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Competition during range expansions is of great interest from both practical and theoretical view points. Experimentally, range expansions are often studied in homogeneous Petri dishes, which lack spatial anisotropy that might be present in realistic populations. Here, we analyze a model of anisotropic growth, based on coupled Kardar-Parisi-Zhang and Fisher-Kolmogorov-Petrovsky-Piskunov equations that describe surface growth and lateral competition. Compared to a previous study of isotropic growth, anisotropy relaxes a constraint between parameters of the model. We completely characterize spatial patterns and invasion velocities in this generalized model. In particular, we find that strong anisotropy results in a distinct morphology of spatial invasion with a kink in the displaced strain ahead of the boundary between the strains. This morphology of the out-competed strain is similar to a shock wave and serves as a signature of anisotropic growth., Comment: 11 pages, 7 figures

A persistent public health challenge is finding immunization schemes that are effective in combating highly mutable pathogens such as HIV and influenza viruses. To address this, we analyze a simplified model of affinity maturation, the Darwinian evolutionary process B cells undergo during immunization. The vaccination protocol dictates selection forces that steer affinity maturation to generate antibodies. We focus on determining the optimal selection forces exerted by a generic time-dependent vaccination protocol to maximize production of broadly neutralizing antibodies (bnAbs) that can protect against a broad spectrum of pathogen strains. The model lends itself to a path integral representation and operator approximations within a mean-field limit, providing guiding principles for optimizing time-dependent vaccine-induced selection forces to enhance bnAb generation. We compare our analytical mean-field results with the outcomes of stochastic simulations and discuss their similarities and differences.

We consider inhomogeneous polymers driven by energy-consuming active processes which encode temporal patterns of athermal kicks. We find that such temporal excitation programs, propagated by tension along the polymer, can effectively couple distinct polymer loci. Consequently, distant loci exhibit correlated motions that fold the polymer into specific conformations, as set by the local actions of the active processes and their distribution along the polymer. Interestingly, active kicks that are canceled out by a time-delayed echo can induce strong compaction of the active polymer.

We introduce a novel, multi-scale model for affinity maturation, which aims to capture the intra-clonal, inter-clonal and epitope-specific organization of the B cell population in a germinal center. We describe the evolution of the B cell population via a quasispecies dynamics, with species corresponding to unique B cell receptors (BCRs), where the desired multi-scale structure is reflected on the mutational connectivity of the accessible BCR space, and on the statistical properties of its fitness landscape. Within this mathematical framework, we study the competition among classes of BCRs targeting different antigen epitopes, and construct an effective \emph{immunogenic space} where epitope immunodominance relations can be universally characterized. We finally study how varying the relative composition of a mixture of antigens with variable and conserved domains allows for a parametric exploration of this space, and identify general principles for the rational design of two-antigen cocktails., Comment: 10 pages + 3 pages (appendix), 6 figures

Active systems are driven out of equilibrium by exchanging energy and momentum with their environment. This endows them with anomalous mechanical properties that we review in this colloquium for the case of dry scalar active matter, which has attracted considerable attention. These unusual properties lead to a rich physics when active fluids are in contact with boundaries, inclusions, tracers, or disordered potentials. Indeed, studies of the mechanical pressure of active fluids and of the dynamics of passive tracers have shown that active systems impact their environment in non-trivial ways, for example, by propelling and rotating anisotropic inclusions. Conversely, the long-ranged density and current modulations induced by localized obstacles show how the environment can have a far-reaching impact on active fluids. This is best exemplified by the propensity of bulk and boundary disorder to destroy bulk phase separation in active matter, showing active systems to be much more sensitive to their surroundings than passive ones. This colloquium aims at providing a unifying perspective on the rich interplay between active systems and their environments., Comment: Review article, feedback is welcome

We develop a theory for heat transport via electromagnetic waves inside media, and use it to derive a spatially nonlocal thermal conductivity tensor, in terms of the electromagnetic Green's function and potential, for any given system. While typically negligible for optically dense bulk media, the electromagnetic component of conductivity can be significant for optically dilute media, and shows regimes of Fourier transport as well as unhindered transport. Moreover, the electromagnetic contribution is relevant even for dense media, when in presence of interfaces, as exemplified for the in-plane conductivity of a nanosheet, which shows a variety of phenomena, including absence of a Fourier regime., Comment: 5 pages, 3 figures, accepted by Phys. Rev. Lett

