Related papers: Calculating Germinal Centre Reactions
A major goal of modern computational biology is to simulate the collective behaviour of large cell populations starting from the intricate web of molecular interactions occurring at the microscopic level. In this paper we describe a…
A persistent public health challenge is finding immunization schemes that are effective in combating highly mutable pathogens such as HIV and influenza viruses. To address this, we analyze a simplified model of affinity maturation, the…
In this article a generalized mathematical model describing the interactions between malignant tumour and immune system with discrete time delay incorporated into the system is considered. Time delay represents the time required to generate…
The adaptive immune system provides a diverse set of molecules that can mount specific responses against a multitude of pathogens. Memory is a key feature of adaptive immunity, which allows organisms to respond more readily upon…
Computational techniques are required for narrowing down the vast space of possibilities to plausible prebiotic scenarios, since precise information on the molecular composition, the dominant reaction chemistry, and the conditions for that…
Processes involving multi-input multi-step reaction cascades are used in developing novel biosensing, biocomputing, and decision making systems. In various applications different changes in responses of the constituent processing steps…
Mathematical modelling of tumor growth is one of the most useful and inexpensive approaches to determine and predict the stage, size and progression of tumors in realistic geometries. Moreover, these models has been used to get an insight…
Regulatory T cells (Treg) have recently been identified as playing a central role in allergy and during allergen-specific immunotherapy. We have extended our previous mathematical model describing the nonlinear dynamics of Th1-Th2…
The genetic regulatory network (GRN) plays a key role in controlling the response of the cell to changes in the environment. Although the structure of GRNs has been the subject of many studies, their large scale structure in the light of…
Many cellular and subcellular biological processes can be described in terms of diffusing and chemically reacting species (e.g. enzymes). Such reaction-diffusion processes can be mathematically modelled using either deterministic…
Chemical reaction networks (CRNs) model the behavior of chemical reactions in well-mixed solutions and they can be designed to perform computations. In this tutorial we give an overview of various computational models for CRNs. Moreover, we…
We establish a link between quantum mechanical molecular simulations and the transfer matrix of a molecule. The transfer matrix (T-matrix) of an object provides a complete description of its electromagnetic response. Once the T-matrices of…
The macroscopic behavior of the solution of a coupled system of partial differential equations arising in the modeling of reaction-diffusion processes in periodic porous media is analyzed. Our mathematical model can be used for studying…
The galactose network is a complex system responsible for galactose metabolism. It has been extensively studied experimentally and mathematically at the unicellular level to broaden our understanding of its regulatory mechanisms at higher…
We suggest a geometric approach to modeling biochemical processes, aiming at those processes that occur in humans with food sensitivities or chemical sensitivities.
The immune system recognizes a myriad of invading pathogens and their toxic products. It does so with a finite repertoire of antibodies and T cell receptors. We here describe theories that quantify the immune system dynamics. We describe…
For the calculation of the partition function $\mathcal{Z}$ of small, isolated and interacting many body systems an improvement with respect to previous formulations is presented. By including anharmonicities and employing a variational…
Genomics methods have uncovered patterns in a range of biological systems, but obscure important aspects of cell behavior: the shape, relative locations of, movement of, and interactions between cells in space. Spatial technologies that…
Cell polarity and movement are fundamental to many biological functions. Experimental and theoretically studies have indicated that interactions of certain proteins lead to the cell polarization which plays a key role in controlling the…
The complexity of biological systems, and the increasingly large amount of associated experimental data, necessitates that we develop mathematical models to further our understanding of these systems. As biological systems are generally not…