Subscribe to the gold package and get unlimited access to Shamra Academy
Register a new userStatistical mechanics of RNA folding: a lattice approach
90
0
0.0
(
0
)
Ask ChatGPT about the research
No Arabic abstract
We propose a lattice model for RNA based on a self-interacting two-tolerant trail. Self-avoidance and elements of tertiary structure are taken into account. We investigate a simple version of the model in which the native state of RNA consists of just one hairpin. Using exact arguments and Monte Carlo simulations we determine the phase diagram for this case. We show that the denaturation transition is first order and can either occur directly or through an intermediate molten phase.
rate research
Read More
We construct a minimalist model of RNA secondary-structure formation and use it to study the mapping from sequence to structure. There are strong, qualitative differences between two-letter and four or six-letter alphabets. With only two kinds of bases, there are many alternate folding configurations, yielding thermodynamically stable ground-states only for a small set of structures of high designability, i.e., total number of associated sequences. In contrast, sequences made from four bases, as found in nature, or six bases have far fewer competing folding configurations, resulting in a much greater average stability of the ground state.
We describe a simple meanfield variational approach to study a number of properties of intrinsically stiff chains which are appropriate models for a large class of biopolymers. We present the calculation of the distribution of end-to-end distance and the elastic response of stiff chains under tension using this approach. In the former example we find that the simple expression almost quantitatively fits the results of computer simulation. For the case of the stiff chain under tension we recover analytically all the known limits. We obtain quantitative agreement with recent experiments on the stretching of DNA. The limitations of our approach are also discussed.
Loops are abundant in native RNA structures and proliferate close to the unfolding transition. By including a statistical weight ~ l^{-c} for loops of length l in the recursion relation for the partition function, we show that the calculated heat capacity depends sensitively on the presence and value of the exponent c, even of short t-RNA. For homo-RNA we analytically calculate the critical temperature and critical exponents which exhibit a non-universal dependence on c.
The mechanical unfolding of a simple RNA hairpin and of a 236--bases portion of the Tetrahymena thermophila ribozyme is studied by means of an Ising--like model. Phase diagrams and free energy landscapes are computed exactly and suggest a simple two--state behaviour for the hairpin and the presence of intermediate states for the ribozyme. Nonequilibrium simulations give the possible unfolding pathways for the ribozyme, and the dominant pathway corresponds to the experimentally observed one.
The statistical properties of protein folding within the {phi}^4 model are investigated. The calculation is performed using statistical mechanics and path integral method. In particular, the evolution of heat capacity in term of temperature is given for various levels of the nonlinearity of source and the strength of interaction between protein backbone and nonlinear source. It is found that the nonlinear source contributes constructively to the specific heat especially at higher temperature when it is weakly interacting with the protein backbone. This indicates increasing energy absorption as the intensity of nonlinear sources are getting greater. The simulation of protein folding dynamics within the model is also refined.
Log in to be able to interact and post comments
comments
Fetching comments
Sign in to be able to follow your search criteria