Kinetic traps are a notorious problem in equilibrium statistical mechanics, where temperature quenches ultimately fail to bring the system to low energy configurations. Using multifarious self-assembly as a model system, we introduce a mechanism to escape kinetic traps by utilizing non-reciprocal interactions between components. Introducing non-equilibrium effects offered by broken action-reaction symmetry in the system, we can push the trajectory of the system out of arrested dynamics. The dynamics of the model is studied using tools from the physics of interfaces and defects. Our proposal can find applications in self-assembly, glassy systems and systems with arrested dynamics., Comment: Updated to published version

In growing populations, the fate of mutations depends on their competitive ability against the ancestor and their ability to colonize new territory. Here we present a theory that integrates both aspects of mutant fitness by coupling the classic description of one-dimensional competition (Fisher equation) to the minimal model of front shape (KPZ equation). We solved these equations and found three regimes, which are controlled solely by the expansion rates, solely by the competitive abilities, or by both. Collectively, our results provide a simple framework to study spatial competition., Comment: 5 pages, 4 figures

As a population grows, spreading to new environments may favor specialization. In this paper, we introduce and explore a model for specialization at the front of a colony expanding synchronously into new territory. We show through numerical simulations that, by gaining fitness through accumulating mutations, progeny of the initial seed population can differentiate into distinct specialists. With competition and selection limited to the growth front, the emerging specialists first segregate into sectors, which then expand to dominate the entire population. We quantify the scaling of the fixation time with the size of the population and observe different behaviors corresponding to distinct universality classes: unbounded and bounded gains in fitness lead to superdiffusive ($z=3/2$) and diffusive ($z=2$) stochastic wanderings of the sector boundaries, respectively., Comment: 6+3 pages, 3+3 figures

We study how walls confining active fluids interact with asymmetric passive objects placed in their bulk. We show that the objects experience non-conservative long-ranged forces mediated by the active bath. To leading order, these forces can be computed using a generalized image theorem. The walls repel asymmetric objects, irrespective of their microscopic properties or their orientations. For circular cavities, we demonstrate how this may lead to the localization of asymmetric objects in the center of the cavity, something impossible for symmetric ones.

We discuss and analyze the properties of Casimir forces acting between nonreciprocal objects in thermal equilibrium. By starting from the fluctuation-dissipation theorem and splitting the force into those arising from individual sources, we show that if all temperatures are equal, the resulting force is reciprocal and is derivable as the gradient of a Casimir (free) energy. While the expression for the free energy is identical to the one for reciprocal objects, there are several distinct features: To leading order in reflections, the free energy can be decomposed as the sum of two terms, the first corresponding to two reciprocal objects, and the second corresponding to two anti-reciprocal objects. The first term is negative and typically yields attraction, while the second can have either sign. For the case of two objects that are each other's mirror images, the second term is positive and yields repulsion. The sum of terms can lead to overall repulsive forces, in agreement with previous observations. Stable configurations, ruled out for reciprocal cases, appear possible for nonreciprocal objects. We show that for three objects, a three-body free energy exists, indicating that previously found persistent heat currents in situations of three objects cannot be used to produce persistent torques.

The Casimir force provides a striking example of the effects of quantum fluctuations in a mesoscopic system. Because it arises from the objects' electromagnetic response, the necessary calculations in quantum field theory are most naturally expressed in terms of electromagnetic scattering from each object. In this review we illustrate a variety of such techniques, with a focus on those that can be expressed in terms of surface effects, including both idealized boundary conditions and their physical realization in terms of material properties., Comment: 29 pages, 2 figures; invited contribution to Annual Reviews in Nuclear and Particle Science; v2: minor editing of version for publication

We show that disordered boundaries destroy bulk phase separation in scalar active systems in dimension $d

