Showing papers by "David A. Kessler published in 2016"

Mechanical bounds to transcriptional noise.

Abstract: Over the past several decades it has been increasingly recognized that stochastic processes play a central role in transcription. Although many stochastic effects have been explained, the source of transcriptional bursting (one of the most well-known sources of stochasticity) has continued to evade understanding. Recent results have pointed to mechanical feedback as the source of transcriptional bursting, but a reconciliation of this perspective with preexisting views of transcriptional regulation is lacking. In this article, we present a simple phenomenological model that is able to incorporate the traditional view of gene expression within a framework with mechanical limits to transcription. By introducing a simple competition between mechanical arrest and relaxation copy number probability distributions collapse onto a shared universal curve under shifting and rescaling and a lower limit of intrinsic noise for any mean expression level is found.

Heavy-tailed phase-space distributions beyond Boltzmann-Gibbs: Confined laser-cooled atoms in a nonthermal state.

Abstract: The Boltzmann-Gibbs density, a central result of equilibrium statistical mechanics, relates the energy of a system in contact with a thermal bath to its equilibrium statistics. This relation is lost for nonthermal systems such as cold atoms in optical lattices, where the heat bath is replaced with the laser beams of the lattice. We investigate in detail the stationary phase-space probability for Sisyphus cooling under harmonic confinement. In particular, we elucidate whether the total energy of the system still describes its stationary state statistics. We find that this is true for the center part of the phase-space density for deep lattices, where the Boltzmann-Gibbs density provides an approximate description. The relation between energy and statistics also persists for strong confinement and in the limit of high energies, where the system becomes underdamped. However, the phase-space density now exhibits heavy power-law tails. In all three cases we find expressions for the leading-order phase-space density and corrections which break the equivalence of probability and energy and violate energy equipartition. The nonequilibrium nature of the steady state is corroborated by explicit violations of detailed balance. We complement these analytical results with numerical simulations to map out the intricate structure of the phase-space density.

Communities as cliques.

Abstract: High-diversity species assemblages are very common in nature, and yet the factors allowing for the maintenance of biodiversity remain obscure. The competitive exclusion principle and May’s complexity-diversity puzzle both suggest that a community can support only a small number of species, turning the spotlight on the dynamics of local patches or islands, where stable and uninvadable (SU) subsets of species play a crucial role. Here we map the question of the number of different possible SUs a community can support to the geometric problem of finding maximal cliques of the corresponding graph. This enables us to solve for the number of SUs as a function of the species richness in the regional pool, N, showing that the growth of this number is subexponential in N, contrary to long-standing wisdom. To understand the dynamics under noise we examine the relaxation time to an SU. Symmetric systems relax rapidly, whereas in asymmetric systems the relaxation time grows much faster with N, suggesting an excitable dynamics under noise.

Quantum Renewal Equation for the first detection time of a quantum walk

Abstract: We investigate the statistics of the first detected passage time of a quantum walk. The postulates of quantum theory, in particular the collapse of the wave function upon measurement, reveal an intimate connection between the wave function of a process free of measurements, i.e. the solution of the Schrodinger equation, and the statistics of first detection events on a site. For stroboscopic measurements a quantum renewal equation yields basic properties of quantum walks. For example, for a tight binding model on a ring we discover critical sampling times, diverging quantities such as the mean time for first detection, and an optimal detection rate. For a quantum walk on an infinite line the probability of first detection decays like $(\mbox{time})^{-3}$ with a superimposed oscillation, critical behavior for a specific choice of sampling time, and vanishing amplitude when the sampling time approaches zero due to the quantum Zeno effect.

Nonlinear self-adapting wave patterns

Abstract: We propose a new type of traveling wave pattern, one that can adapt to the size of physical system in which it is embedded. Such a system arises when the initial state has an instability for a range of wavevectors, k, that extends down to k = 0, connecting at that point to two symmetry modes of the underlying dynamical system. The Min system of proteins in E. coli is such a system with the symmetry emerging from the global conservation of two proteins, MinD and MinE. For this and related systems, traveling waves can adiabatically deform as the system is increased in size without the increase in node number that would be expected for an oscillatory version of a Turing instability containing an allowed wavenumber band with a finite minimum.

Nonlinear self-adapting wave patterns

Abstract: We propose a new type of traveling wave pattern, one that can adapt to the size of physical system in which it is embedded. Such a system arises when the initial state has an instability that extends down to zero wavevector, connecting at that point to two symmetry modes of the underlying dynamical system. The Min system of proteins in E. coli is such as system with the symmetry emerging from the global conservation of two proteins, MinD and MinE. For this and related systems, traveling waves can adiabatically deform as the system is increased in size without the increase in node number that would be expected for an oscillatory version of a Turing instability containing an allowed wavenumber band with a finite minimum.

The effect of environmental stochasticity on species richness in neutral communities

Abstract: Environmental stochasticity is known to be a destabilizing factor, increasing abundance fluctuations and extinction rates of populations. However, the stability of a community may benefit from the differential response of species to environmental variations due to the storage effect. This paper provides a systematic and comprehensive discussion of these two contradicting tendencies, using the metacommunity version of the recently proposed time-average neutral model of biodiversity which incorporates environmental stochasticity and demographic noise and allows for extinction and speciation. We show that the incorporation of demographic noise into the model is essential to its applicability, yielding realistic behavior of the system when fitness variations are relatively weak. The dependence of species richness on the strength of environmental stochasticity changes sign when the correlation time of the environmental variations increases. This transition marks the point at which the storage effect no longer succeeds in stabilizing the community.

