Cell physiology is orchestrated, on a molecular level, through complex networks of biochemical reactions. The propagation of random fluctuations through these networks can significantly impact cell behavior, raising challenging questions about how network design shapes the cell's ability to suppress or exploit these fluctuations. Here, drawing on insights from statistical physics, fluid dynamics, and systems biology, we explore how transient amplification phenomena arising from network connectivity naturally limit a biochemical system's ability to suppress small fluctuations around steady-state behaviors. We find that even a simple system consisting of two variables linked by a single interaction is capable of amplifying small fluctuations orders of magnitude beyond the levels predicted by linear stability theory. We also find that adding additional interactions can promote further amplification, even when these interactions implement classic design strategies known to suppress fluctuations. These results establish that transient amplification is an essential factor determining baseline noise levels in stable intracellular networks. Significantly, our analysis is not bound to specific systems or interaction mechanisms: we find that noise amplification is an emergent phenomenon found near steady states in any network containing sufficiently strong interactions, regardless of its form or function.

Optogenetics provides a method of neuron stimulation that has high spatial, temporal, and cell-type specificity. Here we present a model of optogenetic feedback control that targets the inhibitory population, which expresses light-sensitive channelrhodopsin-2 channels, in a mean-field model of undifferentiated cortex that is driven to seizures. The inhibitory population is illuminated with an intensity that is a function of electrode measurements obtained via the cortical model. We test the efficacy of this control method on seizurelike activity observed in two parameter spaces of the cortical model that most closely correspond to seizures observed in patients. We also compare the effect of closed-loop and open-loop control on seizurelike activity using a less-complicated ordinary differential equation model of the undifferentiated cortex in parameter space. Seizurelike activity is successfully suppressed in both parameter planes using optimal illumination intensities less likely to have adverse effects on cortical tissue.

The physical approach of a small particle (virus, medical drug) to the cell membrane represents the crucial first step before active internalization and is governed by thermal diffusion. Using a fully analytical theory we show that the stretching and bending of the elastic membrane by the approaching particle induces a memory in the system, which leads to anomalous diffusion, even though the particle is immersed in a purely Newtonian liquid. For typical cell membranes the transient subdiffusive regime extends beyond 10 ms and can enhance residence times and possibly binding rates up to 50%. Our analytical predictions are validated by numerical simulations.

We demonstrate both theoretically and experimentally propagation dynamics of surface gravity water-wave pulses, having Hermite-Gauss envelopes. We show that these waves propagate self-similarly along an 18-m wave tank, preserving their general Hermite-Gauss envelopes in both the linear and the nonlinear regimes. The measured surface elevation wave groups enable observing the envelope phase evolution of both nonchirped and linearly frequency chirped Hermite-Gauss pulses, hence allowing us to measure Gouy phase shifts of high-order Hermite-Gauss pulses for the first time. Finally, when increasing pulse amplitude, nonlinearity becomes essential and the second harmonic of Hermite-Gauss waves was observed. We further show that these generated second harmonic bound waves still exhibit self-similar Hermite-Gauss shapes along the tank.

Because of the coupling between local lipid composition and the thickness of the membrane, microphase separation in two-component lipid membranes can take place; such effects may underlie the formation of equilibrium nanoscale rafts. Using a kinetic description, this phenomenon is analytically and numerically investigated. The phase diagram is constructed through the stability analysis for linearized kinetic equations, and conditions for microphase separation are discussed. Simulations of the full kinetic model reveal the development of equilibrium membrane nanostructures with various morphologies from the initial uniform state.

A symmetry-based theory is developed for the description of (streamwise) kinetic energy $K$ in turbulent pipes at extremely high Reynolds numbers (Re's). The theory assumes a mesolayer with continual deformation of wall-attached eddies which introduce an anomalous dissipation, breaking the exact balance between production and dissipation. An outer peak of $K$ is predicted above a critical Re of ${10}^4$, in good agreement with experimental data. The theory offers an alternative explanation for the recently discovered logarithmic distribution of $K$. The concept of anomalous dissipation is further supported by a significant modification of the $k-\omega$ equation, yielding an accurate prediction of the entire $K$ profile.

We study a generic model of coupled oscillators. In the model there is competition between phase synchronization and diffusive effects. For a model with a finite number of states we derive how a phase transition occurs when the coupling parameter is varied. The phase transition is characterized by a symmetry breaking and a discontinuity in the first derivative of the order parameter. We quantitatively account for how the synchronized pulse is a low-entropy structure that facilitates the production of more entropy by the system as a whole. For a model with many states we apply a continuum approximation and derive a potential Burgers' equation for a propagating pulse. No phase transition occurs in that case. However, positive entropy production by diffusive effects still exceeds negative entropy production by the shock formation.

Using the Wilson renormalization group, we show that if no integrated vector operator of scaling dimension $-1$ exists, then scale invariance implies conformal invariance. By using the Lebowitz inequalities, we prove that this necessary condition is fulfilled in all dimensions for the Ising universality class. This shows, in particular, that scale invariance implies conformal invariance for the three-dimensional Ising model.

