arXiv subjects

Mehdi Yahyanejad

Publications and source records attributed to Mehdi Yahyanejad.

3 recordsLinked to original sources

arXiv2004

Untangling influences of hydrophobicity on protein sequences and structures

We fit the Fourier transforms of solvent accessibility and hydrophobicity profiles of a representative set of proteins to a joint multi-variable Gaussian. This allows us to separate the intrinsic tendencies of sequence and structure profiles from the interactions that correlate them; for example, the $α$-helix periodicity in sequence hydrophobicity is dictated by the solvent accessibility of structures. The distinct intrinsic tendencies of sequence and structure profiles are most pronounced at long periods, where sequence hydrophobicity fluctuates more, while solvent accessibility fluctuations are less than average. Interestingly, correlations between the two profiles can be interpreted as the Boltzmann weight of the solvation energy at room temperature.

q-bio.BM↗

arXiv2003

Symmetry considerations and development of pinwheels in visual maps

Neurons in the visual cortex respond best to rod-like stimuli of given orientation. While the preferred orientation varies continuously across most of the cortex, there are prominent pinwheel centers around which all orientations a re present. Oriented segments abound in natural images, and tend to be collinear}; neurons are also more likely to be connected if their preferred orientations are aligned to their topographic separation. These are indications of a reduced symmetry requiring joint rotations of both orientation preference and the underl ying topography. We verify that this requirement extends to cortical maps of mo nkey and cat by direct statistical analysis. Furthermore, analytical arguments and numerical studies indicate that pinwheels are generically stable in evolving field models which couple orientation and topography.

cond-mat.stat-mech↗

arXiv2002

Structure Space of Model Proteins --A Principle Component Analysis

We study the space of all compact structures on a two-dimensional square lattice of size $N=6\times6$. Each structure is mapped onto a vector in $N$-dimensions according to a hydrophobic model. Previous work has shown that the designabilities of structures are closely related to the distribution of the structure vectors in the $N$-dimensional space, with highly designable structures predominantly found in low density regions. We use principal component analysis to probe and characterize the distribution of structure vectors, and find a non-uniform density with a single peak. Interestingly, the principal axes of this peak are almost aligned with Fourier eigenvectors, and the corresponding Fourier eigenvalues go to zero continuously at the wave-number for alternating patterns ($q=π$). These observations provide a stepping stone for an analytic description of the distribution of structural points, and open the possibility of estimating designabilities of realistic structures by simply Fourier transforming the hydrophobicities of the corresponding sequences.

physics.bio-ph↗