Mathematical and biological modelling of RNA secondary structure and its effects on gene expression.
Mathematical and numerical modeling of early atherosclerotic lesions***
This article is devoted to the construction of a mathematical model describing the early formation of atherosclerotic lesions. The early stage of atherosclerosis is an inflammatory process that starts with the penetration of low density lipoproteins in the intima and with their oxidation. This phenomenon is closely linked to the local blood flow dynamics. Extending a previous work [5] that was mainly restricted to a one-dimensional setting, we couple...
Mathematical models and numerical simulations for the P53-Mdm2 network.
Mathematical properties of DNA structure in 3-dimensional space.
Modeling and Simulating Asymmetrical Conductance Changes in Gramicidin Pores
Gramicidin A is a small and well characterized peptide that forms an ion channel in lipid membranes. An important feature of gramicidin A (gA) pore is that its conductance is affected by the electric charges near the its entrance. This property has led to the application of gramicidin A as a biochemical sensor for monitoring and quantifying a number of chemical and enzymatic reactions. Here, a mathematical model of conductance changes of gramicidin A pores in response to the presence of electrical...
Modélisation mathématique de la division méiotique des ovocytes de Xénope induite par la progestérone
Modelling DNA and RNA secondary structures using matrix insertion-deletion systems
Insertion and deletion are operations that occur commonly in DNA processing and RNA editing. Since biological macromolecules can be viewed as symbols, gene sequences can be represented as strings and structures can be interpreted as languages. This suggests that the bio-molecular structures that occur at different levels can be theoretically studied by formal languages. In the literature, there is no unique grammar formalism that captures various bio-molecular structures. To overcome this deficiency,...
Multi-bump ground states of the Gierer–Meinhardt system in R2
Multi-core CPU or GPU-accelerated Multiscale Modeling for Biomolecular Complexes
Multi-scale modeling plays an important role in understanding the structure and biological functionalities of large biomolecular complexes. In this paper, we present an efficient computational framework to construct multi-scale models from atomic resolution data in the Protein Data Bank (PDB), which is accelerated by multi-core CPU and programmable Graphics Processing Units (GPU). A multi-level summation of Gaussian kernel functions is employed to generate implicit models for biomolecules. The coefficients...
Multiphoton response of retinal rod photoreceptors.