| 1. |
- Eriksson, A., et al.
(författare)
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A method for estimating the interactions in dissipative particle dynamics from particle trajectories
- 2009
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Ingår i: Journal of Physics Condensed Matter. - : IOP Publishing. - 0953-8984 .- 1361-648X. ; 21:9, s. art. no. 095401-
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Tidskriftsartikel (refereegranskat)abstract
- 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 timescale 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 bootstrapping 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 timescale separation.
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| 2. |
- Eriksson, Anders, 1975, et al.
(författare)
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Bottom-up derivation of an effective thermostat for united atoms simulations of water
- 2009
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Ingår i: JOURNAL OF CHEMICAL PHYSICS. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 130:16
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Tidskriftsartikel (refereegranskat)abstract
- 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. © 2009 American Institute of Physics.
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| 3. |
- Eriksson, A., et al.
(författare)
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Determining interaction rules in animal swarms
- 2010
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Ingår i: Behavioral Ecology. - : Oxford University Press (OUP). - 1465-7279 .- 1045-2249. ; 21:5, s. 1106-1111
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Tidskriftsartikel (refereegranskat)abstract
- 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, as for example, a rule for aligning with neighbors. The parameter values are optimized so that the deviation between the observed movements in an animal swarm and the movements predicted by the assumed rule set is minimal. We demonstrate the method by reconstructing the interaction rules from the trajectories produced by a computer simulation.
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| 4. |
- Eriksson, Anders, 1975, et al.
(författare)
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Effective thermostat induced by coarse graining of simple point charge water
- 2008
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 129:2
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Tidskriftsartikel (refereegranskat)abstract
- We investigate how the transport properties of a united atom fluid with a dissipative particle dynamics thermostat depend on the functional form and magnitude of both the conservative and the stochastic interactions. We demonstrate how the thermostat strongly affects the hydrodynamics, especially diffusion, viscosity, and local escape times. As model system we use simple point charge (SPC) water, from which projected trajectories are used to determine the effective interactions in the united atom model. The simulation results support our argument that the thermostat should be viewed as an integral part of the coarse-grained dynamics rather than a tool for approaching thermal equilibrium. As our main result we show that the united atom model with the adjusted effective interactions approximately reproduces the diffusion constant and the viscosity of the underlying detailed SPC water model.
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| 5. |
- Eriksson, Anders, 1975, et al.
(författare)
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On the microscopic foundation of dissipative particle dynamics
- 2009
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Ingår i: Europhysics Letters. - : IOP Publishing. - 0295-5075 .- 1286-4854. ; 86:4
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Tidskriftsartikel (refereegranskat)abstract
- Mesoscopic-particle-based fluid models, such as dissipative particle dynamics, are usually assumed to be coarse-grained representations of an underlying microscopic fluid. A fundamental question is whether there exists a map from microscopic particles in these systems to the corresponding coarse-grained particles, such that the coarse-grained system has the same bulk and transport properties as the underlying system. In this letter, we investigate the coarse-graining of microscopic fluids using a Voronoi-type projection that has been suggested in several studies. The simulations show that the projection fails in defining coarse-grained particles that have a physically meaningful connection to the microscopic fluid. In particular, the Voronoi projection produces identical coarse-grained equilibrium properties when applied to systems with different microscopic interactions and different bulk properties. © EPLA, 2009
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| 6. |
- Eriksson, Anders, 1975, et al.
(författare)
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Using force covariance to derive effective stochastic interactions in dissipative particle dynamics.
- 2008
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Ingår i: Physical Review E. - 2470-0045 .- 2470-0053. ; 77:1
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Tidskriftsartikel (refereegranskat)abstract
- 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 the model system we study does not correctly represent transport properties. 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 RDF and a force covariance function can be used to determine all interactions in dissipative particle dynamics (DPD). Furthermore, we use the method to test whether the effective interactions in DPD can be adjusted to produce a force covariance consistent with the 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.
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| 7. |
- Gerlee, Philip, 1980, et al.
(författare)
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Impact of anticipation in dynamical systems
- 2017
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Ingår i: Physical Review E. - 2470-0045 .- 2470-0053. ; 96:6
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Tidskriftsartikel (refereegranskat)abstract
- Many animals, including humans, have predictive capabilities and, presumably, base their behavioral decisions-at least partially-upon an anticipated state of their environment. We explore a minimal version of this idea in the context of particles that interact according to a pairwise potential. Anticipation enters the picture by calculating the interparticle forces from linear extrapolations of the particle positions some time tau in the future. Simulations show that for intermediate values of t, compared to a transient time scale defined by the potential and the initial conditions, the particles form rotating clusters in which the particles are arranged in a hexagonal pattern. Analysis of the system shows that anticipation induces energy dissipation and we show that the kinetic energy asymptotically decays as 1/t. Furthermore, we show that the angular momentum is not necessarily conserved for tau > 0, and that asymmetries in the initial condition therefore can cause rotational movement. These results suggest that anticipation could play an important role in collective behavior, since it may induce pattern formation and stabilizes the dynamics of the system.
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| 8. |
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| 9. |
- Strömbom, Daniel, et al.
(författare)
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Bistability and Switching Behavior in Moving Animal Groups
- 2022
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Ingår i: Northeast Journal of Complex Systems. - : Binghamton University. - 2577-8439. ; 4:1
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 10. |
- Tunström, Kolbjörn, 1974
(författare)
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Estimating Effective Interactions from Particle Trajectories
- 2009
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The theoretical and practical understanding of molecular systems is strongly dependent on computer simulations. All-atom molecular dynamics techniques are capable of sim- ulating systems on the scale of millions of particles up to about 100 ns. Beyond this scale, into the mesoscopic regime, the all-atom approach is strongly limited by computational complexity. A fundamental challenge in the field of molecular computation is to construct coarse-grained models that can bridge the gap between the atomistic and mesoscopic scale. One of the mesoscopic simulation methods that have gained momentum the last decade is dissipative particle dynamics (DPD). The work contained in this thesis mainly concerns two questions: First, how does the dynamics of a DPD system relate to the dynamics of the underlying system? Second, how can the effective interactions on the mesoscale be determined? For coarse-grained systems in general, the first question is answered formally by the Mori-Zwanzig ( MZ) theory of projection operators. In our work we establish the link between DPD and the MZ theory, which shows that the dissipative and stochastic forces in the DPD equations are a direct consequence of coarse- graining and must therefore be interpreted as integral parts of the coarse-grained dynamics. We argue that a consistent coarse-graining scheme for molecular systems need to take this into account. Moreover, we design a coarse-graining scheme for deriving the different interaction terms in DPD, based on the theoretical connection between DPD and MZ theory. In Paper II the DPD thermostat is used to represent united atom SPC water. We show that the dynamical properties of the coarse-grained system can be matched with those of the underlying system by heuristically tuning the thermostat. Paper I and Paper III contains the theoretical derivations behind the coarse-graining scheme and discussions on how to practically apply it. Paper IV presents an application of the coarse-graining scheme to united atom SPC water. The resulting effective thermostat is consistent with the results in Paper II. Paper V is an investigation of the so-called fluid particle view of DPD. The study shows that this view is at best uncertain and poses a serious challenge to the mesoscopic simulation community. In Paper VI we deviate from the coarse-graining perspective and propose to use existing techniques from molecular coarse-graining as a platform for testing hypotheses of behavioral rules in animal swarms.
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