Sökning: "URDME"

Hittade 5 uppsatser innehållade ordet URDME.

  1. 1. Computational modelling of quorum sensing using cascade delay

    Kandidat-uppsats,

    Författare :Nils Axelsson; David Mårsäter; [2022]
    Nyckelord :Quorum sensing; URDME;

    Sammanfattning : The scope of this project was to implement a quorum sensing model capable of synchronised oscillations from the article ”A synchronized quorum of genetic clocks” [1] in the software framework URDME [2]. The model consists of a system of partial differential equations describing time delayed and coupled biochemical reactions. LÄS MER

  3. 2. Comparing priority queues with support for priority updates at arbitrary indexes

    Kandidat-uppsats, Uppsala universitet/Institutionen för informationsteknologi

    Författare :Erik Granberg; [2021]
    Nyckelord :;

    Sammanfattning : The research software URDME makes use of a priority queue that has support for updating the priority of enqueued elements at arbitrary indexes. To achieve this URDME currently relies on a Binary Heap. LÄS MER

  4. 3. A parallel implementation of spatially distributed stochastic chemical kinetics

    Kandidat-uppsats, Uppsala universitet/Institutionen för informationsteknologi

    Författare :Pontus Melin; [2020]
    Nyckelord :;

    Sammanfattning : Stochastic simulation of reaction kinetics has emerged as animportant computational tool in molecular systems biology and will likely continue to grow in importance as experimental techniques are further developed and spatial models can be calibrated to biological data. Many applications require a large number of sample realizations to be generated in order to allow for useful statistical analysis. LÄS MER

  5. 4. Multiscale Stochastic Neuron Modeling : with applications in deep brain stimulation

    Uppsats för yrkesexamina på avancerad nivå, Uppsala universitet/Avdelningen för beräkningsvetenskap

    Författare :Aleksandar Senek; [2017]
    Nyckelord :;

    Sammanfattning : In recent years deep brain stimulation (DBS) has seen success in curing adverseeffects of several diseases, among those Parkinson. Current method for treatmentuses implanted electrodes of the brain which stimulate neurons via potential fields.The precise mechanism with which DBS works is still being researched. LÄS MER

  7. 5. Computational Stochastic Morphogenesis

    Uppsats för yrkesexamina på avancerad nivå, Uppsala universitet/Avdelningen för beräkningsvetenskap

    Författare :Yakup Saygun; [2015]
    Nyckelord :computational morphogenesis; computational biology; biological pattern formation; stochastic simulations; stochastic Turing patterns; stochastic models; reaction-diffusion master equation; intrinsic noise; URDME; next subvolume method;

    Sammanfattning : Self-organizing patterns arise in a variety of ways in nature, the complex patterning observed on animal coats is such an example. It is already known that the mechanisms responsible for pattern formation starts at the developmental stage of an embryo. However, the actual process determining cell fate has been, and still is, unknown. LÄS MER