Related papers: Collective mode mining from molecular dynamics sim…
Photonic condensates are complex systems exhibiting phase transitions due to the interaction with their molecular environment. Given the macroscopic number of molecules that form a reservoir of excitations, numerical simulations are…
We review the observations and the basic laws describing the essential aspects of collective motion -- being one of the most common and spectacular manifestation of coordinated behavior. Our aim is to provide a balanced discussion of the…
Understanding kinetics and thermodynamics profile of biomolecules is necessary to understand their functional roles which has a major impact in mechanism driven drug discovery. Molecular dynamics simulation has been routinely used to…
The collective motion of a finite nuclear system is investigated by numerical simulation and by linear response theory. Using a pseudo-particle simulation technique we analyze the giant resonances with a multipole decomposition scheme. We…
Collective motion is a manifestation of emergent phenomena in medium-heavy and heavy nuclei. A relatively large number of constituent nucleons contribute coherently to nuclear excitations (vibrations, rotations) that are characterized by…
We consider use of collective variables for description of composite fields as collective phenomena due to the strong coupling regime. We discuss two approaches, where identification of collective variables of complex quantum system does…
Controlling polymorphism in molecular crystals is crucial in the pharmaceutical, dye, and pesticide industries. However, its theoretical description is extremely challenging, due to the associated long timescales ($ > 1 \, \mu s$). We…
In this work we aim to highlight a close analogy between cooperative behaviors in chemical kinetics and cybernetics; this is realized by using a common language for their description, that is mean-field statistical mechanics. First, we…
This study deals with the understanding of hydrogen atom scattering from graphene, a process critical for exploring C-H bond formation and energy transfer during the atom surface collision. In our previous work (J.Chem.Phys \textbf{159},…
We present a molecular dynamics study of the collective dynamics of a flexible model for the fragile glass-former orthoterphenyl [ S. Mossa, R. Di leonardo, G. Ruocco, and M. Sampoli, Phys. Rev. E 62, 612 (2000)]. We study the behavior of…
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…
The traditional picture of heat transfer in solids by atomic vibrations, also known as phonons, involves phonons scattering with each other like gas particles and is commonly referred to as the phonon gas model (PGM). This physical picture…
We propose a new approach to comparing simulated observations that enables us to determine the significance of the underlying physical effects. We utilize the methodology of experimental design, a subfield of statistical analysis, to…
We aim to automatize the identification of collective variables to simplify and speed up enhanced sampling simulations of conformational dynamics in biomolecules. We focus on anharmonic low-frequency vibrations that exhibit fluctuations on…
Normal mode dynamics are ubiquitous underlying the motions of diverse systems from rotating stars to crystal structures. These behaviors are composed of simple collective motions of particles which move with the same frequency and phase,…
We use topological data analysis and machine learning to study a seminal model of collective motion in biology [D'Orsogna et al., Phys. Rev. Lett. 96 (2006)]. This model describes agents interacting nonlinearly via attractive-repulsive…
Clustering is widely used in unsupervised learning to find homogeneous groups of observations within a dataset. However, clustering mixed-type data remains a challenge, as few existing approaches are suited for this task. This study…
Understanding the movement behaviours of individuals and the way they react to the external world is a key component of any problem that involves the modelling of human dynamics at a physical level. In particular, it is crucial to capture…
Ferromagnetic models are harmonic oscillators in statistical mechanics. Beyond their original scope in tackling phase transition and symmetry breaking in theoretical physics, they are nowadays experiencing a renewal applicative interest as…
The analysis of live-cell single-molecule imaging experiments can reveal valuable information about the heterogeneity of transport processes and interactions between cell components. These characteristics are seen as motion changes in the…