Related papers: Predictive Modeling of Non-Viral Gene Transfer
Heterogeneous diffusion processes occur in many different fields such as transport in living cells or diffusion in porous media. A characterization of the transport parameters of such processes can be achieved by ensemble-based methods,…
Bistable biochemical switches are ubiquitous in gene regulatory networks and signal transduction pathways. Their switching dynamics, however, are difficult to study directly in experiments or conventional computer simulations, because…
Gene expression datasets offer insights into gene regulation mechanisms, biochemical pathways, and cellular functions. Additionally, comparing gene expression profiles between disease and control patients can deepen the understanding of…
Translational diffusion coefficients are routinely estimated from molecular dynamics simulations. Linear fits to mean squared displacement (MSD) curves have become the de facto standard, from simple liquids to complex biomacromolecules.…
We consider the propagation of a single particle in a random chain, assisted by the coupling to dispersive bosons. Time evolution treated with rate equations for hopping between localized states reveals a qualitative difference between…
We used various analytical and numerical techniques to elucidate signal propagation in a small enzymatic cascade which is subjected to external and internal noise. The nonlinear character of catalytic reactions, which underlie protein…
Signal transduction networks can form highly interconnected systems within cells due to network crosstalk, the sharing of input signals between multiple downstream responses. To better understand the evolutionary design principles…
This paper discusses temporally continuous and discrete forms of the speed-limited particle-in-cell (SLPIC) method first treated by Werner et al. [Phys. Plasmas 25, 123512 (2018)]. The dispersion relation for a 1D1V electrostatic plasma…
We provide evidence that for some values of the parameters a simple agent based model, describing herding behavior, yields signals with 1/f power spectral density. We derive a non-linear stochastic differential equation for the ratio of…
We model the quantum electron transfer (ET) in the photosynthetic reaction center (RC), using a non-Hermitian Hamiltonian approach. Our model includes (i) two protein cofactors, donor and acceptor, with discrete energy levels and (ii) a…
A transfer matrix method is developed for optical calculations of non-interacting graphene layers. Within the framework of this method, optical properties such as reflection, transmission and absorption for single-, double- and multi-layer…
Bayesian models based on Gaussian processes (GPs) offer a flexible framework to predict spatially distributed variables with uncertainty. But the use of nonstationary priors, often necessary for capturing complex spatial patterns, makes…
Mobile genetic elements like conjugative plasmids play a crucial role in shaping the genetic content and population dynamics of bacterial species. Bacterial populations often contain not one, but multiple co-circulating MGEs, which modify…
We calculate the quantum state of the plasmon field excited by an ensemble of molecular emitters, which are driven by exchange of electrons with metallic nano-particle electrodes. Assuming identical emitters that are coupled collectively to…
A random graph model with prescribed degree distribution and degree dependent edge weights is introduced. Each vertex is independently equipped with a random number of half-edges and each half-edge is assigned an integer valued weight…
When it is polarised, a cell develops an asymmetric distribution of specific molecular markers, cytoskeleton and cell membrane shape. Polarisation can occur spontaneously or be triggered by external signals, like gradients of signalling…
In this letter, we characterize the distribution of the number of users associated with the typical base station (BS), termed the typical cell load, in a cellular network where the BSs are distributed as a homogeneous Poisson point process…
Generative modeling of non-negative, discrete data, such as symbolic music, remains challenging due to two persistent limitations in existing methods. Firstly, many approaches rely on modeling continuous embeddings, which is suboptimal for…
Several recent experiments, including our own in the fission yeast, S. pombe, have characterized the motions of gene loci within living nuclei by measuring the locus position over time, then proceeding to obtain the statistical properties…
In the simplest view of transcriptional regulation, the expression of a gene is turned on or off by changes in the concentration of a transcription factor (TF). We use recent data on noise levels in gene expression to show that it should be…