Related papers: Periodic correlation structures in bacterial and a…
We study the propagation of very large amplitude localized excitations in a model of DNA that takes explicitly into account the helicoidal structure. These excitations represent the ``transcription bubble'', where the hydrogen bonds between…
Protein folding, peptide aggregation and crystallization, as well as adsorption of molecules on soft or solid substrates have an essential feature in common: In all these processes, structure formation is guided by a collective, cooperative…
The biological world, especially its majority microbial component, is strongly interacting and may be dominated by collective effects. In this review, we provide a brief introduction for statistical physicists of the way in which living…
Recurrence is a fundamental characteristic of dynamical systems with complicated behavior. Understanding the inner structure of recurrence is challenging, especially if the system has many degrees of freedom and is subject to noise. We…
String barcoding is a recently introduced technique for genomic-based identification of microorganisms. In this paper we describe the engineering of highly scalable algorithms for robust string barcoding. Our methods enable distinguisher…
Maximum-length sequences (m-sequences for short) over finite fields are generated by linear feedback shift registers with primitive characteristic polynomials. These sequences have nice mathematical structures and good randomness properties…
An approximation to the ~4 Mbp basic genome shared by 32 strains of E. coli representing six evolutionary groups has been derived and analyzed computationally. A multiple-alignment of the 32 complete genome sequences was filtered to remove…
We quantize graphs (networks) which consist of a finite number of bonds and vertices. We show that the spectral statistics of fully connected graphs is well reproduced by random matrix theory. We also define a classical phase space for the…
The spectrum and scale of fluctuations in protein structures affect the range of cell phenomena, including stability of protein structures or their fragments, allosteric transitions and energy transfer. The study presents a…
Exchange of biochemical substances is essential way in establishing communication between bacterial cells. It is noticeable that all phases of the process are heavily influenced by perturbations of either internal or external parameters.…
The primary structure of a ribonucleic acid (RNA) molecule can be represented as a sequence of nucleotides (bases) over the alphabet {A, C, G, U}. The secondary or tertiary structure of an RNA is a set of base pairs which form bonds between…
Bootstrap percolation on a graph iteratively enlarges a set of occupied sites by adjoining points with at least $\theta$ occupied neighbors. The initially occupied set is random, given by a uniform product measure, and we say that spanning…
In this paper, we determine periodicity of quantum walks defined by mixed paths and mixed cycles. By the spectral mapping theorem of quantum walks, consideration of periodicity is reduced to eigenvalue analysis of $\eta$-Hermitian adjacency…
Hard spheres in Newtonian fluids serve as paradigms for Non-Newtonian materials phenomena exhibited by colloidal suspensions. A recent experimental study (Cheng et al. 2011 Science, 333, 1276) showed that upon application of shear to such a…
Motile cells often explore natural environments characterized by a high degree of structural complexity. Moreover cell motility is also intrinsically noisy due to spontaneous random reorientation and speed fluctuations. This interplay of…
The control of complex systems is an ongoing challenge of complexity research. Recent advances using concepts of structural control deduce a wide range of control related properties from the network representation of complex systems. Here,…
We calculate the conductance of atomic chains as a function of their length. Using the Density Matrix Renormalization Group algorithm for a many-body model which takes into account electron-electron interactions and the shape of the…
Dynamical patterns in complex networks of coupled oscillators are both of theoretical and practical interest, yet to fully reveal and understand the interplay between pattern emergence and network structure remains to be an outstanding…
Background/ Objectives: Resolving the origin of the genetic code is fundamental to understanding how life began its journey out of the chemical world. Since its deciphering some 60 years ago, there is still no general theory of the…
One of the main challenges in the study of time-varying networks is the interplay of memory effects with structural heterogeneity. In particular, different nodes and dyads can have very different statistical properties in terms of both link…