Related papers: Allovalency revisited: an analysis of multisite ph…
Ultrasensitive response motifs, which are capable of converting graded stimulus in binary responses, are very well-conserved in signal transduction networks. Although it has been shown that a cascade arrangement of multiple ultrasensitive…
Speciation is fundamental to the huge diversity of life on Earth. Evidence suggests reproductive isolation arises most commonly in allopatry with a higher speciation rate in small populations. Current theory does not address this dependence…
The biological effects of electromagnetic fields on proteins remain controversial beyond well-established thermal mechanisms, particularly with respect to frequency-dependent responses. Here, we propose that electromagnetic waves can…
Hybrid molecular dynamics/Monte Carlo simulations used to study melts of unentangled, thermoreversibly associating supramolecular polymers. In this first of a series of papers, we describe and validate a model that is effective in…
The coil-globule transition of hetero-polymer chains is studied here. By means of extensive Molecular Dynamics simulations, we show that the transition is directly linked to the complexity of the chain, which depends on the number of…
The explicit evaluation of linear response coefficients for interacting many-particle systems still poses a considerable challenge to theoreticians. In this work we use a novel many-particle renormalization technique, the so-called…
The essential features of the in vitro refolding of myoglobin are expressed in a solvable physical model. Alpha helices are taken as the fundamental collective coordinates of the system, while the refolding is assumed to be mainly driven by…
Correlations between two variables of a high-dimensional system can be indicative of an underlying interaction, but can also result from indirect effects. Inverse Ising inference is a method to distinguish one from the other. Essentially,…
Cells rely on the ability to sense and respond to small spatial differences in chemoattractant concentrations for survival. There is growing evidence that this is accomplished by setting the signaling system near the threshold for…
In many non-linear systems, such as plasma oscillation, boson condensation, chemical reaction, and even predatory-prey oscillation, the coarse-grained dynamics are governed by an equation containing anti-symmetric transitions, known as the…
Multivalent particles bind to targets via many independent ligand-receptor bonding interactions. This microscopic design spans length scales in both synthetic and biological systems. Classic examples include interactions between cells,…
The state of many physical, biological and socio-technical systems evolves by combining smooth local transitions and abrupt resetting events to a set of reference values. The inclusion of the resetting mechanism not only provides the…
Two recent streams of work suggest that pairwise interactions may be sufficient to capture the complexity of biological systems ranging from protein structure to networks of neurons. In one approach, possible amino acid sequences in a…
The study of the interplay between the structure and dynamics of complex multilevel systems is a pressing challenge nowadays. In this paper, we use a semi-annealed approximation to study the stability properties of Random Boolean Networks…
Most sensory cells use surface receptors to detect environmental stimuli and initiate downstream signaling. Cooperative interactions among sensory receptors is known to play a crucial role in enhancing the sensitivity of biochemical…
We analyze Axelrod's model of social interactions on coevolving complex networks. We introduce four extensions with different mechanisms of edge rewiring. The models are intended to catch two kinds of interactions - preferential attachment,…
Multivalent binding employs multiple simultaneous supramolecular interactions, increasing avidity and selectivity compared with monovalent binding. While equilibrium aspects of multivalency are well characterized, non-equilibrium behavior…
For a paradigmatic model of chemotaxis, we analyze the effect how a nonzero affinity driving receptors out of equilibrium affects sensitivity. This affinity arises whenever changes in receptor activity involve ATP hydrolysis. The…
A model for positron binding to polar molecules is considered by combining the dipole potential outside the molecule with a strongly repulsive core of a given radius. Using existing experimental data on binding energies leads to…
Coarse-graining of fully atomistic molecular dynamics simulations is a long-standing goal in order to allow the description of processes occurring on biologically relevant timescales. For example, the prediction of pathways, rates and…