First proposed as an empirical rule over half a century ago, the Richards growth equation has been frequently invoked in population modeling and pandemic forecasting. Central to this model is the advent of a fractional exponent $\gamma$, typically fitted to the data. While various motivations for this non-analytical form have been proposed, it is still considered foremost an empirical fitting procedure. Here, we find that Richards-like growth laws emerge naturally from generic analytical growth rules in a distributed population, upon inclusion of {\bf (i)} migration (spatial diffusion) amongst different locales, and {\bf (ii)} stochasticity in the growth rate, also known as "seascape noise." The latter leads to a wide (power-law) distribution in local population number that, while smoothened through the former, can still result in a fractional growth law for the overall population. This justification of the Richards growth law thus provides a testable connection to the distribution of constituents of the population., Comment: 12 pages, 7 figures

Arguments based on symmetry and thermodynamics may suggest the existence of a ratchet-like lateral Casimir force between two plates at different temperatures and with broken inversion symmetry. We find that this is not sufficient, and at least one plate must be made of nonreciprocal material. This setup operates as a heat engine by transforming heat radiation into mechanical force. Although the ratio of the lateral force to heat transfer in the near field regime diverges inversely with the plates separation, $d$, an Onsager symmetry, which we extend to nonreciprocal plates, limits the engine efficiency to the Carnot value $\eta_c$. The optimal velocity of operation in the far field is of the order of $c\eta_c$, where $c$ is the speed of light. In the near field regime, this velocity can be reduced to the order of $\bar\omega d \eta_c$, where $\bar\omega$ is a typical material frequency., Comment: V2 and V3 Minor corrections

We study the impact of a random quenched potentials and torques on scalar active matter. Microscopic simulations reveal that motility-induced phase separation is replaced in two-dimensions by an asymptotically homogeneous phase with anomalous long-ranged correlations and non-vanishing steady-state currents. Using a combination of phenomenological models and a field-theoretical treatment, we show the existence of a lower-critical dimension, $d_c=4$, below which phase separation is only observed for systems smaller than an Imry-Ma length-scale. We identify a weak-disorder regime in which the structure factor scales as $S(q) \sim 1/q^2$ which accounts for our numerics. In $d=2$ we predict that, at larger scales, the behaviour should cross over to a strong-disorder regime. In $d>2$, these two regimes exist separately, depending on the strength of the potential., Comment: 14 pages, 8 figures

Models of population growth and extinction are an increasingly popular subject of study. However, consequences of stochasticity and noise in shaping distributions and outcomes are not sufficiently explored. Here we consider a distributed population with logistic growth at each location, subject to "seascape" noise, wherein the population's fitness randomly varies with {\it location and time}. Despite its simplicity, the model actually incorporates variants of directed percolation, and directed polymers in random media, within a mean-field perspective. Probability distributions of the population can be computed self-consistently; and the extinction transition is shown to exhibit novel critical behavior with exponents dependent on the ratio of the strengths of migration and noise amplitudes. The results are compared and contrasted with the more conventional choice of demographic noise due to stochastic changes in reproduction.

We study Eigen's model of quasi-species, characterized by sequences that replicate with a specified fitness and mutate independently at single sites. The evolution of the population vector in time is then closely related to that of quantum spins in imaginary time. We employ multiple perspectives and tools from interacting quantum systems to examine growth and collapse of realistic viral populations, specifically certain HIV proteins. All approaches used, including the simplest perturbation theory, give consistent results.

Perturbations of fluid media can give rise to non-equilibrium dynamics, which may in turn cause motion of immersed inclusions. We consider perturbations ("activations") that are local in space and time, of a fluid density which is conserved, and study the resulting diffusiophoretic phenomena that emerge at a large distance. Specifically, we consider cases where the perturbations propagate diffusively, providing examples from passive and active matter for which this is expected to be the case. Activations can, for instance, be realized by sudden and local changes in interaction potentials of the medium, or by local changes of its activity. Various analytical results are provided for the case of confinement by two parallel walls. We investigate the possibility of extracting work from inclusions which are moving through the activated fluid. Further, we show that a time-dependent density profile, created via suitable activation protocols, allows for conveyance of inclusions along controlled and stable trajectories. In contrast, in states with a steady density, inclusions cannot be held at stable positions, reminiscent of Earnshaw's theorem of electrostatics. We expect these findings to be applicable in a range of experimental systems., Comment: 14 pages (12+2), 14 Figures

The effects of quenched disorder on a single and many active run-and-tumble particles is studied in one dimension. For a single particle, we consider both the steady-state distribution and the particle's dynamics subject to disorder in three parameters: a bounded external potential, the particle's speed, and its tumbling rate. We show that in the case of a disordered potential, the behavior is like an equilibrium particle diffusing on a random force landscape, implying a dynamics that is logarithmically slow in time. In the situations of disorder in the speed or tumbling rate, we find that the particle generically exhibits diffusive motion, although particular choices of the disorder may lead to anomalous diffusion. Based on the single-particle results, we find that in a system with many interacting particles, disorder in the potential leads to strong clustering. We characterize the clustering in two different regimes depending on the system size and show that the mean cluster size scales with the system size, in contrast to non-disordered systems.

