Local rule simulations of capsid assembly.
Locating the boundary peaks of least-energy solutions to a singularly perturbed Dirichlet problem
We consider the problemwhere is a smooth and bounded domain,
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.
Negative control of cell proliferation. Growth arrest versus apoptosis. Role of GBP.
New insights into viral architecture via affine extended symmetry groups.
Node assignment problem in Bayesian networks
This paper deals with the problem of searching for the best assignments of random variables to nodes in a Bayesian network (BN) with a given topology. Likelihood functions for the studied BNs are formulated, methods for their maximization are described and, finally, the results of a study concerning the reliability of revealing BNs' roles are reported. The results of BN node assignments can be applied to problems of the analysis of gene expression profiles.
Nonlinear modelling and qualitative analysis of a real chemostat with pulse feeding.
Numerical simulation of chemotactic bacteria aggregation via mixed finite elements
We start from a mathematical model which describes the collective motion of bacteria taking into account the underlying biochemistry. This model was first introduced by Keller-Segel [13]. A new formulation of the system of partial differential equations is obtained by the introduction of a new variable (this new variable is similar to the quasi-Fermi level in the framework of semiconductor modelling). This new system of P.D.E. is approximated via a mixed finite element technique. The solution algorithm...
Numerical simulation of chemotactic bacteria aggregation via mixed finite elements
We start from a mathematical model which describes the collective motion of bacteria taking into account the underlying biochemistry. This model was first introduced by Keller-Segel [13]. A new formulation of the system of partial differential equations is obtained by the introduction of a new variable (this new variable is similar to the quasi-Fermi level in the framework of semiconductor modelling). This new system of P.D.E. is approximated via a mixed finite element technique. The solution...
Numerical simulation of the coagulation dynamics of blood.
On singular perturbation problems with Robin boundary condition
We consider the following singularly perturbed elliptic problemwhere satisfies some growth conditions, , and () is a smooth and bounded domain. The cases (Neumann problem) and (Dirichlet problem) have been studied by many authors in recent years. We show that, there exists a generic constant such that, as , the least energy solution has a spike near the boundary if , and has an interior spike near the innermost part of the domain if . Central to our study is the corresponding problem...