Related papers: Deconstructing the energy landscape: new algorithm…
We propose a novel phase-field model to predict elastic microphase separation in polymer gels. To this end, we extend the Cahn-Hilliard free-energy functional to incorporate an elastic strain energy and a coupling term. These contributions…
The folding pathway and rate coefficients of the folding of a knotted protein are calculated for a potential energy function with minimal energetic frustration. A kinetic transition network is constructed using the discrete path sampling…
Field-theoretical method is efficient in predicting the assembling structures of polymeric systems. However, for the polymer/nanoparticle mixture, the continuous density description is not suitable to capture the realistic assembly of…
Applying multicanonical simulations we investigated folding properties of off-lattice heteropolymers employing a mesoscopic hydrophobic-polar model. We study for various sequences folding channels in the free-energy landscape by comparing…
Chain molecules play a key role in the polymer field and in living cells. Our focus is on a new homopolymer model of a linear chain molecule subject to an attractive self-interaction promoting compactness. We analyze the model using simple…
A recently developed lattice field theory approach to the statistical mechanics of charged polymers in electrolyte solutions [S. Tsonchev, R. D. Coalson, and A. Duncan, Phys. Rev. E {\bf{60}}, 4257, (1999)] is generalized to the case where…
While stretching of most polymer chains leads to rather featureless force-extension diagrams, some, notably DNA, exhibit non-trivial behavior with a distinct plateau region. Here we propose a unified theory that connects force-extension…
We consider self-avoiding lattice polygons, in the hypercubic lattice, as a model of a ring polymer adsorbed at a surface and either being desorbed by the action of a force, or pushed towards the surface. We show that, when there is no…
Phase separation in polymer solutions often correlates with single-chain and two-chain properties, such as the single-chain radius of gyration, Rg, and the pairwise second virial coefficient, B22. However, recent studies have shown that…
Semiflexible polymers in poor solvents exhibit a rich variety of collapsed morphologies, including globules, toroids, and rodlike bundles, arising from the competition between attractive interactions and chain stiffness. Computer…
The equilibrium free energy landscape of an off-lattice model protein as a function of an internal (reaction) coordinate is reconstructed from out-of-equilibrium mechanical unfolding manipulations. This task is accomplished via two…
A method to reconstruct the energy landscape of small peptides is presented with reference to a 2d off--lattice model. The starting point is a statistical analysis of the configurational distances between generic minima and directly…
The energy landscapes of proteins have evolved to be different from most random heteropolymers. Many studies have concluded that evolutionary selection for rapid and reliable folding to a given structure that is stable at biological…
We study algorithms for solving quadratic systems of equations based on optimization methods over polytopes. Our work is inspired by a recently proposed convex formulation of the phase retrieval problem, which estimates the unknown signal…
We have analyzed the dependence of average ground state energy per monomer, $e$, of the complex of two random heteropolymers with quenched sequences, on chain length, $n$, in the ensemble of chains with uniform distribution of primary…
Phase diagram of the ground states of DNA in a bad solvent is studied for a semi-flexible polymer model with a generalized local elastic bending potential characterized by a nonlinearity parameter $x$ and effective self-attraction promoting…
Protein folding is analyzed using a replica variational formalism to investigate some free energy landscape characteristics relevant for dynamics. A random contact interaction model that satisfies the minimum frustration principle is used…
A system of two self and mutual interacting ring polymers, close together in space, can display several competing equilibrium phases and phase transitions. Using Monte Carlo simulations and combinatorial arguments on a corresponding lattice…
The self-avoid random walk algorithm has been extensively used in the study of polymers. In this work we study the basic properties of the trajectories generated with this algorithm when two interactions are added to it: contact and folding…
In this paper we analyse both the dynamics and the high density physics of the infinite dimensional lattice gas model for random heteropolymers recently introduced in \cite{jort}. Restricting ourselves to site-disordered heteropolymers, we…