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Trellises are crucial graphical representations of codes. While conventional trellises are well understood, the general theory of (tail-biting) trellises is still under development. Iterative decoding concretely motivates such theory. In…
In previous works [physics/0204035, physics/0404052, physics/0509126] a procedure was described for dividing the $3 \times N$-dimensional conformational space of a molecular system into a number of discrete cells, this partition allowed the…
Intrinsically disordered proteins (IDPs) constitute a broad set of proteins with few uniting and many diverging properties. IDPs-and intrinsically disordered regions (IDRs) interspersed between folded domains-are generally characterized as…
We present analysis of a novel tool for protein secondary structure prediction using the recently-investigated Neural Machine Translation framework. The tool provides a fast and accurate folding prediction based on primary structure with…
A framework is presented for understanding the common character of proteins. Proteins are linear chain molecules. However, the simple model of a polymer viewed as spheres tethered together does not account for many of the observed…
We present a novel technique for encoding and decoding constant weight binary codes that uses a geometric interpretation of the codebook. Our technique is based on embedding the codebook in a Euclidean space of dimension equal to the weight…
We develop methods for investigating protein drift-diffusion dynamics in heterogeneous cell membranes and the roles played by geometry, diffusion, chemical kinetics, and phase separation. Our hybrid stochastic numerical methods combine…
The correct prediction of protein secondary structures is one of the key issues in predicting the correct protein folded shape, which is used for determining gene function. Existing methods make use of amino acids properties as indices to…
The protein design problem involves finding polypeptide sequences folding into a given threedimensional structure. Its rigorous algorithmic solution is computationally demanding, involving a nested search in sequence and structure spaces.…
The Automated Protein Structure Analysis (APSA) method is used for the classification of supersecondary structures. Basis for the classification is the encoding of three-dimensional (3D) residue conformations into a 16-letter code (3D-1D…
We introduce a new formalism and a number of new results in the context of geometric computational vision. The classical scope of the research in geometric computer vision is essentially limited to static configurations of points and lines…
This work is the first in a series of papers that, among other things, extends the formalism of diolic differential calculus, wherein a new context for obtaining differential calculus in vector bundles was established. Here we provide a…
The evolutionary trajectory of a protein through sequence space is constrained by function and three-dimensional (3D) structure. Residues in spatial proximity tend to co-evolve, yet attempts to invert the evolutionary record to identify…
We propose a novel and efficient algorithm to model high-level topological structures of neuronal fibers. Tractography constructs complex neuronal fibers in three dimensions that exhibit the geometry of white matter pathways in the brain.…
Mapping between sequence and structure is currently an open problem in structural biology. Despite many experimental and computational efforts it is not clear yet how the structure is encoded in the sequence. Answering this question may…
For every linear binary code $C$, we construct a geometric triangular configuration $\Delta$ so that the weight enumerator of $C$ is obtained by a simple formula from the weight enumerator of the cycle space of $\Delta$. The triangular…
We introduce the notion of "binary" positive and complex geometries, giving a completely rigid geometric realization of the combinatorics of generalized associahedra attached to any Dynkin diagram. We also define open and closed "cluster…
Proteins are the fundamental macromolecules that play diverse and crucial roles in all living matter and have tremendous implications in healthcare, manufacturing, and biotechnology. Their functions are largely determined by the sequences…
In this work, following the Discrete de Rham (DDR) paradigm, we develop an arbitrary-order discrete divdiv complex on general polyhedral meshes. The construction rests 1) on discrete spaces that are spanned by vectors of polynomials whose…
The aim of this paper is to find an optimal matching between manifold-valued curves, and thereby adequately compare their shapes, seen as equivalent classes with respect to the action of reparameterization. Using a canonical decomposition…