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Monte Carlo (MC) simulations of lattice models are a widely used way to compute thermodynamic properties of substitutional alloys. A limitation to their more widespread use is the difficulty of driving a MC simulation in order to obtain the…
Understanding how highly symmetric, robust, monodisperse protein cages self-assemble can have major applications in various areas of bio-nanotechnology, such as drug delivery, biomedical imaging and gene therapy. We develop a model to…
We present a review on the study of metastable silicon, primarily focusing mainly on the aspects of liquid-liquid transition, critical point and phase behaviour, structural and dynamic properties of liquid phase as well as crystal…
This paper presents a large-scale $ab$ $initio$ simulation study of amorphous silicon hydride ($a$-Si$_{\text{1-x}}$H$_{\text{x}}$) with an emphasis on the structure and properties of the material across a range of hydrogen concentration by…
The theory of transition between $\alpha$-helix, $\beta$-sheet and random coil conformation of a protein is discussed through a simple model, that includes both short and long-range interactions. Besides the bonding parameter and helical…
Mesoscopic molecular dynamics simulations are used to determine the large scale structure of several binary polymer mixtures of various chemical architecture, concentration, and thermodynamic conditions. By implementing an analytical…
Within the frame of an effective, coarse-grained hydrophobic-polar protein model, we employ multicanonical Monte Carlo simulations to investigate free-energy landscapes and folding channels of exemplified heteropolymer sequences, which are…
Path integral Monte Carlo (PIMC) simulations with very simple models were used in order to unveil the physics behind the isotope effects in H-bonded ferroelectrics. First, we studied geometrical effects in the H-bonds caused by deuteration…
An implementation of the Reverse Monte Carlo algorithm is presented for the study of amorphous tetrahedral semiconductors. By taking into account a number of constraints that describe the tetrahedral bonding geometry along with the radial…
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 E. coli glucose-galactose chemosensory receptor is a 309 residue, 32 kDa protein consisting of two distinct structural domains. In this computational study, we studied the protein's thermal fluctuations, including both the large scale…
We describe a simple ansatz to approximate the low temperature behavior of proteins and peptides by a mean-field-like model which is analytically solvable. For a small peptide some thermodynamic quantities are calculated and compared with…
Mesoscale simulations of woven composites using parameterized analytical geometries offer a way to connect constituent material properties and their geometric arrangement to effective composite properties and performance. However, the…
Lattice models, for their coarse-grained nature, are best suited for the study of the ``designability problem'', the phenomenon in which most of the about 16,000 proteins of known structure have their native conformations concentrated in a…
We extend the applicability range of fermionic path integral Monte Carlo simulations to heavier elements and lower temperatures by introducing various localized nodal surfaces. Hartree-Fock nodes yield the most accurate prediction for…
Semiconductor artificial graphene nanostructures where Hubbard model parameter $U/t$ can be of the order of 100, provide a highly controllable platform to study strongly correlated quantum many-particle phases. We use accurate variational…
Restricted path integral Monte Carlo simulations are used to calculate the equilibrium properties of hydrogen in the density and temperature range of $9.83 \times 10^{-4}\rm \leq \rho \leq 0.153 \rm gcm^{-3}$ and $5000 \leq T \leq 250 000…
This paper is the last in a series of three papers which investigate pseudoholomorphic strips in the symplectisation of a three dimensional closed contact manifold with a mixed boundary condition. We will prove a compactness and an…
Mono- and poly-disperse melts of oligomers (average length 10 monomers) of trans-1,4-polyisoprene are simulated in full atomistic detail. The force-field is developed by means of a mixture of ab initio quantum-chemistry and an automatic…
We study the finite size scaling behaviour of the specific heat of thin films in the neighbourhood of the lambda-transition. To this end we have simulated the improved two-component phi^4 model on the simple cubic lattice. We employ free…