Related papers: Structural Properties of Small Semiconductor-Bindi…
A minimal off-lattice model for alpha-helical proteins is presented. It is based on hydrophobicity forces and sequence independent local interactions. The latter are chosen so as to favor the formation of alpha-helical structure. They model…
Simulation of transport properties of confined, low-dimensional fluids can be performed efficiently by means of Multi-Particle Collision (MPC) dynamics with suitable thermal-wall boundary conditions. We illustrate the effectiveness of the…
Two-state cooperativity is an important characteristic in protein folding. It is defined by a depletion of states lying energetically between folded and unfolded conformations. While there are different ways to test for two-state…
The investigation of freezing transitions of single polymers is computationally demanding, since surface effects dominate the nucleation process. In recent studies we have systematically shown that the freezing properties of flexible,…
Protein folding, peptide aggregation and crystallization, as well as adsorption of molecules on soft or solid substrates have an essential feature in common: In all these processes, structure formation is guided by a collective, cooperative…
We perform a generalized-ensemble simulation of a small peptide taking the interactions among all atoms into account. From this simulation we obtain thermodynamic quantities over a wide range of temperatures. In particular, we show that the…
Hybrid molecular dynamics/Monte Carlo simulations used to study melts of unentangled, thermoreversibly associating supramolecular polymers. In this first of a series of papers, we describe and validate a model that is effective in…
We study conformational transitions of simple coarse-grained models for protein-like heteropolymers on the simple cubic lattice and off-lattice, respectively, by means of multicanonical sampling algorithms. The effective hydrophobic/polar…
A reduced protein model with five to six atoms per amino acid and five amino acid types is developed and tested on a three-helix-bundle protein, a 46-amino acid fragment from staphylococcal protein A. The model does not rely on the widely…
Thermodynamical properties of the helix-coil transition were successfully described in the past by the model of Lifson, Poland and Sheraga. Here we compute the corresponding structure factor and show that it possesses a universal scaling…
An atomic protein model with a minimalistic potential is developed and then tested on an alpha-helix and a beta-hairpin, using exactly the same parameters for both peptides. We find that melting curves for these sequences to a good…
We perform Monte Carlo simulation of the thermodynamic and structural properties of Hard-, Square-Well, and Square-Shoulder Disks in narrow channels. For the thermodynamics we study the internal energy per particle and the longitudinal and…
We present extensive new \emph{ab initio} path integral Monte Carlo (PIMC) simulations of normal liquid $^3$He without any nodal constraints. This allows us to study the effects of temperature on different structural properties like the…
In a recent work we proposed a coarse-grained methodology for studying the response of peptides when simulated at different values of pH; in this work we extend the methodology to analyze the pH-dependent behavior of coiled coils. This…
The structural and thermodynamic properties of fluids whose molecules interact via potentials with a hard-core plus a square well, a square shoulder, and a second square well, are considered. Those properties are derived by using a…
One-dimensional Heisenberg spin 1/2 chains with random ferro- and antiferromagnetic bonds are realized in systems such as $Sr_3 CuPt_{1-x} Ir_x O_6$. We have investigated numerically the thermodynamic properties of a generic random bond…
The helix-coil transition is modified by grafting to a surface. This modification is studied for short peptides capable of forming $\alpha$-helices. Three factors are involved: (i) the grafting can induced change of the boundary free energy…
Variational methods are used to calculate structural and thermodynamical properties of a titrating polyelectrolyte in a discrete representation. The Coulomb interactions are emulated by harmonic repulsive forces, the force constants being…
A small model polypeptide represented in atomic detail is folded using Monte Carlo dynamics. The polypeptide is designed to have a native conformation similar to the central part of the helix-turn-helix protein ROP. Starting from a…
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…