PROTEIN FOLDING AS A PHYSICAL STOCHASTIC PROCESS

Physical Modeling of Protein Folding

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Modelling Breakage-Fusion-Bridge Cycles as a Stochastic Paper Folding Process

Breakage-Fusion-Bridge cycles in cancer arise when a broken segment of DNA is duplicated and an end from each copy joined together. This structure then ‘unfolds’ into a new piece of palindromic DNA. This is one mechanism responsible for the localised amplicons observed in cancer genome data. The process has parallels with paper folding sequences that arise when a piece of paper is folded severa...

Stochastic dynamics and dominant protein folding pathways

Free energy adopted stochastic optimization protein folding

Optimal structure of proteins is described by linear stochastic differential equation with mean decrease of free energy and volatility. Structure determining strategy is given by a twin of stochastic variables for which empirical conditions are not postulated. Optimal structure determination will be deformed to be adoptive to trading strategy employing martingale property where stochastic integ...

Protein folding with stochastic L-systems

Protein molecules adopt a specific global 3D structure in order to carry out their biological function. To achieve this native state a newly formed protein molecule has to fold. The folding process and the final fold are both determined by the sequence of amino acids making up the protein chain. It is not currently possible to predict the conformation of the native state from the amino acid seq...