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The pair approach applied to kinetics in restricted geometries: strengths and weaknesses of the method Abstract In the rapidly emerging field of nanotechnology, as well as in biology where chemical reaction phenomena take place in systems with 1 characteristic length scales on the nanometer range, understanding of chemical kinetics in restricted geometries(More)
BACKGROUND A dose-response curve depicts the fraction of bound proteins as a function of unbound ligands. Dose-response curves are used to measure the cooperativity degree of a ligand binding process. Frequently, the Hill function is used to fit the experimental data. The Hill function is parameterized by the value of the dissociation constant and the Hill(More)
BACKGROUND The Hill function and the related Hill model are used frequently to study processes in the living cell. There are very few studies investigating the situations in which the model can be safely used. For example, it has been shown, at the mean field level, that the dose response curve obtained from a Hill model agrees well with the dose response(More)
In recent years considerable portion of the computer science community has focused its attention on understanding living cell biochemistry and efforts to understand such complication reaction environment have spread over wide front, ranging from systems biology approaches, through network analysis (motif identification) towards developing language and(More)
The X-level Approach Reaction Noise Estimator (XARNES) method has been developed previously to study reaction noise in well mixed reaction volumes. The method is a typical moment closure method and it works by closing the infinite hierarchy of equations that describe moments of the particle number distribution function. This is done by using correlation(More)
Unconventional computing explores multi-scale platforms connecting molecular-scale devices into networks for the development of scal-able neuromorphic architectures, often based on new materials and components with new functionalities. We review some work investigating the functionalities of locally connected networks of different types of switching(More)
The HIV-1 virus can enter a dormant state and become inactive, which reduces accessibility by antiviral drugs. We approach this latency problem from an unconventional point of view, with the focus on understanding how intrinsic chemical noise (copy number fluctuations of the Tat protein) can be used to assist the activation process of the latent virus.(More)