Related papers: Automated analysis of continuum fields from atomis…
We present simulation results on the structure and dynamics of micromagnetic point singularities with atomistic resolution. This is achieved by embedding an atomistic computational region into a standard micromagnetic algorithm. Several…
A variety of enhanced statistical and numerical methods are now routinely used to extract comprehensible and relevant thermodynamic information from the vast amount of complex, high-dimensional data obtained from intensive molecular…
Activity or spin patterns on random scale-free network are studied by mean field analysis and computer simulations. These activity patterns evolve in time according to local majority-rule dynamics which is implemented using (i) parallel or…
We describe a novel coarse-grained simulation method for modelling the dynamics of globular macromolecules, such as proteins. The macromolecule is treated as a continuum that is subject to thermal fluctuations. The model includes a…
The recent experimental progresses in handling microscopic systems have allowed to probe them at levels where fluctuations are prominent, calling for stochastic modeling in a large number of physical, chemical and biological phenomena. This…
We review the recent literature on the simulation of the structure and deformation of amorphous glasses, including oxide and metallic glasses. We consider simulations at different length and time scales. At the nanometer scale, we review…
Identifying the relevant coarse-grained degrees of freedom in a complex physical system is a key stage in developing powerful effective theories in and out of equilibrium. The celebrated renormalization group provides a framework for this…
Seismogenic plate boundaries are presumed to behave in a similar manner to a densely packed granular medium, where fault and blocks systems rapidly rearrange the distribution of forces within themselves, as particles do in slowly sheared…
As a complementary tool to laboratory experiments, discrete numerical simulation, applied to granular materials, provides valuable information on the grain and contact scale microstructure, thereby enabling one to better understand the…
Coarse-graining or model reduction is a term describing a range of approaches used to extend the time-scale of molecular simulations by reducing the number of degrees of freedom. In the context of molecular simulation, standard…
To develop, calibrate and/or validate continuum models from experimental or numerical data, micro-macro transition methods are required. These methods are used to obtain the continuum fields (such as density, momentum, stress) from the…
We present a coupled atomistic-continuum method for the modeling of defects and interface dynamics of crystalline materials. The method uses atomistic models such as molecular dynamics near defects and interfaces, and continuum models away…
Understanding large amounts of spatiotemporal data from particle-based simulations, such as molecular dynamics, often relies on the computation and analysis of aggregate measures. These, however, by virtue of aggregation, hide structural…
The native structures of proteins, except for notable exceptions of intrinsically disordered proteins, in general take their most stable conformation in the physiological condition to maintain their structural framework so that their…
We demonstrate how direct simulation of stochastic, individual-based models can be combined with continuum numerical analysis techniques to study the dynamics of evolving diseases. % Sidestepping the necessity of obtaining explicit…
All-atom dynamics simulations are an indispensable quantitative tool in physics, chemistry, and materials science, but large systems and long simulation times remain challenging due to the trade-off between computational efficiency and…
Machine learning models often require large datasets and struggle to generalize beyond their training distribution. These limitations pose significant challenges in scientific and engineering contexts, where generating exhaustive datasets…
We introduce machine learning models of quantum mechanical observables of atoms in molecules. Instant out-of-sample predictions for proton and carbon nuclear chemical shifts, atomic core level excitations, and forces on atoms reach…
A general procedure to investigate the elastic response and calculate the elastic constants of stressed and unstressed materials through continuum field modeling, particularly the phase field crystal (PFC) models, is presented. It is found…
The equilibrium amorphous solid state -- formed, e.g., by adequately randomly crosslinking the constituents of a macromolecular fluid -- is a heterogeneous state characterized by a universal distribution of particle localization lengths.…