arXiv subjects

Veronika Bierbaum

Publications and source records attributed to Veronika Bierbaum.

4 recordsLinked to original sources

arXiv2012

Deterministic and stochastic descriptions of gene expression dynamics

A key goal of systems biology is the predictive mathematical description of gene regulatory circuits. Different approaches are used such as deterministic and stochastic models, models that describe cell growth and division explicitly or implicitly etc. Here we consider simple systems of unregulated (constitutive) gene expression and compare different mathematical descriptions systematically to obtain insight into the errors that are introduced by various common approximations such as describing cell growth and division by an effective protein degradation term. In particular, we show that the population average of protein content of a cell exhibits a subtle dependence on the dynamics of growth and division, the specific model for volume growth and the age structure of the population. Nevertheless, the error made by models with implicit cell growth and division is quite small. Furthermore, we compare various models that are partially stochastic to investigate the impact of different sources of (intrinsic) noise. This comparison indicates that different sources of noise (protein synthesis, partitioning in cell division) contribute comparable amounts of noise if protein synthesis is not or only weakly bursty. If protein synthesis is very bursty, the burstiness is the dominant noise source, independent of other details of the model. Finally, we discuss two sources of extrinsic noise: cell-to-cell variations in protein content due to cells being at different stages in the division cycles, which we show to be small (for the protein concentration and, surprisingly, also for the protein copy number per cell) and fluctuations in the growth rate, which can have a significant impact.

q-bio.MN↗

arXiv2007

Localization of coherent exciton transport in phase space

We study numerically the dynamics of excitons on discrete rings in the presence of static disorder. Based on continuous-time quantum walks we compute the time evolution of the Wigner function (WF) both for pure diagonal (site) disorder, as well as for diagonal and off-diagonal (site and transfer) disorder. In both cases, large disorder leads to localization and destroys the characteristic phase space patterns of the WF found in the absence of disorder.

quant-ph↗

arXiv2006

Coherent dynamics on hierarchical systems

We study the coherent transport modeled by continuous-time quantum walks, focussing on hierarchical structures. For these we use Husimi cacti, lattices dual to the dendrimers. We find that the transport depends strongly on the initial site of the excitation. For systems of sizes $N\le21$, we find that processes which start at central sites are nearly recurrent. Furthermore, we compare the classical limiting probability distribution to the long time average of the quantum mechanical transition probability which shows characteristic patterns. We succeed in finding a good lower bound for the (space) average of the quantum mechanical probability to be still or again at the initial site.

cond-mat.stat-mech↗

arXiv2006

Coherent exciton transport in dendrimers and continuous-time quantum walks

We model coherent exciton transport in dendrimers by continuous-time quantum walks (CTQWs). For dendrimers up to the second generation the coherent transport shows perfect recurrences, when the initial excitation starts at the central node. For larger dendrimers, the recurrence ceases to be perfect, a fact which resembles results for discrete quantum carpets. Moreover, depending on the initial excitation site we find that the coherent transport to certain nodes of the dendrimer has a very low probability. When the initial excitation starts from the central node, the problem can be mapped onto a line which simplifies the computational effort. Furthermore, the long time average of the quantum mechanical transition probabilities between pairs of nodes show characteristic patterns and allow to classify the nodes into clusters with identical limiting probabilities. For the (space) average of the quantum mechanical probability to be still or again at the initial site, we obtain, based on the Cauchy-Schwarz inequality, a simple lower bound which depends only on the eigenvalue spectrum of the Hamiltonian.

cond-mat.stat-mech↗