Related papers: Autocatalytic Sets and RNA Secondary Structure
As a model of temporally evolving networks, we consider a globally coupled logistic map with variable connection weights. The model exhibits self-organization of network structure, reflected by the collective behavior of units. Structural…
Both natural ecosystems and biochemical reaction networks involve populations of heterogeneous agents whose cooperative and competitive interactions lead to a rich dynamics of species' abundances, albeit at vastly different scales. The…
For the investigation of chemical reaction networks, the efficient and accurate determination of all relevant intermediates and elementary reactions is mandatory. The complexity of such a network may grow rapidly, in particular if reactive…
Complex network formalism allows to explain the behavior of systems composed by interacting units. Several prototypical network models have been proposed thus far. The small-world model has been introduced to mimic two important features…
The potential number of drug like small molecules is estimated to be between 10^23 and 10^60 while current databases of known compounds are orders of magnitude smaller with approximately 10^8 compounds. This discrepancy has led to an…
Interconnected ensembles of biological entities are perhaps some of the most complex systems that modern science has encountered so far. In particular, scientists have concentrated on understanding how the complexity of the interacting…
The statistical mechanics of heteropolymer structure formation is studied in the context of RNA secondary structures. A designed RNA sequence biased energetically towards a particular native structure (a hairpin) is used to study the…
Many real-world complex networks contain a significant amount of structural redundancy, in which multiple vertices play identical topological roles. Such redundancy arises naturally from the simple growth processes which form and shape many…
Gene Regulatory Networks are networks of interactions in biological organisms responsible for determining the production levels of proteins and peptides. Proteins are workers of a cell factory, and their production defines the goal of a…
A great variety of molecular components is encapsulated in cells. Each of these components is replicated for cell reproduction. To address an essential role of the huge diversity of cellular components, we study a model of protocells that…
Modern biological tools have made it possible to unequivocally demonstrate the deep relationship among species in terms of genes and basic molecular mechanisms. In addition, results from genetic, physical and physiological approaches…
The recent discovery of universal principles underlying many complex networks occurring across a wide range of length scales in the biological world has spurred physicists in trying to understand such features using techniques from…
Chemical reaction systems are dynamical systems that arise in chemical engineering and systems biology. In this work, we consider the question of whether the minimal (in a precise sense) multistationary chemical reaction networks, which we…
This study introduces a novel theoretical framework, the Stacked Autoencoder Evolution Hypothesis, which proposes that biological evolutionary systems operate through multi-layered self-encoding and decoding processes, analogous to stacked…
Ab initio RNA secondary structure predictions have long dismissed helices interior to loops, so-called pseudoknots, despite their structural importance. Here, we report that many pseudoknots can be predicted through long time scales RNA…
Biological cells with all of their surface structure and complex interior stripped away are essentially vesicles - membranes composed of lipid bilayers which form closed sacs. Vesicles are thought to be relevant as models of primitive…
Reduction of information entropy along with ever-increasing complexity are among the key signatures of living matter. Understanding the onset of such behavior in early prebiotic world is essential for solving the problem of origins of life.…
Let Sn denote the network of all RNA secondary structures of length n, in which undirected edges exist between structures s, t such that t is obtained from s by the addition, removal or shift of a single base pair. Using context-free…
Under suitable assumptions, the dynamic behaviour of a chemical reaction network is governed by an autonomous set of polynomial ordinary differential equations over continuous variables representing the concentrations of the reactant…
Random graph models have been instrumental in characterizing complex networks, but chemical reaction networks (CRNs) are better represented as hypergraphs. Traditional models of random CRNs often reduce CRNs to bipartite graphs,…