Related papers: Entropy-driven phase behaviour of all-DNA associat…
The percentage and sequence of AT and GC base pairs and charges on the DNA backbone contribute significantly to the stiffness of DNA. This elastic property of DNA also changes with small interacting ligands. The single-molecule force…
Computing equilibrium concentrations of molecular complexes is generally analytically intractable and requires numerical approaches. In this work we focus on the polymer-monomer level, where indivisible molecules (monomers) combine to form…
Understanding how the vibrational and thermal properties of solids are influenced by atomistic structural disorder is of fundamental scientific interest, and paramount to designing materials for next-generation energy technologies. While…
In systems such as block copolymer mesophases or physical gels formed by associating copolymers, the dynamical properties are often controlled by the extraction/association of a sticking group. We propose a description of the…
The 3D folding of a mammalian gene can be studied by a polymer model, where the chromatin fibre is represented by a semiflexible polymer which interacts with multivalent proteins, representing complexes of DNA-binding transcription factors…
Polar flocks in discrete active systems are often assumed to be robust, yet recent studies reveal their fragility under both imposed and spontaneous fluctuations. Here, we revisit the four-state active Potts model (APM) and show that its…
We propose a new method for electrophoretic separation of DNA in which adsorbed polymers are driven over a disordered two-dimensional substrate which contains attractive sites for the polymers. Using simulations of a model for long polymer…
There is increasing evidence that protein binding to specific sites along DNA can activate the reading out of genetic information without coming into direct physical contact with the gene. There also is evidence that these distant but…
We have investigated interlayer interactions in the bilayer PtTe$_{2}$ system, which influence the electronic energy bands near the Fermi levels. Our diffusion Monte Carlo (DMC) calculations for the high-symmetry bilayer stackings (AA, AB,…
Polymer composites are ideal candidates for next generation biomimetic soft materials because of their exquisite bottom-up designability. However, the richness of behaviours comes at a price: the need for precise and extensive…
Synthetic methods to control the structure of materials at sub-micron scales are typically based on the self-assembly of structural building blocks with precise size and morphology. On the other hand, many living systems can generate…
DNA interactions with polycations are not only important for our understanding of chromatin compaction but also for characterizing DNA-binding proteins involved in transcription, replication and repair. DNA is known to form several types of…
The pair interaction between two stiff parallel linear DNA molecules depends not only on the distance between their axes but on their azimuthal orientation. The positional and orientational order in columnar B-DNA assemblies in solution is…
The mechanics of complex soft matter often cannot be understood in the classical physical frame of flexible polymers or rigid rods. The underlying constituents are semiflexible polymers, whose finite bending stiffness ($\kappa$) leads to…
Whereas entropy can induce phase behavior that is as rich as seen in energetic systems, microphase separation remains a very rare phenomenon in entropic systems. In this paper, we present a density functional approach to study the…
Motivated by the idea that intrinsically disordered proteins (IDPs) condense into liquid-like droplets within cells, we carry out Monte Carlo simulations of a polymer lattice model to study the relationship between charge patterning and…
One of the best known causes of dissipation in ac driven quantum systems stems from photon absorption. Dissipation can also be caused by the retarded response to the time-dependent excitation, and in general gives insight into the system's…
Phase separation within polymer networks plays a central role in shaping the structure and mechanics of both synthetic materials and living cells, including the formation of biomolecular condensates within cytoskeletal networks. Previous…
This study investigates the suitability of the annealed approximation in high-dimensional systems characterized by dense networks with quenched link disorder, employing models of coupled oscillators. We demonstrate that dynamic equations…
The liquid-liquid phase separation of biomolecules is an important process for intracellular organization. Biomolecular sequence combinatorics leads to a large variety of proteins and nucleic acids which can interact to form a diversity of…