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Register a new userA variational conformational dynamics approach to the selection of collective variables in metadynamics
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In this paper we combine two powerful computational techniques, well-tempered metadynamics and time lagged independent component analysis. The aim is to develop a new tool for studying rare events and exploring complex free energy landscapes. Metadynamics is a well-established and widely used enhanced sampling method whose efficiency depends on an appropriate choice of collective variables. Often the initial choice is not optimal leading to slow convergence. However by analyzing the dynamics generated in one such a run with a time-lagged independent component analysis and the techniques recently developed in the area of conformational dynamics, we obtain much more efficient collective variables, that are also better capable of illuminating the physics of the system. We demonstrate the power of this approach in two paradigmatic examples.
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Recently, based on the method of collective variables the statistical field theory for multicomponent inhomogeneous systems was formulated [O. Patsahan, I. Mryglod, J.-M. Caillol, Journal of Physical Studies, 2007, 11, 133]. In this letter we establish a link between this approach and the classical density functional theory for inhomogeneous fluids.
Sampling complex potential energies is one of the most pressing challenges of contemporary computational science. Inspired by recent efforts that use quantum effects and discretized Feynmans path integrals to overcome large barriers we propose a replica exchange method. In each replica two copies of the same system with halved potential strengths interact via inelastic springs. The strength of the spring is varied in the different replicas so as to bridge the gap between the infinitely strong spring, that corresponds to the Boltzmann replica and the less tight ones. We enhance the spring length fluctuations using Metadynamics. We test the method on simple yet challenging problems.
We propose a variational approach to study renormalized phonons in momentum conserving nonlinear lattices with either symmetric or asymmetric potentials. To investigate the influence of pressure to phonon properties, we derive an inequality which provides both the lower and upper bound of the Gibbs free energy as the associated variational principle. This inequality is a direct extension to the Gibbs-Bogoliubov inequality. Taking the symmetry effect into account, the reference system for the variational approach is chosen to be harmonic with an asymmetric quadratic potential which contains variational parameters. We demonstrate the power of this approach by applying it to one dimensional nonlinear lattices with a symmetric or asymmetric Fermi-Pasta- Ulam type potential. For a system with a symmetric potential and zero pressure, we recover existing results. For other systems which beyond the scope of existing theories, including those having the symmetric potential and pressure, and those having the asymmetric potential with or without pressure, we also obtain accurate sound velocity.
In this paper, we demonstrate the existence of topological states in a new collective dynamics model. This individual-based model (IBM) describes self-propelled rigid bodies moving with constant speed and adjusting their rigid-body attitude to that of their neighbors. In previous works, a macroscopic model has been derived from this IBM in a suitable scaling limit. In the present work, we exhibit explicit solutions of the macroscopic model characterized by a non-trivial topology. We show that these solutions are well approximated by the IBM during a certain time but then the IBM transitions towards topologically trivial states. Using a set of appropriately defined topological indicators, we reveal that the breakage of the non-trivial topology requires the system to go through a phase of maximal disorder. We also show that similar but topologically trivial initial conditions result in markedly different dynamics, suggesting that topology plays a key role in the dynamics of this system.
We report the observation of harmonic generation and strong nonlinear coupling of two collective modes of a condensed gas of rubidium atoms. Using a modified TOP trap we changed the trap anisotropy to a value where the frequency of the m=0 high-lying mode corresponds to twice the frequency of the m=0 low-lying mode, thus leading to strong nonlinear coupling between these modes. By changing the anisotropy of the trap and exciting the low-lying mode we observed significant frequency shifts of this fundamental mode and also the generation of its second harmonic.
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