Related papers: Collective mode mining from molecular dynamics sim…

Communities are clusters of nodes with a higher than average density of internal connections. Their detection is of great relevance to better understand the structure and hierarchies present in a network. Modularity has become a standard…

Living systems exhibit complex yet organized behavior on multiple spatiotemporal scales. To investigate the nature of multiscale coordination in living systems, one needs a meaningful and systematic way to quantify the complex dynamics, a…

A theory for chemical reaction dynamics in condensed phase systems based on the generalized Langevin formalism of Grote and Hynes is presented. A microscopic approach to calculate the dynamic friction is developed within the framework of a…

Quantum Molecular Dynamics (QMD) calculations of central collisions between heavy nuclei are used to study fragment production and the creation of collective flow. It is shown that the final phase space distributions are compatible with the…

The complexity of biological systems, and the increasingly large amount of associated experimental data, necessitates that we develop mathematical models to further our understanding of these systems. As biological systems are generally not…

Fractonic phases of matter, a class of states in which collective excitations with constrained mobility exist, were originally discovered in the study of quantum error-correcting codes in solvable lattice spin models such as Haah's code and…

Dynamical systems in the life sciences are often composed of complex mixtures of overlapping behavioral regimes. Cellular subpopulations may shift from cycling to equilibrium dynamics or branch towards different developmental fates. The…

All-atom simulations can provide molecular-level insights into the dynamics of gas-phase, condensed-phase and surface processes. One important requirement is a sufficiently realistic and detailed description of the underlying intermolecular…

We introduce a new method to accurately and efficiently estimate the effective dynamics of collective variables in molecular simulations. Such reduced dynamics play an essential role in the study of a broad class of processes, ranging from…

Anharmonicities provide a wealth of information about the vibrational dynamics, mode coupling and energy transfer within a polyatomic system. In this contribution we show how driven molecular dynamics trajectories can be used to extract…

An analytical method to compute thermodynamic properties of a given Hamiltonian system is proposed. This method combines ideas of both dynamical systems and ensemble approaches to thermodynamics, providing de facto a possible alternative to…

A key overall goal of biomolecular simulations is the characterization of "mechanism" -- the pathways through configuration space of processes such as conformational transitions and binding. Some amount of heterogeneity is intrinsic to the…

Understanding biological network dynamics is a fundamental issue in various scientific and engineering fields. Network theory is capable of revealing the relationship between elements and their propagation; however, for complex collective…

Extending the famous Model B for the time evolution of a liquid mixture, we derive an approximate expression for the mobility matrix that couples the different mixture components. This approach is based on a single component fluid with…

Protein function does not solely depend on structure but often relies on dynamical transitions between distinct conformations. Despite this fact, our ability to characterize or predict protein dynamics is substantially less developed…

We study a system of two-mode stochastic oscillators coupled through their collective output. As a function of a relevant parameter four qualitatively distinct regimes of collective behavior are observed. In an extended region of the…

We study the interplay between collective and incoherent single-particle motion in a model of two chains of particles whose interaction comprises a non-integrable part. In the perturbative regime, but for a general form of the interaction,…

Many collective systems exist in nature far from equilibrium, ranging from cellular sheets up to flocks of birds. These systems reflect a form of active matter, whereby individual material components have internal energy. Under specific…

In order to understand the physics phenomea on the fundamental aspects, the software simulations are a good exercise to succed in this way. Some work of heat transport and molecular physics laboratory are studied in a comparative mode…

Molecular dynamics simulations use statistical mechanics at the atomistic scale to enable both the elucidation of fundamental mechanisms and the engineering of matter for desired tasks. The behavior of molecular systems at the microscale is…