Related papers: Simulation based estimation of branching models fo…
Transposable elements, or transposons, are DNA sequences that can jump from site to site in the genome during the life cycle of a cell, usually encoding the very enzymes which perform their excision. However, some transposons are parasitic,…
In this paper we consider a model based on branching process theory for the proliferation and the dissemination network of T cells in the adaptive immune response. A multi-type Galton Watson branching process is assumed as the basic…
We employ the diffusing transcription factors model for numerical simulation of chromatin topology conformations and transcriptional processes of human chromatin. Simulations of a short chromatin filament reveal different possible pathways…
An open source software package for simulating thermal neutron propagation in geometry is presented. In this system, neutron propagation can be treated by either the particle transport method or the ray-tracing method. Supported by an…
Radio propagation modeling and prediction is fundamental for modern cellular network planning and optimization. Conventional radio propagation models fall into two categories. Empirical models, based on coarse statistics, are simple and…
It is possible to discuss the propagation of an electronic current through certain layered nanostructures modeling them as a collection of random one-dimensional interfaces, through which a coherent signal can be transmitted or reflected…
This paper presents an algorithm for the efficient simulation of ductile crack propagation through heterogeneous structures, as e.g. metallic microstructures, which are given as voxel data. These kinds of simulations are required for e.g.,…
Electroporation is a very useful tool for drug delivery into various diseased tissues of the human body. This technique helps to improve the clinical treatment by transferring drugs into the targeted cells rapidly. In electroporation, drug…
Motivation: We introduce TRONCO (TRanslational ONCOlogy), an open-source R package that implements the state-of-the-art algorithms for the inference of cancer progression models from (epi)genomic mutational profiles. TRONCO can be used to…
The development of effective explainability tools for Transformers is a crucial pursuit in deep learning research. One of the most promising approaches in this domain is Layer-wise Relevance Propagation (LRP), which propagates relevance…
Drug delivery through electroporation could be highly beneficial for the treatment of different types of diseased tissues within the human body. In this work, a mathematical model of reversible tissue electroporation is presented for…
Diffusion models have shown strong competitiveness in offline reinforcement learning tasks by formulating decision-making as sequential generation. However, the practicality of these methods is limited due to the lengthy inference processes…
The evolution of molecular and phenotypic traits is commonly modelled using Markov processes along a phylogeny. This phylogeny can be a tree, or a network if it includes reticulations, representing events such as hybridization or admixture.…
Stem cells, through their ability to produce daughter stem cells and differentiate into specialized cells, are essential in the growth, maintenance, and repair of biological tissues. Understanding the dynamics of cell populations in the…
Stochastic processes can model many emerging phenomena on networks, like the spread of computer viruses, rumors, or infectious diseases. Understanding the dynamics of such stochastic spreading processes is therefore of fundamental interest.…
Continuous-time birth-death-shift (BDS) processes are frequently used in stochastic modeling, with many applications in ecology and epidemiology. In particular, such processes can model evolutionary dynamics of transposable elements -…
We study propagating mode-I fracture in two dimensional amorphous materials using atomistic simulations. We used the continuous random network (CRN) model of an amorphous material, creating samples using a two dimensional analogue of the…
Cosmic ray (CR) transport is usually modeled with a single diffusion coefficient, but this description captures only the growth of the variance and not the full transport process. Distinct transport mechanisms can share the same effective…
An empirical numerical model that includes nuclear absorption, multiple Coulomb scattering, and energy loss is presented in this work to calculate the transmission of the thick objects in high energy proton radiography, and in this…
Whole genome sequencing of pathogens from multiple hosts in an epidemic offers the potential to investigate who infected whom with unparalleled resolution, potentially yielding important insights into disease dynamics and the impact of…