How does removal of sites by a random walk lead to blockage of percolation? To study this problem of correlated site percolation, we consider a random walk (RW) of $N=uL^d$ steps on a $d$-dimensional hypercubic lattice of size $L^d$ (with periodic boundaries). We systematically explore dependence of the probability $\Pi_d(L,u)$ of percolation (existence of a spanning cluster) of sites not removed by the RW on $L$ and $u$. The concentration of unvisited sites decays exponentially with increasing $u$, while the visited sites are highly correlated -- their correlations decaying with the distance $r$ as $1/r^{d-2}$ (in $d>2$). Upon increasing $L$, the percolation probability $\Pi_d(L,u)$ approaches a step function, jumping from 1 to 0 when $u$ crosses a percolation threshold $u_c$ that is close to 3 for all $3\le d\le6$. Within numerical accuracy, the correlation length associated with percolation diverges with exponents consistent with $\nu=2/(d-2)$. There is no percolation threshold at the lower critical dimension of $d=2$, with the percolation probability approaching a smooth function $\Pi_2(\infty,u)>0$., Comment: RevTex, 12 pages, 13 figures

Diffusion-driven patterns appear on curved surfaces in many settings, initiated by unstable modes of an underlying Laplacian operator. On a flat surface or perfect sphere, the patterns are degenerate, reflecting translational/rotational symmetry. Deformations, e.g. by a bulge or indentation, break symmetry and can pin a pattern. We adapt methods of conformal mapping and perturbation theory to examine how curvature inhomogeneities select and pin patterns, and confirm the results numerically. The theory provides an analogy to quantum mechanics in a geometry-dependent potential and yields intuitive implications for cell membranes, tissues, thin films, and noise-induced quasipatterns., Comment: substantial re-write of arXiv:1710.00103

Directed Percolation (DP) is a classic model for nonequilibrium phase transitions into a single absorbing state (fixation). It has been extensively studied by analytical and numerical techniques in diverse contexts. Recently, DP has appeared as a generic model for the evolutionary/ecological dynamics of competing bacterial populations. Range expansion -- the stochastic reproduction of bacteria competing for space to be occupied by their progeny -- leads to a fluctuating and rough growth front, which is known from experiment and simulation to affect the underlying critical behavior of the DP transition. In this work, we employ symmetry arguments to construct a pair of non-linear stochastic partial differential equations describing the co-evolution of surface roughness with the composition field of DP. Macroscopic manifestations (phenomenology) of these equations on growth patterns and genealogical tracks of range expansion are discussed; followed by a renormalization group analysis of possible scaling behaviors at the DP transition., Comment: 13+9 pages, 5+5 figures, 1 table

Ensembles of biological and artificial microswimmers produce long-range velocity fields with strong nonequilibrium fluctuations, which result in dramatic increase diffusivity of embedded particles (tracers). While such enhanced diffusivity may point to enhanced mixing of the fluid, a rigorous quantification of the mixing efficiency requires analysis of pair dispersion of tracers, rather than simple one-particle diffusivity. Here, we calculate analytically the scale-dependent coefficient of relative diffusivity of passive tracers embedded in a dilute suspension of run-and-tumble microswimmers. Although each tracer is subject to strong fluctuations resulting in large absolute diffusivity, the small-scale relative dispersion is suppressed due to the correlations in fluid velocity which are relevant when the inter-tracers separation is below the persistence length of the swimmers motion. Our results suggest that the reorientation of swimming direction plays an important role in biological mixing and should be accounted in design of potential active matter devices capable of effective fluid mixing at microscale., Comment: 9 pages, 3 figures

