Related papers: Ising model description of long range correlations…
At present, there have been suggested two types of physical mechanism that may facilitate preferential pairing between DNA molecules, with identical or similar base pair texts, without separation of base pairs. One solely relies on base…
Repetitive elements are important in genomic structures, functions and regulations, yet effective methods in precisely identifying repetitive elements in DNA sequences are not fully accessible, and the relationship between repetitive…
The distances over which biological molecules and their complexes can function range from a few nanometres, in the case of folded structures, to millimetres, for example during chromosome organization. Describing phenomena that cover such…
We investigate the melting transition of non-supercoiled circular DNA of different lengths, employing Brownian dynamics simulation. In the absence of supercoiling, we find that melting of circular DNA is driven by a large bubble, which…
A tight-binding model together with a novel statistical method are used to investigate the relation between the sequence-dependent electric transport properties and the sequences of protein-coding regions of complete genomes. A correlation…
Synchronization across long neural distances is a functionally important phenomenon. In order to access the mechanistic basis of long-range synchrony, we constructed an experimental model that enables monitoring of spiking activities over…
Protein-protein interactions are fundamental to many biological processes. Experimental screens have identified tens of thousands of interactions and structural biology has provided detailed functional insight for select 3D protein…
DNA looping plays a fundamental role in a wide variety of biological processes, providing the backbone for long range interactions on DNA. Here we develop the first model for DNA looping by an arbitrarily large number of proteins and solve…
Tools that effectively analyze and compare sequences are of great importance in various areas of applied computational research, especially in the framework of molecular biology. In the present paper, we introduce simple geometric criteria…
We propose a method for detecting differential gene expression that exploits the correlation between genes. Our proposal averages the univariate scores of each feature with the scores in correlation neighborhoods. In a number of real and…
We examine in detail the theoretical foundations of striking long-range couplings emerging in arrays of fluid cells connected by narrow channels by using a lattice gas (Ising model) description of a system. We present a reexamination of the…
Intermittent density fluctuations of nucleotide molecules (adenine, guanine, cytosine and thymine) along DNA sequences are studied in the framework of a hierarchical structure (HS) model originally proposed for the study of fully developed…
We have considered as a theoretical possibility for the development of a nanobiochip the operation principle of which is based on measuring conductance in single-stranded and double-stranded DNA. Calculations have demonstrated that in the…
Short-range correlations between nucleon pairs in different spin-isospin channels are investigated for light nuclei using the Argonne V8' interaction. At distances below 1 fm a universal behavior is found for the deuteron, 3H, 3He and for…
It has long been noticed that high dimension data exhibits strange patterns. This has been variously interpreted as either a "blessing" or a "curse", causing uncomfortable inconsistencies in the literature. We propose that these patterns…
Modern genomics experiments measure functional behaviors for many thousands of DNA sequences. We suggest that, especially when these sequences are chosen at random, it is natural to compute correlation functions between sequences and…
The Heisenberg scaling is typically associated with nonclassicality and entanglement. In this work, however, we discuss how classical long-range correlations between lattice sites in many-body systems may lead to a 1/N scaling in precision…
Sequencing by synthesis is the underlying technology for many next-generation DNA sequencing platforms. We developed a new model, the fixed flow cycle model, to derive the distributions of sequence length for a given number of flow cycles…
We examine the conformations of a model for a short segment of closed DNA. The molecule is represented as a cylindrically symmetric elastic rod with a constraint corresponding to a specification of the linking number. We obtain analytic…
The one-dimensional Ising model in an external magnetic field with uniform long-range interactions and random short-range interactions satisfying bimodal annealed distributions is studied. This generalizes the random model discussed by…