Related papers: From Collapse to Freezing in Random Heteropolymers
Contrary to expectations based on Harris' criterion, chain disorder with frustration can modify the universality class of scaling at the theta transition of heteropolymers. This is shown for a model with random two-body potentials in 2D on…
Biological molecules can form hydrogen bonds between nearby residues, leading to helical secondary structures. The associated reduction of configurational entropy leads to a temperature dependence of this effect: the "helix-coil…
We study the holographic entanglement entropy in a homogeneous falling shell background, which is dual to the strongly coupled field theory following a global quench. For d=2 conformal field theories, it is known that the entropy has a…
Block copolymer melts self-assemble in the bulk into a variety of nanostructures, making them perfect candidates to template the position of nanoparticles. The morphological changes of block copolymers are studied in the presence of a…
We study numerically a lattice model of semiflexible homopolymers with nearest neighbor attraction and energetic preference for straight joints between bonded monomers. For this we use a new algorithm, the "Pruned-Enriched Rosenbluth…
We solve a model that takes into account entropic barriers, frustration, and the organization of a protein-like molecule. For a chain of size $M$, there is an effective folding transition to an ordered structure. Without frustration, this…
The free energy landscape of a protein-like chain in a fluid was studied by combining discontinuous molecular dynamics and parallel tempering. The model protein is a repeating sequence of four different beads, with interactions mimicking…
The study of real-life network modeling has become very popular in recent years. An attractive model is the scale-free percolation model on the lattice $\mathbb{Z}^d$, $d\ge1$, because it fulfills several stylized facts observed in large…
Model off-lattice sequences in two dimensions are constructed so that their native states are close to an on-lattice target. The Hamiltonian involves the Lennard-Jones and harmonic interactions. The native states of these sequences are…
Self-avoiding polymers in strictly two-dimensional ($d=2$) melts are investigated by means of molecular dynamics simulation of a standard bead-spring model with chain lengths ranging up to N=2048. % The chains adopt compact configurations…
We present an analytical theory for heteropolymer deformation, as exemplified experimentally by stretching of single protein molecules. Using a mean-field replica theory, we determine phase diagrams for stress-induced unfolding of typical…
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…
Mean field replica theory is employed to analyze the freezing transition of random heteropolymers comprised of an arbitrary number ($q$) of types of monomers. Our formalism assumes that interactions are short range and heterogeneity comes…
We consider ideal chains in a hypercubic lattice \mathbb{Z}^{d}, d\geq3, with a fixed ratio m of self-intersection per monomer. Despite the simplicity of the geometrical constraint, this model shows some interesting properties, such as a…
Through extensive Monte Carlo simulations, we systematically study the effect of chain stiffness on the packing ability of linear polymers composed of hard spheres in extremely confined monolayers, corresponding effectively to 2D films.…
We study the problem of "phantom" folding of the two-dimensional square lattice, in which the edges and diagonals of each face can be folded. The non-vanishing thermodynamic folding entropy per face $s \simeq .2299(1)$ is estimated both…
The scaling of entanglement entropy is computationally studied in several $1\le d \le 2$ dimensional free fermion systems that are connected by one or more point contacts (PC). For both the $k$-leg Bethe lattice $(d =1)$ and $d=2$…
While the $\Theta$-collapse of single long polymers in bad solvents is usually a continuous (tri-critical) phase transition, there are exceptions where it is preempted by a discontinuous crystallization (liquid $\leftrightarrow$ solid)…
De novo prediction of protein folding is an open scientific challenge. Many folding models and force fields have been developed, yet all face difficulties converging to native conformations. Hydrophobicity scales (HSs) play a crucial role…
We study holographic entanglement entropy in 5-dimensional charged black brane geometry obtained from Einstein-SU(2)Yang-Mills theory defined in asymptotically AdS space. This gravity system undergoes second order phase transition near its…