When a biological population expands into new territory, genetic drift develops an enormous influence on evolution at the propagating front. In such range expansion processes, fluctuations in allele frequencies occur through stochastic \textit{spatial} wandering of both genetic lineages and the boundaries between genetically segregated sectors. Laboratory experiments on microbial range expansions have shown that this stochastic wandering, transverse to the front, is superdiffusive due to the front's growing roughness, implying much faster loss of genetic diversity than predicted by simple flat front diffusive models. We study the evolutionary consequences of this superdiffusive wandering using two complementary numerical models of range expansions: the stepping stone model, and a new interpretation of the model of directed paths in random media, in the context of a roughening population front. Through these approaches we compute statistics for the times since common ancestry for pairs of individuals with a given spatial separation at the front, and we explore how environmental heterogeneities can locally suppress these superdiffusive fluctuations.

We consider localization of a random walk (RW) when attracted or repelled by multiple extended manifolds of different dimensionalities. In particular, we focus on $(d-1)$- and $(d-2)$-dimensional manifolds in $d$-dimensional space, where attractive interactions are (fully or marginally) relevant. The RW can then be in one of four phases where it is localized to neither, one, or both manifolds. The four phases merge at a special multi-critical point where (away from the manifolds) the RW spreads diffusively. Extensive numerical analyses on two dimensional RWs confined inside or outside a rectangular wedge confirm general features expected from a continuum theory, but also exhibit unexpected attributes, such as a reentrant localization to the corner while repelled by it.

T cell receptors (TCRs) bind foreign or self-peptides attached to major histocompatibility complex (MHC) molecules, and the strength of this interaction determines T cell activation. Optimizing the ability of T cells to recognize a diversity of foreign peptides yet be tolerant of self-peptides is crucial for the adaptive immune system to properly function. This is achieved by selection of T cells in the thymus, where immature T cells expressing unique, stochastically generated TCRs interact with a large number of self-peptide-MHC; if a TCR does not bind strongly enough to any self-peptide-MHC, or too strongly with at least one self-peptide-MHC, the T cell dies. Past theoretical work cast thymic selection as an extreme value problem, and characterized the statistical enrichment or depletion of amino acids in the post-selection TCR repertoire, showing how T cells are selected to be able to specifically recognize peptides derived from diverse pathogens, yet have limited self-reactivity. Here, we investigate how the degree of enrichment is modified by nonuniform contacts that a TCR makes with peptide-MHC. Specifically, we were motivated by recent experiments showing that amino acids at certain positions of a TCR sequence have large effects on thymic selection outcomes, and crystal structure data that reveal a nonuniform contact profile between a TCR and its peptide-MHC ligand. Using a representative TCR contact profile as an illustration, we show via simulations that the degree of enrichment now varies by position according to the contact profile, and, importantly, it depends on the implementation of nonuniform contacts during thymic selection. We explain these nontrivial results analytically. Our study has implications for understanding the selection forces that shape the functionality of the post-selection TCR repertoire., Comment: 10 pages, 4 figures, submitted to Phys. Rev. E

Non-equilibrium systems are known to exhibit long-ranged correlations due to conservation of quantities like density or momentum. This, in turn, leads to long-ranged fluctuation-induced (Casimir) forces, predicted to arise in a variety of non-equilibrium settings. Here, we study such forces, which arise transiently between parallel plates or compact inclusions in a gas of particles, following a change ("quench") in temperature or activity of the medium. Analytical calculations, as well as numerical simulations of passive or active Brownian particles, indicate two distinct forces: (i) The immediate effect of the quench is adsorption or desorption of particles of the medium to the immersed objects, which in turn initiates a front of relaxing (mean) density. This leads to time-dependent {\it density-induced forces}. (ii) A long-term effect of the quench is that density fluctuations are modified, manifested as transient (long-ranged) (pair-)correlations that relax diffusively to their (short-ranged) steady-state limit. As a result, transient {\it fluctuation-induced forces} emerge. We discuss the properties of fluctuation-induced and density-induced forces as regards universality, relaxation as a function of time, and scaling with distance between objects. Their distinct signatures allow us to distinguish the two types of forces in simulation data. Finally, we propose several scenarios for their experimental observation., Comment: - Added Journal reference and DOI - Modified title - Fixed minor typos - Added plot of Eq. (32) [16 pages, 11 figures]

A polymer repelled by unfavorable interactions with a uniform flat surface may still be pinned to attractive edges and corners. This is demonstrated by considering adsorption of a two-dimensional ideal polymer to an attractive corner of a repulsive wedge. The well-known mapping between the statistical mechanics of an ideal polymer and the quantum problem of a particle in a potential is then used to analyze the singular behavior of the unbinding transition of the polymer. The divergence of the localization length is found to be governed by an exponent that varies continuously with the angle (when reflex). Numerical treatment of the discrete (lattice) version of such an adsorption problem confirms this behavior.

