Related papers: The interplay between phase-separation and gene-en…
Non-equilibrium selection pressures were proposed for the formation of oligonucleotides with rich functionalities encoded in their sequences, such as catalysis. Since phase separation was shown to direct various chemical processes, we ask…
Recent progress in coherent quantum interactions between free-electron pulses and laser-induced near-field light have revolutionized electron wavepacket shaping. Building on these advancements, we numerically explore the potential of…
Next-generation sequencing technology enables the identification of thousands of gene regulatory sequences in many cell types and organisms. We consider the problem of testing if two such sequences differ in their number of binding site…
Simulations and Mode-Coupling Theory calculations, for a large range of the arm number $f$ and packing fraction $\eta$ have shown that the structural arrest and the dynamics of star polymers in a good solvent are extremely rich: the systems…
Transcriptional activity has been shown to relate to the organization of chromosomes in the eukaryotic nucleus and in the bacterial nucleoid. In particular, highly transcribed genes, RNA polymerases and transcription factors gather into…
By means of extensive replica-exchange simulations of generic coarse-grained models for helical polymers, we systematically investigate the structural transitions into all possible helical phases for flexible and semiflexible elastic…
We theoretically study mixtures of chemically-interacting particles, which produce or consume a chemical to which they are attracted or repelled, in the most general case of many coexisting species. We find a new class of active phase…
The adhesion of biomembranes is mediated by the binding of membrane-anchored receptor and ligand proteins. The proteins can only bind if the separation between apposing membranes is sufficiently close to the length of the protein complexes,…
Cytoskeletal motors known as motor proteins are molecules that drive cellular transport along several parallel cytoskeletal filaments and support many biological processes. Experimental evidences suggest that they interact with the nearest…
Partitioning of (bio)materials in polymeric mixtures is a key phenomenon both in cellular environments, as well as in industrial applications. In cells, several macromolecules are suspended within different biomolecular phases. On the other…
In this paper, we consider the relationship between phase-type distributions and positive systems through practical examples. Phase-type distributions, commonly used in modelling dynamic systems, represent the temporal evolution of a set of…
The phase behavior of charged rods in the presence of inter-rod linkers is studied theoretically as a model for the equilibrium behavior underlying the organization of actin filaments by linker proteins in the cytoskeleton. The presence of…
Statistical-mechanical lattice models for protein-DNA binding are well established as a method to describe complex ligand binding equilibriums measured in vitro with purified DNA and protein components. Recently, a new field of applications…
We discuss a realistic scenario, accounting for the existence of sub-micrometric protein domains in cell membranes. At the biological level, such membrane domains have been shown to be specialized, in order to perform a determined…
We present a theoretical study of a system with competing short-range ferromagnetic attraction and a long-range anti-ferromagnetic repulsion, in the presence of a uniform external magnetic field. The interplay between these interactions, at…
Quenched or frozen-in structural disorder is ubiquitous in real experimental systems. Much of the progress is achieved in understanding the phase separation of such systems using the diffusion-driven coarsening in Ising model with quenched…
We present a detailed numerical study of multi-component colloidal gels interacting sterically and obtained by arrested phase separation. Under deformation, we found that the interplay between the different intertwined networks is key.…
Usually, we expect large particles to sediment faster than small of the same material. Contrary to this intuition, we report a dynamical competition between sedimentation and phase ordering which leads to smaller particles settling faster…
The phase behavior of a cross-linked polymer blend made of two incompatible species, $A$ and $B$, of different chemical nature is analyzed. Besides a homogeneous phase, this system also exhibits two microphases and a phase of total…
We study the stability, the clustering and the phase-diagram of free cooling granular gases. The systems consist of mono-disperse particles with additional non-contact (long-range) interactions, and are simulated here by the event-driven…