Related papers: Cooperative ligation breaks sequence symmetry and …
A continuing frustration for origin of life scientists is that abiotic and, by extension, pre-biotic attempts to develop self-sustaining, evolving molecular systems tend to produce more dead-end substances than macromolecular products with…
Self-organization, the ability of a system of microscopically interacting entities to shape macroscopically ordered structures, is ubiquitous in Nature. Spatio-temporal patterns are abundantly observed in a large plethora of applications,…
The discerning behavior of living systems relies on accurate interactions selected from the lot of molecular collisions occurring in the cell. To ensure the reliability of interactions, binding partners are classically envisioned as finely…
The bacterium Escherichia coli initiates replication once per cell cycle at a precise volume per origin and adds an on average constant volume between successive initiation events, independent of the initiation size. Yet, a molecular model…
A mechanism of the replication of proto-RNAs in oligomer world is proposed. The replication is carried out by a minimum cycle which is sustained by a ligase and a helicase. We expect that such a cycle actually worked in the primordial soup…
The complex interactions underlying collective motion in biological systems give rise to emergent behaviours such as flocking, sorting, and cooperative transport. These dynamics often involve species with different motilities coordinating…
Genome organization in eukaryotes during interphase stems from the delicate balance between non-random correlations present in the DNA polynucleotide linear sequence and the physico/chemical reactions which shape continuously the form and…
The onset of synchronization in networks of networks is investigated. Specifically, we consider networks of interacting phase oscillators in which the set of oscillators is composed of several distinct populations. The oscillators in a…
Synthetic biology sets out to implement new functions in cells, and to develop a deeper understanding of biological design principles. In 2000, Elowitz and Leibler showed that by rational design of the reaction network, and using existing…
The protein folding problem has attracted an increasing attention from physicists. The problem has a flavor of statistical mechanics, but possesses the most common feature of most biological problems -- the profound effects of evolution. I…
When a population inhabits an inhomogeneous environment, the fitness value of traits can vary with the position in the environment. Gene flow caused by random mating can nevertheless prevent that a sexually reproducing population splits…
Biomolecular networks have already found great utility in characterizing complex biological systems arising from pair-wise interactions amongst biomolecules. Here, we review how graph theoretical approaches can be applied not only for a…
Molecular biology explains function of molecules by their geometrical and electronical structures that are mainly determined by utilization of quantum effects in chemistry. However, further quantum effects are not thought to play any…
Molecular biology is a nanotechnology that works--it has worked for billions of years and in an amazing variety of circumstances. At its core is a system for acquiring, processing and communicating information that is universal, from…
The emergence of macroscopic order and patterns is a central paradigm in systems of (self-)propelled agents, and a key component in the structuring of many biological systems.The relationships between the ordering process and the underlying…
The formation of DNA loops by proteins and protein complexes that bind at distal DNA sites plays a central role in many cellular processes, such as transcription, recombination, and replication. Here we review the basic thermodynamic…
Interactions between neighboring cells are essential for generating or refining patterns in a number of biological systems. We propose a discrete filtering approach to predict how networks of cells modulate spatially varying input signals…
Cooperation is ubiquitous ranging from multicellular organisms to human societies. Population structures indicating individuals' limited interaction ranges are crucial to understand this issue. But it is still at large to what extend…
Living creatures exhibit a remarkable diversity of locomotion mechanisms, evolving structures specialised for interacting with their environment. In the vast majority of cases, locomotor behaviours such as flying, crawling, and running, are…
Mathematical models play an increasingly important role in the interpretation of biological experiments. Studies often present a model that generates the observations, connecting hypothesized process to an observed pattern. Such generative…