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The free energy of globular protein chain is considered to be a functional defined on smooth curves in three dimensional Euclidean space. From the requirement of geometrical invariance, together with basic facts on conformation of helical proteins and dynamical characteristics of the protein chains, we are able to determine, in a unique way, the exact form of the free energy functional. Namely, the free energy density should be a linear function of the curvature of curves on which the free energy functional is defined. This model can be used, for example, in Monte Carlo simulations of exhaustive searching the native stable state of the protein chain.
Nearly a quarter of genomic sequences and almost half of all receptors that are likely to be targets for drug design are integral membrane proteins. Understanding the detailed mechanisms of the folding of membrane proteins is a largely unsolved, key
We study the distribution of first-passage functionals ${cal A}= int_0^{t_f} x^n(t), dt$, where $x(t)$ is a Brownian motion (with or without drift) with diffusion constant $D$, starting at $x_0>0$, and $t_f$ is the first-passage time to the origin. I
We present a theoretical model of facilitated diffusion of proteins in the cell nucleus. This model, which takes into account the successive binding/unbinding events of proteins to DNA, relies on a fractal description of the chromatin which has been
Protein-fragment seqlets typically feature about 10 amino acid residue positions that are fixed to within conservative substitutions but usually separated by a number of prescribed gaps with arbitrary residue content. By quantifying a general amino a
The beautiful structures of single and multi-domain proteins are clearly ordered in some fashion but cannot be readily classified using group theory methods that are successfully used to describe periodic crystals. For this reason, protein structures