain an analytical prediction for the scaling of the diffusion coefficient with the parameters of the active force. Our study sheds light on the effect of a flow-field on the diffusion of active particles, such as living microorganisms and motile phytoplankton in fluids.

Derivation of a Langevin equation in a system with multiple scales: The case of negative temperatures.

We consider the problem of building a continuous stochastic model, i.e., a Langevin or Fokker-Planck equation, through a well-controlled coarse-graining procedure. Such a method usually involves the elimination of the fast degrees of freedom of the "bath" to which the particle is coupled. Specifically, we look into the general case where the bath may be at negative temperatures, as found, for instance, in models and experiments with bounded effective kinetic energy. Here, we generalize previous studies by considering the case in which the coarse graining leads to (i) a renormalization of the potential felt by the particle, and (ii) spatially dependent viscosity and diffusivity. In addition, a particular relevant example is provided, where the bath is a spin system and a sort of phase transition takes place when going from positive to negative temperatures. A Chapman-Enskog-like expansion allows us to rigorously derive the Fokker-Planck equation from the microscopic dynamics. Our theoretical predictions show excellent agreement with numerical simulations.

Characterization of high- and low-risk hepatocellular adenomas by magnetic resonance imaging in an animal model of glycogen storage disease type 1A.

Hepatocellular adenomas (HCAs) are benign tumors, of which the most serious complications are hemorrhage and malignant transformation to hepatocellular carcinoma (HCC). Among the various subtypes of HCA, the ß-catenin-activated subtype (bHCA) is associated with greatest risk of malignant transformation. Magnetic resonance imaging (MRI) is an important tool to differentiate benign and malignant hepatic lesions, and preclinical experimental approaches may help to develop a method to identify MRI features associated with bHCA. HCAs are associated with various pathologies, including glycogen storage disease 1a (GSD1a). Here, we utilized a mouse model for GSD1a that develops HCA and HCC, and analyzed the mice in order to distinguish low-risk from high-risk tumors. Animals were scanned by MRI using a hepato-specific contrast agent. The mice were sacrificed after MRI and their lesions were classified using immunohistochemistry. We observed that 45% of the animals developed focal lesions, and MRI identified four different patterns after contrast administration: isointense, hyperintense and hypointense lesions, and lesions with peripheral contrast enhancement. After contrast administration, only bHCA and HCC were hypointense in T1-weighted imaging and mildly hyperintense in T2-weighted imaging. Thus, high-risk adenomas display MRI features clearly distinguishable from those exhibited by low-risk adenomas, indicating that MRI is a reliable method for early diagnosis and classification of HCA, necessary for correct patient management.

Langevin equations from experimental data: The case of rotational diffusion in granular media.

A model has two main aims: predicting the behavior of a physical system and understanding its nature, that is how it works, at some desired level of abstraction. A promising recent approach to model building consists in deriving a Langevin-type stochastic equation from a time series of empirical data. Even if the protocol is based upon the introduction of drift and diffusion terms in stochastic differential equations, its implementation involves subtle conceptual problems and, most importantly, requires some prior theoretical knowledge about the system. Here we apply this approach to the data obtained in a rotational granular diffusion experiment, showing the power of this method and the theoretical issues behind its limits. A crucial point emerged in the dense liquid regime, where the data reveal a complex multiscale scenario with at least one fast and one slow variable. Identifying the latter is a major problem within the Langevin derivation procedure and led us to introduce innovative ideas for its solution.

Activity induced delocalization and freezing in self-propelled systems.

We study a system of interacting active particles, propelled by colored noises, characterized by an activity time τ, and confined by a single-well anharmonic potential. We assume pair-wise repulsive forces among particles, modelling the steric interactions among microswimmers. This system has been experimentally studied in the case of a dilute suspension of Janus particles confined through acoustic traps. We observe that already in the dilute regime - when inter-particle interactions are negligible - increasing the persistent time, τ, pushes the particles away from the potential minimum, until a saturation distance is reached. We compute the phase diagram (activity versus interaction length), showing that the interaction does not suppress this delocalization phenomenon but induces a liquid- or solid-like structure in the densest regions. Interestingly a reentrant behavior is observed: a first increase of τ from small values acts as an effective warming, favouring fluidization; at higher values, when the delocalization occurs, a further increase of τ induces freezing inside the densest regions. An approximate analytical scheme gives fair predictions for the density profiles in the weakly interacting case. The analysis of non-equilibrium heat fluxes reveals that in the region of largest particle concentration equilibrium is restored in several aspects.

Active escape dynamics: The effect of persistence on barrier crossing.

We study a system of non-interacting active particles, propelled by colored noises, characterized by an activity time τ, and confined by a double-well potential. A straightforward application of this system is the problem of barrier crossing of active particles, which has been studied only in the limit of small activity. When τ is sufficiently large, equilibrium-like approximations break down in the barrier crossing region. In the model under investigation, it emerges as a sort of "negative temperature" region, and numerical simulations confirm the presence of non-convex local velocity distributions. We propose, in the limit of large τ, approximate equations for the typical trajectories which successfully predict many aspects of the numerical results. The local breakdown of detailed balance and its relation with a recent definition of non-equilibrium heat exchange is also discussed.

Development and characterization of an inducible mouse model for glycogen storage disease type Ib.

BACKGROUND AND AIMS: Glycogen storage disease type Ib (GSD1b) is a rare metabolic and immune disorder caused by a deficiency in the glucose-6-phosphate transporter (G6PT) and characterized by impaired glucose homeostasis, myeloid dysfunction, and long-term risk of hepatocellular adenomas. Despite maximal therapy, based on a strict diet and on granulocyte colony-stimulating factor treatment, long-term severe complications still develop. Understanding the pathophysiology of GSD1b is a prerequisite to develop new therapeutic strategies and depends on the availability of animal models. The G6PT-KO mouse mimics the human disease but is very fragile and rarely survives weaning. We generated a conditional G6PT-deficient mouse as an alternative model for studying the long-term pathophysiology of the disease. We utilized this conditional mouse to develop an inducible G6PT-KO model to allow temporally regulated G6PT deletion by the administration of tamoxifen (TM). METHODS: We generated a conditional G6PT-deficient mouse utilizing the CRElox strategy. Histology, histochemistry, and phenotype analyses were performed at different times after TM-induced G6PT inactivation. Neutrophils and monocytes were isolated and analyzed for functional activity with standard techniques. RESULTS: The G6PT-inducible KO mice display the expected disturbances of G6P metabolism and myeloid dysfunctions of the human disorder, even though with a milder intensity. CONCLUSIONS: TM-induced inactivation of G6PT in these mice leads to a phenotype which mimics that of human GSD1b patients. The conditional mice we have generated represent an excellent tool to study the tissue-specific role of the G6PT gene and the mechanism of long-term complications in GSD1b.

Hydrodynamics of granular particles on a line.

We investigate a lattice model representing a granular gas in a thin channel. We deduce the hydrodynamic description for the model from the microscopic dynamics in the large-system limit, including the lowest finite-size corrections. The main prediction from hydrodynamics, when finite-size corrections are neglected, is the existence of a steady "uniform longitudinal flow" (ULF), with the granular temperature and the velocity gradient both uniform and directly related. Extensive numerical simulations of the system show that such a state can be observed in the bulk of a finite-size system by attaching two thermostats with the same temperature at its boundaries. The relation between the ULF state and the shocks appearing in the late stage of a cooling gas of inelastic hard rods is discussed.

Erratum: Heat, temperature and Clausius inequality in a model for active Brownian particles.

This corrects the article DOI: 10.1038/srep46496.