Related papers: Deciphering general characteristics of residues co…
Residue-wise contact order (RWCO) is a new kind of one-dimensional protein structures which represents the extent of long-range contacts. We have recently shown that a set of three types of one-dimensional structures (secondary structure,…
Biological neural systems encode and transmit information as patterns of activity tracing complex trajectories in high-dimensional state-spaces, inspiring alternative paradigms of information processing. Heteroclinic networks, naturally…
Ambient AI "scribe" systems promise to reduce clinical documentation burden, but automatic speech recognition (ASR) errors can remain unnoticed without careful review, and high-quality human reference transcripts are often unavailable for…
Semiconductor crosshatch patterns in thin film heterostructures form as a result of strain relaxation processes and dislocation pile-ups during growth of lattice mismatched materials. Due to their connection with the internal misfit…
The increasing capacity of high-throughput genomic technologies for generating time-course data has stimulated a rich debate on the most appropriate methods to highlight crucial aspects of data structure. In this work, we address the…
Phase separation mechanisms can produce a variety of complicated and intricate microstructures, which often can be difficult to characterize in a quantitative way. In recent years, a number of novel topological metrics for microstructures…
One of the most challenging and long-standing problems in computational biology is the prediction of three-dimensional protein structure from amino acid sequence. A promising approach to infer spatial proximity between residues is the study…
Communicating cells can coordinate their gene expressions to form spatial patterns. 'Secrete-and-sense cells' secrete and sense the same molecule to do so and are ubiquitous. Here we address why and how these cells, from disordered…
Coded caching is able to exploit accumulated cache size and hence superior to uncoded caching by distributing different fractions of a file in different nodes. This work investigates coded caching in a large-scale small-cell network (SCN)…
Theoretical studies of protein folding on lattice models relie on the assumption that water close to amino-acids is always in thermal equilibrium all along the folding pathway. Within this framework, it has always been considered that…
High-pressure research is a productive route to new structures and emergent properties. However, crucial high-pressure structural information remains highly fragmented across individual publications and heterogeneous computational…
The primary structure of proteins, that is their sequence, represents one of the most abundant set of experimental data concerning biomolecules. The study of correlations in families of co--evolving proteins by means of an inverse…
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…
A typical protein structure is a compact packing of connected alpha-helices and/or beta-strands. We have developed a method for generating the ensemble of compact structures a given set of helices and strands can form. The method is tested…
Dynamical systems containing heteroclinic cycles and networks can be invoked as models of intransitive competition between three or more species. When populations are assumed to be well-mixed, a system of ordinary differential equations…
Naively, one expects the information communicated by an enzyme downstream within a signaling network, in which the enzyme is embedded, to grow monotonically with the enzyme's rate of product formation. However, here we observe that this…
The intricate three-dimensional geometries of protein tertiary structures underlie protein function and emerge through a folding process from one-dimensional chains of amino acids. The exact spatial sequence and configuration of amino…
Is protein secondary structure primarily determined by local interactions between residues closely spaced along the amino acid backbone, or by non-local tertiary interactions? To answer this question we have measured the entropy densities…
In the present article we carry out a molecular dynamics study of the core-softened system and show that the existence of the water-like anomalies in this system depends on the trajectory in $P-\rho-T$ space along which the behavior of the…
Previous investigation of coding sequence lengths (CDS) in the bacterial circular chromosome revealed short range correlation in the series of these data. We have further analyzed the averaged periodograms of these series and we found that…