Turing patterns emerge from a spatially uniform state following a linear instability driven by diffusion. Features of the eventual pattern (stabilized by non-linearities) are already present in the initial unstable modes. On a uniform flat surface or perfect sphere, the unstable modes and final patterns are degenerate, reflecting translational/rotational symmetry. This symmetry can be broken, e.g. by a bump on a flat substrate or by deforming a sphere. As the diffusion operator on a two dimensional manifold depends on the underlying curvature, the degeneracy of the initial unstable mode is similarly reduced. Different shapes can pin different modes. We adapt methods of conformal mapping and perturbation theory to analytically examine how bumps and ripples entrain modes of the diffusion operator on cylinders and spheres. We confirm these results numerically, and provide closed form expressions that describe how non-uniformities in curvature pin diffusion-driven instabilities and the resulting patterns., Comment: arXiv:1901.09900 is a substantial re-write such that replacement isn't correct

We consider forces acting on objects immersed in, or attached to, long fluctuating polymers. The confinement of the polymer by the obstacles results in polymer-mediated forces that can be repulsive (due to loss of entropy) or attractive (if some or all surfaces are covered by adsorbing layers). The strength and sign of the force in general depends on the detailed shape and adsorption properties of the obstacles, but assumes simple universal forms if characteristic length scales associated with the objects are large. This occurs for scale-free shapes (such as a flat plate, straight wire, or cone), when the polymer is repelled by the obstacles, or is marginally attracted to it (close to the depinning transition where the absorption length is infinite). In such cases, the separation $h$ between obstacles is the only relevant macroscopic length scale, and the polymer mediated force equals ${\cal A} \, k_{B}T/h$, where $T$ is temperature. The amplitude ${\cal A}$ is akin to a critical exponent, depending only on geometry and universality of the polymer system. The value of ${\cal A}$, which we compute for simple geometries and ideal polymers, can be positive or negative. Remarkably, we find ${\cal A}=0$ for ideal polymers at the adsorption transition point, irrespective of shapes of the obstacles, i.e. at this special point there is no polymer-mediated force between obstacles (scale-free or not)., Comment: RevTeX, 10 pages, 10 figures

We compute fluctuation-induced (Casimir) forces for classical systems after a temperature quench. Using a generic coarse-grained model for fluctuations of a conserved density, we find that transient forces arise even if the initial and final states are force-free. In setups reminiscent of Casimir (planar walls) and van der Waals (small inclusions) interactions, we find comparable exact universal expressions for the force. Dynamical details only scale the time axis of transient force curves. We propose that such quenches can be achieved, for instance, in experiments on active matter, employing tunable activity or interaction protocols., Comment: 5 pages, 2 figures, added equation references/comments

We study the shift of rotational levels of a diatomic polar molecule due to its van der Waals (vdW) interaction with a gently curved dielectric surface at temperature $T$, and submicron separations. The molecule is assumed to be in its electronic and vibrational ground state, and the rotational degrees are described by a rigid rotor model. We show that under these conditions retardation effects and surface dispersion can be neglected. The level shifts are found to be independent of $T$, and given by the quantum state averaged classical electrostatic interaction of the dipole with its image on the surface. We use a derivative expansion for the static Green's function to express the shifts in terms of surface curvature. We argue that the curvature induced line splitting is experimentally observable, and not obscured by natural line widths and thermal broadening., Comment: 8 pages, 2 figures, version accepted for publication in Phys. Rev. A

The probability distribution for the free energy of directed polymers in random media (DPRM) with uncorrelated noise in $d=1+1$ dimensions satisfies the Tracy-Widom distribution. We inquire if and how this universal distribution is modified in the presence of spatially correlated noise. The width of the distribution scales as the DPRM length to an exponent $\beta$, in good (but not full) agreement with previous renormalization group and numerical results. The scaled probability is well described by the Tracy-Widom form for uncorrelated noise, but becomes symmetric with increasing correlation exponent. We thus find a class of distributions that continuously interpolates between Tracy-Widom and Gaussian forms.