Scroll waves in a three-dimensional media may develop into turbulence due to negative tension of the filament. Such negative tension-induced instability of scroll waves has been observed in the Belousov-Zhabotinsky reaction systems. Here we propose a method to restabilize scroll wave turbulence caused by negative tension in three-dimensional chemical excitable media using a circularly polarized (rotating) external field. The stabilization mechanism is analyzed in terms of phase-locking caused by the external field, which makes the effective filament tension positive. The phase-locked scroll waves that have positive tension and higher frequency defy the turbulence and finally restore order. A linear theory for the change of filament tension caused by a generic rotating external field is presented and its predictions closely agree with numerical simulations.

Rippling patterns of myxobacteria appear in starving colonies before they aggregate to form fruiting bodies. These periodic traveling cell density waves arise from the coordination of individual cell reversals, resulting from an internal clock regulating them and from contact signaling during bacterial collisions. Here we revisit a mathematical model of rippling in myxobacteria due to Igoshin et al. [Proc. Natl. Acad. Sci. USA 98, 14913 (2001) and Phys. Rev. E 70, 041911 (2004)]. Bacteria in this model are phase oscillators with an extra internal phase through which they are coupled to a mean field of oppositely moving bacteria. Previously, patterns for this model were obtained only by numerical methods, and it was not possible to find their wave number analytically. We derive an evolution equation for the reversal point density that selects the pattern wave number in the weak signaling limit, shows the validity of the selection rule by solving numerically the model equations, and describes other stable patterns in the strong signaling limit. The nonlocal mean-field coupling tends to decohere and confine patterns. Under appropriate circumstances, it can annihilate the patterns leaving a constant density state via a nonequilibrium phase transition reminiscent of destruction of synchronization in the Kuramoto model.

We report on the formation of tubular membrane protrusions from giant unilamellar vesicles in alternating electric fields. The construction of the experimental chamber permitted the application of external AC fields with strength of dozens of V/mm and kHz frequency during relatively long time periods (several minutes). Besides the vesicle electrodeformation from quasispherical to prolate ellipsoidal shape, the formation of long tubular membrane protrusions with length of up to several vesicle diameters, arising from the vesicular surface in the field direction, was registered and analyzed. The threshold electric field at which the electro-induced protrusions appeared was lower than the field strengths inducing membrane electroporation.

We show systematic electrical impedance measurements of single motile cells on microelectrodes. Wild-type cells and mutant strains were studied that differ in their cell-substrate adhesion strength. We recorded the projected cell area by time-lapse microscopy and observed irregular oscillations of the cell shape. These oscillations were correlated with long-term variations in the impedance signal. Superposed to these long-term trends, we observed fluctuations in the impedance signal. Their magnitude clearly correlated with the adhesion strength, suggesting that strongly adherent cells display more dynamic cell-substrate interactions.

Particle rheology is used to extract the linear viscoelastic properties of an entangled polymer melt from molecular dynamics simulations. The motion of a stiff, approximately spherical particle is tracked in both passive and active modes. We demonstrate that the dynamic modulus of the melt can be extracted under certain limitations using this technique. As shown before for unentangled chains [Karim et al., Phys. Rev. E 86, 051501 (2012)], the frequency range of applicability is substantially expanded when both particle and medium inertia are properly accounted for by using our inertial version of the generalized Stokes-Einstein relation (IGSER). The system used here introduces an entanglement length $d_T$, in addition to those length scales already relevant: monomer bead size $d$, probe size $R$, polymer radius of gyration $R_g$, simulation box size $L$, shear wave penetration length $\mathrm{\Delta }$, and wave period $\mathrm{\Lambda }$. Previously, we demonstrated a number of restrictions necessary to obtain the relevant fluid properties: continuum approximation breaks down when $d\gtrsim \mathrm{\Lambda }$; medium inertia is important and IGSER is required when $R\gtrsim \mathrm{\Lambda }$; and the probe should not experience hydrodynamic interaction with its periodic images, $L\gtrsim \mathrm{\Delta }$. These restrictions are also observed here. A simple scaling argument for entangled polymers shows that the simulation box size must scale with polymer molecular weight as $M_w^3$. Continuum analysis requires the existence of an added mass to the probe particle from the entrained medium but was not observed in the earlier work for unentangled chains. We confirm here that this added mass is necessary only when the thickness $L_S$ of the shell around the particle that contains the added mass, $L_S>d$. We also demonstrate that the IGSER can be used to predict particle displacement over a given timescale from knowledge of medium viscoelasticity; such ability will be of interest for designing nanoparticle-based drug delivery.

