Condensation is the phenomenon whereby one of a sum of random variables contributes a finite fraction to the sum. It is manifested as an aggregation phenomenon in diverse physical systems such as coalescence in granular media, jamming in traffic, and gelation in networks. We show here that the same condensation scenario, which normally happens only if the underlying probability distribution has tails heavier than exponential, can occur for light-tailed distributions in the presence of additional constraints. We demonstrate this phenomenon on the sample variance, whose probability distribution conditioned on the particular value of the sample mean undergoes a phase transition. The transition is manifested by a change in behavior of the large deviation rate function.

In small volumes, the kinetics of filamentous protein self-assembly is expected to show significant variability, arising from intrinsic molecular noise. This is not accounted for in existing deterministic models. We introduce a simple stochastic model including nucleation and autocatalytic growth via elongation and fragmentation, which allows us to predict the effects of molecular noise on the kinetics of autocatalytic self-assembly. We derive an analytic expression for the lag-time distribution, which agrees well with experimental results for the fibrillation of bovine insulin. Our expression decomposes the lag-time variability into contributions from primary nucleation and autocatalytic growth and reveals how each of these scales with the key kinetic parameters. Our analysis shows that significant lag-time variability can arise from both primary nucleation and from autocatalytic growth and should provide a way to extract mechanistic information on early-stage aggregation from small-volume experiments.

One of the greatest challenges in biophysical models of translation is to identify coding sequence features that affect the rate of translation and therefore the overall protein production in the cell. We propose an analytic method to solve a translation model based on the inhomogeneous totally asymmetric simple exclusion process, which allows us to unveil simple design principles of nucleotide sequences determining protein production rates. Our solution shows an excellent agreement when compared to numerical genome-wide simulations of S. cerevisiae transcript sequences and predicts that the first 10 codons, which is the ribosome footprint length on the mRNA, together with the value of the initiation rate, are the main determinants of protein production rate under physiological conditions. Finally, we interpret the obtained analytic results based on the evolutionary role of the codons' choice for regulating translation rates and ribosome densities.

Abstract. Real space condensation is known to occur in stochastic models of mass transport in the regime in which the globally conserved mass density is greater than a critical value. It has been shown within models with factorised stationary states that the condensation can be understood in terms of sums of independent and identically distributed random variables: these exhibit condensation when they are conditioned to a large deviation of their sum. It is well understood that the condensation, whereby one of the random variables contributes a finite fraction to the sum, occurs only if the underlying probability distribution (modulo exponential) is heavy-tailed, i.e. decaying slower than exponential. Here we study a similar phenomenon in which condensation is exhibited for non-heavy-tailed distributions, provided random variables are additionally conditioned on a large deviation of certain linear statistics. We provide a detailed theoretical analysis explaining the phenomenon, which is supported by Monte Carlo simulations (for the case where the additional constraint is the sample variance) and demonstrated in several physical systems. Our results suggest that the condensation is a generic phenomenon that pertains to both typical and rare events.

We study stochastic processes in which the trajectories are constrained so that the process realises a large deviation of the unconstrained process. In particular we consider stochastic bridges and the question of inequivalence of path ensembles between the microcanonical ensemble, in which the end points of the trajectory are constrained, and the canonical or s ensemble in which a bias or tilt is introduced into the process. We show how ensemble inequivalence can be manifested by the phenomenon of temporal condensation in which the large deviation is realised in a vanishing fraction of the duration (for long durations). For diffusion processes we find that condensation happens whenever the process is subject to a confining potential, such as for the Ornstein-Uhlenbeck process, but not in the borderline case of dry friction in which there is partial ensemble equivalence. We also discuss continuous-space, discrete-time random walks for which in the case of a heavy tailed step-size distribution it is known that the large deviation may be achieved in a single step of the walk. Finally we consider possible effects of several constraints on the process and in particular give an alternative explanation of the interaction-driven condensation in terms of constrained Brownian excursions.

We develop a power series method for the nonequilibrium steady state of the inhomogeneous one-dimensional totally asymmetric simple exclusion process (TASEP) in contact with two particle reservoirs and with site-dependent hopping rates in the bulk. The power series is performed in the entrance or exit rates governing particle exchange with the reservoirs, and the corresponding particle current is computed analytically up to the cubic term in the entry or exit rate, respectively. We also show how to compute higher-order terms using combinatorial objects known as Young tableaux. Our results address the long outstanding problem of finding the exact nonequilibrium steady state of the inhomogeneous TASEP. The findings are particularly relevant to the modeling of mRNA translation in which the rate of translation initiation, corresponding to the entrance rate in the TASEP, is typically small.

We consider a discrete-time continuous-space random walk under the constraints that the number of returns to the origin (local time) and the total area under the walk are fixed. We first compute the joint probability of an excursion having area a and returning to the origin for the first time after time τ . We then show how condensation occurs when the total area constraint is increased: an excursion containing a finite fraction of the area emerges. Finally we show how the phenomena generalises previously studied cases of condensation induced by several constraints and how it is related to interaction-driven condensation which allows us to explain the phenomenon in the framework of large deviation theory.

Generalization of the one-dimensional totally asymmetric exclusion process (TASEP) with open boundary conditions in which particles are allowed to jump l sites ahead with the probability pl approximately 1l/sigma+1 is studied by Monte Carlo simulations and the domain-wall approach. For sigma>1 the standard TASEP phase diagram is recovered, but the density profiles display additional features when 1