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Hard helices can be regarded as a paradigmatic elementary model for a number of natural and synthetic soft matter systems, all featuring the helix as their basic structural unit: from natural polynucleotides and polypeptides to synthetic…
We show how to use the multiple histogram method to combine canonical ensemble Monte Carlo simulations made at different temperatures and densities. The method can be applied to study systems of particles with arbitrary interaction…
We propose an off-lattice model for a self-avoiding homopolymer chain with two different competing attractive interactions, mimicking the hydrophobic effect and the hydrogen bond formation respectively. By means of Monte Carlo simulations,…
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…
The basic models of helix-coil transitions in biomolecules are introduced. These include phenomenological, zipper (Bragg-Zimm) models of polypeptides, loop-entropy (Poland-Scheraga) and Hamiltonian (Peyrard-Bishop) models of homogeneous DNA…
We present the first review of the current state of the literature on electronic properties and phase transitions in TlX and TlMX2 (M = Ga, In; X = Se, S, Te) compounds. These chalcogenides belong to a family of the low-dimensional…
Polymer blends consisting of two or more polymers are important for a wide variety of industries and processes, but, the precise mechanism of their thermomechanical behaviour is incompletely understood. In order to understand clearly, it is…
The structural and dynamical properties of OCS molecules solvated in Helium clusters are studied using reptation quantum Monte Carlo, for cluster sizes n=3-20 He atoms. Computer simulations allow us to establish a relation between the…
Microgels are soft colloids that, in virtue of their polymeric nature, can react to external stimuli such as temperature or pH by changing their size. The resulting swelling/deswelling transition can be exploited in fundamental research as…
Purpose: From the myofibrils to the whole muscle scale, muscle micro-constituents exhibit passive and active mechanical properties, potentially coupled to electrical, chemical, and thermal properties. Experimental characterization of some…
Thermoresponsive microgels are soft colloids that find widespread use as model systems for soft matter physics. Their complex internal architecture, made of a disordered and heterogeneous polymer network, has been so far a major challenge…
In this manuscript, we describe a new configurational bias Monte Carlo technique for the simulation of peptides. We focus on the biologically relevant cases of linear and cyclic peptides. Our approach leads to an efficient,…
We study the phase behavior of single homopolymers in a simple hydrophobic/hydrophilic off-lattice model with sequence independent local interactions. The specific heat is, not unexpectedly, found to exhibit a pronounced peak well below the…
We present a new, biased Monte Carlo scheme for simulating complex, cyclic peptides. Backbone atoms are equilibrated with a biased rebridging scheme, and side-chain atoms are equilibrated with a look-ahead configurational bias Monte Carlo.…
The boundaries of cooperative helix--coil transitions directly affect protein allostery and conformational dynamics, yet the physical origin of the persistent one-to-two-residue assignment ambiguity at these structural interfaces remains…
A wide survey has been performed, concerning atomic binding energies and ionization energies used by well- known general purpose Monte Carlo codes and a few specialized electromagnetic models for track structure simulation. Validation…
Being motivated by the surge of fermionic quantum Monte Carlo simulations at finite temperature, we present a detailed analysis of the permutation-cycle properties of path integral Monte Carlo (PIMC) simulations of degenerate electrons.…
We use Monte Carlo simulations to investigate the thermodynamical behaviour of aggregates consisting of few superparamagnetic particles in a colloidal suspension. The potential energy surface of this classical two-level system with a stable…
Most helix-coil transition theories can be characterized by a set of three parameters: energetic, describing the (free) energy cost of forming a helical state in one repeating unit; entropic, accounting for the decrease of entropy due to…
We have systematically studied the thermodynamic properties of a two-dimensional half-filled SU(2N) Hubbard model on a square lattice by using the determinant quantum Monte Carlo method. The entropy-temperature relation, the isoentropy…