We study, from first principles, the pressure exerted by an active fluid of spherical particles on general boundaries in two dimensions. We show that, despite the non-uniform pressure along curved walls, an equation of state is recovered upon a proper spatial averaging. This holds even in the presence of pairwise interactions between particles or when asymmetric walls induce ratchet currents, which are accompanied by spontaneous shear stresses on the walls. For flexible obstacles, the pressure inhomogeneities lead to a modulational instability as well as to the spontaneous motion of short semi-flexible filaments. Finally, we relate the force exerted on objects immersed in active baths to the particle flux they generate around them., Comment: 6 pages, 5 figures and 8 pages of supplementary information

Human immunodeficiency virus (HIV) evolves with extraordinary rapidity. However, its evolution is constrained by interactions between mutations in its fitness landscape. Here we show that an Ising model describing these interactions, inferred from sequence data obtained prior to the use of antiretroviral drugs, can be used to identify clinically significant sites of resistance mutations. Successful predictions of the resistance sites indicate progress in the development of successful models of real viral evolution at the single residue level, and suggest that our approach may be applied to help design new therapies that are less prone to failure even where resistance data is not yet available., Comment: 5 pages, 3 figures

Fluctuation and dissipation are by-products of coupling to the `environment.' The Caldeira-Leggett model, a successful paradigm of quantum Brownian motion, views the environment as a collection of harmonic oscillators linearly coupled to the system. However, symmetry considerations may forbid a linear coupling, e.g. for a neutral particle in quantum electrodynamics. We argue that nonlinear couplings can lead to a fundamentally different behavior. Specifically, we consider a heavy particle quadratically coupled to quantum fluctuations of the bath. In one dimension the particle undergoes anomalous diffusion, unfolding as a power-law distribution in space, reminiscent of L\'evy flights. We suggest condensed matter analogs where similar effects may arise., Comment: Introduction expanded. Appendices added

The Casimir--Polder interaction between an anisotropic particle and a surface is orientation dependent. We study novel orientational effects that arise due to curvature of the surface for distances much smaller than the radii of curvature by employing a derivative expansion. For nanoparticles we derive a general short distance expansion of the interaction potential in terms of their dipolar polarizabilities. Explicit results are presented for nano-spheroids made of SiO$_2$ and gold, both at zero and at finite temperatures. The preferred orientation of the particle is strongly dependent on curvature, temperature, as well as material properties., Comment: 9 pages, 10 encapsulated figures

The rapid collapse of a polymer, due to external forces or changes in solvent, yields a long-lived `crumpled globule.' The conjectured fractal structure shaped by hierarchical collapse dynamics has proved difficult to establish, even with large simulations. To unravel this puzzle, we study a coarse-grained model of in-falling spherical blobs that coalesce upon contact. Distances between pairs of monomers are assigned upon their initial coalescence, and do not `equilibrate' subsequently. Surprisingly, the model reproduces quantitatively the dependence of distance on segment length, suggesting that the slow approach to scaling is related to the wide distribution of blob sizes.

Thermal fluctuations in non-equilibrium steady states generically lead to power law decay of correlations for conserved quantities. Embedded bodies which constrain fluctuations in turn experience fluctuation induced forces. We compute these forces for the simple case of parallel slabs in a driven diffusive system. The force falls off with slab separation $d$ as $k_B T/d$ (at temperature $T$, and in all spatial dimensions), but can be attractive or repulsive. Unlike the equilibrium Casimir force, the force amplitude is non-universal and explicitly depends on dynamics. The techniques introduced can be generalized to study pressure and fluctuation induced forces in a broad class of non-equilibrium systems., Comment: 5 pages, 2 figures

