Search

We present a two-species population model in a well-mixed environment where the dynamics involves, in addition to birth and death, changes due to environmental factors and inter-species interactions. The novel dynamical components are motivated by two common mechanisms for developing antibiotic resistance in bacteria: plasmid {\it transformation}, where external genetic material in the form of a plasmid is transferred inside a host cell; and {\it conjugation} by which one cell transfers genetic material to another by direct cell-to-cell contact. Through analytical and numerical methods, we identify the effects of transformation and conjugation individually. With transformation only, the two-species system will evolve towards one species' extinction, or a stable co-existence in the long-time limit. With conjugation only, we discover interesting oscillations for the system. Further, we quantify the combined effects of transformation and conjugation, and chart the regimes of stable co-existence, a result with ecological implications., Comment: 11 pages, 10 figures, J. Phys. Commun (2020)

We investigate the quasiparticle dynamics in the prototype heavy fermion CeCoIn$_5$ using ultrafast optical pump-probe spectroscopy. Our results indicate that this material system undergoes hybridization fluctuations before full establishment of the heavy electron coherence, as the temperature decreases from $\sim$120 K ($T^\dagger$) to $\sim$55 K ($T^*$ ). We reveal that the observed anomalous phonon softening and damping reduction below $T^*$ are directly associated with opening of an indirect hybridization gap. We also discover a distinct collective mode with an energy of $\sim$8 meV, which may be the experimental evidence of the predicted unconventional density wave. Our observations provide critical informations for understanding the hybridization dynamics in heavy fermion materials.

Spatial patterning can be crucially important for understanding the behavior of interacting populations. Here we investigate a simple model of parasite and host populations in which parasites are random walkers that must come into contact with a host in order to reproduce. We focus on the spatial arrangement of parasites around a single host, and we derive using analytics and numerical simulations the necessary conditions placed on the parasite fecundity and lifetime for the populations long-term survival. We also show that the parasite population can be pushed to extinction by a large drift velocity, but, counterintuitively, a small drift velocity generally increases the parasite population., Comment: 6 pages, 6 figures

When particle flux is regulated by multiple factors such as particle supply and varying transport rate, it is important to identify the respective dominant regimes. We extend the well-studied totally asymmetric simple exclusion model to investigate the interplay between a controlled entrance and a local defect site. The model mimics cellular transport phenomena where there is typically a finite particle pool and non-uniform moving rates due to biochemical kinetics. Our simulations reveal regions where, despite an increasing particle supply, the current remains constant while particles redistribute in the system. Exploiting a domain wall approach with mean-field approximation, we provide a theoretical ground for our findings. The results in steady state current and density profiles provide quantitative insights into the regulation of the transcription and translation process in bacterial protein synthesis. We investigate the totally asymmetric simple exclusion model with controlled entrance and a defect site in the bulk to mimic the finite particle pool and non-uniform moving rates in particle transport processes., Comment: 9 pages, 12 figures; v2: minor format changes; v3: major revision, additional references; v4: minor format change to figures, additional references

The phenomenon of protein synthesis has been modeled in terms of totally asymmetric simple exclusion processes (TASEP) since 1968. In this article, we provide a tutorial of the biological and mathematical aspects of this approach. We also summarize several new results, concerned with limited resources in the cell and simple estimates for the current (protein production rate) of a TASEP with inhomogeneous hopping rates, reflecting the characteristics of real genes., Comment: 25 pages, 7 figures

The totally asymmetric simple exclusion process (TASEP) with a localized defect is revisited in this article with attention paid to the power spectra of the particle occupancy N(t). Intrigued by the oscillatory behaviors in the power spectra of an ordinary TASEP in high/low density phase(HD/LD) observed by Adams et al. (2007 Phys. Rev. Lett. 99 020601), we introduce a single slow site with hopping rate q<1 to the system. As the power spectrum contains time-correlation information of the particle occupancy of the system, we are particularly interested in how the defect affects fluctuation in particle number of the left and right subsystems as well as that of the entire system. Exploiting Monte Carlo simulations, we observe the disappearance of oscillations when the defect is located at the center of the system. When the defect is off center, oscillations are restored. To explore the origin of such phenomenon, we use a linearized Langevin equation to calculate the power spectrum for the sublattices and the whole lattice. We provide insights into the interactions between the sublattices coupled through the defect site for both simulation and analytical results., Comment: 16 pages, 6 figures; v2: Minor revisions

We study a totally asymmetric simple exclusion process (TASEP) with one defect site, hopping rate $q<1$, near the system boundary. Regarding our system as a pair of uniform TASEP's coupled through the defect, we study various methods to match a \emph{finite} TASEP and an \emph{infinite} one across a common boundary. Several approximation schemes are investigated. Utilizing the finite segment mean-field (FSMF) method, we set up a framework for computing the steady state current $J$ as a function of the entry rate $% \alpha $ and $q$. For the case where the defect is located at the entry site, we obtain an analytical expression for $J(\alpha, q) $ which is in good agreement with Monte Carlo simulation results. When the defect is located deeper in the bulk, we refined the scheme of MacDonald, et.al. [Biopolymers, \textbf{6}, 1 (1968)] and find reasonably good fits to the density profiles before the defect site. We discuss the strengths and limitations of each method, as well as possible avenues for further studies., Comment: 16 pages, 4 figures

We study the effects of local inhomogeneities, i.e., slow sites of hopping rate $q<1$, in a totally asymmetric simple exclusion process (TASEP) for particles of size $\ell \geq 1$ (in units of the lattice spacing). We compare the simulation results of $\ell =1$ and $\ell >1$ and notice that the existence of local defects has qualitatively similar effects on the steady state. We focus on the stationary current as well as the density profiles. If there is only a single slow site in the system, we observe a significant dependence of the current on the \emph{location} of the slow site for both $\ell =1$ and $\ell >1$ cases. When two slow sites are introduced, more intriguing phenomena emerge, e.g., dramatic decreases in the current when the two are close together. In addition, we study the asymptotic behavior when $q\to 0$. We also explore the associated density profiles and compare our findings to an earlier study using a simple mean-field theory. We then outline the biological significance of these effects., Comment: 14 pages; 14 figures

This submission is a duplicate of arXiv:q-bio/0602024 and has been removed., Comment: 8 pages, 8 figures; This submission is a duplicate of arXiv:q-bio/0602024, and has been removed