Related papers: Collective Variables for the Study of Crystallizat…
The data torrent unleashed by current and upcoming astronomical surveys demands scalable analysis methods. Many machine learning approaches scale well, but separating the instrument measurement from the physical effects of interest, dealing…
Variable selection in cluster analysis is important yet challenging. It can be achieved by regularization methods, which realize a trade-off between the clustering accuracy and the number of selected variables by using a lasso-type penalty.…
We systematically study the relationship between equilibrium and non-equilibrium phase diagrams of a system of short-ranged attractive colloids. Using Monte Carlo and Brownian dynamics simulations we find a window of enhanced…
Molecular dynamics simulations are widely used across chemistry, physics, and biology, providing quantitative insight into complex processes with atomic detail. However, their limited timescale of a few microseconds is a significant…
Based on multiple simulation trajectories, which started from dispersively selected initial conformations, the weighted ensemble dynamics method is designed to robustly and systematically explore the hierarchical structure of complex…
We consider several patchy particle models that have been proposed in literature and we investigate their candidate crystal structures in a systematic way. We compare two different algorithms for predicting crystal structures: (i) an…
Molecular dynamics (MD) simulations are useful in obtaining thermodynamic and kinetic properties of bio-molecules but are limited by the timescale barrier, i.e., we may be unable to efficiently obtain properties because we need to run…
In the present work, crystallization in melts and poor-solvent solutions of semiflexible polymers with different concentration was studied by means of dissipative particle dynamics simulation technique. We use a coarse-grained polymer model…
We present a methodology for simulating dilute suspensions of particles settling under gravity, with the main purpose of overcoming limitations of triply periodic configurations, mainly the strong vertical correlation that hinders the study…
In this tutorial-style review we discuss basic concepts of coupled cluster theory and recent developments that increase its computational efficiency for calculations of molecules, solids and materials in general. We will touch upon the…
Jamming is a phenomenon shared by a wide variety of systems, such as granular materials, foams, and glasses in their high density regime. This has motivated the development of a theoretical framework capable of explaining many of their…
This paper exposes a novel exploratory formalism, which end goal is the numerical simulation of the dynamics of a cloud of particles weakly or strongly coupled with a turbulent fluid. Giventhe large panel of expertise of the list of…
We present an investigation into data selection methods for the efficient sampling of configuration space as applied to the development of inter-atomic potentials for scale bridging in molecular dynamics (MD) simulations. This investigation…
We use Monte Carlo and molecular dynamics simulations to study phase behavior and transport properties in a symmetric binary fluid where particles interact via Lennard-Jones potential. Our results for the critical behavior of collective…
When fitting statistical models, some predictors are often found to be correlated with each other, and functioning together. Many group variable selection methods are developed to select the groups of predictors that are closely related to…
The computational study of conformational transitions in RNA and proteins with atomistic molecular dynamics often requires suitable enhanced sampling techniques. We here introduce a novel method where concurrent metadynamics are integrated…
Enhanced sampling algorithms have emerged as powerful methods to extend the utility of molecular dynamics simulations and allow the sampling of larger portions of the configuration space of complex systems in a given amount of simulation…
A widely spread method of crystal preparation is to precipitate it from a supersaturated solution. In such a process, control of solution concentration is of paramount importance. Nucleation process, polymorph selection, and crystal habits…
We propose a hybrid deterministic and stochastic approach to achieve extended time scales in atomistic simulations that combines the strengths of molecular dynamics (MD) and Monte Carlo (MC) simulations in an easy-to-implement way. The…
We perform experiments with a granular system that consists of a collection of identical hollow spheres (ping-pong balls). Particles rest on a horizontal metallic grid and are confined within a circular region. Fluidization is achieved by…