22 research outputs found
Bottom-up derivation of an effective thermostat for united atoms simulations of water
In this article we derive the effective pairwise interactions in a Langevin
type united atoms model of water. The interactions are determined from the
trajectories of a detailed molecular dynamics simulation of simple point charge
water. A standard method is used for estimating the conservative interaction,
whereas a new "bottom-up" method is used to determine the effective dissipative
and stochastic interactions. We demonstrate that, when compared to the standard
united atoms model, the transport properties of the coarse-grained model is
significantly improved by the introduction of the derived dissipative and
stochastic interactions. The results are compared to a previous study, where a
"top-down" approach was used to obtain transport properties consistent with
those of the simple point charge water model.Comment: Submitted to J. Chem. Phy
Bistability and Switching Behavior in Moving Animal Groups
Moving animal groups such as schools of fish and flocks of birds frequently switch between different group structures. Standard models of collective motion have been used successfully to explain how stable groups form via local interactions between individuals, but they are typically unable to produce groups that exhibit spontaneous switching. We are only aware of one model, constructed for barred flagtail fish that are known to rely on alignment and attraction to organize their collective motion, that has been shown to generate this type of behavior in 2D (or 3D). Interestingly, another species of fish, golden shiners, do exhibit switching but have been shown to use attraction and repulsion, not alignment, to coordinate themselves in schools. Suggesting that switching may be explained by attraction and repulsion alone, without an alignment interaction. Here we introduce a model based on attraction and repulsion only and show that groups exhibiting switching similar to that observed in experiments with golden shiners emerges. We also establish that switching occur in two boundary-free extensions of the model. Our work suggests that the bistability and switching behavior observed in golden shiners and other moving animal groups may be explained via attractive and repulsive interactions alone
A method for estimating the interactions in dissipative particle dynamics from particle trajectories
We introduce a method for determining the functional form of the stochastic
and dissipative interactions in a dissipative particle dynamics (DPD) model
from projected phase space trajectories. The DPD model is viewed as a coarse
graining of a detailed dynamics that displays a clear time scale separation.
Based on the Mori-Zwanzig projection operator method we derive a consistency
equation for the stochastic interaction in DPD. The consistency equation can be
solved by an iterative boot strapping procedure. Combined with standard
techniques for estimating the conservative interaction, our method makes it
possible to reconstruct all the forces in a coarse grained DPD model. We
demonstrate how the method works by recreating the interactions in a DPD model
from its phase space trajectory. Furthermore, we discuss how our method can be
used in realistic systems with finite time scale separation
Using force covariance to derive effective stochastic interactions in dissipative particle dynamics
There exist methods for determining effective conservative interactions in
coarse grained particle based mesoscopic simulations. The resulting models can
be used to capture thermal equilibrium behavior, but in the model system we
study do not correctly represent transport properties. In this article we
suggest the use of force covariance to determine the full functional form of
dissipative and stochastic interactions. We show that a combination of the
radial distribution function and a force covariance function can be used to
determine all interactions in dissipative particle dynamics. Furthermore we use
the method to test if the effective interactions in dissipative particle
dynamics (DPD) can be adjusted to produce a force covariance consistent with a
projection of a microscopic Lennard-Jones simulation. The results indicate that
the DPD ansatz may not be consistent with the underlying microscopic dynamics.
We discuss how this result relates to theoretical studies reported in the
literature.Comment: 10 pages, 10 figure
Determining interaction rules in animal swarms
In this paper we introduce a method for determining local interaction rules
in animal swarms. The method is based on the assumption that the behavior of
individuals in a swarm can be treated as a set of mechanistic rules.
The principal idea behind the technique is to vary parameters that define a
set of hypothetical interactions to minimize the deviation between the forces
estimated from observed animal trajectories and the forces resulting from the
assumed rule set. We demonstrate the method by reconstructing the interaction
rules from the trajectories produced by a computer simulation.Comment: v3: text revisions to make the article more comprehensibl