We investigated the effects of varying the volume fraction of large particles $\left(r\right)$ on the linear rheology and microstructure of mixtures of polymers and bidisperse colloids, in which the ratio of the small and large particle diameters was $\alpha =0.31$ or $\alpha =0.45$. Suspensions formulated at a total volume fraction of ${\varphi }_T=0.15$ and a constant concentration of polymer in the free volume $c/c^{*}\approx 0.7$ contained solid-like gels for small $r$ and fluids or fluids of clusters at large $r$. The solid-like rheology and microstructure of these suspensions changed little with $r$ when $r$ was small, and fluidized only when $r>0.8$. By contrast, dense suspensions with ${\varphi }_T=0.40$ and $\alpha =0.31$ contained solid-like gels at all concentrations of large particles and exhibited only modest rheological and microstructural changes upon varying the volume fraction of large particles. These results suggest that the effect of particle-size dispersity on the properties of colloid-polymer mixtures are asymmetric in particle size and are most pronounced near a gelation boundary.

Enzymatic “machines,” such as catalytic rods or colloids, can self-propel and interact by generating gradients of their substrates. We theoretically investigate the behaviors of such machines in a chemically active environment where their catalytic substrates are continuously synthesized and destroyed, as occurs in living cells. We show how the kinetic properties of the medium modulate self-propulsion and pairwise interactions between machines, with the latter controlled by a tunable characteristic interaction range analogous to the Debye screening length in an electrolytic solution. Finally, we discuss the effective force arising between interacting machines and possible biological applications, such as partitioning of bacterial plasmids.

The Brownian diffusion of micron-scale inclusions in freely suspended smectic-$A$ liquid crystal films a few nanometers thick and several millimeters in diameter depends strongly on the air surrounding the film. Near atmospheric pressure, the three-dimensionally coupled film-gas system is well described by Hughes-Pailthorpe-White hydrodynamic theory but at lower pressure ($p\lesssim 70$ torr), the diffusion coefficient increases substantially, tending in high vacuum toward the two-dimensional limit where it is determined by film size. In the absence of air, the films are found to be a nearly ideal physical realization of a two-dimensional, incompressible Newtonian fluid.

We present a numerical calculation of the total number of disordered jammed configurations $\mathrm{\Omega }$ of $N$ repulsive, three-dimensional spheres in a fixed volume $V$. To make these calculations tractable, we increase the computational efficiency of the approach of Xu et al. [Phys. Rev. Lett. 106, 245502 (2011)] and Asenjo et al. [Phys. Rev. Lett. 112, 098002 (2014)] and we extend the method to allow computation of the configurational entropy as a function of pressure. The approach that we use computes the configurational entropy by sampling the absolute volume of basins of attraction of the stable packings in the potential energy landscape. We find a surprisingly strong correlation between the pressure of a configuration and the volume of its basin of attraction in the potential energy landscape. This relation is well described by a power law. Our methodology to compute the number of minima in the potential energy landscape should be applicable to a wide range of other enumeration problems in statistical physics, string theory, cosmology, and machine learning that aim to find the distribution of the extrema of a scalar cost function that depends on many degrees of freedom.

We study head-on impacts of equal-speed but unequal-width incompressible jets in two dimensions with a focus on dense granular jets. We use discrete particle simulations to show that head-on impact of granular jets produces a quasi-steady-state where a fraction of the excess incident momentum from the larger jet is captured by an impact center that drifts steadily over time. By varying the dissipation in our discrete particle simulations and through additional analogous continuum jet impacts of different rheologies, we show that this central drift speed is remarkably dependent primarily on the total dissipation rate to the power $1.5$, and largely independent of the dissipation mechanism. We finish by presenting a simple control volume analysis that qualitatively captures the emergence of the drift speed but not the scaling.

Mechanical impulse propagation in granular media depends strongly on the imposed confinement conditions. In this work, the propagation of sound in a granular packing contained by flexible walls that enable confinement under hydrostatic pressure conditions is investigated. This configuration also allows the form of the input impulse to be controlled by means of an instrumented impact pendulum. The main characteristics of mechanical wave propagation are analyzed, and it is found that the wave speed as function of the wave amplitude of the propagating pulse obeys the predictions of the Hertz contact law. Upon increasing the confinement pressure, a continuous transition from nonlinear to linear propagation is observed. Our results show that in the low-confinement regime, the attenuation increases with an increasing impulse amplitude for nonlinear pulses, whereas it is a weak function of the confinement pressure for linear waves.

Linear and nonlinear mechanisms for conical wave propagation in two-dimensional lattices are explored in the realm of phononic crystals. As a prototypical example, a statically compressed granular lattice of spherical particles arranged in a hexagonal packing configuration is analyzed. Upon identifying the dispersion relation of the underlying linear problem, the resulting diffraction properties are considered. Analysis both via a heuristic argument for the linear propagation of a wave packet and via asymptotic analysis leading to the derivation of a Dirac system suggests the occurrence of conical diffraction. This analysis is valid for strong precompression, i.e., near the linear regime. For weak precompression, conical wave propagation is still possible, but the resulting expanding circular wave front is of a nonoscillatory nature, resulting from the complex interplay among the discreteness, nonlinearity, and geometry of the packing. The transition between these two types of propagation is explored.