Recently, theoretical models to employ physical interactions between monomers for the selection of appropriate heteropolymer sequences have been suggested. The Shakhnovich-Gutin model simulates the in vivo creation of natural proteins by molecular evolution. Our model suggests a method for the in vitro synthesis of heteropolymers which are “protein-like” in the sense that they have unique 3D fo...

I use a Landau theory to study the behavior of A – B heteropolymers with disordered sequences immersed in a binary solvent mixture. Segments of type A are preferentially solvated in one type of solvent, and those of type B prefer the other type of solvent. At high temperatures, the behavior is qualitatively the same as that in a single solvent. As the temperature approaches the critical tempera...

1.1. Definition of the model. We start with the definition of the model. The dimension is denoted by d+1, d≥ 1. Then our model has three random ingredients: (1) a (d+ 1)-dimensional random medium, described by η; (2) a (d+1)-dimensional directed random walk, described by S; (3) a sequence of random variables ω, taking values ±1 describing the random monomers. So let us formally define all these...

The folding of a protein-like heteropolymer is studied by using direct simulation of a lattice model that folds rapidly to a well-defined "native" structure. The details of each molecular folding event depend on the random initial conformation as well as the random thermal fluctuations of the polymer. By analyzing the statistical properties of hundreds of folding events, a classical folding "pa...

By means of multicanonical computer simulations, we investigate thermodynamic properties of the aggregation of interacting semiflexible polymers. We analyze a mesoscopic beadstick model, where nonbonded monomers interact via Lennard-Jones forces. Aggregation turns out to be a process, in which the constituents experience strong structural fluctuations, similar to peptides in coupled folding-bin...

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 transition between the native and molten phase of the RNA as a function of temperature. The transition is driven by a competition between the energy gained from th...

We analyze the equilibrium response of random heteropolymers to mechanical deformation. In contrast to homopolymer response, the stress-induced transformation of a heteropolymer from globule to coil need not be sharp. For chain lengths relevant to biological macromolecules, intermediate necklace-like structures dominate over a range of applied force. Stability of these conformations is primaril...