相关论文: The self-referring DNA and protein: a remark on ph…
Natural protein sequences contain a record of their history. A common constraint in a given protein family is the ability to fold to specific structures, and it has been shown possible to infer the main native ensemble by analyzing…
In nature the three-dimensional structure of a protein is encoded in the corresponding gene. In this paper we describe a new method for encoding the three-dimensional structure of a protein into a binary sequence. The feature of the method…
The structure and function of a protein are determined by its amino acid sequence. While random mutations change a protein's sequence, evolutionary forces shape its structural fold and biological activity. Studies have shown that neutral…
In the course of evolution, proteins undergo important changes in their amino acid sequences, while their three-dimensional folded structure and their biological function remain remarkably conserved. Thanks to modern sequencing techniques,…
The interactions between DNA, RNA, and proteins are fundamental to biological processes, as illustrated by the central dogma of molecular biology. Although modern biological pre-trained models have achieved great success in analyzing these…
A simple DNA-based data storage scheme is demonstrated in which information is written using "addressing" oligonucleotides. In contrast to other methods that allow arbitrary code to be stored, the resulting DNA is suitable for downstream…
Fluorescence microscopy reveals that the contents of many (membrane-free) nuclear "bodies" exchange rapidly with the soluble pool whilst the underlying structure persists; such observations await a satisfactory biophysical explanation. To…
Protein-protein interactions (protein functionalities) are mediated by water, which compacts individual proteins and promotes close and temporarily stable large-area protein-protein interfaces. Proteins are peptide chains decorated by amino…
The three dimensional structure of a protein is an outcome of the interactions of its constituent amino acids in 3D space. Considering the amino acids as nodes and the interactions among them as edges we have constructed and analyzed…
Recent experimental and theoretical approaches have attempted to quantify the physical organization (compaction and geometry) of the bacterial chromosome with its complement of proteins (the nucleoid). The genomic DNA exists in a complex…
The functionality of proteins is related to their structure in the native state. Protein structures are made up of emergent building blocks of helices and almost planar sheets. A simple coarse-grained geometrical model of a flexible tube…
Proteins are an important class of biomolecules that serve as essential building blocks of the cells. Their three-dimensional structures are responsible for their functions. In this thesis we have investigated the protein structures using a…
Natural supports of information are given by random copolymers such as DNA or RNA where information is coded in the sequence of covalent bonds. At the molecular scale, the stochastic growth of a single copolymer with or without a template…
Motivated by the wide ranging experimental results on the conductivity of DNA, we have investigated extraordinary configurations and chemical environments in which DNA might become a true molecular wire, perticularly from enhanced…
Recent progress has been made in the understanding of the physical properties of chromatin -- the dense complex of DNA and histone proteins that occupies the nuclei of plant and animal cells. Here I will focus on the two lowest levels of…
The influence of decoherence and bonding on the linear conductance of single double-stranded DNA molecules is examined by fitting a phenomenological statistical model developed recently (EPJB {\bf 68}, 237 (2009)) to experimental results.…
Enzymatic DNA labeling is a powerful tool with applications in biochemistry, molecular biology, biotechnology, medical science, and genomic research. This paper contributes to the evolving field of DNA-based data storage by presenting a…
The structures of proteins exhibit secondary elements composed of helices and loops. Comparison of several water-only hydrophobicity scales with the functionalities of two repeat proteins shows that these secondary elements possess…
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…
In molecular phylogeny, relationships among organisms are reconstructed using DNA or protein sequences and are displayed as trees. A linear increase in the number of sequences results in an exponential increase of possible trees. Thus,…