We use a derivative expansion for gently curved surfaces to compute the leading and the next-to-leading curvature corrections to the Casimir-Polder interaction between a polarizable small particle and a non-planar surface. While our methods apply to any homogeneous and isotropic surface, explicit results are presented here for perfect conductors. We show that the derivative expansion of the Casimir-Polder potential follows from a resummation of its perturbative series, for small in-plane momenta. We consider the retarded, non-retarded and classical high temperature limits., Comment: 6 pages, 1 Figure

We study the implications of quantum fluctuations of a dispersive medium, under steady rotation, either in or out of thermal equilibrium with its environment. A rotating object exhibits a quantum instability by dissipating its mechanical motion via spontaneous emission of photons, as well as internal heat generation. Universal relations are derived for the radiated energy and angular momentum as trace formulas involving the object's scattering matrix. We also compute the quantum noise by deriving the full statistics of the radiated photons out of thermal and/or dynamic equilibrium. The (entanglement) entropy generation is quantified, and the total entropy is shown to be always increasing. Furthermore, we derive a Fokker-Planck equation governing the stochastic angular motion resulting from the fluctuating back-reaction frictional torque. As a result, we find a quantum limit on the uncertainty of the object's angular velocity in steady rotation. Finally, we show in some detail that a rotating object drags nearby objects, making them spin parallel to its axis of rotation. A scalar toy model is introduced in the first part to simplify the technicalities and ease the conceptual complexities; a detailed discussion of quantum electrodynamics is presented in the second part.

Near field radiative heat transfer and dynamic Casimir forces are just two instances of topics of technological and fundamental interest studied via the formalism of fluctuational electrodynamics. From the perspective of experiment and simulations, it is hard to precisely control and probe such non-equilibrium situations. Fluctuations in equilibrium are easier to measure, and can typically be related to non-equilibrium response functions by Green-Kubo relations. We consider a collection of arbitrary objects in vacuum, perturbed by changing the temperature or velocity of one object. Developing a method for computation of higher order correlation functions in fluctuational electrodynamics, we explicitly compare linear response and equilibrium fluctuations. We obtain a Green-Kubo relation for the radiative heat transfer, as well as a closed formula for the vacuum friction in arbitrary geometries in the framework of scattering theory. We comment on the signature of the radiative heat conductivity in equilibrium fluctuations., Comment: Main article: 5 pages, 2 figures; Supplemental Material: 2 pages

Mutational escape from vaccine induced immune responses has thwarted the development of a successful vaccine against AIDS, whose causative agent is HIV, a highly mutable virus. Knowing the virus' fitness as a function of its proteomic sequence can enable rational design of potent vaccines, as this information can focus vaccine induced immune responses to target mutational vulnerabilities of the virus. Spin models have been proposed as a means to infer intrinsic fitness landscapes of HIV proteins from patient-derived viral protein sequences. These sequences are the product of non-equilibrium viral evolution driven by patient-specific immune responses, and are subject to phylogenetic constraints. How can such sequence data allow inference of intrinsic fitness landscapes? We combined computer simulations and variational theory \'{a} la Feynman to show that, in most circumstances, spin models inferred from patient-derived viral sequences reflect the correct rank order of the fitness of mutant viral strains. Our findings are relevant for diverse viruses., Comment: 10 pages, 4 figures and supplementary methods file

We present a number of arguments to demonstrate that a quantum analog of Cherenkov effect occurs when two dispersive objects are in relative motion. Specifically we show that two semi-infinite plates experience friction beyond a threshold velocity which, in their center-of-mass frame, is the phase speed of light within their medium. The loss in mechanical energy is radiated away through the plates before getting fully absorbed in the form of heat. By deriving various correlation functions inside and outside the two plates, we explicitly compute the radiation, and discuss its dependence on the reference frame., Comment: Typos and Fig. 2 corrected. Manuscript improved. References added

We show that roughness or surface modulations change the distance dependence of (power-law) interactions between curved objects at proximity. The modified scaling law is then simply related to the order of the first non-vanishing coefficient of the Taylor expansion of the distribution of separations between the surfaces. The latter can in principle be estimated by scanning measurements, or computed for well characterized modulations, and then used to predict short-distance scaling behavior in disparate experiments. For example, we predict that the radiative heat transfer between a rough sphere and a plate approaches a constant with decreasing separation. Similar saturation is expected for the Casimir force between dielectric or metallic surfaces with appropriate modulations over distinct length scales., Comment: 5 pages, 2 figures