Related papers: Puckering Free Energy of Pyranoses Using a Combine…
We present the results of a combined metadynamics--umbrella sampling investigation of the puckered conformers of pyranoses described using the gromos 45a4 force field. The free energy landscape of Cremer--Pople puckering coordinates has…
Cremer-Pople puckering coordinates appear to be the natural candidate variables to explore the conformational space of cyclic compounds, and in literature different parametrizations have been used to this end. However, while every…
This paper deals with the comparative use of the chemical shift surfaces to simulate experimental 13C CPMAS data on amorphous solid state disaccharides, paying particular attention to -1-1 linkage of trehalose, to -1,4…
We present a simulation protocol that allows for efficient sampling of the degrees of freedom of a solute in explicit solvent. The protocol involves using a non-equilibrium umbrella sampling method, in this case the recently developed…
Ordered graphene has been extensively studied. In this paper we undertake a first density functional study of it topologically disordered analogues of graphene, in the form of a random network, consisting predominantly of hexagonal rings,…
We present the results of a large-scale numerical study of the equilibrium three-dimensional Edwards-Anderson Ising spin glass with Gaussian disorder. Using parallel tempering (replica exchange) Monte Carlo we measure various static, as…
We report the folding thermodynamics of ccUUCGgg and ccGAGAgg RNA tetraloops using atomistic molecular dynamics simulations. We obtain a previously unreported estimation of the folding free energy using parallel tempering in combination…
Common force fields overestimate the hydration free energies of hydrophobic solutes, leading to an exaggerated hydrophobic effect. We compute the hydration free energies of linear alkanes from methane to eicosane (C${20}$H${42}$) using free…
Molecular dynamics methods have proven their applicability for the reproduction and prediction of molecular conformations during the last decades. However, most of works considered dilute solutions and relatively short trajectories that…
We use computer simulations to investigate the stability of a two-component polymer brush de-mixing on a curved template into phases of different morphological properties. It has been previously shown via molecular dynamics simulations that…
The computational study of conformational transitions in nucleic acids still faces many challenges. For example, in the case of single stranded RNA tetranucleotides, agreement between simulations and experiments is not satisfactory due to…
We study the magnetic properties of a frustrated Heisenberg spin chain with a dynamic spin-phonon interaction. By Lanczos diagonalization, preserving the full lattice dynamics, we explore the non-adiabatic regime with phonon frequencies…
We investigate conformations and dynamics of a polymer considering its monomers to be active Brownian particles. This active polymer shows very intriguing physical behavior which is absent in an active Rouse chain. The chain initially…
Monte Carlo computer simulations are used to study the segregation behaviour of two polymers under cylindrical confinement. Using a multiple-histogram method, the conformational free energy, F, of the polymers was measured as a function of…
We investigate the coarse-graining of host-guest systems under the perspective of the local distribution of pore occupancies, along with the physical meaning and actual computability of the coarse-interaction terms. We show that the widely…
The conformational free energy landscape of a system is a fundamental thermodynamic quantity of importance particularly in the study of soft matter and biological systems, in which the entropic contributions play a dominant role. While…
A puckered sheet is a freestanding crystalline membrane with an embedded array of bistable buckled units. Recent work has shown that the bistable units behave like spins in a two-dimensional compressible Ising antiferromagnet with, however,…
This thesis is an attempt to provide a new outlook on complex systems, as well as some physical answers for certain models, taking a computational approach. We have focused on disordered systems, addressing two traditional problems in three…
In this paper, we investigated the annealing experiments of poly(mercaptopropylmethylsiloxane, PMMS) confined within two types of porous templates (anodic aluminium oxide, AAO, and silica) characterized by different pore diameter, d=…
Monte Carlo computer simulations are used to study the conformational free energy of a folded polymer confined to a long cylindrical tube. The polymer is modeled as a hard-sphere chain. Its conformational free energy $F$ is measured as a…