Size distribution of ring polymers

Abstract: We present an exact solution for the distribution of sample averaged monomer to monomer distance of ring polymers. For non-interacting and local-interaction models these distributions correspond to the distribution of the area under the reflected Bessel bridge and the Bessel excursion respectively, and are shown to be identical in dimension d ≥ 2, albeit with pronounced finite size effects at the critical dimension, d = 2. A symmetry of the problem reveals that dimension d and 4 - d are equivalent, thus the celebrated Airy distribution describing the areal distribution of the d = 1 Brownian excursion describes also a polymer in three dimensions. For a self-avoiding polymer in dimension d we find numerically that the fluctuations of the scaled averaged distance are nearly identical in dimension d = 2, 3 and are well described to a first approximation by the non-interacting excursion model in dimension 5.

Communities as cliques

Abstract: High-diversity assemblages are very common in nature, and yet the factors allowing for the maintenance of biodiversity remain obscure. The competitive exclusion principle and May's complexity-diversity puzzle both suggest that a community can support only a small number of species, turning the spotlight at the dynamics of local patches or islands, where stable and uninvadable (SU) subsets of species play a crucial role. Here we map the community SUs question to the geometric problem of finding maximal cliques of the corresponding graph. We solve for the number of SUs as a function of the species richness in the regional pool, $N$, showing that this growth is subexponential, contrary to long-standing wisdom. We show that symmetric systems relax rapidly to an SU, where the system stays until a regime shift takes place. In asymmetric systems the relaxation time grows much faster with $N$, suggesting an excitable dynamics under noise.

Theory of pinned fronts.

Abstract: The properties of a front between two different phases in the presence of a smoothly inhomogeneous external field that takes its critical value at the crossing point is analyzed. Two generic scenarios are studied. In the first, the system admits a bistable solution and the external field governs the rate in which one phase invades the other. The second mechanism corresponds to a continuous transition that, in the case of reactive systems, takes the form of a transcritical bifurcation at the crossing point. We solve for the front shape and for the response of competitive fronts to external noise, showing that static properties and also some of the dynamical features cannot discriminate between the two scenarios. A reliable indicator turns out to be the fluctuation statistics. These take a Gaussian form in the bifurcation case and a double-peaked shape in a bistable system. Our results are discussed in the context of biological processes, such as species and communities dynamics in the presence of a resource gradient.

Darwinian Selection Induces Lamarckian Adaptation in a Holobiont Model

Abstract: Current models of animal evolution focus on selection of individuals, ignoring the much faster selection of symbiotic bacteria. Here we take host-symbiont interactions into account by introducing a Population Genetics-like model of holobionts exposed to toxic stress. The stress can be alleviated by selection of resistant individuals (host and bacteria) and by secretion of a detoxification agent (″detox″). By defining a new measure, termed the ′Lamarckian′, we show that selection of resistant bacteria over one generation of hosts leads to stress-dependent increase in the tolerance of the hosts′ offspring. This benefit is mediated by co-alleviation of toxic and physiologic stress. Prolonged exposure leads to further adaptation by ′group selection′ of bacterial communities with higher detox per bacterium. These findings show that Lamarckian adaptation can arise via interactions between two levels of Darwinian selection within a holobiont system. The conclusions and modelling framework are applicable to diverse types of holobiont systems.

Darwinian Selection Induces Lamarckian Adaptation in a Holobiont Model

Abstract: Current models of animal evolution focus on selection of individuals, ignoring the much faster selection of symbiotic bacteria. Here we take host-symbiont interactions into account by introducing a Population Genetics-like model of holobionts exposed to toxic stress. The stress can be alleviated by selection of resistant individuals (host and bacteria) and by secretion of a detoxification agent ("detox"). By defining a new measure, termed the Lamarckian, we show that selection of resistant bacteria over one generation of hosts leads to stress-dependent increase in the tolerance of the host's offspring. This benefit is mediated by co-alleviation of toxic and physiologic stress. Prolonged exposure leads to further adaptation by 'group selection' of bacterial communities with higher detox per bacterium. These findings show that Lamarckian adaptation can arise via interactions between two levels of Darwinian selection within a holobiont system. The conclusions and modelling framework are applicable to diverse types of holobiont systems.

Stability of two-species communities: drift, environmental stochasticity, storage effect and selection

Abstract: The dynamics of two competing species in a finite size community is one of the most studied problems in population genetics and community ecology. Stochastic fluctuations lead, inevitably, to the extinction of one of the species, but the relevant timescale depends on the underlying dynamics. The persistence time of the community has been calculated for neutral models, where the only drive of the system is drift (demographic stochasticity) and for models with strong selection. Following recent analyses that stress the importance of environmental stochasticity in empirical systems, we present here a general theory of persistence time of two-species community where drift, environmental variations and time independent selective advantage are all taken into account.