Related papers: Visualizing Conformations in Molecular Dynamics
Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…
This paper describes the method of visualization of periodic constituents and instability areas in series of measurements, being based on the algorithm of smoothing out and concept of one-dimensional cellular automata. A method can be used…
We present the complete phase diagram for one-dimensional binary mixtures of bosonic ultracold atomic gases in a harmonic trap. We obtain exact results with direct numerical diagonalization for small number of atoms, which permits us to…
Molecular Dynamics simulations are essential tools for understanding the dynamic behavior of biomolecules, yet extracting meaningful molecular pathways from these simulations remains challenging due to the vast amount of generated data. In…
We extend the phase field crystal model to accommodate exact atomic configurations and vacancies by requiring the order parameter to be non-negative. The resulting theory dictates the number of atoms and describes the motion of each of…
We study the geometry of the critical clusters in fully coordinated percolation on the square lattice. By Monte Carlo simulations (static exponents) and normal mode analysis (dynamic exponents), we find that this problem is in the same…
The nucleation of crystals in liquids is one of nature's most ubiquitous phenomena, playing an important role in areas such as climate change and the production of drugs. As the early stages of nucleation involve exceedingly small time and…
Virtual screening can accelerate drug discovery by identifying promising candidates for experimental evaluation. Machine learning is a powerful method for screening, as it can learn complex structure-property relationships from experimental…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
Merging galaxy clusters have become one of the most important probes of dark matter, providing evidence for dark matter over modified gravity and even constraints on the dark matter self-interaction cross-section. To properly constrain the…
Assessing the convergence of a biomolecular simulation is an essential part of any computational investigation. This is because many important quantities (e.g., free energy differences) depend on the relative populations of different…
The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…
An important aspect of astrophysical MHD turbulence research is developing diagnostics to connect simulations with the observable universe. Turbulent systems are by definition structurally complex in all fluid variables (density, velocity,…
Molecular building blocks interacting at the nanoscale organize spontaneously into stable mono- layers that display intriguing long-range ordering motifs on the surface of atomic substrates. The patterning process, if appropriately…
Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with…
Dynamical behavior of the clusters during relaxation is studied in two-dimensional Potts model using cluster algorithm. Average cluster size and cluster formation velocity are calculated on two different lattice sizes for different number…
Superellipse sector particles (SeSPs) are segments of superelliptical curves that form a tunable set of hard-particle shapes for granular and colloidal systems. SeSPs allow for continuous parameterization of corner sharpness, aspect ratio,…
In this work we report on the Monte Carlo study performed to understand and reproduce experimental measurements of a new plastic \b{eta}-detector with cylindrical geometry. Since energy deposition simulations differ from the experimental…
Pixel-space full spectrum fitting exploiting non-linear $\chi^2$ minimization became a \emph{de facto} standard way of deriving internal kinematics from absorption line spectra of galaxies and star clusters. However, reliable estimation of…
One of the molecular properties most intuitive to the human perception is the geometrical shape. However, when exploring a large chemical space the determination of shape needs to be automated. We present a fast and simple approach to…