Related papers: Local Interactions and Protein Folding: A Model St…
Exact results for the scaling properties of compact polymers on the square lattice are obtained from an effective field theory. The entropic exponent \gamma=117/112 is calculated, and a line of fixed points associated with interacting…
The square lattice with central-force springs on nearest-neighbor bonds is isostatic. It has a zero mode for each row and column, and it does not support shear. Using the Coherent Potential Approximation (CPA), we study how the random…
Proteins are minimally frustrated polymers. However, for realistic protein models non-native interactions must be taken into account. In this paper we analyze the effect of non-native interactions on the folding rate and on the folding free…
Floppy microscale spring networks are widely studied in theory and simulations, but no well-controlled experimental system currently exists. Here, we show that square lattices consisting of colloid-supported lipid bilayers functionalized…
We study the statistics of matrix elements of local operators in the basis of energy eigenstates in a paradigmatic integrable many-particle quantum theory, the Lieb-Liniger model of bosons with repulsive delta-function interaction. Using…
Protein representation and potential function are essential ingredients for studying proteins folding and protein prediction. We introduce a novel geometric representation of contact interactions using the edge simplices from alpha shape of…
We study a process of pattern formation for a generic model of species anchored to the nodes of a network where local reactions take place, and that experience non-reciprocal long-range interactions, encoded by the network directed links.…
In structure-based models of proteins, one often assumes that folding is accomplished when all contacts are established. This assumption may frequently lead to a conceptual problem that folding takes place in a temperature region of very…
In part I of this contribution we have reported how the Flory-Huggins interaction parameter chi can be modeled as a function of chain length within the composition range of pair interaction between the macromolecules by means of the three…
We recently introduced a physical model [Hoang et al., P. Natl. Acad. Sci. USA (2004), Banavar et al., Phys. Rev. E (2004)] for proteins which incorporates, in an approximate manner, several key features such as the inherent anisotropy of a…
We study theoretically the spatiotemporal response of a lipid membrane submitted to a local chemical change of its environment, taking into account the time-dependent profile of the reagent concentration due to diffusion in the solution…
The presence of one or more species at some spatial locations but not others is a central matter in ecology. This phenomenon is related to ecological pattern formation. Nonlocal interactions can be considered as one of the mechanisms…
Protein folds are built primarily from the packing together of two types of structures: alpha-helices and beta-sheets. Neither structure is rigid, and the flexibility of helices and sheets is often important in determining the final fold…
We present calculations of the localisation length, $\lambda_{2}$, for two interacting particles (TIP) in a one-dimensional random potential, presenting its dependence on disorder, interaction strength $U$ and system size. $\lambda_{2}(U)$…
Thermoresponsive polymers hold both fundamental and technological importance, but the essential physics driving their intriguing behavior is not wholly understood. We introduce a lattice framework that incorporates elements of Flory-Huggins…
Isolated long-range interacting particle systems appear generically to relax to non-equilibrium states ("quasi-stationary states" or QSS) which are stationary in the thermodynamic limit. A fundamental open question concerns the "robustness"…
The conformations of interacting linear polymers on a dynamical planar random lattice are studied using a random two-matrix model. An exact expression for the partition function of self-avoiding chains subject to attractive contact…
We calculate the dynamical structure factor S(q, {\omega}) of a weakly interacting helical edge state in the presence of a magnetic field B. The latter opens a gap of width 2B in the single-particle spectrum, which becomes strongly…
In this article the configurational space of two simple protein models consisting of polymers composed of a periodic sequence of four different kinds of monomers is studied as a function of temperature. In the protein models, hydrogen bond…
Using Monte Carlo dynamics and the Monte Carlo Histogram Method, the simple three-dimensional 27 monomer lattice copolymer is examined in depth. The thermodynamic properties of various sequences are examined contrasting the behavior of good…