The asymmetric exclusion process: Comparison of update procedures

The asymmetric exclusion process (ASEP) has attracted a lot of interest not only because its many applications, e.g. in the context of the kinetics of biopolymerization and traffic flow theory, but also because it is a paradigmatic model for nonequilibrium systems. Here we study the ASEP for different types of updates, namely random-sequential, sequential, sublattice-parallel and parallel. In order to compare the effects of the different update procedures on the properties of the stationary state, we use large-scale Monte Carlo simulations and analytical methods, especially the so-called matrix-product Ansatz (MPA). We present in detail the exact solution for the model with sublattice-parallel and sequential updates using the MPA. For the case of parallel update, which is important for applications like traffic flow theory, we determine the phase diagram, the current, and density profiles based on Monte Carlo simulations. We furthermore suggest a MPA for that case and derive the corresponding matrix algebra.Comment: 47 pages (11 PostScript figures included), LATEX, Two misprints in equations correcte

The asymmetric exclusion model with sequential update

We present a solution for the stationary state of an asymmetric exclusion model with sequential update and open boundary conditions. We solve the model exactly for random hopping in both directions by applying a matrix-product formalism which was recently used to solve the model with sublattice-parallel update[1]. It is shown that the matrix-algebra describing the sequential update and sublattice-parallel update are identical and can be mapped onto the random sequential case treated by Derrida et al[2].Comment: 7 pages, Late

Exact density profiles for fully asymmetric exclusion process with discrete-time dynamics

Exact density profiles in the steady state of the one-dimensional fully asymmetric simple exclusion process on semi-infinite chains are obtained in the case of forward-ordered sequential dynamics by taking the thermodynamic limit in our recent exact results for a finite chain with open boundaries. The corresponding results for sublattice parallel dynamics follow from the relationship obtained by Rajewsky and Schreckenberg [Physica A 245, 139 (1997)] and for parallel dynamics from the mapping found by Evans, Rajewsky and Speer [J. Stat. Phys. 95, 45 (1999)]. By comparing the asymptotic results appropriate for parallel update with those published in the latter paper, we correct some technical errors in the final results given there.Comment: About 10 pages and 3 figures, new references are added and a comparison is made with the results by de Gier and Nienhuis [Phys. Rev. E 59, 4899(1999)

Stochastic boundary conditions in the deterministic Nagel-Schreckenberg traffic model

We consider open systems where cars move according to the deterministic Nagel-Schreckenberg rules and with maximum velocity ${v}_{max} > 1$, what is an extension of the Asymmetric Exclusion Process (ASEP). It turns out that the behaviour of the system is dominated by two features: a) the competition between the left and the right boundary b) the development of so-called "buffers" due to the hindrance an injected car feels from the front car at the beginning of the system. As a consequence, there is a first-order phase transition between the free flow and the congested phase accompanied by the collapse of the buffers and the phase diagram essentially differs from that of ${v}_{max} = 1$ (ASEP).Comment: 29 pages, 26 figure

Application of the Density Matrix Renormalization Group Method to a Non-Equilibrium Problem

We apply the density matrix renormalization group (DMRG) method to a non-equilibrium problem: the asymmetric exclusion process in one dimension. We study the stationary state of the process to calculate the particle density profile (one-point function). We show that, even with a small number of retained bases, the DMRG calculation is in excellent agreement with the exact solution obtained by the matrix-product-ansatz approach.Comment: 8 pages, LaTeX (using jpsj.sty), 4 non-embedded figures, submitted to J. Phys. Soc. Jp

Exact solution of an exclusion process with three classes of particles and vacancies

We present an exact solution for an asymmetric exclusion process on a ring with three classes of particles and vacancies. Using a matrix product Ansatz, we find explicit expressions for the weights of the configurations in the stationary state. The solution involves tensor products of quadratic algebras.Comment: 18 pages, no figures, LaTe

Single-cell transcriptomics characterizes cell types in the subventricular zone and uncovers molecular defects impairing adult neurogenesis

