Related papers: Exactly Solvable Model for Helix-Coil-Sheet Transi…
We have performed chain-growth simulations of minimalistic hybrid lattice models for polymers interacting with interfaces of attractive solid substrates in order to gain insights into the conformational transitions of the polymers in the…
The Flory-Huggins theory describes the phase separation of solutions containing polymers. Although it finds widespread application from polymer physics to materials science to biology, the concentrations that coexist in separate phases at…
Hybrid particle-field methods are computationally efficient approaches for modelling soft matter systems. So far applications of these methodologies have been limited to constant volume conditions. Here, we reformulate particle-field…
We consider a model of two (fully) compact polymer chains, coupled through an attractive interaction. These compact chains are represented by Hamiltonian paths (HP), and the coupling favors the existence of common bonds between the chains.…
Molecular dynamics simulations are used to study structure formation in simple model polymer chains that are subject to excluded volume and torsional interactions. The changing conformations exhibited by chains of different lengths under…
Using Wang-Landau sampling with suitable Monte Carlo trial moves (pull moves and bond-rebridging moves combined) we have determined the density of states and thermodynamic properties for a short sequence of the HP protein model. For free…
In this report, we explore the use of a quantum optimization algorithm for obtaining low energy conformations of protein models. We discuss mappings between protein models and optimization variables, which are in turn mapped to a system of…
Port-Hamiltonian systems theory provides a structured approach to modelling, optimization and control of multiphysical systems. Yet, its relationship to thermodynamics seems to be unclear. The Hamiltonian is traditionally thought of as…
We describe an approach to the study of phase transitions in Potts models based on an estimate of the complexity of the locus of real zeros of the partition function, computed in terms of the classes in the Grothendieck ring of the affine…
We describe and test an implicit solvent all-atom potential for simulations of protein folding and aggregation. The potential is developed through studies of structural and thermodynamic properties of 17 peptides with diverse secondary…
The Cahn-Hilliard system has been used to describe a wide number of phase separation processes, from co-polymer systems to lipid membranes. In this work the convergence properties of a closest-point based scheme is investigated. In place of…
We test a simplified, local version of the helix model on two synthetic and two natural proteins, to study its efficiency in predicting the native secondary structure. The results we obtain are very good for the synthetic sequences, poorer…
The experimental calorimetric two-state criterion requires the van't Hoff enthalpy $\Delta H_{\rm vH}$ around the folding/unfolding transition midpoint to be equal or very close to the calorimetric enthalpy $\Delta H_{\rm cal}$ of the…
We have investigated the potential energy surfaces for alanine chains consisting of three and six amino acids. For these molecules we have calculated potential energy surfaces as a function of the Ramachandran angles Phi and Psi, which are…
Using multicanonical simulations, the authors study the effect of charged end groups on helix formation in alanine based polypeptides. They confirm earlier reports that neutral polyalanine exhibits a pronounced helix-coil transition in gas…
A self-consistent field theory was developed in the grand-canonical ensemble formulation to study transitions in a helix-coil multiblock globule. Helical and coil parts are treated as stiff rods and self-avoiding walks of variable lengths…
To what extent do general features of folding/unfolding kinetics of small globular proteins follow from their thermodynamic properties? To address this question, we investigate a new simplifed protein chain model that embodies a cooperative…
We discuss general thermodynamic properties of molecular structure formation processes like protein folding by means of simplified, coarse-grained models. The conformational transitions accompanying these processes exhibit similarities to…
The packing of elastic sheets is investigated in a quasi two-dimensional experimental setup: a sheet is pulled through a rigid hole acting as a container, so that its configuration is mostly prescribed by the cross-section of the sheet in…
We derive and validate a partition function for low-dimensional systems interacting with a heat bath, addressing the general issue of thermodynamic modeling of nanoscale systems. In contrast to bulk systems in the canonical (NVT) ensemble…