Related papers: Collective mode mining from molecular dynamics sim…
Using molecular dynamics simulations we study the slow dynamics of a hard sphere fluid confined in a disordered porous matrix. The presence of both discontinuous and continuous glass transitions as well as the complex interplay between…
Collective phenomena arise from interactions within complex systems, leading to behaviors absent in individual components. Observing quantum collective phenomena with macroscopic mechanical oscillators has been impeded by the stringent…
Isoscalar collective modes in a relativistic meson-nucleon system are investigated in the framework of the time-dependent Thomas-Fermi method. The energies of the collective modes are determined by solving consistently the dispersion…
We here discuss the outcome of an hypothetic experiments of populations dynamics, where a set of independent realizations is made available. The importance of ensemble average is clarified with reference to the registered time evolution of…
In this paper, we address the normal mode analysis on the linearized Boltzmann equation for massive particles in the relaxation time approximation. One intriguing feature of massive transport is the coupling of the secular equations between…
In complex systems with many degrees of freedom such as peptides and proteins there exist a huge number of local-minimum-energy states. Conventional simulations in the canonical ensemble are of little use, because they tend to get trapped…
Recently there has been a lot of interest in monitoring and identifying changes in dynamic networks, which has led to the development of a variety of monitoring methods. Unfortunately, these methods have not been systematically compared;…
The internal dynamics of strongly interacting systems and that of biomolecules such as proteins display several important analogies, despite the huge difference in their characteristic energy and length scales. For example, in all such…
Coarse-graining has become an area of tremendous importance within many different research fields. For molecular simulation, coarse-graining bears the promise of finding simplified models such that long-time simulations of large-scale…
Integrative modeling of macromolecular assemblies allows for structural characterization of large assemblies that are recalcitrant to direct experimental observation. A Bayesian inference approach facilitates combining data from…
We discuss three different aspects of the quantum dynamics of bio-molecular systems and more generally complex networks in the presence of strongly coupled environments. Firstly, we make a case for the systematic study of fundamental…
The number of modes in a probability density function is representative of the complexity of a model and can also be viewed as the number of subpopulations. Despite its relevance, there has been limited research in this area. A novel…
The combination of multiple classifiers using ensemble methods is increasingly important for making progress in a variety of difficult prediction problems. We present a comparative analysis of several ensemble methods through two case…
It is often difficult to quantitatively determine if a new molecular simulation algorithm or software properly implements sampling of the desired thermodynamic ensemble. We present some simple statistical analysis procedures to allow…
Understanding the electron dynamics and transport in metallic and semiconductor nanostructures -- such as metallic nanoparticles, thin films, quantum wells and quantum dots -- represents a considerable challenge for today's condensed matter…
We present a molecular simulation method to simultaneously find multiple transition pathways, and their associated free-energy profiles. The scheme extends path-metadynamics (PMD) [Phys. Rev. Lett. 109, 020601 (2012)] with multiple paths…
We study the emergence of a collective optical response of a cold and dense $^{87}$Rb atomic cloud to a near-resonant low-intensity light when the atom number is gradually increased. Experimental observations are compared with microscopic…
We review a selection of methods for performing enhanced sampling in molecular dynamics simulations. We consider methods based on collective variable biasing and on tempering, and offer both historical and contemporary perspectives. In…
We present a proof-of-concept of a model comparison approach for analyzing spatio-temporal observations of interacting populations. Our model variants are a collection of structurally similar Bayesian networks. Their distinct Noisy-Or…
We report a computational study of the anharmonicity of the vibrational modes of various individual fullerenes using the "moments method" [Y. Gao and M. Daw, Modelling Simul. Mater. Sci. Eng. 23 045002 (2015)] with a Tersoff-style potential…