Neural stem cells (NSCs) contribute to plasticity and repair of the adult brain. Niches harboring NSCs regulate stem cell self-renewal and differentiation. We used comprehensive and untargeted single-cell RNA profiling to generate a molecular cell atlas of the largest germinal region of the adult mouse brain, the subventricular zone (SVZ). We characterized >20 neural and non-neural cell types and gained insights into the dynamics of neurogenesis by predicting future cell states based on computational analysis of RNA kinetics. Furthermore, we applied our single-cell approach to document decreased numbers of NSCs, reduced proliferation activity of progenitors, and perturbations in Wnt and BMP signaling pathways in mice lacking LRP2, an endocytic receptor required for SVZ maintenance. Our data provide a valuable resource to study adult neurogenesis and a proof of principle for the power of single-cell RNA sequencing to elucidate neural cell-type-specific alterations in loss-of-function models

LifeTime and improving European healthcare through cell-based interceptive medicine

Here we describe the LifeTime Initiative, which aims to track, understand and target human cells during the onset and progression of complex diseases, and to analyse their response to therapy at single-cell resolution. This mission will be implemented through the development, integration and application of single-cell multi-omics and imaging, artificial intelligence and patient-derived experimental disease models during the progression from health to disease. The analysis of large molecular and clinical datasets will identify molecular mechanisms, create predictive computational models of disease progression, and reveal new drug targets and therapies. The timely detection and interception of disease embedded in an ethical and patient-centred vision will be achieved through interactions across academia, hospitals, patient associations, health data management systems and industry. The application of this strategy to key medical challenges in cancer, neurological and neuropsychiatric disorders, and infectious, chronic inflammatory and cardiovascular diseases at the single-cell level will usher in cell-based interceptive medicine in Europe over the next decade

RCAS: an RNA centric annotation system for transcriptome-wide regions of interest

In the field of RNA, the technologies for studying the transcriptome have created a tremendous potential for deciphering the puzzles of the RNA biology. Along with the excitement, the unprecedented volume of RNA related omics data is creating great challenges in bioinformatics analyses. Here, we present the RNA Centric Annotation System (RCAS), an R package, which is designed to ease the process of creating gene-centric annotations and analysis for the genomic regions of interest obtained from various RNA-based omics technologies. The design of RCAS is modular, which enables flexible usage and convenient integration with other bioinformatics workflows. RCAS is an R/Bioconductor package but we also created graphical user interfaces including a Galaxy wrapper and a stand-alone web service. The application of RCAS on published datasets shows that RCAS is not only able to reproduce published findings but also helps generate novel knowledge and hypotheses. The meta-gene profiles, gene-centric annotation, motif analysis and gene-set analysis provided by RCAS provide contextual knowledge which is necessary for understanding the functional aspects of different biological events that involve RNAs. In addition, the array of different interfaces and deployment options adds the convenience of use for different levels of users. RCAS is available at http://bioconductor.org/packages/release/bioc/html/RCAS.html and http://rcas.mdc-berlin.de

TET enzymes control antibody production and shape the mutational landscape in germinal centre B cells

Upon activation by antigen, B cells form germinal centers where they clonally expand and introduce affinity-enhancing mutations into their B cell receptor genes. Somatic mutagenesis and class switch recombination in germinal center B cells are initiated by the activation-induced cytidine deaminase (AID). Upon germinal center exit, B cells differentiate into antibody-secreting plasma cells. Germinal center maintenance and terminal fate choice require transcriptional reprogramming that associates with a substantial reconfiguration of DNA methylation patterns. Here we examine the role of TET proteins, enzymes that facilitate DNA demethylation and promote a permissive chromatin state by oxidizing 5-methylcytosine, in antibody-mediated immunity. Using a conditional gene ablation strategy, we show that TET2 and TET3 guide the transition of germinal center B cells to antibody-secreting plasma cells. Optimal AID expression requires TET function, and TET2 and TET3 double-deficient germinal center B cells show defects in class switch recombination. However, TET2/TET3 double-deficiency does not prevent the generation and selection of high-affinity germinal center B cells. Rather, combined TET2 and TET3 loss-of-function in germinal center B cells favors C-to-T and G-to-A transition mutagenesis, a finding that may be of significance for understanding the etiology of B cell lymphomas evolving in conditions of reduced TET function