Related papers: Visualizing Conformations in Molecular Dynamics
In order to characterize molecular structures we introduce configurational fingerprint vectors which are counterparts of quantities used experimentally to identify structures. The Euclidean distance between the configurational fingerprint…
The structural dynamics of macromolecules is important for most microbiological processes, from protein folding to the origins of neurodegenerative disorders. Noninvasive measurements of these dynamics are highly challenging. Recently,…
Dynamic bonding is an essential feature of many soft materials. Molecular simulations have proven to be a powerful tool for modeling bonding kinetics and thermodynamics in these materials, providing insights into their properties that…
The motivation for this study came from the task of analysing the kinetic behavior of single molecules in a living cell based on Single Molecule Localization Microscopy. Given measurements of both the motion of clusters and molecules, the…
Conformational transitions are ubiquitous in biomolecular systems, have significant functional roles and are subject to evolutionary pressures. Here we provide a first theoretical framework for topological transition, i.e. conformational…
In this paper I propose a new model for representing the formation energies of multicomponent crystalline alloys as a function of atom types. In the cases when displacements of atoms from their equilibrium positions are not large, the…
Sequential Monte Carlo methods, also known as particle methods, are a popular set of techniques for approximating high-dimensional probability distributions and their normalizing constants. These methods have found numerous applications in…
We discuss the efficiency of Monte Carlo methods in solving continuum radiative transfer problems. The sampling of the radiation field and convergence of dust temperature calculations in the case of optically thick clouds are both studied.…
Rigid bodies, made of smaller composite beads, are commonly used to simulate anisotropic particles with molecular dynamics or Monte Carlo methods. To accurately represent the particle shape and to obtain smooth and realistic effective pair…
Understanding the behavior of numerical metaheuristic optimization algorithms is critical for advancing their development and application. Traditional visualization techniques, such as convergence plots, trajectory mapping, and fitness…
This chapter is devoted to the computation of equilibrium (thermodynamic) properties of quantum systems. In particular, we will be interested in the situation where the interaction between particles is so strong that it cannot be treated as…
Understanding protein dynamics are essential for deciphering protein functional mechanisms and developing molecular therapies. However, the complex high-dimensional dynamics and interatomic interactions of biological processes pose…
The basic ingredients of models for the internal dynamics of globular clusters are reviewed, with an emphasis on the description of equilibrium configurations. The development of progressive complexity in the models is traced, concentrating…
Through extensive molecular simulations we determine a phase diagram of attractive, flexible polymer chains in two and three dimensions. A surprisingly rich collection of distinct crystal morphologies appear, which can be finely tuned…
There is increasing interest in using high-energy collisions to probe the structure of nuclei, in particular with the high-precision data made possible by collisions performed with pairs of isobaric species. A systematic study requires a…
Rapidly growing data sizes of scientific simulations pose significant challenges for interactive visualization and analysis techniques. In this work, we propose a compact probabilistic representation to interactively visualize large…
We explore the morphological and dynamical evolution of galaxy clusters in simulations using scalar and vector-valued Minkowski valuations and the concept of fundamental plane relations. In this context, three questions are of fundamental…
Tailoring the performance of next-generation high entropy materials requires a deep understanding of the competition between entropy-driven random solid solution and enthalpy-driven chemical ordering. Investigating such order and disorder…
In this work, we present a new computational approach to characterize and classify molecular packing in the solid states. The key idea is to project each neighboring molecule (or short contact) from the centered molecule into a unit sphere…
The microscopic calculation of nuclear level densities in the presence of correlations is a difficult many-body problem. The shell model Monte Carlo method provides a powerful technique to carry out such calculations using the framework of…