Related papers: Thermodynamic Sampling of Molecular Conformations
Using the conventional approach of superposing plane waves, it is not possible to create a strictly isotropic turbulent magnetic field structure that obeys all physical constraints, which are (i) equal mean of all magnetic field components;…
In particle-based algorithms, the effect of binary collisions is commonly described in a statistical way, using Monte Carlo techniques. It is shown that, in the relativistic regime, stringent constraints should be considered on the sampling…
In Monte Carlo simulations with a local update algorithm, the auto-correlation with respect to the topological charge tends to become very long. In the extreme case one can only perform reliable measurements within fixed sectors. We…
With the help of lattice Monte Carlo modelling of heteropolymers, we show that the necessary condition for a protein to fold on short call is to proceed through partially folded intermediates. These elementary structures are formed at an…
The rates of protein folding with photon absorption or emission and the cross section of photon -protein inelastic scattering are calculated from the quantum folding theory by use of standard field-theoretical method. All these protein…
We solve a model that takes into account entropic barriers, frustration, and the organization of a protein-like molecule. For a chain of size $M$, there is an effective folding transition to an ordered structure. Without frustration, this…
Despite their importance for precision QCD calculations, correlations between in- and out-of-jet regions of phase space have never directly been observed. These so-called non-global effects are present generically whenever a collider…
Solvent-free coarse grained models represent one of the most promising approaches for molecular simulations of mesoscopically large membranes. In these models, the size of the simulated membrane is limited by the slow relaxation time of…
The integration time step is a critical determinant of performance in molecular dynamics simulations, governing the trade-off between speed and fidelity. Although 2 fs remains the standard in atomistic biomolecular simulations, the push for…
Equilibrium adsorption of disk-like particles on patterned adhesive surfaces is studied using Monte Carlo simulations. The surface is represented as a two-dimensional plane with circular adhesive domains arranged either regularly or…
We study the molecular mode coupling theory for a liquid of diatomic molecules. The equations for the critical tensorial nonergodicity parameters ${\bf F}_{ll'}^m(q)$ and the critical amplitudes of the $\beta$ - relaxation ${\bf…
Molecular rotors form twisted conformations upon photoexcitation, with their fluorescent relaxation time serving as a measure of viscosity. They have been used to assess membrane viscosities but yield higher values compared to other…
Configurational entropy is an important factor in the free energy change of many macromolecular recognition and binding processes, and has been intensively studied. Despite great progresses that have been made, the global sampling remains…
De novo prediction of protein folding is an open scientific challenge. Many folding models and force fields have been developed, yet all face difficulties converging to native conformations. Hydrophobicity scales (HSs) play a crucial role…
Magnetic molecules are investigated with respect to their usability as units in future quantum devices. In view of quantum computing, a necessary prerequisite is a long coherence time of superpositions of low-lying levels. In this article,…
Three-dimensional single-component ideal gas systems composed of model homogeneous rigid molecules in various molecular shapes and sizes are simulated by a molecular Monte Carlo simulation technique. We reveal that percolation thresholds of…
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…
In this work we study the thermodynamic properties of ultrathin ferromagnetic dots using Monte Carlo simulations. We investigate the vortex density as a function of the temperature and the vortex structure in monolayer dots with…
Monte Carlo methods play important part in modern statistical physics. The application of these methods suffer from two main difficulties.The first is caused by the relatively small number of particles that can participate in any numerical…
We study a sequential Monte Carlo algorithm to sample from the Gibbs measure with a non-convex energy function at a low temperature. We use the practical and popular geometric annealing schedule, and use a Langevin diffusion at each…